ANIMAL MODEL FOR HIV INDUCED DISEASE

Abstract
HIV does not cause disease in any non-human species. Thus, there is no animal model system to evaluate the efficacy of strategies aimed at preventing, treating or curing disease caused by this virus. The present invention provides compositions and a method for producing an animal model for HIV induced disease. The present invention is an animal adapted to simulate a human-like immune response to HIV, which is accomplished by activation and inactivation of complement of proteins within the animal. Accordingly, the present invention stages certain human proteins within an animal by way of its gut associated lymphoid tissue followed by infection of live HIV.
Description
FIELD OF THE INVENTION

The present invention relates to a composition and method for producing an animal model for HIV.


BACKGROUND OF THE INVENTION

HIV is a viral infection. Therefore, by definition, HIV is an intra cellular parasite. The virus must assimilate a variety of host cellular proteins, lipids, carbohydrates and nucleic acids into its own structure and reproductive cycle. Attempts at inoculating animals with HIV have all failed. Animals such as mice lack one or more cellular proteins or other cellular derived molecules necessary for viral replication, immune evasion and immune suppression. The purpose of this invention is to produce an animal that possesses the full complement of HIV immune mediated molecules in a manner that the animal can assimilate in trans the human derived proteins necessary for an HIV infection to proliferate. The animal will not recognize these foreign molecules as being foreign, and therefore, will not develop an immune response towards them. Furthermore, these human derived molecules will be directed towards Peyer's patches, the very site of HIV replication. The animal will be susceptible to HIV disease.


Rationale Behind an HIV Animal Model

    • 1. Allow for an in depth and ethical study of the natural course of HIV infection. Currently all studies are on human subjects and are therefore limited by ethical considerations.
    • 2. A testing ground for anti-retroviral drugs and other technology.
    • 3. A testing ground for HIV based vaccines.
    • 4. Allow the development and manufacture of effective HIV vaccines. In 1794, Edward Jenner demonstrated that inoculation of humans with extracts from cowpox lesions produce minimal systemic disease but protected the recipient from smallpox. Initially, the only way to supply the population with enough cowpox vaccine was to pass the infection (cowpox) from person to person by serial infection. This methodology, however, was complicated by transmission of other diseases such as syphilis and hepatitis and fell into disfavor. The cowpox vaccine was later passed into sheep and water buffalos in an attempt to obtain enough inoculum for the population. Recently, an unused smallpox vaccine was uncovered in New York dating back to 1876. This virus was identified as vaccinia. By 1876, the original cowpox vaccine was replaced by vaccinia virus. Vaccinia is not found in any animal studied to date. It most likely resulted as a recombination of cowpox with other pox vectors, animal and human. The U.S. Smallpox Vaccine (Dryvax by Wyeth) reserve is over thirty years old and was derived from a seed stock of a New York City Board of Health strain that was passed between twenty-two to twenty-eight times on young calves. Distribution of Dryvax ceased in 1983. Multiple retroviral vectors infect animals. Passage of HIV and one or more animal retroviruses will allow for multiple recombinant events to occur. In a manner that parallels the vaccinia vaccine derivation an HIV vaccine can be developed. Such an animal model can also be a continuous inexpensive reliable source of new fresh vaccine.


Overview of HIV Lifecycle and Protein Requirements

A retroviral life cycle can be divided into an afferent and efferent limb. The afferent limb starts with viral attachment and ends with viral DNA integration into the host genome. The efferent limb commences with the production of viral messenger RNA and culminates with viral fission releasing immature virions.


The afferent lifecycle of the virus will be arbitrarily divided into the following steps:

    • 1. Attachment to a target cell by its surface (SU) and transmembrane (TM) proteins. The surface protein binds to the CD4 receptor and to either the CCR5 or CXCR4 coreceptor.
    • 2. Fusion of viral envelope and cell plasma membrane.
    • 3. Deposition of viral core into cytoplasm.
    • 4. Reverse transcription of viral RNA.
    • 5. Translocation of viral pre-integration complex across nuclear membrane.
    • 6. Integration of viral DNA into host DNA.


The efferent lifecycle of the virus will be arbitrarily divided into the following steps:

    • 7. Transcription of viral RNA into RNA.
    • 8. Splicing of viral RNA.
    • 9. Translocation of early viral completely spliced RNA products (Tat, Rev and Nef) across nuclear membrane into cytoplasm.
    • 10. Rev mediated translocation of singly spliced and unspliced viral RNA across the nuclear membrane to the cytoplasm.
    • 11. Viral env proteins produced in cytoplasmic rough endoplasmic reticulum (RER).
    • 12. Glycosylation and folding of env proteins in Golgi apparatus.
    • 13. Targeting of mature envelope proteins to cytoplasmic side of plasma membrane.
    • 14. Translation of Gag and Gag-Pol polyprotein.
    • 15. Targeting of Gag and Gag-Pol polyprotein to host endosomal machinery.
    • 16. Gag and Gag-Pol polyprotein cleaved by viral protease.
    • 17. Assembly of Gag and Gag-Pol polyprotein precursors and envelope proteins at budding site.
    • 18. Viral fission.
    • 19. Viral maturation.


Each step delineated above relies on host derived proteins, lipids, carbohydrates and/or nucleic acids. Animals do not support the HIV lifecycle because they lack one or more necessary host derived molecules.


HIV, as with all significant viral pathogens, is able to evade the host immune response. Furthermore, HIV down regulates or deregulates the host immunologic response.


For an animal model to be successful for HIV disease, three correlates of the disease must be expressed:

    • 1. Viral replication
    • 2. Viral immune evasion
    • 3. Viral immune deregulation and/or suppression


Many proteins necessary for viral replication of the host immune response are human host derived proteins that are not found in animals. These include, but are not limited to, tRNA synthetase, tRNAlys, Tsg101, Tal, Staufen, LEDGF/p75, Cyclin T, CDK9 and RNA polymerase II. To create an animal model capable of not only supporting HIV replication, but also reproducing HIV disease in the animal requires the assimilation of these proteins into the animal without the animal recognizing these proteins as foreign. Success of such an animal model would rely on the lack of an immunologic response to these human proteins. Furthermore, assimilation or targeting of these proteins into the proper target tissues, predominantly Peyer's patches, the principal site of HIV replication, is necessary to reproduce an HIV infection in an alternate host.


Viral evasion of the host's immune response requires the active participation of host derived cellular proteins such as the complement control proteins CD55, CD46 and Factor H. These proteins are necessary to prevent the host's immune cells from reacting to and destroying normal tissue. By incorporating these molecules into an intact HIV virion, the virus is able to fool the immune system in a “cloak-and-dagger” method that avoids virolysis.


Immune disregulation is accomplished by the virus skewing the host towards a Th2 immune response. This is accomplished by the virus hijacking the endosomal pathway by incorporating molecules such as Tsg101, Tal and Ubiquitin. Furthermore, the viral envelope incorporates MHC-11 and CD86 molecules which are consistent with a Th2 response.


As a corollary to the above paragraph, any given protein may exhibit different and at times divergent and conflicting functions, complicating the challenge to an animal model for HIV.


DESCRIPTION OF THE INVENTION
Summary of the Invention

The present invention provides compositions and a method for producing an animal model for HIV induced disease. The present invention is an animal adapted to simulate a human-like immune response to HIV, which is accomplished by activation and inactivation of complement of proteins within the animal. Accordingly, the present invention stages certain human proteins within an animal by way of its gut associated lymphoid tissue followed by infection of live HIV.







DETAILED DESCRIPTION

The present invention is directed to an animal model for HIV and the method of producing the same. Preferably, the present invention is a mouse adapted to simulate a human-like immune response to HIV, which is generated by appropriate protein behavior within the mouse. The mouse genome has been published.1 Extensive linkage conservation/synteny between mouse and human DNA has been established.2 The present invention stages certain human proteins within a mouse by way of its gut associated lymphoid tissue (GALT).


A key to protein variability lies in the primary, secondary, tertiary and quaternary structure of the protein itself. The protein may assume different secondary, tertiary and quaternary structures in various environmental conditions. Changes in ph, temperature, as well as the presence, absence, or concentration of cellular cofactors, such as calcium and magnesium, alter the structure and function of the protein. Most importantly however, proteins can be divided into basic building blocks or subunits known as motifs, each which possesses a specific function which is independent of the rest of the molecule. In some instances only a portion of the protein is directly involved in a certain metabolic process. The whole protein may or may not be needed to produce the desired effect. The subunits not directly involved in the cellular activity may affect the overall structure, stability, intracellular location and often function as a scaffold.


However it has also been demonstrated in other circumstances that a subunit of a protein that carries a significant function maintains that function when physically separated from the rest of the molecule. In such circumstances one may envision that only a portion of the protein is needed to perform the desired effect and is necessary to be encoded by recombinant DNA technology to develop an animal model for HIV. Invariant amino acids in each protein are always noted. For example, the cystine residue occupying the position of amino acid 261 of Cyclin T is absolutely required for interaction with Tat.3


The above conclusion has been demonstrated with in vitro models of human CyclinT1 (hCycT1) as it interacts with the Tat protein. A heterodimer of human CyclinT1 and Tat protein is a prerequisite to the binding of the heterodimer to the TAR sequence that initiates HIV RNA replication. The first 272 amino acids of the 726-aa hCycT1 protein are sufficient to support Tat function, TAR recognition and binding and ultimately viral replication. Even more specifically a critically defined region of hCycT1 located between residues 250 and 262 is critical for Tat and TAR binding and has been termed the Tat-TAR recognition motif (TRM).


All proteins have a characteristic half life usually measured in minutes or hours. Therefore, these proteins that support HIV replication and immune evasion need to be produced within the animal in a continuous pattern with a steady state level. The tissue concentration of the proteins supplied in trans should mirror that found in the normal human immunologic milieu.


All proteins administered to the animal model are encoded within the DNA. Recombinant technology allows introduction of human DNA into bacteria, fungi, yeast or viruses. Utilizing commensal organisms, found normally in the gut of an animal such as a mouse, rat or rabbit for this recombination the proteins of human origin necessary for HIV replication and immune evasion and immune disregulation can be introduced into the animal without the animal rejecting the proteins as foreign. The mechanisms of suppressor cells and regulatory cells found within the gut associated lymphoid tissue (GALT) prevent immunologic response to ingested food, commensal organisms and the products of the commensal organisms. Commensal organisms often produce vitamins necessary for the host to survive. Vitamins are protein based structures. By reasonable inference other proteins produced by the commensals would be assimilated into the host without an ensuing immunologic response. To replicate and survive the commensal bacteria continually produce protein and other components of its structure in excess of what is needed or incorporated into the replicating bacteria. These excess proteins do not elicit an immunologic response from the host animal.


GALT constitutes nearly 80% of the total body's immune cell population. GALT is the most comprehensive lymphoid organ system in humans. The function of GALT is a paradox and at times is in conflict with the systemic immune system. The systemic immune apparatus, under normal conditions, functions in a sterile environment devoid of pathogens and pathogen associated toxins. Therefore, any foreign matter encountered by the systemic immune system is regarded as a potentially harmful invader and the appropriate immunologic response follows. GALT, however, stands as a barrier between the human organism and an external environment replete with foreign tissue. The foreign matter includes a variety of commensal organisms, commensal derived products, pathogens, and pathogen derived products and ingested food. The entire GI tract from the mouth to the anus is functionally external to the human body. Unlike the systemic immune system, which responds vigorously to any foreign matter, GALT must differentiate between commensal organisms and their products, as well as ingested food to which an immunologic response would have adverse consequences and invading pathogens potentially lethal to the host.4


To affect this diversity of function, GALT is compartmentalized and, in contrast to the systemic and peripheral immune system (spleen & lymph nodes), is characterized by non-homogeneously distributed B and T cells. The phenotypic behavior, cell surface markers, developmental origins, secretory products, and hence function of the T and B cells of GALT, is markedly different from the T and B cells of the systemic system. Furthermore, GALT contains certain subsets of non-conventional lymphocytes such as γ/δ T cells. Overall GALT is characterized by afferent and efferent conduits not found in the systemic system.5


GALT (armed with a variety of immunologic cells not found in the systemic circulation, and patterned or clustered into characteristic vehicles not found elsewhere in the body) is capable of immunologic suppression as well as classically based Th-1 and Th-2 immune responses. Antigen uptake in GALT occurs through specialized epithelial cells known as “M” cells or “membranous” cells. Antigen uptake in GALT can also occur directly by epithelial cells in close proximity to underlying T and B cells. The uptake or assimilation of antigens through the “M” cells or epithelial cells may result in localized immune response, disseminated immune response and/or tolerance or immunosuppression. The vast majority of antigens interacting with GALT results in specific suppression of immunity for that antigenic structure. This is necessary because the primary function of GALT is to prevent an immunologic reaction to innocuous, and at times beneficial, foreign material.6


The final determination in GALT of immunity versus tolerance rests on many variables. These include but are not limited to the chemical structure of the antigen, the dose of the antigen administered, and the cytokine environment. Whether this phenomenon is termed suppression, anergy, deletion, ignorance, and/or immunologic deviation is irrelevant. Importantly, immunologic tolerance within GALT depends on an intact epithelial barrier.7


Many mechanisms have been described in the literature detailing the immune suppression observed with antigens derived from the large and small intestine. In classic immunology dendritic cells exposed to peripherally derived antigen assimilate the antigen (by a variety of mechanisms including but not limited to endocytosis, macrocytosis, pinocytosis, and cross presentation). Dendritic cells (DCs) lining the tissue have been described. The DCs then undergo a process of maturation and migrate to the most proximal lymph nodes. Expressing a “danger signal” the cells of the lymph node respond and eliminate the antigen expressed by the DCs. Recently however, DCs lining the GALT with an opposite function, one of tolerance have been described in the literature. These cells stimulate a protective immune response when stimulated by pathogens whose tropism (i.e., the phenomena observed in living organisms of moving towards each other) is confined to pathogens that infect or are confined to epithelial cells.8


The incorporation of the DNA encoding these human derived proteins into the commensals, herein referred to as incorporated DNA, can be done through recombinant technology with the following seven methodologies commonly used and known by those in the art.

    • 1. Incorporation of the DNA into the bacterial, viral, yeast or fungal DNA utilizing restriction enzymes, endonucleases, exonucleases, deoxyribonucleases, ribonucleases, alkaline phosphatases, polynucleotide kinases, terminal transferases, and DNA ligases, all commercially available.9
    • 2. The formation of a plasmid encoding the human protein. A plasmid is a genetic particle physically separate from the chromosomal DNA of the host cell that is stable and can function and replicate independently of the nucleus.10
    • 3. Incorporation of the DNA into a bacteriophage. A bacteriophage is a virus with a specific affinity for bacteria and has been found in association with essentially all groups of bacteria. Like other viruses, they contain either RNA or DNA but never both.11
    • 4. Hybrid plasmid/phage vectors such as cosmids, phagemids or phasmids.12
    • 5. Bacterial artificial chromosomes.13
    • 6. Yeast artificial chromosomes.14
    • 7. A combination of the above.


If incorporated into a plasmid, a promoter/regulatory region controlling the plasmid activity would need to be included. The assimilation of the protein produced by the commensal into the animal may occur by passive (ATP independent) or active (ATP dependent) means. The DNA encoding a cell penetrating peptide (CPP) may be fused with the DNA encoding the human protein(s) prior to the recombinant process incorporating the DNA into the bacteria. Many cell penetrating peptides have been defined in the literature and have been used to carry cargos (attached protein, carbohydrate or lipid molecules) into cells which would normally be impermeable to these attached structures. Cell penetrating peptides can pass through cell walls, nuclear membranes, as well as the membranes enclosing other intracellular organelles with ease.15


Alternatively, the DNA encoding the below mentioned human proteins necessary for HIV viral replication, immune evasion and immune disregulation can be spliced into the DNA of an animal. Intuitively this may seem to be the most logical answer. For some proteins such as the CD4 receptor and the CCR5 and CXCR4 co-receptor, this would be workable and perhaps preferable, since the proteins would be a component of the host cell plasma membrane. Many potential problems arise using that conceptualized framework for all the proteins. Most difficult would be the targeting of the needed proteins to the sites of HIV replication (i.e., Peyer's patches). Furthermore, encoding a protein into the DNA of an organism does not equate to transcription and translation of the DNA and protein production. 70% of the DNA in a mammal is not transcribed and has been termed “junk DNA”. Production of a transgenic or chimeric animal does not equate to tissue targeting. External control of animals genetically modified at the level of embryonic cells is problematic.


These issues may be addressed as the science relating to models progresses. However, the present invention, as a first conceptualized model, involves splicing the DNA for the needed human proteins into commensal organisms.


The host proteins necessary for HIV to attach to a target cell, penetrate the target cell and replicate within the target cell, include and are not limited to the following list. The following proteins, or the nucleotide sequences encoding these proteins, preferably should be included in a working animal model for HIV:


1. Transcription factors.

    • a. NFK B
    • b. NFAT
    • c. Sp1


2. Cellular cofactors.

    • a. Cyclin T
    • b. CDK9/PITALRE
    • c. RNA polymerase II
    • d. Exportin 1/Crm1
    • e. Ran GTP
    • f. Ran GTPase activating protein (RanGAP)


g. Ran Binding Protein (RanBP1)


3. Cellular receptors.

    • a. CD4


4. Cellular coreceptors.

    • a. CCR5
    • b. CXCR4
    • c. CCR2B
    • d. CCR3
    • e. CCR8
    • f. GPR1
    • g. GPR15 (Bob)
    • h. STRL33 (Bonzo)
    • i. US28
    • j. CX3CR1 (V28)
    • k. APJ
    • l. chemR23


5. Cellular proteases.

    • a. Furin


6. Cellular proteins involved in the ubiquitin-proteasome pathway.

    • a. H-β-TrCP
    • b. Skp1p


7. Cellular adaptor protein.

    • a. AP-2


8. Human ribosomal RNA.


The host derived proteins necessary for HIV to evade the immune response include but are not limited to the following, and preferably should be included in a workable animal model for HIV. (See Table in Appendix A for a complete list of “Host Proteins Incorporated into the Intact Virus and for Pre-Integration Complex (PIC)”.


1. Plasma proteins.

    • a. C4 binding protein (C4b protein)
    • b. Factor H (Includes FHL-1, FHR1, FHR2, FHR3, FHR4, FHR5)


2. Cell membrane bound proteins.

    • a. Membrane cofactor protein (MCP) or CD46
    • b. Decay accelerating factor (CD55)
    • c. Complement-receptor 1 (CD35)
    • d. Complement-receptor 2 (CD21)
    • 3. Homologous restriction factor (HRF).


Finally and in addition to the proteins listed above the table located in Appendix A lists the host proteins incorporated into the intact virus, the pre-integration complex (PIC) and those involved in the HIV lifecycle. It is not exhaustive as new viral protein/host protein interactions are reported in the literature with regularity. The genetic loci of the human proteins have been described in the literature and allow for restriction enzyme splicing into yeast, bacteria or plasmid DNA.


In an alternative embodiment, the activity of Human Factor H in an animal can be limited by administration of soluble complement-receptor 1 (sCR1) by adding sCR1 exogenously or by splicing the genomic sequence for sCR1 into a commensal organism. This protein binds to C3b and C4b and facilitates the breakdown of these proteins by Factor 1. By binding to C3b, sCR1 prevents complement activation by the C3 convertase. The activity of Human Factor H in thwarting the complement cascade is mimicked by sCR1.


The administration of soluble CR1 is a controlled element or variable in the animal model. sCR1 allows control of tissue levels of C3b thereby limiting the activity of the C3 and C5 convertases which mirrors the function of Factor H.


In some animal models (e.g., old world primates), and particularly cell cultures derived thereof, TRIM-α confers a potent post entry (i.e., meaning after entry into the cell) block to HIV-1 infection. Cyclophilin A (CypA) binding to viral capsid proteins results in a similar response observed in vitro for certain human cell lines. Among new world primates, only owl monkeys exhibit post-entry restriction of HIV-1 replication. More specifically, monkey kidney cells of the Aotus trivirgatus owl restrict HIV infection, but are permissive for SIV infection. HIV restriction in these cells is completely abrogated when the interaction of the HIV-1 capsid and the cellular protein CypA is disrupted. Paradoxically, the opposite is seen in human cells where capsid-CypA interaction is required for efficient intracellular HIV-1 replication. Therefore if such an animal model is used the viral capsid interaction with the host CypA protein must be severed. The use of the CypA-binding drug cyclosporine A (CsA) would be necessary if these animal models were used. Similar findings may exist in other animals but have not yet been delineated.16


The most effective weapon for immune perturbation within the HIV arsenal is the Tat protein. The Tat protein is necessary for viral replication as well. A multiplicity of immune down modulating effects of the Tat protein has been well documented in human studies. An accurate model of HIV must include Tat mediated immune suppression. This will involve the Tat protein and the host cell receptors for the Tat protein.


Expression of MHC class II genes is inhibited by the Tat protein resulting in profound immunosuppression. A central protein in class II expression is the class II trans-activator (CIITA) protein. CIITA is responsible for integrating several proteins at the promoters of MHC class II genes enhancing MHC II gene transcription and ultimately MHC II gene expression.


In human models, the Tat protein inhibits CIITA function down regulating the expression of MHC II genes. Human cyclin T1 (hCycT1) is involved in this Tat mediated immunosuppression.


In mice however, the Tat protein does not interact with the human counterpart of hCycT1, mouse cyclin T1 (mCycT1). However, the Tat protein in mice does inhibit the activity of CIITA in a mechanism that is not dependent on mCycT1. The results are the same: the down regulation of the CIITA protein, decreased MHC II production, and immunosuppression.


Co-expression of transfected human CD4, CCR5 and CXCR4 molecules into murine cell cultures allows entry of HIV-1 but replication is blocked. Murine cyclin T1 binds Tat but does not bind TAR. Transfection with human cyclin T1 restored Tat function.17


Murine cyclin T2 can bind HIV-1 Tat and facilitate TAR binding if a single residue, asparagine 260 is replaced with a cysteine residue. Interestingly, Tat from HIV-2 does bind murine cyclin T1 and murine cyclin T2. However, neither complex binds effectively the TAR residue. With both HIV-1 and HIV-2 Tat effective binding and activity of Tat on HIV replication is rescued in murine cells by the above-mentioned mutation of Cyclin T2 at amino acid number 260. Therefore, if a murine model is anticipated, mutation of Cyclin T2 at residue 260 would equate to human Cyclin T1 supplied in trans. In an alternate murine animal model, another single amino acid difference between human Cyclin T1 and murine Cyclin T1 determines species restriction of HIV-1 Tat function. In this model, replacing the tyrosine residue at amino acid 261 in the murine Cyclin T1 with a cysteine conferred effective Cyclin T1 function with Tat and TAR.18


A competent Cyclin T1 is necessary but not sufficient for HIV viral replication. This can be provided to a murine model by either one of the above-mentioned mutations in the mouse genome or by providing human Cyclin T1 in trans.


An effective block of HIV replication in a murine model is the inability of the virion to assimilate murine Factor H. HIV directly activates the classical complement pathway in rabbit, mouse and guinea pig serum. This activation results in viral neutralization by lysis.19 Factor H is bound at multiple sites to gp120 and gp41 in the intact virus.20 Factor His the main contributor to HIV evasion of complement mediated lysis.21 Murine and human Factor His composed of twenty repetitive units and each unit is approximately sixty amino acids long.22 Neither murine Factor H nor human Factor H is characterized by an alpha helix or a beta pleated sheet. Both human and murine Factor H exists in two different confomiational states (φ1 and φ2) that can be separated by hydrophobic chromatography. Both have equal function.23 Although murine Factor H possesses a high degree of homology to human Factor H, it does not bind to the HIV virus. Establishing an effective HIV infection in a murine model would require the assimilation of human Factor H.


A variety of sialic acids (characterized by a 9 carbon backbone) and/or a glycan chain (composed of mostly 5 and 6 carbon sugars) are expressed on the surfaces of animals, fungi, plants, protozoa, bacteria and viruses. Mammals possess a variety of sialic acid recognizing proteins known as Siglecs. To date, eleven functional Siglecs and one Siglecs like molecule (Siglec L1) have been characterized. Macrophages express Siglec 1 (sialoadhesin), B cells express Siglec 2 (CD22) and monocytes express Siglec 3 (CD33). Cells involved in the innate immune response including natural killer cells and granulocytes are characterized by Siglecs 1, 3, 5, 7 and 10. The function of a protein and its potential immunogenicity are in part related to its surface glycan or sialic acid residues. Therefore, a potential rejection and function issue exists if proteins from animals expressing different surface sugar molecules co-exist in the same animal. Interestingly, the CMP-Neu5Ac synthetase genes that encode the enzymatic machinery necessary for sialic acids are found with one exception only in fruit flies, rainbow trout, mice and humans. Surprisingly, one bacteria Streptomyces coelicolor also expresses this genetic machinery. Lateral gene transfer between this bacterium and a eukaryotic host best explains this anomaly.24 Therefore, a murine model obviates this overwhelming concern.


The mucosa of the murine GI tract has been well described. The surface of Peyer's patches is covered by epithelium associated with a variety of lymphoid cells known as the follicle-associated epithelium (FAE). The FAE is composed of a variety of cells including cells known as M cells. These cells exhibit slender cytoplasmic extensions around lymphoid cells. The basolateral surface of the M cell is deeply invaginated forming a pocket that shortens the distance from the apical to the basolateral surface. The pocket is rich in B cells, T cells, macrophages and dendritic cells. Antigen uptake by M cells does not result in intracellular degradation but rather delivery of the intact molecule to the underlying lymphoid tissue. The apical surface of the M cell lacks the brush border of typical gut lining enterocytes. Furthermore, the M cells are not coated with the thick glycocalyx found on enterocytes. Finally, the distribution of actin-associated protein villin in M cells differs from enterocytes. These characteristics make M cells ideal targets for absorption of proteins produced by recombinant commensal organisms needed for HIV replication.25


A variety of methods will target the M cells for absorption of defined proteins. These include, but are not limited to: (1) cholera toxin-B subunit, (2) carbohydrate lectins, (3) genetically engineered IgA or the secretory component of IgA. Splicing the genetic DNA sequence for a defined protein needed for HIV replication and linking that protein to 1, 2 or 3, above, will target the protein to the M cells and ultimately to the underlying immune tissue.26


Alternatively, attenuated viruses particularly the mouse reovirus, attenuated Poliovirus type 1 and the attenuated Sabin strain selectively adhere to M cells. These viruses can be exploited for transporting a defined protein into Peyer's patches.27


Certain attenuated bacteria also target the M cell apical membrane. These include Vibrio Cholerae, Salmonella, Shigella, Yersinia and BCG. Attenuation of these organisms renders them non-virulent. They can be exploited in targeting recombinant proteins to the M cells and the underlying immune tissue.28


As a final step, the described proteins are administered to the animal by way of its GALT followed by infection of live HIV. Infection with live HIV will result in Tat protein transcription and translation with the resulting Tat mediated immune suppression. Alternatively, Tat protein or the incorporation of the DNA encoding the Tat protein can be administered directly in combination with other proteins or incorporated into the commensal through recombinant technology described above.


Administration and Supplements

It is possible for the proteins, composition of proteins and or compositions of incorporated DNA encoding the proteins to be administered as a pharmaceutical formulation or preparation, optionally with supplements or other compositions as described above. If protein carriers are used they must be “pharmaceutically acceptable” in the sense of being compatible with the other ingredients of the formulation and not deleterious to the recipient thereof. The coupling of protein carriers (e.g., complement proteins) is known within pharmacology.


Administration may be made in a variety of routes, for example orally, transbucally, transmucosally, sublingually, nasally, rectally, vaginally, intraocularly, intramuscularly, intralymphatically, intravenously, subcutaneously, transdermally, intradermally, intra tumor, topically, transpulmonarily, by inhalation, by injection, or by implantation, etc. Various forms of the composition may include, without limitation, capsule, gel cap, tablet, enteric capsule, encapsulated particle, powder, suppository, injection, ointment, cream, implant, patch, liquid, inhalant, or spray, systemic, topical, or other oral media, solutions; suspensions, infusion, etc. Because some of the first targets for infection with HIV are epithelial cells and Langerhans cells in the skin and rectal mucosa, then a preferable embodiment of delivery is dermal combined with rectal suppositories.


Those skilled in the art will recognize that for administration by injection, formulation in aqueous solutions, such as Ringer's solution or a saline buffer may be appropriate. Liposomes, emulsions, and solvents are other examples of delivery vehicles. Oral administration would require carriers suitable for capsules, tablets, liquids, pills, etc, such as sucrose, cellulose, etc.


The preferred method of administration would be via commensal organisms genetically modified to express one or more human derived proteins needed for HIV replication. The preferred area of administration would be the intestines targeting Peyer's patches. The delivery and deliberate infection of live HIV is well known in the art and includes intra vaginal, rectal and systemic portals.


In conclusion, the present invention provides compositions and a method for producing an animal model for HIV induced disease. The present invention is an animal adapted to simulate a human-like immune response to HIV, which is accomplished by activation and inactivation of complement of proteins within the animal. Accordingly, the present invention stages certain human proteins within an animal by way of its GALT followed by infection of live HIV.


The analysis and development of the animal model for HIV induced disease should incorporate a wide range of doses of the proteins necessary for viral replication and immune evasion, deregulation and/or suppression for evaluation. Animal trials should consider differences in size, species, and immunological characteristics.


The above examples should be considered to be exemplary embodiments, and are in no way limiting of the present invention. Thus, while the description above refers to particular embodiments, it will be understood that many modifications may be made without departing from the spirit thereof.


Prokaryotic organisms lack the post translational modification machinery found in eukaryotic organisms. Yeast such as Saccharomyces cerevisiae are eukaryotes often found as commensal organisms in GALT. Yeast may therefore be preferable as recombinatorial vectors.


A blend of genetic manipulations may yield the optimal animal model. A mouse with one or the other above-mentioned amino acid substitutions in the Cyclin T protein that renders it Tat and TAR processive would be a good starting point. This murine model could then assimilate the CD4 receptor and the CCR5 and CXCR4 co-receptors by transgenic technology. Other proteins the mouse is lacking to affect HIV replication, immune evasion and immune disregulation could be supplied in trans via recombinatorial GALT vectors.


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APPENDIX A

The following information is generally known by those in the art and can be found in medical texts generally including by way of example, Mucosal Vaccines, Hematology Basic Principles and Practices, and Immunology, Infection and Immunity and journals such as Immunologic Reviews, Nature, Virology, and Molecular Immunology.












HIV-1











FUNCTION(S) OF





HOST
COMPONENT
FUNCTION(S) OF


HOST
MOLECULE IN HOST
OF INTACT
HOST MOLECULE IN


MOLECULE
CELL
VIRION
HIV VIRION





Membrane
A type 1 transmembrane
Yes, envelope
Protects virion against


Cofactor of
protein present on

complement cascade.


Proteolysis
thymocytes, T cells, B

Mechanism employed


(MCP/CD46)
cells, natural killer cells,

by HIV identical to that



monocytes, neutrophils,

found on host cellular



platelets, endothelial

proteins.



cells, epithelial cells,



fibroblasts and placenta.



Complement control



protein prevents



convertase (C4b, 2b or



C3 convertase and C4b,



2b, 3b or C5 convertase)



production by cleaving



C3b into iC3b, an



inactive protein.



Therefore controls both



classical and alternative



complement pathways.



Cofactor for factor I.



Found on chromosome 1



location 1q32. Has a



role in tailoring innate



immune recognition of



apoptotic and necrotic



cells. Bridges innate



and acquired immunity



by regulating T cell-



induced inflammatory



reactions.


Decay
A
Yes, envelope
Protects virion against


Accelerating
glycosylphosphatidylinositol

complement cascade.


Factor
(GPI)-anchored

Mechanism employed


(DAF/CD55)
membrane protein

by HIV identical to that



present on all

found on host cellular



hemopoietic cells.

proteins.



Complement control



protein competes with



factor B for binding to



C3b on the cell surface



and displaces Bb protein



from a convertase C3 or



C5 convertase that has



already formed. Found



on chromosome 1



location 1q32. Antigen-



presenting cell



exosomes are protected



from complement-



mediated lysis by



expression of CD55 and



CD59.


20-kd
A GPI-anchored
Yes, envelope
Protects virion against


homologous
membrane present on

complement cascade.


restriction factor
many hemopoietic cells.

Mechanism employed


(HRF-20/CD59)
Complement control

by HIV identical to that



protein inhibits cell

found on host cellular



surface membrane

proteins.



attack complex.



Recognizes specific



domains within C8 and



C9. Found on



chromosome 11 location



11p13. Antigen-



presenting cell



exosomes are protected



from complement-



mediated lysis by



expression of CD55 and



CD59.


Factor H
Complement control
Yes, envelope
Protects virion against



protein inhibits C3 and

complement cascade.



C5 convertase formation

Mechanism employed



and promotes

by HIV identical to that



degradation of C3

found on host cellular



convertase. Found on

proteins.



chromosome 1 location



1q32. Factor H domains



19-20 alone are capable



of discriminating



between host-like and



complement-activating



cells. Three heparin-



binding sites were



identified in complement



factor H1. Factor H is



cleaved by a dermatan



sulfate-mediated



protease identified in



blood. The site and



putative residues on



factor H (FH) essential



for the interaction of the



C-terminal end of FH



with C3d, C3b, and



heparin have been



identified; the heparin-



and C3d-binding sites



are overlapping.


Thy-1 (CD90)
A GPI-anchored
Yes, envelope
HIV-1 Matrix co-



membrane protein
and Matrix
localizes with Thy-1 in



present on
protein
lipid rafts, the site of



prothymocytes, brain

virus particle budding



and other non lymphoid

from cells, and Thy-1 is



tissue. Found on

incorporated into virus



chromosome 11 location

particles as a result of



11q22.3-q23. Role of

this process.



endothelial cell receptor



Thy1 in cell adhesion



has been defined.



AlphaX-beta2



specifically interacts with



Thy-1. Thy-1 and Mac-1



interact and are involved



in the adhesion of



leukocytes to activated



endothelial cells as well



as in subsequent trans



endothelial migration of



leukocytes into the



perivascular tissue.


GM1 (β-
Gangliosides are
Yes, envelope
May facilitate


galactosidase)
glycosphingolipids found

gp120/gp41/CD4



in neuronal and synaptic

membrane fusion.



membranes. Basic



structure consists of an



oligosaccharide chain



attached to a hydroxyl



(OH) group of ceramide



and sialic acid bound to



galactose. Gangliosides



are degraded



sequentially by specific



exoglycosidases. Found



on chromosome 3



location 3p21.33.



Catalyzes the enzymatic



conversion of gal-



NAcglc-gal-glc-



ceramide→NAcglc-gal-



glc-ceramide. Involved



in cell-cell interaction,



signal transduction, and



cell activation.


HLA-DR
Antigen presentation,
Yes, envelope
Interacts with CD4



MHC class II directly

glycoprotein on target



presents peptide

cells. Without



antigens to CD4 T cells.

associated antigen in



Highly polymorphic.

the peptide binding



Heterodimer consisting

cleft of HLA-DR and



of an alpha (DRA) and a

co-stimulating



beta (DRB) chain, both

molecular interactions,



anchored in the

CD4 cell will be



membrane. Presents

rendered anergic.



peptides derived from

HIV-1 Gag expression



extracellular proteins by

is able to induce HLA-



antigen presenting cells,

DR cell-surface



B cells, dendritic cells

localization in H78-



and macrophages.

C10.0 cells. In human



Found on chromosome 6

macrophages, HIV-1



location 6p21.3.

Gag proteins co-





localize with MHC II





(HLA-DR), CD63, and





Lamp1 in MHC II





compartments. HIV-1





Capsid (p24) inhibits





interferon gamma





induced increases in





HLA-DR and





cytochrome B heavy





chain mRNA levels in





the human monocyte-





like cell line THP1.





HIV-1 Tat down





regulates expression of





MHC class II genes in





antigen-presenting





cells (APC) by





inhibiting the





transactivator of MHC





class II genes, CIITA.





HIV-1 Tat up regulates





HLA-DR expression in





monocyte-derived





dendritic cells and T





cells, thereby driving T





cell-mediated immune





responses and





activation. Associates





with HIV-1 gp41.





Enhances HIV-1





infectivity. Not affected





by viral tropism which





is determined by the





V3 loop of gp120.





Amino acids 708-750





of gp41 required for





MHC-II incorporation





into the HIV-1





envelope.





Approximately 375 to





600 molecules of HLA





II are incorporated into





each HIV-1 virion.





HLA II DR is the





predominant if not only





subtype of HLA II





detected on the





surface of most HIV-1





virions. Therefore,





HLA II DR is





selectively





incorporated into the





viral envelope.


ICAM-1
A type 1 transmembrane
Yes, envelope
Increases HIV


(Intercellular
protein present on

infectivity by a factor of


adhesion
leukocytes and

5 to 10 in T cells not


molecule 1 also
endothelial cells and

expressing the LFA


known as CD54)
inducible on

(lymphocyte function-


ICAM-2 ICAM-3
lymphocytes, dendritic

associated antigen)-1



cells, keratinocytes,

ligand. In T cells



chondrocytes,

expressing the LFA-1



fibroblasts, and epithelial

ligand, infectivity



cells. A ligand for CD11

increases one hundred



and CD18. Adhesion

fold. ICAM-1



molecule binds to LFA-1

increases the stability



(lymphocyte function

of virion/cell



antigen 1 also known as

interaction. The ICAM-



CD11a/CD18)

1/LFA-1 association



contributes to T and B

was a more efficient



cell activation. Found on

transmission factor for



chromosome 19 location

HIV-1 bearing ICAM-1



19p13.3-p13.2.

than combined



Signaling via ICAM-1

gp120/DC-SIGN &



induces adhesiveness of

ICAM-3/DC-SIGN. The



mononuclear

finding was confirmed



phagocytes. Direct

in human lymphoid



interaction of ICAM-1

tissues.29 ICAM-1 co-



with cytoplasmic alpha-

localizes with HIV-1



actinin-1 and -4 is

Matrix at sites of cell-



essential for leukocyte

to-cell membrane



extravasation. Functions

contact and is



with VCAM-1 (vascular

incorporated into virus



cell adhesion molecule-

particles. Expression



1), activated moesin,

of HIV-1 Nef in



actin, alpha-actinin,

macrophages induces



vinculin, ezrin and VASP

the release of soluble



(vasodilator-stimulated

ICAM, which



phosphoprotein) to

upregulates the



facilitate leukocyte

expression of co-



adhesion. An inducible

stimulatory receptors



ligand for both LFA-1

on B lymphocytes.



(αLβ2) and Mac-1

Interacts with Tat and



(αMβ2). Interacts with

Nef. Tat up regulates



the actin cytoskeleton

the expression of



using ezrin as an

ICAM-1 on endothelial



intermediate.

cells and astrocytes, in





part regulated by





NFKB. May be





correlated with the





development of AIDS-





related Kaposi's





sarcoma. Increases





HIV infectivity.





Interacts directly or





indirectly with Gag





polyprotein precursor





Pr55Gag in newly





formed virions. May





allow virion fusion with





CD4 negative cells.


LFA-1
A type I transmembrane
Yes, envelope
The incorporation of


(CD11A/LFA1A/I
protein found on

adhesion molecules


TGAL [integrin,
lymphocytes,

may allow virion fusion


alpha L (antigen
neutrophils, monocytes,

with CD4 negative


CD11A [p180]),
and macrophages,

cells.


lymphocyte
facilitates cell adhesion


function-
and cell activation.


associated
Contributes to B cell/T


antigen 1; alpha
cell interactions. Natural


polypeptide]
ligand, ICAM-1. Found



on chromosome 16



location 16p11.2. NK



cells receive early



activation signals directly



through LFA-1 without



co-stimulatory signals.


VCAM-1
A member of the Ig
Yes, envelope
B-lymphomas


(vascular cell
superfamily, a cell

characterize HIV.


adhesion
surface sialoglycoprotein

Endothelial cells (EC's)


molecule 1; also
expressed by cytokine-

bind firmly to malignant


known as
activated endothelial

B cells. The key event


CD106)
cells, macrophages,

promoting EC-BL-cell



dendritic cells and

adhesion was Vpu of



marrow stroma. Type I

HIV-1 upregulates



membrane protein

endothelial CD40,



mediating leukocyte-

facilitating increased



endothelial cell adhesion

expression of vascular



and signal transduction.

cell adhesion molecule



Two alternatively spliced

1 (VCAM-1).



transcripts encoding

Therefore, Vpu may



different isoforms have

enhance the metastatic



been described.

potential of B



Interacts with α4β1

lymphomas.



(VCAM-1 counterpart or



ligand). Found on



chromosome 1 location



1p32-p31.


VLA-4

Yes, envelope


(CD29/CD49d)


MHC-1
In humans, six MHC
Yes, envelope
Enhances HIV



class 1 isotypes have

infectivity and changes



been identified: HLA-A,

gp120 conformation.



HLA-B, HLA-C, HLA-E,

Without antigen in



HLA-F and HLA-G.

MHC-1 binding groove



HLA-A, HLA-B and HLA-

and co-stimulatory



C function to present

activity, anergy results.



antigens to CD8 T cells

HIV-1 Nef down



and to form ligands for

regulates surface



natural killer (NK) cell

expression of CD4 and



receptors. HLA-E and

MHC-1 in resting CD4+



HLA-G also ligands for

T lymphocytes. Nef up



NK-cell receptors. HLA-

regulates cell surface



A is found on

levels of the MHC-2



chromosome 6 location

invariant chain CD74.



6p21.3.

Nef down regulates





HLA class I expression





and therefore





suppresses the





cytolytic activity of HIV-





1-specific cytotoxic T-





lymphocyte (CTL)





clones. Macrophage-





tropic (M-tropic) HIV-1





Nef down regulates





expression of HLA-A2





on the surface of





productively infected





macrophages. HIV-1





group N and group O





Nef weakly down





regulates CD4, CD28,





and class I and II MHC





molecules and up





regulates surface





expression of the





invariant chain (Ii)





associated with





immature major





histocompatibility





complex (MHC) class





II. Nef interrupts MHC-





I trafficking to the





plasma membrane and





inhibits antigen





presentation. Nef





interacts with the μ1





subunit of adaptor





protein (AP) AP-1A, a





cellular protein





complex implicated in





TGN linking





endosome/lysosome





pathways. HIV-1 Nef





binds to the MHC-I





(HLA-A2) hypo





phosphorylated





cytoplasmic tails in the





endoplasmic reticulum;





this Nef-MHC-I





complex migrates into





the Golgi apparatus





then into the lysosomal





compartments for





degradation. Nef





promotes a physical





interaction between





endogenous AP-1 and





MHC-I. The Pro-X-X-





Pro motif in HIV-1 Nef





induces the





accumulation of CCR5





(HIV-1 M-tropic





coreceptor) in a





perinuclear





compartment where





both molecules co-





localize with MHC-1.





The Pro-X-X-Pro motif





interacts with src





homology region-3





domains of src-like





kinases interfering with





cell signaling





pathways. HIV-1 Nef





selectively down





regulates HLA-A and





HLA-B but does not





significantly affect





HLA-C or HLA-E,





which allows HIV-





infected cells to avoid





NK cell-mediated lysis.





Nef decreases the





incorporation of MHC-1





molecules into virions.





Furthermore, Nef down





regulates MHC-1





expression on human





dendritic cells.





Therefore, HIV-1 Nef





impairs antigen





presentation to HIV-





specific CD8+ T





lymphocytes. HIV-1





Nef-induced down





regulation of MHC-I





expression and MHC-I





targeting to the trans-





Golgi network (TGN)





require the binding of





Nef to PACS-1





(phosphofurin acidic





cluster sorting protein





1). PACS-1 is a





protein with a putative





role in the localization





of proteins to the trans-





Golgi network (TGN)





including furin which





cleaves gp160. HIV-1





Nef down regulates





MHC-1 on lymphoid,





monocytic and





epithelial cells. Nef





expression results in





rapid internalization





and accumulation of





MHC-1 in endosomal





vesicles which degrade





MHC-1 molecules. Nef





blocks transport of





MHC-I molecules to





the cell surface,





leading to





accumulation of MHC-





1 in intracellular





organelles.





Furthermore, the effect





of Nef on MHC-1





molecules (but not on





CD4) requires





phosphoinositide 3-





kinase (PI 3-kinase)





activity found on the





cytoplasmic side of the





plasma membrane.


CD63
A type III
Yes, envelope
The efferent arm of



transmembrane protein

viral replication occurs



present on activated

in the endosomes.



platelets, monocytes,

The CD63 marker is



macrophages, and in

the result of the



secretory granules of

endosomal sorting



vascular endothelial

machinery and



cells. Facilitates

facilitates further



adhesion to activated

endosomal viral



endothelium. A marker

maturation. CD63 may



of late endosomes.

facilitate HIV-1



Found on chromosome

penetration of



12 location 12q12-q13.

macrophages.



Regulates cell



development, activation,



growth and motility.



CD63 represents an



activation-induced



reinforcing element,



whose triggering



promotes sustained and



efficient T cell activation



and expansion. CD63



serves as an adaptor



protein that links its



interaction partners to



the endocytic machinery



of the cell.


CD81
A type III
Yes, envelope
The efferent arm of



transmembrane protein

viral replication occurs



found on lymphocytes

in the endosomes.



which facilitates signal

The CD81 marker is



transduction. A marker

the result of the



of late endosomes.

endosomal sorting



Found on chromosome

machinery and



11 location 11p15.5.

facilitates endosomal



CD81 signaling events

viral maturation.



could be mediated by



14-3-3 adapter proteins,



and these signals may



be dependent on cellular



redox. 14-3-3 Proteins



recognize



phosphoserine/threonine



amino acids in specific



primary amino acid



sequences. Control cell



cycle, apoptosis, gene



transcription, DNA



replication and



chromatin remodeling.


CD82
A type III
Yes, envelope
The efferent arm of



transmembrane protein

viral replication occurs



present on epithelial

in the endosomes.



cells, endothelial cells,

The CD82 marker is



and activated

the result of the



lymphocytes. May be

endosomal sorting



involved in intracellular

machinery and



calcium fluctuations. A

facilitates endosomal



marker of late

viral maturation. HIV-1



endosomes. Found on

Gag proteins co-



chromosome 11 location

localize with the type III



11p11.2. CD82

transmembrane



facilitates transcription of

proteins CD9, CD81,



IL-2 gene. Coordinates

CD82 and CD63.



activity with β1 integrin



in IL-2 gene



transcription.


CD107a (LAMP-
A type I transmembrane
Yes, envelope
The efferent arm of


1 [Lysosome-
protein present on

viral replication occurs


associated
activated platelets. A

in the endosomes.


membrane
marker of late

The LAMP-1 marker is


glycoprotein 1
endosomes. Found on

the result of the


precursor])
chromosome X location

endosomal sorting



Xp21.1.

machinery and





facilitates endosomal





viral maturation.


HP68
RNase L inhibitor. A
Present in
Interacts with HIV-1



member of the
immature
Gag. Protects viral



superfamily of ATP-
capsid
RNA from intracellular



binding cassette (ABC)
assembly
RNAse degradation.



transporters. ABC
intermediates.
Also interacts with Vif.



proteins transport

Essential for post-



various molecules

translational events in



across extra- and intracellular

immature HIV-1 capsid



membranes.

assembly. Interaction



Inhibits protein synthesis

of Vif involved in virion



in the 2-5A/RNase L

morphogenesis and



system, the central

infectivity. Basic



pathway for viral

residues in NC recruit



interferon action. Two

both viral RNA and



transcript variants

HP68 facilitating



encoding the same

capsid assembly.



protein have been found



for this gene. Found on



chromosome 4 location



4q31.


Ezrin (villin 2)
Cytoskeletal protein
Yes, virion,
Facilitates viral fusion



linking the actin
specifically
with target cell and



cytoskeleton with the
internal
possibly endocytosis of



plasma membrane.
nucleocapsid
virion. Incorporated



Found on chromosome 6
and reverse
into HIV-1 particles via



location 6q25.2-q26.
transcription
interaction with actin



Binds directly to CD95
complex
which binds to the p7



(APO-1/Fas) mediating

domain of HIV-1 Gag.



apoptosis in CD4+ T



cells. Part of the



ezrin/radixin/moesin



(ERM) family proteins.



Links the actin



cytoskeleton to the



dystroglycan adhesion



receptor complex.



Functions in cell



adhesion, cell survival



and motility. Function



regulated by



phosphorylation on two



tyrosine residues, one at



the amino-terminal, the



other in the carboxyl-



terminal domain.



Involved in signal



transduction pathways



that involve tyrosine



kinases, including PI3K



(phosphatidyl inositide 3-



kinase) and c-Src (the



proto-oncogene of Src



tyrosine kinase).


Moesin
Cytoskeletal protein
Yes, virion,
Facilitates viral fusion



component of the ERM
specifically
and PIC directional



protein family. Localizes
internal
translocation into the



beneath the cell
nucleocapsid
nucleus. Incorporated



membrane and cross
and reverse
into HIV-1 particles via



links the plasma
transcription
interaction with actin



membrane and the
complex
which binds to the p7



cortical actin

domain of HIV-1 Gag.



cytoskeleton. Involved



in cell adhesion and



motility. Widely



expressed in B and T



cells. As with Ezrin,



phosphorylation of both



the N- and C-terminal



domains serves as



activating signals.



Moesin interacts with



CD43, CD44, CD50 and



other proteins containing



the PDZ (PSD-95, DIgA



and ZO-1) dimerization



domain. Found on



chromosome X location



Xq11.2-q12.


Actin (beta and
Cytoskeletal protein,
Yes, virion,
An intact actin


gamma)
most abundant protein in
specifically
cytoskeleton of host



mammalian cells, up to
internal
cell is essential for



15% of the total protein
nucleocapsid
efficient reverse



content, highly
and reverse
transcription of HIV-1.



conserved among
transcription
The viral proteins Rev



species. Three major
complex
and Vpr effect actin



isoforms have been

polymerization



identified - alpha, beta

facilitating the



and gamma. Alpha

preintegration complex



predominantly in muscle

(PIC) entry into the



tissue. Beta and gamma

nucleus. The matrix



are ubiquitous. Multiple

protein, p17, also



functions including

interacts with actin in



changes in cell structure,

the PIC. Actin is



pliability and motility.

necessary for the



Actin depolymerizing

clustering of the HIV



factor (ADF)/cofilin and

CD4 receptor and the



gelsolin in actin-filament

CXCR4 co-receptor



are primarily responsible

with gp120 binding.



for remodeling the actin

Interaction between



cytoskeleton.

Nef, Actin and Vav, a



ADF/cofilins are also

guanine nucleotide



necessary for

exchange factor of



cytokinesis. Involved in

Cdc42 and Rac (two



cellular mitosis. Intra

small GTPases



cellular cytoplasmic

regulating the actin



streaming is largely

cytoskeleton) modify



dependent upon actin.

the actin cortex before



Endocytosis,

viral budding. N-



phagocytosis and

terminal myristoylated



pinocytosis are actin

HIV-1 Nef associates



dependent. Beta actin

with actin in human B



found on chromosome 7

and T lymphocytes.



location 7p15-p12.

This influences the



Gamma actin found on

subcellular localization



chromosome 17 location

of Nef. Nuclear beta-



17q25.

actin bundles may be





involved in the Rev-





dependent





nuclear/cytoplasmic





transport of intron-





containing (unspliced





and incompletely





spliced) HIV-1 gag





mRNA.


Ubiquitin
Vesicular transport
Yes, virion
Monoubiquitination of



protein, 76 amino acid

late domains (L



protein ubiquitous in all

domains) of viral



mammalian cells

proteins targets the



correlated with multiple

proteins to the host



cellular functions,

intracellular endocytic



including, but not limited

pathway. HIV-1 L



to, degradation of

domain is a highly



proteins under

conserved Pro-Thr-



conditions of stress,

Ala-Pro (PTAP)



degradation of

sequence in the p6



denatured or damaged

domain of Gag.



proteins, targeted



degradation of regulatory



proteins, transmembrane



receptors, mitotic



cyclins, transcription



activating proteins,



modulation of cell



surface receptor activity,



import of proteins into



cellular organelles, DNA



repair, processing and



presenting of antigens



and ribosomal assembly.



Monoubiquitination of



plasma membrane



receptors targets



intracellular proteins to



the endocytic pathway



and functions as a



sorting signal directing



the movement of



proteins between



different endocytic



compartments.


Pin1 (protein
A parvulin, a peptidyl-
Yes, virion
Increases intra cellular


[peptidyl prolyl
prolyl isomerase binds to

NFKB levels. NFKB


cis/trans
phosphoserine-proline

binding sites are found


isomerase] NIMA
and phosphothreonine-

in the HIV-1 core


[never in mitosis
proline motifs, essential

enhancer.


gene a)-related
in mitosis, facilitates


kinase]-
proline cis/trans


interacting 1)
isomerizations and



subsequent tertiary and



quaternary protein



structures. Proline



isomerization of cell



cycle protein Cdc25



phosphatase facilitates



dephosphorylation of



phosphorylated Cdc25



protein by the protein



phosphatase PP2A.



Found on chromosome



19 location 19p13.



Mediates GM-CSF



production. Binds c-Fos



through specific pS/T-P



sites within the c-Fos



TAD (carboxyl terminal



transactivation domain)



resulting in enhanced



transcriptional response



of c-Fos to polypeptide



growth factors that



stimulate ERK



(extracellular regulated



kinases). Involved in the



cooperative activity of c-



Jun and c-Fos to



regulate AP-1-



dependent gene



transcription upon



phosphorylation by



mitogen-activated kinase



(MAPK) family members.



Binds to the pThr254-



Pro motif in p65 and



inhibits p65 binding to



IKBα, resulting in



increased nuclear



accumulation and



protein stability of p65



and enhanced NFKB



activity. Interacts with



transcription factor β-



catenin (cadherin-



associated protein) and



increases the



transcription activity of



cyclin D1. Interacts with



the carboxyl terminal



domain (CTD) of RNA



polymerase II (RNAPII).



Inhibits the CTD



dephosphorylation by



FCP1. Enhances the



phosphorylation of the



CTD domain of RNAP II



by the cdc2/cyclinB



complex. Co-localizes



with the splicing factor



SC35 in the cell nucleus.



These protein



aggregates known as



“speckles” contain



transcription factors and



pre-mRNA. Speckles



are intra nuclear



warehouses storing



components of



transcription and the



RNA editing.


tRNA synthetase
Ligase, charges or
Yes, virion
tRNAlys3 binds to the


or aminoacyl
aminoacylates key RNA

primer binding site


tRNA synthetase
molecules linking the

initiating reverse



molecule to the

transcription. In HIV-1



respective amino acid.

an RNA loop formed



One synthetase for each

by the tRNAlys3



amino acid found in

anticodon and an



mammalian cells. ATP

adenine rich RNA loop



dependent.

initiates reverse





transcription.


tRNAlys
Allows incorporation of
Yes, virion
Induces three



lysine into proteins by
associated
dimensional structural



the host translational
attached to
changes in the



apparatus.
primer binding
unspliced viral RNA to




site (PBS)
allow reverse





transcription to





proceed.


GAPDH
In glycolysis,
Yes, virion
??????


(Glyceraldehyde-
enzymatically converts


3-phosphate
Glyceraldehyde-3-


dehydrogenase)
phosphate to 1,3-



bisphosphoglycerate.



Also involved in cell



cycle regulation by



modulating cyclin B-



cdk1, apoptosis,



membrane fusion,



microtubule bundling,



phosphotransferase



activity, nuclear RNA



export, programmed



neuronal cell death, DNA



replication, and DNA



repair. Found on



chromosome 12 location



12p13.


MAPK/ERK2
Serine/threonine kinases
Yes, virion
Phosphorylates


(mitogenic
important in regulation of

p6(gag), involved in


activated protein
growth and cellular

the budding stage of


kinase/extracellular
differentiation via a

HIV-1 life cycle. MAPK


regulated
cascade of sequential

(ERK1 and ERK2)


kinases)
protein kinases and

regulates HIV-1



scaffold proteins. Found

infectivity by



on chromosome 22

phosphorylating Vif.



locations 22q11.2;



22q11.21.


HSP60 (Heat
Chaperone intracellular
Yes, virion
Enhances 3′


shock protein 60)
protein produced in

processing and strand



response to intracellular

transfer in HIV-1 DNA



stress. Found on

integration.



chromosome 2 location



2q33.1. A member of



the chaperonin family. A



mitochondrial protein



that may function as a



signaling molecule in the



innate immune system.



Essential for folding and



assembly of newly



imported proteins into



the mitochondria. Two



transcript variants



encoding the same



protein have been



identified for this gene.


HSP70 (Heat
Chaperone intracellular
Yes, virion
May bind HIV-1 gag


shock protein 70)
protein produced in

polyprotein chain and



response to intracellular

maintain proper tertiary



stress. Found on

confirmation during



chromosome 19 location

intracellular transport



19q13.42. Binds to and

from nucleus to plasma



regulates Hsp70 activity.

membrane. May



The carboxyl terminus of

participate in early



Hsp70-interacting

events in infection.



protein (CHIP) is an

Might participate in



Hsp70-associated

uncoating the viral



ubiquitin ligase which

capsid. May target



ubiquitinates misfolded

HIV-1 PIC to the



proteins associated with

nucleus.



cytoplasmic chaperones.


HSC70 (also
Chaperone, heat shock
Yes, virion
May bind HIV-1 gag


called Hsp73)
protein, works with

polyprotein chain and



auxilin to remove clathrin

maintain proper tertiary



coated vesicles. Found

confirmation during



on chromosome 11

intracellular transport



location 11q24.1. Heat-

from nucleus to plasma



inducible and

membrane. May



constitutively expressed

participate in early



proteins identified.

events in infection.



Binds to nascent

Might participate in



polypeptides to facilitate

uncoating the viral



correct folding.

capsid. May target



Functions as an ATPase

HIV-1 PIC to the



in the disassembly of

nucleus.



clathrin-coated vesicles



during transport of



membrane components



through the cell. Two



alternatively spliced



variants have been



characterized.


CypA
Immunophilin, peptidyl-
Yes, virion
Incorporated as a


(Cyclophilin A)
prolyl isomerase. Found

component of the Gag



on chromosome 7

molecule at a 1/10



location 7p13.

ratio. Also interacts



Catalyzes the cis-trans

with Vpr, Vif, MA, Nef



isomerization of proline

and gp120env. Binds



imidic peptide bonds in

to the central region of



oligopeptides,

the CA protein



accelerates the folding of

(residues 85 to 93).



proteins.

Catalyzes the cis/trans





isomerization of the





Gly-89-Pro-90 peptide





bond. The capsid





sequence 87His-Ala-





Gly-Pro-Ile-Ala92





(87HAGPIA92)





encompasses the





primary cyclophilin A





binding site. Inhibits





Itk (Interleukin-2





tyrosine kinase)





catalytic activity, a





cytoplasmic non-





receptor protein





tyrosine kinase of the





Tec (Molecular class:





tyrosine kinase,





Molecular Function:





protein-tyrosine kinase





activity, Biological





Process: cell





communication, signal





transduction) family





that participates in the





intracellular signaling





events leading to T cell





activation. A proline-





dependent





conformational switch





within the Itk SH2





domain regulates





substrate recognition





and mediates





regulatory interactions





with the active site of





CypA. Regulates the





cis/trans





interconversion of the





imidic bond within the





conserved proline





residues of Vpr in vivo.





Implicated in capsid





final assembly and





defense of HIV-1





against innate host





restriction factors





specifically Ref-1.





CypA/CD147 (Type I





integral membrane





glycoprotein found on





hemopoietic,





microglial, endothelial





and peripheral blood





cells) interaction





follows CypA





interaction with surface





heparins. Facilitates





viral/host cell binding





prior to gp120/CD4





and gp120/CXCR4 or





CCR5 co-receptor





interaction. Increases





probability of





successful infection





when a small amount





of virus has been





transmitted.


FKBP12 (FK506
A peptidyl prolyl
Yes, virion
Growth of chronically


binding proteins)
isomerase. Found on

infected HIV-1 cells



chromosome 20 location

dependent on FKBP12



20p13. There is

in vitro.



evidence of multiple



alternatively spliced



transcript variants for



this gene.


Tsg101 (Tumor
Vesicular transport
Yes, virion
Helix-1 of p6 binds to


specific gene)
protein, a component of

the binding groove in


(VPS28
the endosomal sorting

Tsg101. The PTAP


homolog)
complex known as

motif of p6 binds



ESCRT-I which activates

Tsg101 linking the



formation of ESCRT-II,

efferent virion to the



which in turn recruits

host endosomal



ESCRT-III, all

process. AIP1



components of the multi

interacts with Tsg101



vesicular body (MVB)

and p6 forming a



formation process.

ternary complex that





recruits CHMP





(charges multi





vesicular body





proteins) proteins





leading to the





endosomal cascade





culminating in viral





fission. The proline





rich motif in p6 mimics





the adapter protein Hrs





(hepatocyte growth





factor-regulated





tyrosine kinase





substrate), a





component of the





MVB.


Tal (Tsg101-
Vesicular transport
Yes, virion
Regulates a Tsg101-


associated ligase
protein. Found on

associated complex


also known as
chromosome 9 location

responsible for the


LRSAM1/leucine
9q33.3-q34.11.

sorting of cargo into


rich repeat and
Regulates vesicular

cytoplasm-containing


sterile alpha
trafficking processes in

vesicles that bud at


motif containing
mammals. RING (really

multi vesicular bodies


1)
interesting new gene)

and at the plasma



finger necessary for

membrane. The



multiple

ubiquitin E2 variant



monoubiquitination of

(UEV region) of



Tsg101. Bivalent

Tsg101 binds to the



binding of Tsg101 to a

PTAP-PSAP motif of



PTAP motif and to a

Tal near the COOH



central region of Tal is

terminus. Monomeric



essential for Tal-

ubiquitin binds to



mediated ubiquitination

Tsg101 at a site



of Tsg101. RING finger

outside the UEV. The



motifs are found in

coiled coil (CC) region



proteins of regulatory

of Tal interacts with the



function linked to

steadiness box (SB) of



ubiquitin proteasome

Tsg101. Tal mediated



system. Promotes

ubiquitination of



ubiquitination of target

Tsg101 inactivates



proteins that have been

sorting/endosomal



recognized by the E3

directed function of



enzymes. RING

Tsg101 and



functions as a scaffold

translocates Tsg101



positioning the substrate

from the plasma



and the E2 enzyme

membrane. Enzymes



facilitating ubiquitin

that remove the



transfer. RING finger

ubiquitin on Tsg101



E3s perform three

work in concert with



functions: (1)

Tal. The coordinated



recognition and binding

activity of Tal and a Tal



of the substrate, (2)

specific



recognition and binding

deubiquitination



of the E2 enzyme, and

enzyme control the



(3) transfer ubiquitin.

recycling of the Tsg101





and the reloading of





Tsg101 mediated





cargo. Ubiquitination





of Tsg101 may allow





transient dissociation





of Tsg101 from its





cargo allowing for the





next step in the





ESCRT complex to





assimilate the cargo of





Tsg101 facilitating the





endosomal pathway





hijacked by the HIV





virus. Therefore Tal





accelerates the





endosomal/sorting





function of Tsg101.


AIP1/ALIX (ALG-
Vesicular transport
Yes, virion
The p6 domain of HIV-


2-interacting
protein. Found on

1 forms a ternary


protein X [also
chromosome 3 location

complex with AIP1 and


known as
3p22.3. Functions in

Tsg101 which recruit


PDCD61P
actin-dependent

CHMP proteins directly


programmed cell
intracellular positioning

via AIP1 and indirectly


death 6
of endosomes. Interacts

via ESCRT-II to form


interacting
with an EF-hand type

ESCRT-III. p6 adopt a


protein])
Ca2+-binding protein,

helix-flexible helix



ALG-2 (apoptosis-linked

structure; a short helix-



gene 2), through its C-

1 (amino acids 14-18)



terminal proline-rich

is connected to a



region. CHMP4a and

pronounced helix-2



CHMP4b (chromatin-

(amino acids 33-44) by



modifying protein;

a flexible hinge region.



charged multi vesicular

Helix-2 binds to



body protein), are also

AIP1/ALIX, the site of



binding partners.

interaction with Vpr.



CHMP4b and Alix

This indicates that the



participate in formation

Vpr binding region of



of multivesicular bodies

p6 adopts different



by cooperating with

three dimension



SKD1 (suppressor of K+

structures dependent



transport defect 1), a

on the viral life cycle



dominant negative form

context.



of the AAA type ATPase.



Involved in calcium-



dependent apoptosis.



Links early endosomal



complexes



(TSG101/ESCRT-I) and



late endosomal



complexes



(CHMP4/ESCRT-III).


VPS4B (vacuolar
Vesicular transport
Yes, virion
Binds to the COOH


protein sorting 4
protein. Member of the

terminal half of


homolog B)
AAA protein family

Tsg101, specifically



(ATPases). Found on

residues 330-377.



chromosome 18 location

Required for HIV



18q21-32-q21.33.

fission. Approximately





5-25 VPS28 molecules





incorporated into each





virion.


APOBEC3G
Member of the cytidine
Yes, virion
Binds to accessory



deaminase gene family,

protein Vif. Vif reduces



Induces viral DNA hyper

viral incorporation and



mutations converting a

cellular expression of



cytosine residue into a

protein limiting viral



uracil residue. Uracil

hyper mutation.



residues in DNA tag the

Incorporated into virion



nucleic acid for nuclease

between the two zinc



destruction. Found on

coordination motifs in



chromosome 22 location

Vif (amino acids 54-124).



22q13.1-q13.2

Also binds to





nucleocapsid





sequence (amino acids





104-156).


APOBEC3F
Member of the cytidine
Yes, virion
Targeted by the COOH



deaminase gene family.

terminus of Vif



Functionally related to

accessory protein



the C to U RNA-editing

limiting viral DNA



cytidine deaminase

hyper mutation.



APOBEC1. Controls

Localization by Vif to



degradation of cell cycle

processing or P-bodies



proteins. Found on

(cytoplasmic



chromosome 22 location

compartments involved



22q13.1.

in the degradation and





storage of non





translating mRNAs).





Induces G to A hyper





mutations in newly





synthesized minus





strand viral cDNA at





the step of reverse





transcription.


UNG (Uracil-
Uracil-DNA glycosylase
Yes, virion
Integrase is required


DNA
removes DNA uracil

for packaging of UNG


glycosylase)
residues. Excises the

into virions. UNG2



uracil residues and

binds the viral reverse



introduces non

transcriptase enzyme.



templated nucleotides

Uracil repair pathway



allowing for somatic

is associated with HIV-



hyper mutation.

1 viral particles.



Increases



immunoglobulin



diversity. Essential for



generation of strand



breaks for class switch



recombination. Both



mitochondrial (UNG1)



and nuclear (UNG2)



isoforms have been



described. UNG1 only



uracil-DNA glycosylase



isolated to date in



mitochondria.



Mitochondrial UNG1 is



encoded by nuclear not



mitochondrial DNA.



UNG2 predominant form



in proliferating cells,



UNG1 predominant form



in non-proliferating cells.



UNG2 levels high in S-



phase and early G2 of



the cell cycle. UNG2



primarily located at



replication foci during S-



phase. A second uracil-



DNA glycosylase,



Single-strand-selective



Monofunctional Uracil-



DNA Glycosylase



(SMUG1) has a



preference for double-



stranded DNA rather



than single-stranded



DNA as with UNG1 and



UNG2. Found on



chromosome 12 location



12q23-q24.1. Not cell



cycle regulated, does not



accumulate at replication



fosi and is not found in



mitochondria. SMUG1



accumulates in nucleoli,



UNG2 excluded from



nucleoli. UNG1, UNG2



and SMUG1 function in



base excision repair.



UNG2 implicated in both



innate and acquired



immunity.


Staufen
Double-stranded RNA
Yes, virion
Binds HIV-1 genomic



binding protein.

RNA. May be involved



Transports mRNAs to

in retroviral genome



intracellular

selection and



compartments/organelles.

packaging into



Found on

assembling virions.



chromosome 20 location

Interaction with the



20q13.1. Binds tubulin.

nucleocapsid domain



Transports mRNA via

of pr55(Gag) in vitro



the microtubule network

and in live cells



to the RER. Five

mediated by Staufen's



transcript variants from

dsRBD3 (RNA binding



alternative splicing of

domain 3), with a



STAU gene encoding

contribution from its C-



three isoforms have

terminal domain.



been described.

Preferentially binds





with the 9-kb non-





spliced viral RNA.





Implicated in the





generation of infectious





virions.


INI1 (Integrase
INI1 is one of four
Yes, virion
INI1 has two highly


interactor
components of the

conserved domains


1)/hSNF5
mammalian SWI (yeast

known as imperfect



mating type switch

repeats (Rpt1 and



gene)/SNF (sucrose non

Rpt2). HIV-1 integrase



fermentable gene)

specifically binds to



complex involved in

Rpt 1, not Rpt 2. INI1



ATP-dependent

is incorporated into the



chromosome

virions and is



remodeling. Found on

necessary for viral



chromosome 22

production. Couples



locations 22q11.23 and

DNA binding of HIV-1



22q11.

PIC to the host cell





transcriptional





apparatus. Possibly





couples integration and





transcription.





Stimulates the





integration protein of





the transcription





coactivator PC4





(LEDGF/p75).


EF-1α
Catalyzes the entry of
Yes,
Interacts with MA (p17)



aminoacyl-tRNA into the
associated
and the nucleocapsid



ribosomal A (aminoacyl
with MA and
protein (p7). Basic



site). Energy source
NC
residues in MA and NC



hydrolysis of GTP.

and possibly viral RNA



Forms ternary complex

are required for



with GTP and all

binding. May allow



aminoacyl-tRNAs except

RNA to be packaged



the initiator tRNAimet.

into virions. Catalyzes



Isolated as an actin-

the binding of RNA



binding and bundling

Polymerase II and



protein in some cell

TRP-185 to HIV-1 TAR



lines. May control cell

RNA. May interact



cycle progression via its

with Tat.



actin interaction. Found



on chromosome 6



location 6q14.1. Multiple



copies found on other



chromosomes



representing pseudo



genes have been



defined.


LEDGF/p75
DNA-binding protein
Yes, PIC
Central core domain


(lens epithelium-
implicated in cellular
(preintegration
and N-terminal zinc


derived growth
differentiation and
complex)
binding domain of


factor/transcription
cellular response to

integrase are involved


coactivator p75
environmental stress.

in the interaction with


[alternate names
Activates transcription of

LEDGF/p75. An


include
stress related genes

essential cofactor for


PC(positive cofactor)
triggering a survival

nuclear targeting of


4 and
response. Protective

HIV-1 integrase.


SFRS1
role in stress-induced

Physically links


interaction
apoptosis. Found on

integrase to host


protein 2
chromosome 9 location

chromatin. The


(PSIP2)]) Prior
9p22.3. A member of

alternatively spliced


journal articles
the hepatoma-derived

protein LEDGF/p52,


differentiate p75
growth factor (HDGF).

does not interact with


from PC4 in
The alternatively spliced

HIV-1 or HIV-2


HELA cells
p52 (PC4 and SFRS1

integrase. LEDGF/p75



interaction protein 1

links the integrase



(PSIP1)) protein

protein to the host



interactions with

chromatin during the



transcriptional

G2 phase of the cell



coactivators, general

cycle. May target the



transcription factors, and

HIV-1 proviral DNA to



splicing factors,

specific genomic sites



modulating pre-mRNA

of actively transcribed



splicing of class II genes.

genes to promote viral



The p75 protein is not a

transcription.



transcriptional factor.

Residues are the



Heparin binds to

integrase binding



LEDGF/p75, facilitating

domain (IBD). Dictates



transport through the

site(s) of HIV



cytoplasm into the

integration, most



nucleus. The N-terminal

favored are areas



PWWP domain and its

undergoing



beta-barrel substructure

transcription, high G-C



are needed for binding to

(guanine-cytosine)



metaphase chromatin.

content, with active





RNA polymerase





subunits and





transcription factors.





Prevents proteasomal





degradation of HIV-1





integrase. The N-





terminal zinc binding





domain (amino acids





1-52) and the central





core domain (amino





acids 53-212) of HIV-1





integrase interact with





LEDGF/p75. The core





domain harbors the





main determinant for





this interaction.


DNA-PK (DNA-
Repairs double-stranded
Yes, virion,
Participates in


dependent
DNA breaks by
PIC
retroviral DNA


protein kinase)
nonhomologous and

integration. Sp1 is a



joining (NHEJ).

mammalian



Composed of DNA

transcription factor



binding protein,

characterized by



Ku70/Ku86 heterodimer

clusters of zinc fingers.



and a large catalytic

Zinc fingers are



subunit, DNA-PKcs (a

essential for correct



serine/threonine protein

folding and DNA



kinase). The DNA-PKcs

binding. Tat amino



is found on chromosome

acids 30 to 55 binds to



8 location 8q11.

the transcription factor



Participates in

Sp1. Tat augments



variable/diversity/joining

double-stranded DNA-



recombination events in

PK-mediated Sp1



T and B cells. The

phosphorylation in a



PRKDC gene encodes

contact-dependent



the catalytic subunit

manner.



DNA-PKcs. The DNA-



binding component is the



autoimmune antigen Ku



(MIM 152690). On its



own, the catalytic



subunit of DNA-PK is



inactive and relies on the



Ku component for



nuclear localization and



kinase activity. DNA-



PKcs is only function



when bound to DNA.


Ku80
86-kDa subunit of
Yes, virion,
Required for the



human DNA-dependent
PIC
formation of the



protein kinase. Ku80

retroviral 2-LTR circle



protein forms

DNA. Protects



heterodimer with the

infected cells from



Ku70 subunit to form a

retrovirus-induced



complex that possesses

apoptosis. Binds to



a DNA end-binding

viral cDNA. Enhances



activity. Ku70/Ku80

binding of reverse



heterodimer can recruit

transcriptase and/or



the catalytic p350

integrase as well as



subunit of the DNA-

the PIC associated



dependent protein

host cellular cofactors.



kinase. Catalyzes DNA

The DNA repair



double-strand break

pathway is another



repair (nonhomologous

cellular process



recombinational

hijacked by HIV to



repair/NHEJ). Found on

complete life cycle.



chromosome 2 location



2q35. Implicated in



transcription,



variable/diversity/joining



gene recombination in T



and B cells and telomere



maintenance.


hRad18
The protein encoded by
Yes, virion,
hRAD18 possesses a



this gene is similar to the
PIC
RING (Really



S. cerevisiae DNA

Interesting New Gene)



damage repair protein

finger domain, a



Rad18. Yeast Rad18

structure associated



interacts with Rad6, an

with E3 ubiquitin



ubiquitin-conjugating

ligases. A 162-residue



enzyme (E2) required for

region of hRad18



post-replication repair of

(amino acids 65-226)



damaged DNA. Similar

binds with and



to its yeast counterpart,

stabilizes integrase.



hRad18 interacts with

Integrase is inherently



the human homolog of

unstable since its N



yeast Rad6 protein

terminal amino acid is



through a conserved

phenylalanine. N



ring-finger motif. Found

terminal phenylalanine



on chromosome 3

is recognized as a



location 3p25-p24.

degradation signal by





the ubiquitin





proteasome system





(N-end Rule). hRad18





interacts with HIV-1





integrase in





replication/translesion





DNA repair in the





retroviral integration





process.


EED (Embryonic
Nuclear protein involved
Yes, virion (?)
Interacts with HIV-1


ectoderm
in transcriptional

matrix and integrase


development)
repression and gene

early in the HIV viral



silencing by histone de-

life cycle. May



acetylation. Found on

facilitate replication.



chromosome 11 location

Nef translocates EED



11q14.2-q22.3. May

from the nucleus to the



regulate integrin

plasma membrane.



function. Two distinct

This stimulates Tat-



isoforms identified. A

dependent HIV



member of the

transcription.



superfamily of WD-40



repeat proteins and of



the Polycomb group



proteins.


HMGA1/HMG-1a
A non-histone protein, a
Yes, virion,
Increases HIV


(high mobility
general coactivator of
PIC
integrase activity by a


group AT-hook1)
transcription, involved in

factor of 10.



many cellular processes,



including regulation of



inducible gene



transcription.



Preferentially binds to



the minor groove of A + T



(adenine + thymine) rich



regions in double-



stranded DNA.



Frequently acetylated



and found in the



nucleus. At least seven



transcript variants



encoding two different



isoforms have been



found for this gene.



Found on chromosome 6



location 6p21. A



characteristic feature is



the ability to bend DNA.


BAF (barrier-to-
Interacts with nuclear
Yes, virion,
Increases HIV


auto integration
proteins that have a
PIC and in
integrase activity by


factor)/BANF1
conserved LEM (LAP2
intact virions
5 × 103. Prevents HIV-1



[lamin-associated
Approximately
cDNA auto integration.



polypeptide 2], emerin,
zero to three
Promotes efficient



MAN1) domain.
copies per
intermolecular



Frequently found in DNA
virion.
recombination of viral



polymerases, ligases,

and host DNA. HIV-1



glycosylases and

cDNA associated with



helicases that bind DNA

emerin in vivo, and the



non-specifically.

interaction of viral



Definitive function

cDNA with chromatin



unknown. May reform

was dependent on



the nuclear envelope

emerin. Required for



during telophase (the

the association of viral



final stage of mitosis

cDNA with emerin (an



characterized by

inner nuclear envelope



cytokinesis or cell

protein) supporting



division). Found on

viral replication.



chromosome 11 location



11q13.1.


p300
A generalized
Yes, PIC
Tat binds two p300



transcriptional co-

and CBP both in vitro



activator with histone

and in vivo. Integrity of



acetylase activity.

the basic domain of



Found on chromosome

Tat is essential for this



22 location 22q13.2.

interaction. HIV-1 Tat



p300 is related by

forms a ternary



sequence to CBP

complex with P/CAF



(CREB-binding protein

and p300. This



[CREB: cyclic-AMP

increases the affinity of



responsive element

p300 for CDK9/P-TEFb



binding protein]). Like

CTD kinase complex.



CBP can stimulate

Tat binds to amino acid



transcription through

1253-1790 of p300.



activation of CREB.

This interaction results





in a structural change





of p300/CBP. Tat-p300





interaction increases





the HAT activity of





p300 on histone H4.





H4 is a component of





nucleosomes. Histone





H4 was acetylated on





lysines 8, 12, and 16.





Acetylation of H4 was





inhibited by Lys-





coenzyme A (CoA), a





selective inhibitor of





p300 acetyltransferase





activity. Tat could auto





acetylate itself, which





was specific to lysine





residues 41 and 71.





Acetylated Tat is





considered to be the





transcriptionally active





form intracellularly.





p300 and PCAF





directly acetylate Tat.





p300 acetylated Lys50





in the TAR RNA





binding domain, while





PCAF acetylated





Lys28 in the activation





domain of Tat.





Acetylation at Lys28 by





PCAF enhanced Tat





binding to the Tat-





associated kinase,





CDK9/P-TEFb, while





acetylation by p300 at





Lys50 of Tat promoted





the dissociation of Tat





from TAR RNA.





Acetylation of Tat





regulates two discrete





and functionally critical





steps in viral





transcription (1)





binding to an RNAP II





CTD-kinase, (2)





release of Tat from





TAR RNA. Vpr





induced G2/M growth





arrest is mediated by





p300 which promotes





cooperative





interactions between





the Rel A subunit of





NFKB and cyclin





B1.Cdc2. Vpr interacts





with p300 which





controls in part intra





cellular NFKB activity.





Therefore, Vpr controls





in part HIV





transcription via p300.


Rev cofactor
Related to nucleoporins
No?
hRIP is an essential


(RCF) (HRB
that mediate nuclear

cellular Rev cofactor


[HIV-1 Rev
cytoplasmic transport.

which functions at a


binding protein]),
Found on chromosome 2

step in HIV-1 RNA


(hRIP [human
location 2q36.3.

export: movement of


Rev-interacting


mRNAs from the


protein])


nucleus. Promotes the





release of incompletely





spliced HIV-1 RNAs





from the perinuclear





region.


HSP90 (Heat
HSPs, chaperone
No
Tat enters T cells toxin,


shock protein 90)
intracellular protein

using clathrin-mediated



produced in response to

endocytosis before



intracellular stress.

low-pH-induced and



Required for

Hsp90-assisted



translocation of FGF-1

endosomal



and FGF-2 across the

translocation. Critical



endosomal membrane.

to the



Involved in types I and II

stabilization/folding of



interferon pathways.

Cdk9 as well as the



Found on chromosome

assembly of an active



14 location 14q32.33.

Cdk9/cyclin T1





complex responsible





for P-TEFb-mediated





Tat transactivation.


CypB
Immunophilin with cis-
No
Interacts with HIV-1


(Cyclophilin B)
trans peptidyl-prolyl

Gag polyprotein



isomerase and

Pr55gag. HIV-1 Gag



chaperone-like activities.

directly contacts



Found on chromosome

residues in the



15 location 15q21-q22.

hydrophobic pocket of



Primarily located within

CyPA. Binds with



the endoplasmic

higher affinity to



reticulum. Associated

mature capsid protein



with the secretory

cleaved from the Gag



pathway and release of

polyprotein.



biological fluids.


HSP27
HSPs, chaperone.
No
May link the efferent



Induced by thermal, free

loop of the replication



radical, and

cycle to the endosomal



inflammatory stress.

pathway.



Chaperone denatured



intracellular proteins,



signal transduction



proteins, modulating



signaling cascades



during repeated stress.



Found on chromosome 7



location 7q11.23.


HSP40
HSPs, chaperone.
No
Interacts with Nef



Found on chromosome

which induces its



19 location 19p13.2.

expression. Nef



Induced by thermal, free

translocates Hsp40



radical, and

into the nucleus of



inflammatory stress.

infected cells. This



Chaperone denatured

facilitates viral gene



intracellular proteins,

expression. Becomes



signal transduction

part of the cyclin-



proteins, modulating

dependent kinase 9-



signaling cascades

associated



during repeated stress.

transcription complex





regulating long





terminal repeat-





mediated gene





expression.


VPS37B
Vesicular transport
No
Ternary complex with



protein. Found on

Tsg 101 and VPS 28



chromosome 12 location

forms the human



12q24.31. Component

ESCRT-I which is



of the human ESCRT-I

required for HIV-1 Gag



complex. Forms a

budding and virus



complex with Ts101 and

infectivity



Vps28.


CD4
A type I transmembrane
Yes, envelope
Interacts with specific



protein found on

domains of gp120



helper/inducer T cells,

facilitating viral fusion.



monocytes,



macrophages, and



dendritic cells that is



involved in T-cell



recognition of antigens.



Found on chromosome



12 location 12pter-p12.


CXCR4
Binds chemokine SDF-1
Yes, envelope
Viral co-receptor



(stromal cell derived

determines viral



factor 1). Found on

tropism for CD4 T



hematopoietic

cells.



precursors, mature white



blood cells and plasma



cells. Found on



chromosome 2 location



2q21. Type III



transmembrane protein



crossing the plasma



membrane seven times.


CCR5
Found on Th1 cells,
Yes, envelope
Viral co-receptor



dendritic cells,

determines viral



monocytes/macrophages.

tropism for



Type III

macrophages.



transmembrane protein



crossing the plasma



membrane seven times.



Ligands include



monocyte chemo



attractant protein 2



(MCP-2), macrophage



inflammatory protein 1



alpha (MIP-1 alpha),



macrophage



inflammatory protein 1



beta (MIP-1 beta) and



regulated on activation



normal T expressed and



secreted protein



(RANTES). Found on



chromosome 3 location



3p21.31


CD86
Member of the
Yes, envelope
Skews the host



immunoglobulin

towards a Th2 biased



superfamily. Membrane

immune response.



protein present on some



germinal-center B cells,



mitogen-activated B



cells, and monocytes



that serves as a B-cell



activator. Found on



chromosome 3 location



3q21. Co-stimulatory



signal necessary for



activation of T cell.


Phosphatidyl
Intermediate in the
No, virion?
Promotes binding of


inositol 4,5-
plasma membrane

Gag to the plasma


bisphosphate
generation of inositol

membrane to facilitate


[PI(4,5)P2]
triphosphate (IP3) and

protein/protein



diacylglycerol (DAG).

interactions involving



IP3 releases calcium

the capsid domains.



from the endoplasmic



reticulum and DAG



activates protein kinase



C (PKC). Found on



chromosome 22 location



22q11.2-q13.2.


NFKB
Cellular transcription

Binding sites in the



factor involved in the

viral LTR necessary for



immune process. Found

viral transcription.



on chromosome *



location *.


NFAT
Cellular transcription

Binding sites in the



factor involved in the

viral LTR necessary for



immune process. Found

viral transcription.



on chromosome 20



location 20q13.2-q13.3.


Sp1
Cellular transcription

Binding sites in the



factor involved in the

viral LTR necessary for



immune process. Found

viral transcription.



on chromosome 12



location 12q13.1.


Cyclin T


CDK9/PITALRE


RNA polymerase


II


Exportin 1/Crm 1


Ran GTP


Ran GTPase


activating protein


(RanGAP)


Ran Binding


Protein


(RanBP1)


CCR2B


CCR3


CCR8


GPR1


GPR15 (Bob)


STRL33 (Bonzo)


US28


CX3CR1 (V28)


APJ


chemR23


Furin


H-β-TrCP


Skp1p


AP-2


C4 binding


protein (C4b


protein)


CD35


(Complement-


receptor 1)


CD21


(Complement-


receptor 2)


sCR1


(Complement-


receptor 1)


Cyclin T


CDK9



















HIV-2


















HLA-DR
Antigen presentation,
Yes, envelope
Interacts with CD4



MHC class II directly

glycoprotein on target



presents peptide

cells. Without



antigens to CD4 T cells.

associated antigen in



Highly polymorphic.

the peptide binding



Heterodimer consisting

cleft of HLA-DR and



of an alpha (DRA) and a

co-stimulating



beta (DRB) chain, both

molecular interactions,



anchored in the

CD4 cell will be



membrane. Presents

rendered anergic.



peptides derived from

HIV-1 Gag expression



extracellular proteins by

is able to induce HLA-



antigen presenting cells,

DR cell-surface



B cells, dendritic cells

localization in H78-



and macrophages.

C10.0 cells. In human



Found on chromosome

macrophages, HIV-1



6 location 6p21.3.

Gag proteins co-





localize with MHC II





(HLA-DR), CD63, and





Lamp1 in MHC II





compartments. HIV-1





Capsid (p24) inhibits





interferon gamma





induced increases in





HLA-DR and





cytochrome B heavy





chain mRNA levels in





the human monocyte-





like cell line THP1.





HIV-1 Tat down





regulates expression





of MHC class II genes





in antigen-presenting





cells (APC) by





inhibiting the





transactivator of MHC





class II genes, CIITA.





HIV-1 Tat up regulates





HLA-DR expression in





monocyte-derived





dendritic cells and T





cells, thereby driving T





cell-mediated immune





responses and





activation. Associates





with HIV-1 gp41.





Enhances HIV-1





infectivity. Not





affected by viral





tropism which is





determined by the V3





loop of gp120. Amino





acids 708-750 of gp41





required for MHC-II





incorporation into the





HIV-1 envelope.


MHC-1
In humans, six MHC
Yes, envelope
Enhances HIV



class 1 isotypes have

infectivity and changes



been identified: HLA-A,

gp120 conformation.



HLA-B, HLA-C, HLA-E,

Without antigen in



HLA-F and HLA-G.

MHC-1 binding groove



HLA-A, HLA-B and HLA-

and co-stimulatory



C function to present

activity, anergy results.



antigens to CD8 T cells

HIV-1 Nef down



and to form ligands for

regulates surface



natural killer (NK) cell

expression of CD4 and



receptors. HLA-E and

MHC-1 in resting CD4+



HLA-G also ligands for

T lymphocytes. Nef



NK-cell receptors. HLA-

up regulates cell



A is found on

surface levels of the



chromosome 6 location

MHC-2 invariant chain



6p21.3.

CD74. Nef down





regulates HLA class I





expression and





therefore suppresses





the cytolytic activity of





HIV-1-specific





cytotoxic T-lymphocyte





(CTL) clones.





Macrophage-tropic (M-





tropic) HIV-1 Nef down





regulates expression





of HLA-A2 on the





surface of productively





infected macrophages.





HIV-1 group N and





group O Nef weakly





down regulates CD4,





CD28, and class I and





II MHC molecules and





up regulates surface





expression of the





invariant chain (Ii)





associated with





immature major





histocompatibility





complex (MHC) class





II. Nef interrupts





MHC-I trafficking to





the plasma membrane





and inhibits antigen





presentation. Nef





interacts with the μ1





subunit of adaptor





protein (AP) AP-1A, a





cellular protein





complex implicated in





TGN linking





endosome/lysosome





pathways. HIV-1 Nef





binds to the MHC-I





(HLA-A2) hypo





phosphorylated





cytoplasmic tails in the





endoplasmic





reticulum; this Nef-





MHC-I complex





migrates into the Golgi





apparatus then into





the lysosomal





compartments for





degradation. Nef





promotes a physical





interaction between





endogenous AP-1 and





MHC-I. The Pro-X-X-





Pro motif in HIV-1 Nef





induces the





accumulation of CCR5





(HIV-1 M-tropic





coreceptor) in a





perinuclear





compartment where





both molecules co-





localize with MHC-1.





The Pro-X-X-Pro motif





interacts with src





homology region-3





domains of src-like





kinases interfering with





cell signaling





pathways. HIV-1 Nef





selectively down





regulates HLA-A and





HLA-B but does not





significantly affect





HLA-C or HLA-E,





which allows HIV-





infected cells to avoid





NK cell-mediated lysis.





Nef decreases the





incorporation of MHC-





1 molecules into





virions. Furthermore,





Nef down regulates





MHC-1 expression on





human dendritic cells.





Therefore, HIV-1 Nef





impairs antigen





presentation to HIV-





specific CD8+ T





lymphocytes. HIV-1





Nef-induced down





regulation of MHC-I





expression and MHC-I





targeting to the trans-





Golgi network (TGN)





require the binding of





Nef to PACS-1





(phosphofurin acidic





cluster sorting protein





1). PACS-1 is a





protein with a putative





role in the localization





of proteins to the





trans-Golgi network





(TGN) including furin





which cleaves gp160.





HIV-1 Nef down





regulates MHC-1 on





lymphoid, monocytic





and epithelial cells.





Nef expression results





in rapid internalization





and accumulation of





MHC-1 in endosomal





vesicles which





degrade MHC-1





molecules. Nef blocks





transport of MHC-I





molecules to the cell





surface, leading to





accumulation of MHC-





1 in intracellular





organelles.





Furthermore, the effect





of Nef on MHC-1





molecules (but not on





CD4) requires





phosphoinositide 3-





kinase (PI 3-kinase)





activity found on the





cytoplasmic side of the





plasma membrane.


HSP70 (Heat
Chaperone intracellular
Yes, virion
May bind HIV-1 gag


shock protein
protein produced in

polyprotein chain and


70)
response to intracellular

maintain proper



stress. Found on

tertiary confirmation



chromosome 19 location

during intracellular



19q13.42. Binds to and

transport from nucleus



regulates Hsp70 activity.

to plasma membrane.



The carboxyl terminus of

May participate in



Hsp70-interacting

early events in



protein (CHIP) is an

infection. Might



Hsp70-associated

participate in



ubiquitin ligase which

uncoating the viral



ubiquitinates misfolded

capsid. May target



proteins associated with

HIV-1 PIC to the



cytoplasmic

nucleus.



chaperones.


UNG (Uracil-
Uracil-DNA glycosylase
Yes, virion
Integrase is required


DNA
removes DNA uracil

for packaging of UNG


glycosylase)
residues. Excises the

into virions. UNG2



uracil residues and

binds the viral reverse



introduces non

transcriptase enzyme.



templated nucleotides

Uracil repair pathway



allowing for somatic

is associated with HIV-



hyper mutation.

1 viral particles.



Increases



immunoglobulin



diversity. Essential for



generation of strand



breaks for class switch



recombination. Both



mitochondrial (UNG1)



and nuclear (UNG2)



isoforms have been



described. UNG1 only



uracil-DNA glycosylase



isolated to date in



mitochondria.



Mitochondrial UNG1 is



encoded by nuclear not



mitochondrial DNA.



UNG2 predominant form



in proliferating cells,



UNG1 predominant form



in non-proliferating cells.



UNG2 levels high in S-



phase and early G2 of



the cell cycle. UNG2



primarily located at



replication foci during S-



phase. A second uracil-



DNA glycosylase,



Single-strand-selective



Monofunctional Uracil-



DNA Glycosylase



(SMUG1) has a



preference for double-



stranded DNA rather



than single-stranded



DNA as with UNG1 and



UNG2. Found on



chromosome 12 location



12q23-q24.1. Not cell



cycle regulated, does



not accumulate at



replication fosi and is



not found in



mitochondria. SMUG1



accumulates in nucleoli,



UNG2 excluded from



nucleoli. UNG1, UNG2



and SMUG1 function in



base excision repair.



UNG2 implicated in both



innate and acquired



immunity.


Staufen
Double-stranded RNA
Yes, virion
Binds HIV-1 genomic



binding protein.

RNA. May be involved



Transports mRNAs to

in retroviral genome



intracellular

selection and



compartments/organelles.

packaging into



Found on

assembling virions.



chromosome 20 location

Interaction with the



20q13.1. Binds tubulin.

nucleocapsid domain



Transports mRNA via

of pr55(Gag) in vitro



the microtubule network

and in live cells



to the RER. Five

mediated by Staufen's



transcript variants from

dsRBD3 (RNA binding



alternative splicing of

domain 3), with a



STAU gene encoding

contribution from its C-



three isoforms have

terminal domain.



been described.

Preferentially binds





with the 9-kb non-





spliced viral RNA.





Implicated in the





generation of





infectious virions.


α-actinin 1


Required for Vpx-





mediated nuclear





import of the PIC.


LEDGF/p75
DNA-binding protein
Yes, PIC
Central core domain


(lens epithelium-
implicated in cellular
(preintegration
and N-terminal zinc


derived growth
differentiation and
complex)
binding domain of


factor/transcription
cellular response to

integrase are involved


coactivator
environmental stress.

in the interaction with


p75 [alternate
Activates transcription of

LEDGF/p75. An


names include
stress related genes

essential cofactor for


PC(positive cofactor)
triggering a survival

nuclear targeting of


4 and
response. Protective

HIV-1 integrase.


SFRS1
role in stress-induced

Physically links


interaction
apoptosis. Found on

integrase to host


protein 2
chromosome 9 location

chromatin. The


(PSIP2)]) Prior
9p22.3. A member of

alternatively spliced


journal articles
the hepatoma-derived

protein LEDGF/p52,


differentiate p75
growth factor (HDGF).

does not interact with


from PC4 in
The alternatively spliced

HIV-1 or HIV-2


HELA cells
p52 (PC4 and SFRS1

integrase.



interaction protein 1

LEDGF/p75 links the



(PSIP1)) protein

integrase protein to



interactions with

the host chromatin



transcriptional

during the G2 phase of



coactivators, general

the cell cycle. May



transcription factors, and

target the HIV-1



splicing factors,

proviral DNA to



modulating pre-mRNA

specific genomic sites



splicing of class II

of actively transcribed



genes. The p75 protein

genes to promote viral



is not a transcriptional

transcription.



factor. Heparin binds to

Residues are the



LEDGF/p75, facilitating

integrase binding



transport through the

domain (IBD).



cytoplasm into the

Dictates site(s) of HIV



nucleus. The N-terminal

integration, most



PWWP domain and its

favored are areas



beta-barrel substructure

undergoing



are needed for binding

transcription, high G-C



to metaphase

(guanine-cytosine)



chromatin.

content, with active





RNA polymerase





subunits and





transcription factors.





Prevents proteasomal





degradation of HIV-1





integrase. The N-





terminal zinc binding





domain (amino acids





1-52) and the central





core domain (amino





acids 53-212) of HIV-1





integrase interact with





LEDGF/p75. The core





domain harbors the





main determinant for





this interaction.


tRNA synthetase
Ligase, charges or
Yes, virion
tRNAlys3 binds to the


or aminoacyl
aminoacylates key RNA

primer binding site


tRNA synthetase
molecules linking the

initiating reverse



molecule to the

transcription. In HIV-1



respective amino acid.

an RNA loop formed



One synthetase for each

by the tRNAlys3



amino acid found in

anticodon and an



mammalian cells. ATP

adenine rich RNA loop



dependent.

initiates reverse





transcription.


tRNAlys
Allows incorporation of
Yes, virion
Induces three



lysine into proteins by
associated
dimensional structural



the host translational
attached to
changes in the



apparatus.
primer binding
unspliced viral RNA to




site (PBS)
allow reverse





transcription to





proceed.


GAPDH
In glycolysis,
Yes, virion
??????


(Glyceraldehyde-
enzymatically converts


3-phosphate
Glyceraldehyde-3-


dehydrogenase)
phosphate to 1,3-



bisphosphoglycerate.



Also involved in cell



cycle regulation by



modulating cyclin B-



cdk1, apoptosis,



membrane fusion,



microtubule bundling,



phosphotransferase



activity, nuclear RNA



export, programmed



neuronal cell death,



DNA replication, and



DNA repair. Found on



chromosome 12 location



12p13.


CD4
A type I transmembrane
Yes, envelope
Interacts with specific



protein found on

domains of gp120



helper/inducer T cells,

facilitating viral fusion.



monocytes,



macrophages, and



dendritic cells that is



involved in T-cell



recognition of antigens.



Found on chromosome



12 location 12pter-p12.


CXCR4
Binds chemokine SDF-1
Yes, envelope
Viral co-receptor



(stromal cell derived

determines viral



factor 1). Found on

tropism for CD4 T



hematopoietic

cells.



precursors, mature



white blood cells and



plasma cells. Found on



chromosome 2 location



2q21. Type III



transmembrane protein



crossing the plasma



membrane seven times.


CCR5
Found on Th1 cells,
Yes, envelope
Viral co-receptor



dendritic cells,

determines viral



monocytes/macrophages.

tropism for



Type III

macrophages.



transmembrane protein



crossing the plasma



membrane seven times.



Ligands include



monocyte chemo



attractant protein 2



(MCP-2), macrophage



inflammatory protein 1



alpha (MIP-1 alpha),



macrophage



inflammatory protein 1



beta (MIP-1 beta) and



regulated on activation



normal T expressed and



secreted protein



(RANTES). Found on



chromosome 3 location



3p21.31


NFKB
Cellular transcription

Binding sites in the



factor involved in the

viral LTR necessary



immune process.

for viral transcription.



Found on chromosome *



location *.


NFAT
Cellular transcription

Binding sites in the



factor involved in the

viral LTR necessary



immune process.

for viral transcription.



Found on chromosome



20 location 20q13.2-q13.3.


Sp1
Cellular transcription

Binding sites in the



factor involved in the

viral LTR necessary



immune process.

for viral transcription.



Found on chromosome



12 location 12q13.1.








Claims
  • 1. A method for the production of a live animal model for HIV comprising the steps of: a. creating and administering to said live animal a first set of HIV related human host proteins necessary for HIV to attach, penetrate, and replicate within said live animal using recombinant technology to encode said first set of proteins into commensal organisms normally found in and derived from gut associated lymphoid tissue of said animal;b. creating and administering to said live animal, a second set of HIV related proteins necessary for HIV to evade said animal's immune response using recombinant technology to encode said second set of HIV related human host proteins into commensal organisms normally found in and derived from gut associated lymphoid tissue of said animal; andc. infecting said animal with live, replication competent HIV.
  • 2. The method of claim 1, wherein said first set and said second set of proteins are administered in trans and mirror concentrations found in normal human immunologic milieu.
  • 3. The method of claim 1, wherein said method further comprises the step of coupling said first set and said second set of proteins with cell penetrating peptides using recombinant technology.
  • 4. The method of claim 1, wherein said method further comprises the step of administering CypA-binding drug Cyclosporine to said live animal.
  • 5. The method of claim 1, wherein said method further comprises the step of administering soluble complement-receptor 1 to said live animal.
  • 6. The method of claim 1, wherein said method further comprises the step of administering Tat protein to said live animal.
  • 7. The method of claim 1, wherein the first set of proteins comprise transcription factors, cellular cofactors, cellular receptors, cellular co-receptors, cellular proteases, cellular proteins involved in the ubiquitin-proteasome pathway, cellular adaptor proteins, and human ribosomal RNA.
  • 8. The method of claim 7, wherein the transcription factors are selected from the group consisting of NFK B, NFAT, Sp1, and combinations thereof.
  • 9. The method of claim 7, wherein the cellular cofactors are selected from the group consisting of Cyclin T, CDK9/PITALRE, RNA polymerase II, Exportin 1/Crm 1, Ran GTP, Ran GTPase activating protein (RanGAP), Ran Binding Protein (RanBP1), and combinations thereof.
  • 10. The method of claim 7, wherein the cellular receptors are CD4.
  • 11. The method of claim 7, wherein the cellular coreceptors are selected from the group consisting of CCR5, CXCR4, CCR2B, CCR3, CCR8, GPR1, GPR15 (Bob), STRL33 (Bonzo), US28, CX3CR1 (V28), APJ, chemR23, and combinations thereof.
  • 12. The method of claim 7, wherein the cellular proteases are Furin.
  • 13. The method of claim 7, wherein the cellular proteins involved in the ubiquitin-proteosome pathway are selected from the group consisting of H-β-TrCP, Skp1p, and combinations thereof.
  • 14. The method of claim 7, wherein the cellular adaptor proteins are AP-2.
  • 15. The method of claim 1, wherein the second set of proteins comprise plasma proteins, cell membrane bound proteins, and homologous restriction factor (HRF).
  • 16. The method of claim 15, wherein the plasma proteins are selected from the group consisting of C4 binding protein (C4b protein), factor H and combinations thereof.
  • 17. The method of claim 15, wherein the cell membrane bound proteins are selected from the group consisting of membrane cofactor protein (MCP), CD46, decay accelerating factor (CD55), complement-receptor 1 (CD35), complement-receptor 2 (CD21), homologous restriction factor, and combinations thereof.
  • 18. The method of claim 1, wherein corresponding to HIV-1 said first set of proteins comprise Thy-1 (CD90), GM1 (β-galactosidase), HLA-DR, VCAM-1, VLA-4, MHC-1, CD63, CD81, CD82, CD107a, HP68, ezrin, moesin, cofilin, actin, ubiquitin, Pin1, tRNA synthetase, aminoacyl tRNA synthetase, GAPDH, MAPK/ERK2, HSP60, HSP70, HSC70, CypA, FKBP12, Tsg101, Tal, VPS28, AIP1/ALIX, VPS4B, UNG, Staufen, INI1, EF-1α, LEDGF/p75, PSIP2, DNA-PK, Ku80, hRad18, EED, HMGA/HMG-1a, BAF/BANF1, p300, Rev cofactor, HSp90, CypB, HSP 27, HSP40, VPS37B, CD4, CXCR4, CCR5, CD86, Phosphatidyl inositol 4,5-bisphosphate, NFK B, NFAT, Sp1, Cyclin T, CDK9/PITALRE, RNA polymerase II, Exportin 1/Crm 1, Ran GTP, Ran GTPase activating protein, Ran Binding Protein, CCR2B, CCR3, CCR8, GPR1, GPR15, STRL33, US28, CX3CR1, APJ, chemR23, Furin, AP-2, CD35, CD21 and tRNAlys; and wherein corresponding to HIV-1 said second set of proteins comprise MCP/CD46, DAF/CD55, HRF-20/CD59, Factor H, HLA-DR, ICAM-1, ICAM-2, ICAM-3, LFA-1, VCAM-1, MHC-1, CD63, CD81, CD82, CD107a, ubiquitin, CypA, Tsg101, Tal, VPS28, AIP1/ALIX APOBEC3G, APOBEC3F, HSp90, CD4, CXCR4, CCR5, CD86, CCR2B, CCR3, CCR8, GPR1, GPR15, STRL33, US28, CX3CR1, APJ, H-β-TrCP, Skp1p, C4 binding protein, CD35, and CD21.
  • 19. The method of claim 1, wherein corresponding to HIV-2 said first Set of proteins comprise HLA-DR, MHC-1, HSP70, UNG, Staufen, α-actinin 1, LEDGF/P75, tRNA synthetase, aminoacyl tRNA synthetase, tRNAlys, GAPDH, CD4, CXCR4, CCR5, NFKB, NFAT, and Sp1, and wherein corresponding to HIV-2 said second set of proteins comprise HLA-DR, MHC-1, CD4, CXCR4, and CCR5.
  • 20. A composition comprising: a. a first set of HIV related human host proteins necessary for a HIV virion to attach, penetrate, and replicate within a live animal, wherein said proteins are encoded in a genetically engineered commensal organism normally found in and derived from gut associated lymphoid tissue of said live animal using recombinant technology;b. a second set of HIV related human host proteins necessary for HIV to evade said animal's immune response, wherein said proteins are encoded in a genetically engineered commensal organism normally found in and derived from gut associated lymphoid tissue of said live animal using recombinant technology; andc. live, replication competent HIV.
  • 21. The composition of claim 20, wherein said first set and said second set of proteins are supplied in trans and mirror concentrations found in the normal human immunologic milieu.
  • 22. The composition of claim 20, wherein said first set and said second set of proteins are coupled with DNA encoding a cell penetrating peptide using recombinant technology.
  • 23. The composition of claim 20, in combination with CypA-binding drug Cyclosporine.
  • 24. The composition of claim 20, in combination with soluble complement-receptor 1.
  • 25. The composition of claim 20, in combination with Tat protein.
  • 26. The composition of claim 20, wherein said first set of proteins comprise transcription factors, cellular cofactors, cellular receptors, cellular co-receptors, cellular proteases, cellular proteins involved in the ubiquitin-proteasome pathway, cellular adaptor proteins, human ribosomal RNA, and combinations thereof.
  • 27. The composition of claim 26, wherein the transcription factors are selected from the group consisting of NFKB, NFAT, Sp1, and combinations thereof.
  • 28. The composition of claim 26, wherein the cellular cofactors are selected from the group consisting of Cyclin T, CDK9/PITALRE, RNA polymerase II, Exportin 1/Crm1, Ran GTP, Ran GTPase activating protein (RanGAP), Ran Binding Protein (RanBP1), and combinations thereof.
  • 29. The composition of claim 26, wherein the cellular receptors are CD4.
  • 30. The composition of claim 26, wherein the cellular coreceptors are selected from the group consisting of CCR5, CXCR4, CCR2B, CCR3, CCR8, GPR1, GPR15 (Bob), STRL33 (Bono), US28, CX3CR1 (V28), APJ, chemR23, and combinations thereof.
  • 31. The composition of claim 26, wherein the cellular proteases are Furin.
  • 32. The composition of claim 26, wherein the cellular proteins involved in the ubiquitin-proteasome pathway are selected from the group consisting of H-β-TrCP, Skp1p, and combinations thereof.
  • 33. The composition of claim 26, wherein the cellular adaptor proteins are AP-2.
  • 34. The composition of claim 20, wherein said second set of proteins comprise plasma proteins, cell membrane bound proteins, and homologous restriction factor (HRF).
  • 35. The composition of claim 34, wherein the plasma proteins are selected from the group consisting of C4 binding protein (C4b protein), factor H, and combinations thereof.
  • 36. The composition of claim 34, wherein the cell membrane bound proteins are selected from the group consisting of membrane cofactor protein (MCP), CD46, decay accelerating factor (CD55), complement-receptor 1 (CD35), complement-receptor 2 (CD21), homologous restriction factor, and combinations thereof.
  • 37. The composition of claim 20, wherein corresponding to HIV-1 said first set of proteins comprise Thy-1 (CD90), GM1 (β-galactosidase), HLA-DR, VCAM-1, VLA-4, MHC-1, CD63, CD81, CD82, CD107a, HP68, ezrin, moesin, cofilin, actin, ubiquitin, Pin1, tRNA synthetase, aminoacyl tRNA synthetase, GAPDH, MAPK/ERK2, HSP60, HSP70, HSC70, CypA, FKBP12, Tsg101, Tal, VPS28, AIP1/ALIX, VPS4B, UNG, Staufen, INI1, EF-1α, LEDGF/p75, PSIP2, DNA-PK, Ku80, hRad18, EED, HMGA/HMG-1α, BAF/BANF1, p300, Rev cofactor, HSp90, CypB, HSP 27, HSP40, VPS37B, CD4, CXCR4, CCR5, CD86, Phosphatidyl inositol 4,5-bisphosphate, NFKB, NFAT, Sp1, Cyclin T, CDK9/PITALRE, RNA polymerase II, Exportin 1/Crm 1, Ran GTP, Ran GTPase activating protein, Ran Binding Protein, CCR2B, CCR3, CCR8, GPR1, GPR15, STRL33, US28, CX3CR1, APJ, chemR23, Furin, AP-2, CD35, CD21 and tRNAlys; and wherein corresponding to HIV-1 said second set of proteins comprise MCP/CD46, DAF/CD55, HRF-20/CD59, Factor H, HLA-DR, ICAM-1, ICAM-2, ICAM-3, LFA-1, VCAM-1, MHC-1, CD63, CD81, CD82, CD107a, ubiquitin, CypA, Tsg101, Tal, VPS28, AIP1/ALIX APOBEC3G, APOBEC3F, HSp90, CD4, CXCR4, CCR5, CD86, CCR2B, CCR3, CCR8, GPR1, GPR15, STRL33, US28, CX3CR1, APJ, H-β-TrCP, Skp1p, C4 binding protein, CD35, and CD21.
  • 38. The composition of claim 20, wherein corresponding to HIV-2 said first set of proteins comprise HLA-DR, MHC-1, HSP70, UNG, Staufen, α-actinin 1, LEDGF/P75, tRNA synthetase, aminoacyl tRNA synthetase, tRNAlys, GAPDH, CD4, CXCR4, CCR5, NFKB, NFAT, and Sp1, and wherein corresponding to HIV-2 said second set of proteins comprise HLA-DR, MHC-1, CD4, CXCR4, and CCR5.
RELATED U.S. APPLICATION DATA

The present application is a Continuation-in-Part of application Ser. No. 11/702,260 filed Feb. 5, 2007 which claims priority to Provisional Application No. 60/765,315, filed on Feb. 3, 2006, which are incorporated herein by reference.

Provisional Applications (1)
Number Date Country
60765315 Feb 2006 US
Continuation in Parts (1)
Number Date Country
Parent 11702260 Feb 2007 US
Child 12794102 US