Patent Grant
7691574
1. Field of the Invention
The present invention relates to methods for monitoring expression of a plurality of genes in Bacillus cells. The present invention also relates to Bacillus genomic sequenced tags and to substrates and computer readable media containing such genomic sequenced tags.
2. Description of the Related Art
Microarray technology is increasingly becoming the method of choice for the quantitative and simultaneous analysis of the expression levels of many thousands of genes. Microarray analyses typically follow the steps of gene selection, microarray synthesis, sample preparation, array hybridization, detection, and data analysis (Watson et al., 1998, Current Opinion in Biotechnology 9: 609-614).
PCR-amplified coding sequences of genomic DNA from an organism are particularly useful in microarrays for obtaining global expression profiles where the genome of the organism has been fully sequenced.
Chu et al., 1998, Science 282: 699-705 disclose the use of microarrays containing PCR-amplified genomic coding sequences for determining the temporal expression of Saccharomyces cerevisiae genes during sporulation.
For other organisms whose genomes have not been sequenced, global expression profiles may be obtained with arraying (1) random genomic DNA segments or clones (e.g., from a genomic DNA library); (2) random cDNA clones (e.g., from one or more cDNA libraries) that are uncharacterized at the DNA sequence level; or (3) random cDNA clones that have been sequenced and partially characterized with respect to putative identification and function.
Genomic sequenced tags (GSTs) are partial genomic DNA sequences. Simply stated, a GST is a segment of a sequence from a random genomic DNA clone that corresponds to part of a specific gene. The use of sequenced GSTs in microarrays compared to genomic clones or random cDNA clones provides several advantages especially for organisms whose genomes have not been fully sequenced. First, since sequence information is available, redundancy and follow-up characterization is minimized. Second, GST microarrays can be organized based on function of the gene products to facilitate analysis of the results (e.g., GSTs encoding enzymes from the same metabolic pathway can be arranged or grouped accordingly).
Ruan et al., 1998, The Plant Journal 15: 821-833, disclose the use of microarrays containing Arabidopsis thaliana EST sequences for determining the temporal expression of Arabidopsis thaliana genes in root, leaf, and two stages of floral development.
Iyer et al., 1999, Science 283; 83-87, disclose the use of microarrays containing human EST sequences for determining the temporal expression of human fibroblast cells in response to serum.
Hayward et al., 2000, Molecular Microbiology 35: 6-14, disclose shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria.
Bacteria are used as host microorganisms for the industrial production of enzymes and other proteins whether endogenous or heterogenous to the microorganisms. There is a need in the art to provide methods for monitoring the global expression of genes from Bacillus cells to improve the production potential of these microorganisms.
It is an object of the present invention to provide alternative methods for monitoring expression of a plurality of genes in Bacillus cells.
The present invention relates to methods for monitoring differential expression of a plurality of genes in a first Bacillus cell relative to expression of the same or similar genes in one or more second Bacillus cells, comprising:
(a) adding a mixture of labeled nucleic acid probes isolated from the Bacillus cells to a substrate containing an array of Bacillus GSTs under conditions where the nucleic acids hybridize to complementary sequences of the Bacillus GSTs in the array, wherein the nucleic acids from the first Bacillus cell and the one or more second Bacillus cells are labeled with a first reporter and one or more different second reporters, respectively; and
(b) examining the array under conditions wherein the relative expression of the genes in the Bacillus cells is determined by the observed hybridization reporter signal of each spot in the array in which (i) the Bacillus GSTs in the array that hybridize to the nucleic acids obtained from either the first or the one or more second Bacillus cells produce a distinct first hybridization reporter signal or one or more second hybridization reporter signals, respectively, and (ii) the GSTs in the array that hybridize to the nucleic acids obtained from both the first and one or more second Bacillus cells produce a distinct combined hybridization reporter signal. In a preferred embodiment, the Bacillus GSTs are the Bacillus licehniformis GSTs of SEQ ID NOs. 1-4448. In another preferred embodiment, the Bacillus GSTs are the Bacillus clausii GSTs of SEQ ID NOs. 4449-8481.
The present invention also relates to computer readable media, substrates containing an array of Bacillus GSTs, and computer-based systems.
The present invention relates to methods for monitoring differential expression of a plurality of genes in a first Bacillus cell relative to expression of the same genes in one or more second Bacillus cells. The methods comprise (a) adding a mixture of labeled nucleic acid probes isolated from two or more Bacillus cells in culture to a substrate containing an array of Bacillus GSTs under conditions where the nucleic acids hybridize to complementary sequences of the Bacillus GSTs in the array; and (b) examining the array under conditions wherein the relative expression of the genes in the two or more cells is determined by the observed hybridization reporter signal of each spot in the array.
The methods of the present invention may be used to monitor global expression of a plurality of genes from a Bacillus cell, discover new genes, identify possible functions of unknown open reading frames, and monitor gene copy number variation and stability. For example, the global view of changes in expression of genes may be used to provide a picture of the way in which Bacillus cells adapt to changes in culture conditions, environmental stress, or other physiological provocation. Other possibilities for monitoring global expression include spore morphogenesis, recombination, metabolic or catabolic pathway engineering.
The methods of the present invention are particularly advantageous when one spot on an array equals one gene or open reading frame because extensive follow-up characterization is unnecessary since sequence information is available, and Bacillus GST microarrays can be organized based on function of the gene products. However, one spot may contain more than one gene especially if random genomic sequences are used.
Genomic Sequenced Tags
The term “genomic sequenced tag” or “GST” is defined herein as a segment of a sequence from a random genomic DNA clone of an expressed Bacillus genome. The term “GST” will be understood to also include two or more Bacillus GSTs assembled into a contig. Bacillus GSTs are generally generated as follows: Total cellular DNA is isolated from a Bacillus cell, digested with a restriction endonuclease or cleaved by sonication, nebulization, or physical methods, size-selected by agarose gel electrophoresis, isolated, and ligated into a vector, e.g., pSGMU2 (Errington, 1986, Journal of General Microbiology 132: 2953-2961). The ligation mixture is used to transform competent E. coli cells and transformants are selected under selective pressure, e.g., ampicillin selection. Plasmids from the genomic DNA libraries are generated from random selected transformants, isolated, and partially sequenced. The partial sequences are then compared to sequences in various publicly available databases, for example GenBank, EMBL, Swissprot etc., for identification of function and annotated accordingly.
In the methods of the present invention, the Bacillus GSTs are preferably at least about 50 bp in length, more preferably at least about 100 bp in length, even more preferably at least about 150 bp in length, and most preferably at least about 200 bp in length.
The Bacillus GSTs may be obtained from any Bacillus cell but preferably from a Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulars, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, or Bacillus thuringiensis cells. In a preferred embodiment, the Bacillus cell is a Bacillus clausii cell.
In a preferred embodiment, the Bacillus GSTs are obtained from a Bacillus licheniformis cell. In a more preferred embodiment, the Bacillus licheniformis GSTs are obtained from Bacillus licheniformis ATCC 14580. In a most preferred embodiment, the Bacillus licheniformis GSTs are selected from the group consisting of SEQ ID NOs. 1-4448, nucleic acid fragments of SEQ ID NOs. 1-4448, and nucleic acid sequences having at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 1-4448.
In another preferred embodiment, the Bacillus GSTs are obtained from a Bacillus clausii cell. In another more preferred embodiment, the Bacillus clausii GSTs are obtained from Bacillus clausii NCIB 10309. In another most preferred embodiment, the Bacillus clausii GSTs are selected from the group consisting of SEQ ID NOs. 4449-8481, nucleic acid fragments of SEQ ID NOs. 4449-8481, and nucleic acid sequences having at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 4449-8481.
Microarrays
The term “an array of Bacillus GSTS” is defined herein as a linear or two-dimensional array of preferably discrete elements of Bacillus GSTs, each having a finite area, formed on the surface of a solid support.
The term “microarray” is defined herein as an array of Bacillus GST elements having a density of discrete GST elements of at least about 100/cm2, and preferably at least about 1000/cm2. The GST elements in a microarray have typical dimensions, e.g., diameters, in the range of between about 10 to about 250 μm, preferably in the range of between about 10 to about 200 μm, more preferably in the range of between about 20 to about 150 μm, even more preferably in the range of between about 20 to about 100 μm, most preferably in the range of between about 50 to about 100 μm, and even most preferably in the range of between about 80 to about 100 μm, and are separated from other GST elements in the microarray by about the same distance.
Methods and instruments for forming microarrays on the surface of a solid support are well known in the art. See, for example, U.S. Pat. No. 5,807,522; U.S. Pat. No. 5,700,637; and U.S. Pat. No. 5,770,151. The instrument may be an automated device such as described in U.S. Pat. No. 5,807,522.
The term “a substrate containing an array of Bacillus GSTs” is defined herein as a solid support having deposited on the surface of the support one or more of a plurality of Bacillus GSTs for use in detecting binding of labeled nucleic acids to the Bacillus GSTs.
The substrate may, in one aspect, be a glass support (e.g., glass slide) having a hydrophilic or hydrophobic coating on the surface of the support, and an array of distinct Bacillus GSTs bound to the coating, where each distinct GST is disposed at a separate, defined position.
Each microarray in the substrate preferably contains at least 103 distinct Bacillus GSTs in a surface area of less than about 5 or 6 cm2. Each distinct Bacillus GST (i) is disposed at a separate, defined position in the array, (ii) has a length of at least 50 bp, and (iii) is present in a defined amount between about 0.1 femtomoles and 100 nanomoles or higher if necessary.
For a hydrophilic coating, the glass slide is coated by placing a film of a polycationic polymer with a uniform thickness on the surface of the slide and drying the film to form a dried coating. The amount of polycationic polymer added should be sufficient to form at least a monolayer of polymers on the glass surface. The polymer film is bound to the surface via electrostatic binding between negative silyl-OH groups on the surface and charged cationic groups in the polymers. Such polycationic polymers include, but are not limited to, polylysine and polyarginine.
Another coating strategy employs reactive aldehydes to couple DNA to the slides (Schena et al., 1996, Proceedings of the National Academy of Science USA 93: 10614-10619; Heller at al., 1997, Proceedings of the National Academy of Science USA 94: 2150-2155).
Alternatively, the surface may have a relatively hydrophobic character, i.e., one that causes aqueous medium deposited on the surface to bead. A variety of known hydrophobic polymers, such as polystyrene, polypropylene, or polyethylene, have desirable hydrophobic properties, as do glass and a variety of lubricant or other hydrophobic films that may be applied to the support surface. A support surface is “hydrophobic” if an aqueous droplet applied to the surface does not spread out substantially beyond the area size of the applied droplet, wherein the surface acts to prevent spreading of the droplet applied to the surface by hydrophobic interaction with the droplet.
In another aspect, the substrate may be a multi-cell substrate where each cell contains a microarray of Bacillus GSTs, and preferably an identical microarray, formed on a porous surface. For example, a 96-cell array may typically have array dimensions between about 12 and 244 mm in width and 8 and 400 mm in length, with the cells in the array having width and length dimension of 1/12 and ⅛ the array width and length dimensions, respectively, i.e., between about 1 and 20 in width and 1 and 50 mm in length.
The solid support may include a water-impermeable backing such as a glass slide or rigid polymer sheet, or other non-porous material. Formed on the surface of the backing is a water-permeable film which is formed of porous material. Such porous materials include, but are not limited to, nitrocellulose membrane nylon, polypropylene, and polyvinylidene difluoride (PVDF) polymer. The thickness of the film is preferably between about 10 and 1000 μm. The film may be applied to the backing by spraying or coating, or by applying a preformed membrane to the backing.
Alternatively, the solid support may be simply a filter composed of nitrocellulose, nylon, polypropylene, or polyvinylidene difluoride (PVDF) polymer, or for that matter any material suitable for use.
The film surface may be partitioned into a desirable array of cells by water-impermeable grid lines typically at a distance of about 100 to 2000 μm above the film surface. The grid lines can be formed on the surface of the film by laying down an uncured flowable resin or elastomer solution in an array grid, allowing the material to infiltrate the porous film down to the backing, and then curing the grid lines to form the cell-array substrate.
The barrier material of the grid lines may be a flowable silicone, wax-based material, thermoset material (e.g., epoxy), or any other useful material. The grid lines may be applied to the solid support using a narrow syringe, printing techniques, heat-seal stamping, or any other useful method known in the art.
Each well preferably contains a microarray of distinct Bacillus GSTs. “Distinct Bacillus GSTs” as applied to the GSTs forming a microarray is defined herein as an array member which is distinct from other array members on the basis of a different GST sequence, and/or different concentrations of the same or distinct GSTs, and/or different mixtures of distinct GSTs or different-concentrations of GSTs. Thus an array of “distinct Bacillus GSTs” may be an array containing, as its members, (i) distinct GSTs, which may have a defined amount in each member, (ii) different, graded concentrations of given-sequence GSTs, and/or (iii) different-composition mixtures of two or more distinct GSTs.
However, any type of substrate known in the art may be used in the methods of the present invention.
The delivery of a known amount of a selected Bacillus GST to a specific position on the support surface is preferably performed with a dispensing device equipped with one or more tips for insuring reproducible deposition and location of the GSTs and for preparing multiple arrays. Any dispensing device known in the art may be used in the methods of the present invention. See, for example, U.S. Pat. No. 5,807,522.
For liquid-dispensing on a hydrophilic surface, the liquid will have less of a tendency to bead, and the dispensed volume will be more sensitive to the total dwell time of the dispenser tip in the immediate vicinity of the support surface.
For liquid-dispensing on a hydrophobic surface, flow of fluid from the tip onto the support surface will continue from the dispenser onto the support surface until it forms a liquid bead. At a given bead size, i.e., volume, the tendency of liquid to flow onto the surface will be balanced by the hydrophobic surface interaction of the bead with the support surface, which acts to limit the total bead area on the surface, and by the surface tension of the droplet, which tends toward a given bead curvature. At this point, a given bead volume will have formed, and continued contact of the dispenser tip with the bead, as the dispenser tip is being withdrawn, will have little or no effect on bead volume.
The desired deposition volume, i.e., bead volume, formed is preferably in the range 2 pl (picoliters) to 2 nl (nanoliters), although volumes as high as 100 nl or more may be dispensed. It will be appreciated that the selected dispensed volume will depend on (i) the “footprint” of the dispenser tip(s), i.e., the size of the area spanned by the tip(s), (ii) the hydrophobicity of the support surface, and (iii) the time of contact with and rate of withdrawal of the tip(s) from the support surface. In addition, bead size may be reduced by increasing the viscosity of the medium, effectively reducing the flow time of liquid from the dispensing device onto the support surface. The drop size may be further constrained by depositing the drop in a hydrophilic region surrounded by a hydrophobic grid pattern on the support surface.
At a given tip size, bead volume can be reduced in a controlled fashion by increasing surface hydrophobicity, reducing time of contact of the tip with the surface, increasing rate of movement of the tip away from the surface, and/or increasing the viscosity of the medium. Once these parameters are fixed, a selected deposition volume in the desired picoliter to nanoliter range can be achieved in a repeatable fashion.
After depositing a liquid droplet of a Bacillus GST sample at one selected location on a support, the tip may be moved to a corresponding position on a second support, the GST sample is deposited at that position, and this process is repeated until the GST sample has been deposited at a selected position on a plurality of supports.
This deposition process may then be repeated with another GST sample at another microarray position on each of the supports.
The diameter of each Bacillus GST region is preferably between about 20-200 μm. The spacing between each region and its closest (non-diagonal) neighbor, measured from center-to-center, is preferably in the range of about 20-400 μm. Thus, for example, an array having a center-to-center spacing of about 250 μm contains about 40 regions/cm or 1,600 regions/cm2. After formation of the array, the support is treated to evaporate the liquid of the droplet forming each region, to leave a desired array of dried, relatively flat GST regions. This drying may be done by heating or under vacuum. The DNA can also be UV-crosslinked to the polymer coating.
Bacterial Cells
In the methods of the present invention, the two or more Bacillus cells may be any Bacillus cell where one of the cells is used as a reference for identifying differences in expression of the same or similar complement of genes in the other cell(s). In one aspect, the two or more cells are the same cell. For example, they may be compared under different growth conditions, e.g., oxygen limitation, nutrition, and/or physiology. In another aspect, one or more cells are mutants of the reference cell. For example, the mutant(s) may have a different phenotype. In a further aspect, the two or more cells are of different species (e.g., Bacillus clausii and Bacillus subtilis). In another further aspect, the two or more cells are of different genera. In an even further aspect, one or more cells are transformants of the reference cell, wherein the one or more transformants exhibit a different property. For example, the transformants may have an improved phenotype relative to the reference cell and/or one of the other transformants. The term “phenotype” is defined herein as an observable or outward characteristic of a cell determined by its genotype and modulated by its environment. Such improved phenotypes may include, but are not limited to, improved secretion or production of a protein or compound, reduced or no secretion or production of a protein or compound, improved or reduced expression of a gene, desirable morphology, an altered growth rate under desired conditions, relief of over-expression mediated growth inhibition, or tolerance to low oxygen conditions.
The Bacillus cells may be any Bacillus cells, but preferably Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulars, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, or Bacillus thuringiensis cells.
In a preferred embodiment, the Bacillus cells are Bacillus alkalophilus cells. In another preferred embodiment, the Bacillus cells are Bacillus amyloliquefaciens cells. In another preferred embodiment, the Bacillus cells are Bacillus brevis cells. In another preferred embodiment, the Bacillus cells are Bacillus circulans cells. In another preferred embodiment, the Bacillus cells are Bacillus clausii cells. In another preferred embodiment, the Bacillus cells are Bacillus coagulans cells. In another preferred embodiment, the Bacillus cells are Bacillus firmus cells. In another preferred embodiment, the Bacillus cells are Bacillus lautus cells. In another preferred embodiment, the Bacillus cells are Bacillus lentus cells. In another preferred embodiment, the Bacillus cells are Bacillus licheniformis cells. In another preferred embodiment, the Bacillus cells are Bacillus megaterium cells. In another preferred embodiment, the Bacillus cells are Bacillus pumilus cells. In another preferred embodiment, the Bacillus cells are Bacillus stearothermophilus cells. In another preferred embodiment, the Bacillus cells are Bacillus subtilis cells. In another preferred embodiment, the Bacillus cells are Bacillus thuringiensis cells.
In a more preferred embodiment, the Bacillus cells are Bacillus licheniformis cells. In a most preferred embodiment, the Bacillus licheniformis cells are Bacillus licheniformis ATCC 14580 cells.
In another more preferred embodiment, the Bacillus cells are Bacillus clausii cells. In another most preferred embodiment, the Bacillus clausii cells are Bacillus clausii NCIB 10309 cells.
In the methods of the present invention, the cells are cultivated in a nutrient medium suitable for growth using methods well known in the art for isolation of the nucleic acids to be used as probes. For example, the cells may be cultivated by shake flask cultivation, small-scale or large-scale fermentation (including continuous, batch, fed-batch, or solid state fermentations) in laboratory or industrial fermentors performed in a suitable medium. The cultivation takes place in a suitable nutrient medium comprising carbon and nitrogen sources and inorganic salts, using procedures known in the art. Suitable media are available from commercial suppliers or may be prepared according to published compositions (e.g., in catalogues of the American Type Culture Collection).
Nucleic Acid Probes
The nucleic acid probes from the two or more Bacillus cells may be any nucleic acid including genomic DNA, cDNA, and RNA, and may be isolated using standard methods known in the art. For example, cDNA probes may be obtained from total RNA isolated from the cells using standard methods and reverse transcribed into total cDNA.
The populations of isolated nucleic acid probes may be labeled with colorimetric, radioactive (for example, 32p, 33p, or 35S), fluorescent reporters, or other reporters using methods known in the art (Chen et al., 1998, Genomics 51: 313-324; DeRisi et al., 1997, Science 278: 680-686; U.S. Pat. No. 5,770,367).
In a preferred embodiment, the probes are labeled with fluorescent reporters. For example, the cDNA probes may be labeled during reverse transcription from the respective RNA pools by incorporation of fluorophores as dye-labeled nucleotides (DeRisi et al., 1997, supra), e.g., Cy5-labeled deoxyuridine triphosphate, or the isolated cDNAs may be directly labeled with different fluorescent functional groups. Fluorescent-labeled nucleotides include, but are not limited to, fluorescein conjugated nucleotide analogs (green fluorescence), lissamine nucleotide analogs (red fluorescence). Fluorescent functional groups include, but are not limited to, Cy3 (a green fluorescent dye) and Cy5 (red fluorescent dye).
Array Hybridization
The labeled nucleic acids from the two or more Bacillus cells are then added to a substrate containing an array of Bacillus GSTs under conditions where the nucleic acid pools from the two or more Bacillus cells hybridize to complementary sequences of the GSTs in the array. For purposes of the present invention, hybridization indicates that the labeled nucleic acids from the two or more cells hybridize to the GSTs under very low to very high stringency conditions.
A small volume of the labeled nucleic acids mixture is loaded onto the substrate. The solution will spread to cover the entire microarray. In the case of a multi-cell substrate, one or more solutions are loaded into each cell which stop at the barrier elements.
For nucleic acid probes of at least about 100 nucleotides in length, miroarray hybridization conditions described by Eisen and Brown, 1999, Methods of Enzymology 303: 179-205, may be used. Hybridization is conducted under a coverslip at 65° C. in 3×SSC for 4-16 hours followed by post-hybridization at room temperature after removal of the coverslip in 2×SSC, 0.1% SDS by plunging the array two or three times in the solution, followed by successive washes in 1×SSC for 2 minutes and 0.2×SSC wash for to or more minutes.
Conventional conditions of very low to very high stringency conditions may also be used. Very low to very high stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/ml sheared and denatured salmon sperm DNA, and either 25% formamide for very low and low stringencies, 35% formamide for medium and medium-high stringencies, or 50% formamide for high and very high stringencies, following standard Southern blotting procedures.
The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS preferably at least at 45° C. (very low stringency), more preferably at least at 50° C. (low stringency), more preferably at least at 55° C. (medium stringency), more preferably at least at 60° C. (medium-high stringency), even more preferably at least at 65° C. (high stringency), and most preferably at least at 70° C. (very high stringency).
For shorter nucleic acid probes which are less than 50 nucleotides, microarray hybridization conditions described by Kane et al., 2000, Nucleic Acids Research 28: 4552-4557, may be used. Hybridization is conducted under a supported coverslip at 42° C. for 16-18 hours at high humidity in 50% formamide, 4.1× Denhardt's, 4.4×SSC, and 100 μg/ml of herring sperm DNA. Arrays are washed after removal of the coverslip in 4×SSC by immersion into 1×SSC, 0.1% SDS for 10 minutes, 0.1×SSC, 0.1% SDS twice for 10 minutes, and 0.1×SSC twice for 10 minutes.
For shorter nucleic acid probes which are about 50 nucleotides to about 100 nucleotides in length, conventional stringency conditions may be used. Such stringency conditions are defined as prehybridization, hybridization, and washing post-hybridization at 5° C. to 10° C. below the calculated Tm using the calculation according to Bolton and McCarthy (1962, Proceedings of the National Academy of Sciences USA 48: 1390) in 0.9 M NaCl, 0.09 M Tris-HCl pH 7.6, 6 mM EDTA, 0.5% NP-40, 1× Denhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per ml following standard Southern blotting procedures.
The carrier material is finally washed once in 6×SSC plus 0.1% SDS for 15 minutes and twice each for 15 minutes using 6×SSC at 5° C. to 10° C. below the calculated Tm.
The choice of hybridization conditions will depend on the degree of homology between the Bacillus GSTs and the nucleic acids obtained from the two or more Bacillus cells. For example, where the nucleic acid probes and the GSTs are obtained from identical Bacillus cells, high stringency conditions may be most suitable. Where the cells are from a genus or species different from which the GSTs were obtained, low or medium stringency conditions may be more suitable.
In a preferred embodiment, the hybridization is conducted under low stringency conditions. In a more preferred embodiment, the hybridization is conducted under medium stringency conditions. In a most preferred embodiment, the hybridization is conducted under high stringency conditions.
The entire solid support is then reacted with detection reagents if needed and analyzed using standard calorimetric, radioactive, or fluorescent detection means. All processing and detection steps are performed simultaneously to all of the microarrays on the solid support ensuring uniform assay conditions for all of the microarrays on the solid support.
Detection
Any detection method known in the art may be used. The most common detection method is laser-induced fluorescence detection using confocal optics (Cheung et al., 1998, Nat. Genet. 18: 225-230). The array is examined under fluorescence excitation conditions such that (i) the Bacillus GSTs in the array that hybridize to the nucleic acid probes obtained from one of the first cell and one or more second cells produces a distinct first fluorescence emission color or one or second fluorescence emission colors, respectively, and (ii) the Bacillus GSTs in the array that hybridize to substantially equal numbers of nucleic acid probes obtained from the first cell and one of the one or more second cells produce a distinct combined fluorescence emission color, respectively; wherein the relative expression of the genes in the two or more cells can be determined by the observed fluorescence emission color of each spot in the array.
The fluorescence excitation conditions are based on the selection of the fluorescence reporters. For example, Cy3 and Cy5 reporters are detected with solid state lasers operating at 532 nm and 632 nm, respectively.
Other methods of detection may be used employing calorimetric and radioactive (for example, 32p, 33p, or 35S) reporters, or other reporters using methods known in the art (Chen et al., 1998, supra; DeRisi et al., 1997, supra; U.S. Pat. No. 5,770,367).
Data Analysis
The fluorescence data obtained from the scanned image may then be analyzed using any of the commercially available image analysis software. The software preferably identifies array elements, subtracts backgrounds, deconvolutes multi-color images, flags or removes artifacts, verifies that controls have performed properly, and normalizes the signals (Chen et al., 1997, Journal of Biomedical Optics 2: 364-374).
Several computational methods have been described for the analysis and interpretation of microarray-based expression profiles including cluster analysis (Eisen et al., 1998, Proc. Nat. Acad. Sci. USA 95: 14863-14868), parametric ordering of genes (Spellman et al., 1998, Mol. Biol. Cell 9: 3273-3297), and supervised clustering methods based on representative hand-picked or computer-generated expression profiles (Chu et al., 1998. Science 282: 699-705).
Computer Readable Media
The Bacillus GSTs described herein may be “provided” in a variety of media to facilitate their use. The term “provided” refers to a manufacture comprising an array of Bacillus GSTs. Such manufactures provide a large portion of the genome of Bacillus and parts thereof (e.g., an open reading frame (ORF)) in a form which allows one skilled in the art to examine the manufacture using means not directly applicable to examining the genome or a subset thereof as it exists in nature or in purified form.
Thus, the present invention also relates to such a manufacture in the form of a computer readable medium comprising an array of Bacillus GSTs selected from the group consisting of SEQ ID NOs. 1-8481, nucleic acid fragments of SEQ ID NOs. 1-8481, and nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 1-8481.
In a preferred embodiment, the computer readable medium comprises an array of Bacillus licheniformis GSTs consisting of nucleic acid sequences of SEQ ID NOs. 1-4448.
In another preferred embodiment, the computer readable medium comprises an array of Bacillus licheniformis GSTs consisting of nucleic acid fragments of SEQ ID NOs. 1-4448.
In another preferred embodiment, the computer readable medium comprises an array of Bacillus licheniformis GSTs consisting of nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 1-4448.
In another preferred embodiment, the computer readable medium comprises an array of Bacillus clausii GSTs consisting of nucleic acid sequences of SEQ ID NOs. 4449-8481.
In another preferred embodiment, the computer readable medium comprises an array of Bacillus clausii GSTs consisting of nucleic acid fragments of SEQ ID NOs. 4449-8481.
In another preferred embodiment, the computer readable medium comprises an array of Bacillus clausii GSTs consisting of nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 4449-8481.
In one application of this embodiment, the Bacillus GSTs of the present invention can be recorded on computer readable media. The term “computer readable media” is defined herein as any medium which can be read and accessed by a computer. Such computer readable media include, but are not limited to, magnetic storage media, e.g., floppy discs, hard disc storage medium, and magnetic tape; optical storage media, e.g., CD-ROM, DVD; electrical storage media, e.g., RAM and ROM; and hybrids of these categories, e.g., magnetic/optical storage media. One skilled in the art can readily appreciate how any of the presently known computer readable media can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. Likewise, it will be clear to those of skill how additional computer readable media that may be developed also can be used to create analogous manufactures having recorded thereon a nucleotide sequence of the present invention.
As used herein, “recorded” refers to a process for storing information on computer readable medium. One skilled in the art can readily adopt any of the presently known methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.
A variety of data storage structures are available for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data-processor structuring formats (e.g., text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.
Various computer software are publicly available that allow a skilled artisan to access sequence information provided in a computer readable medium. Thus, by providing in computer readable form an array of Bacillus clausii GSTs selected from the group consisting of SEQ ID NOs. 4449-8481, nucleic acid fragments of SEQ ID NOs. 4449-8481, and nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 4449-8481 enables one skilled in the art to routinely access the provided sequence information for a wide variety of purposes.
Software utilizing the BLAST (Altschul et al., 1990, Journal of Molecular Biology 215: 403-410), BLAZE (Brutlag et al., 1993, Comp. Chem. 17: 203-207), GENEMARK (Lukashin and Borodovsky, 1998, Nucleic Acids Research 26: 1107-1115), GENSCAN (Burge and Karlin, 1997, Journal of Molecular Biology 268: 78-94), GLIMMER (Salzberg et al., 1998, Nucleic Acids Research 26: 544-548), and GRAIL (Xu et al., 1994, Comput. Appl. Biosci. 10: 613-623) search algorithms may be used to identify open reading frames (ORFs) within a genome of interest, which contain homology to ORFs or proteins from both Bacillus licheniformis and Bacillus clausii and from other organisms. Among the ORFs discussed herein are protein encoding fragments of the Bacillus licheniformis and Bacillus clausii genomes useful in producing commercially important proteins, such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.
The present invention further provides systems, particularly computer-based systems, which contain the sequence information described herein. Such systems are designed to identify, among other things, genes and gene products—many of which could be products themselves or used to genetically modify an industrial expression host through increased or decreased expression of a specific gene sequence(s).
The term “a computer-based system” is herein defined as the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. One skilled in the art can readily appreciate that any currently available computer-based system is suitable for use in the present invention.
As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means.
The term “data storage means” is defined herein as memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.
The term “search means” refers is defined herein as one or more programs which are implemented on the computer-based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of the present genomic sequences which match a particular target sequence or target motif. A variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, MacPattern (Fuchs, 1991, Comput. Appl. Biosci. 7: 105-106), BLASTN and BLASTX National Center for Biotechnology Information (NCBI). One skilled in the art can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems.
The term “target sequence” is defined here as any DNA (genomic DNA, cDNA) or amino acid sequence of six or more nucleotides or two or more amino acids. One skilled in the art can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 100 amino acids or from about 30 to 300 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.
The term “a target structural motif” or “target motif” is defined herein as any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzyme active sites and signal sequences, substrate and cofactor binding domains, transmembrane domains, and sites for post-translational modifications. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences), repeats, palindromes, dyad symmetries, and transcription and translation start and stop sites.
A variety of structural formats for the input and output means can be used to input and output the information in the computer-based systems of the present invention. A preferred format for an output means ranks fragments of the Bacillus licheniformis or Bacillus clausii genomic sequences possessing varying degrees of homology to the target sequence or target motif. Such presentation provides one skilled in the art with a ranking of sequences which contain various amounts of the target sequence or target motif and identifies the degree of homology contained in the identified fragment.
A variety of comparing means can be used to compare a target sequence or target motif with the data storage means to identify sequence fragments of the Bacillus licheniformis and Bacillus clausii genomes. For example, implementing software which utilize the BLAST and BLAZE algorithms, described in Altschul et al., 1990, Journal of Molecular Biology 215: 403-410, may be used to identify open reading frames within the Bacillus licheniformis or Bacillus clausii genome or the genomes of other organisms. A skilled artisan can readily recognize that any one of the publicly available homology search programs can be used as the search means for the computer-based systems of the present invention. Of course, suitable proprietary systems that may be known to those of skill also may be employed in this regard.
Substrates
The present invention also relates to substrates as described herein comprising an array of Bacillus GSTs.
In a preferred embodiment, the substrate comprises an array of Bacillus licheniformis GSTs selected from the group consisting of SEQ ID NOs. 1-4448, nucleic acid fragments of SEQ ID NOs. 1-4448, and nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 1-4448. In a more preferred embodiment, the substrate comprises an array of Bacillus licheniformis GSTs selected from the group consisting of SEQ ID NOs. 1-4448. In another more preferred embodiment, the substrate comprises an array of Bacillus licheniformis GSTs selected from the group consisting of nucleic acid fragments of SEQ ID NOs. 1-4448. In another more preferred embodiment, the substrate comprises an array of Bacillus licheniformis GSTs selected from the group consisting of nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 1-4448.
In a preferred embodiment, the substrate comprises an array of Bacillus clausii GSTs selected from the group consisting of SEQ ID NOs. 4449-8481, nucleic acid fragments of SEQ ID NOs. 4449-8481, and nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 4449-8481. In a more preferred embodiment, the substrate comprises an array of Bacillus clausii GSTs selected from the group consisting of SEQ ID NOs. 4449-8481. In another more preferred embodiment, the substrate comprises an array of Bacillus clausii GSTs selected from the group consisting of nucleic acid fragments of SEQ ID NOs. 4449-8481. In another more preferred embodiment, the substrate comprises an array of Bacillus clausii GSTs selected from the group consisting of nucleic acid sequences having preferably at least 85%, more preferably at least 90%, and most preferably at least 95% homology to SEQ ID NOs. 4449-8481.
Co-linearity of Bacillus licheniformis and Bacillus subtilis Chromosomes
The complete nucleotide sequence of the Bacillus subtilis chromosome was recently published (Kunst et al., 1997, Nature 390: 249-256) and reveals the exact position of more than 4000 genes in this genome. Several public databases are available for searching and graphic representations of the entire genome.
The method of shot-gun sequencing of the Bacillus licheniformis chromosome which is conducted herein does not directly address the specific arrangement of genes on the chromosome. However, since Bacillus subtilis and Bacillus licheniformis are very closely related organisms according to the literature (Ash et al., 1991, Letters in Applied Microbiology 13: 202-206) the linear arrangement of genes on the two chromosomes might be similar.
To investigate this hypothesis, a series of long range PCR amplifications were made using primers to Bacillus licheniformis sequences which were identified as homologues to specific genes in Bacillus subtilis. Each PCR reaction employs Bacillus licheniformis chromosomal DNA as template for primer pairs that hybridizes to two genes in Bacillus licheniformis which has a known location, orientation and distance in the Bacillus subtilis homologs. If a PCR product of the expected size is synthesized, according to the Bacillus subtilis chromosomal map, it can be concluded that the two target genes are placed in the same orientation and at the same distance on both chromosomes.
Multiple PCR reactions as described herein were performed on Bacillus licheniformis to investigate the degree of co-linearity to the model organism Bacillus subtilis. The results of the PCR mapping indicate that approximately 75% of the Bacillus subtilis and Bacillus licheniformis gene content are similar or collinear (Lapidus et al., Poster P67 at The 10th International Conference on Bacilli, Baveno, Italy).
This high degree of co-linearity between these two organisms can be exploited when yet unidentified genes or part of genes from the Bacillus licheniformis chromosome are to be cloned. By using the Bacillus subtilis chromosomal map as model for the Bacillus licheniformis chromosome, it is possible to amplify specific genome regions of Bacillus licheniformis where a certain gene of interest are predicted to be located according to the Bacillus subtilis chromosomal map. Flanking sequence tags to the region can be as far apart as 10-15 kb when long range PCR methods are employed. This method of PCR mapping was used for cloning several genes of specific interest that were not tagged in the primary shot-gun library.
Gene Disrupting/deletion
A plasmid denoted “Deletion plasmid” is constructed by cloning two PCR amplified fragments from given gene X region denoted “Y” on a temperature-sensitive parent plasmid. The PCR fragments are denoted “A” and “B”, wherein A comprises the 5′-part of the Y fragment; and B comprises the 3′-part of DNA fragment Y. The deleted Y DNA between A and B may be varied depending of the size of the Y fragment. The size of the A and B fragment should be larger than 100 basepairs. A spectinomycin resistance gene flanked by resolvase (res) sites is introduced between fragments “A” and “B” on the plasmid. This spectinomycin resistance gene can later be removed by resolvase-mediated site-specific recombination.
The disrupting/deletion is transferred from the “Deletion plasmid” to the chromosome of a Bacillus licheniformis or Bacillus clausii target strain by double homologous recombination via fragments “A” and “B”, mediated by integration and excision of the temperature-sensitive plasmid. The resulting strain is denoted “Deletion strain”.
The present invention is further described by the following examples, which should not be construed as limiting the scope of the invention.
Chemicals used as buffers and substrates were commercial products of at least reagent grade.
Bacillus licheniformis ATCC 14580 was used as source of chromosomal DNA for constructing a library. Strain E. coli JJC 128F′ araD139 Δ(ara-leu)7696 galE15 galK16 Δ(lac)X74 hsdr− hsdm+ StrR F′[laclq Δ(lacZ)M15 traD36] was used as a host to construct the genomic bank (Sorokin et al., 1996, Microbiology 142: 2005-2016).
Chromosomal DNA from Bacillus licheniformis ATCC 14580 was prepared as follows. Bacillus licheniformis strain ATCC 14580 was cultivated overnight at 37° C. in 125 ml shake flasks containing 25 ml of LB medium (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, NY, 1989). The cells were harvested and treated with 10 μg of lysozyme per ml of 50 mM Tris-HCl pH 8.0, 50 mM EDTA, 25% sucrose. SDS was then added to a final concentration of 0.5% followed by proteinase K to 100 μg/ml. The mixture was incubated at 50° C. for 4 hours, and then extracted three times with water-saturated phenol-chloroform (1:1 v/v) at pH 8.0. After precipitation with two volumes of ethanol in 0.3 M sodium acetate pH 4.8, the DNA was removed with a glass rod, washed in 70% ethanol, and stored at −20° C. in water at 100 μg/ml.
Plasmid pSGMU2 (Errington, 1986, Journal of General Microbiology 132: 2953-2961) was used as a vector for constructing the chromosomal bank. pSGMU2 was isolated as follows. Cells of E. coli JJC 128F′, containing pSGMU2, were grown in 4 ml of 2×YT medium (Sambrook et al., 1989, supra) overnight. The cell pellet was resuspended in 100 μl of 50 mM glucose, 25 mM Tris/HCl pH 8.0, 10 mM EDTA solution (TE). Then a 100 μl volume of 10 mg/ml lysozyme was added. After 30 minutes 400 μl of 1% (w/v) SDS, 0.2 M NaOH were added. After cell lysis, 300 μl of 3 M sodium acetate pH 4.8, was added. After 30 minutes on ice, tubes were centrifuged at 13,000 rpm (5000×g) for 1 hour and 0.6 ml of isopropanol was added to the supernatant. After centrifugation as before for 10 minutes, the pellet was dissolved in 100 μl of water and then 100 μl of 9 M lithium chloride was added. After 1 hour at −20° C., tubes were centrifuged at 13,000 rpm (5000×g) for 10 minutes. The pellet was discarded and 500 μl of absolute ethanol was added to the supernatant. The pellet was redissolved in 300 μl of 0.3 M sodium acetate pH 4.8 and precipitated again. After dissolving the pellet in 100 μl of TE, the plasmid preparation was sufficiently pure for fluorescent sequencing.
A library with insert sizes in the range from 1 to 2 kb, was constructed by using pSGMU2. A 20 μg quantity of Bacillus licheniformis chromosomal DNA was sonicated using a VibraCell 72408 sonicator (Bioblock Scientific) at minimal amplitude for 10 seconds. The sonication was performed in 300 μl of Bal31 buffer (600 mM NaCl, 20 mM Tris-HCl pH 8.0, 12 mM CaCl2, 12 mM MgCl2, 1 mM EDTA) in a 1.5 ml Eppendorf tube. After sonication the chromosomal DNA was treated with Bal31 exonuclease (New England Biolabs, Inc., Beverly, MA) for 5 minutes at 25° C. After water-saturated phenol extraction and ethanol precipitation the DNA was treated by Klenow fragment of DNA polymerase I under the following conditions: 10 mM Tris HCl pH 7.6, 10 mM MgCl2, 0.2 mM each dNTP, at 37° C for 1 hour. After water-saturated phenol extraction and ethanol precipitation, the DNA was ligated with SmaI-digested pSGMU2 and treated with bacterial alkaline phosphatase. The ligation was performed in 10 mM Tris HCl pH 7.6, 10 mM MgCl2, 1 mM DTT, 1 mM ATP at 10° C. for 6 hours. DNA from the ligation mixture was precipitated with ethanol in the presence of 1 mM glycogen at −20° C.
The DNA was then electroporated into E. coli JJC128F′ cells using 2.5kV and 25 mF. The cells were plated on LB agar medium containing 50 μg/ml of ampicillin for selection of transformants and 20 μg/ml of 5-bromo-4-chloro-3-indolyl beta-D-galactopyranoside (XGAL) and 20 μg/ml of isopropyl beta-D-thiogalactopyranoside (IPTG) for selection of inserts. The ratio of white to blue colonies in a successful experiment was 4 to 1. A total of 25.244 plasmids were extracted from the white colonies and were sequenced by forward (M13-21) primer and 877 plasmids by reverse (M13RP1) primer using a Perkin-Elmer Applied Biosystems Model 377 XL Automatic DNA Sequencer, Perkin-Elmer Applied Biosystems, Inc., Foster City, Calif.) with successful sequencing rate of about 90%. The sequencing produced a total of 13.227.856 bases. The total accumulated nonredundant contig length was 3.723.871 basepairs in 1.239 contigs randomly distributed over the chromosome.
Oligonucleotides were synthesized using a DNA Synthesizer “Oligo 1000” (Beckman-Coulter, Fullerton, Calif.). Primers used for Long Accurate PCR were 20-22-mers, chosen to contain 12 GC-bases.
Plasmid DNA for sequencing was prepared as described above. PCR products used for sequencing with dye terminators were purified by the Wizard™ PCR Preps kit (Promega, Madison, Wis.) or agarose gel electrophoresis. Forward and reverse PCR sequencing was performed using BigDye terminator Cycle Sequencing Ready Reaction Kit (Perkin-Elmer Applied Biosystems, Inc., Foster City, Calif.) and a “Perkin Elmer” 9600 thermal cycler or the “Catalyst” station (Perkin-Elmer Applied Biosystems, Inc., Foster City, Calif.). The fragment separation was conducted using an Applied Biosystems Model 377 XL Automatic DNA Sequencer.
The Long Accurate PCR reaction (50 μl) contained the following components as described by Sorokin et al. (1996, Genome Research 6: 448-453): 20 mM Tricine, pH 8.7; 85 mM potassium acetate; 1 mM magnesium acetate; 8% glycerol; 2% dimethylsulfoxide; 0.2 mM each dNTP; 0.2 μM each primer; 0.1 μg chromosomal DNA; 2 U rTth (Perkin-Elmer Applied Biosystems, Inc., Foster City, Calif.); and 0.05 U of Vent polymerase (New England Biolabs, Inc., Beverly, Mass.). The Long Accurate PCR used the following cycling conditions: One cycle at 94° C. for 5 minutes; 12 cycles of 10 second melting at 94° C., and 12 minutes annealing-polymerisation-repair at 68° C., and 24 cycles with increasing the extension time 15 seconds for each cycle.
The overall results are summarized in Table 1.
Bacillus licheniformis ATCC 14580
Nucleotide sequence data were scrutinized for quality, and samples giving improper spacing or ambiguity levels exceeding 2% were discarded or re-run. Vector sequences were removed with the crossmatch program from the Phred/Phrap package (Ewing and Green, 1998, Genome Research 8: 186-194). The sequences were assembled with Phrap also from the Phred/Phrap package.
Annotation of a gene means assignment of a function to a given sequence. The protein encoded genes were found and annotated the following way: The assembled sequences were searched with BLASTX (Pearson and Lipman, 1988, Proceedings of the National Academy of Science USA 85: 2444-2448; Pearson, 1990, Methods in Enzymology 183: 63-98) against a customized database consisting of protein sequences from SWISSPROT, SWISSPROTNEW, TREMBL, TREMBLNEW, REMTREMBL, PDB and GeneSeqP. The matrix used was BL50. The start and stop position of each hit and the score of the hit where temporarily marked in the sequence. All open reading frames starting with ATG, GTG or TTG where temporarily marked with the start and stop position and a score. The score of the ORF was calculated as 0.5 times the length of the ORF for ORF starting with ATG and 0.25 times the length of the ORF for ORFs starting with GTG or TTG. A non overlapping set of regions with maximal score larger than 100 was found from the temporarily marked sequence. Each region represents a gene. The best hit for each gene is shown in Appendix 1. Functional category assignment was done by fastx homology search against clusters of orthologous genes from ncbi. In Appendix 1, the assignment to a particular functional category is represented by a single letter. “C” means energy production and conversion. “D” means cell division and chromosome partitioning. “E” means amino acid transport and metabolism. “F” means nucleotide transport and metabolism. “G” means carbohydrate transport and metabolism. “H” means coenzyme metabolism. “I” means lipid metabolism. “J” means translation, ribosomal structure and biogenesis. “K” means transcription. “L” means DNA replication, recombination and repair. “M” means cell envelope biogenesis, outer membrane. “N” means cell motility and secretion. “O” means posttranslational modification, protein turnover, chaperones. “P” means inorganic ion transport and metabolism. “Q” means secondary metabolites biosynthesis, transport and catabolism. “R” means general function prediction only. “S” means function unknown. “T” means signal transduction mechanisms.
Structural RNA encoding genes were found by homology (blastn) to tRNA and rRNA genes in Bacillus subtilis.
The Bacillus licheniformis GST sequences are designated SEQ ID NOs. 14448. An “N” in a nucleic acid sequence means that the nucleotide is an A, C, G, or T.
Bacillus clausii NCIB 10309 (National Collections of Industrial and Marine Bacteria Ltd., 23 St. Machar Drive, Aberdeen, Scotland, UK AB2 1RY) was used as source of chromosomal DNA for constructing a library. Strain E. coli JJC 128F′ araD139 Δ(ara-leu)7696 galE15 galK16 Δ(lac)X74 hsdr− hsdm+ StrR F′[laclq (lacZ)M15 traD36] was used as a host to construct the genomic bank (Sorokin et al., 1996, Microbiology 142: 2005-2016).
Chromosomal DNA from Bacillus clausii NCIB 10309 was prepared as follows. Bacillus clausii strain NCIB 10309 was cultivated overnight at 37° C. in 125 ml shake flasks containing 25 ml of LB medium (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, NY, 1989). The cells were harvested and treated with 10 μg of lysozyme per ml of 50 mM Tris-HCl pH 8.0, 50 mM EDTA, 25% sucrose. SDS was then added to a final concentration of 0.5% followed by proteinase K to 100 μg/ml. The mixture was incubated at 50° C. for 4 hours, and then extracted three times with water-saturated phenol-chloroform (1:1 v/v) at pH 8.0. After precipitation with two volumes of ethanol in 0.3 M sodium acetate pH 4.8, the DNA was removed with a glass rod, washed in 70% ethanol, and stored at −20° C. in water at 100 μg/ml.
Plasmid pSGMU2 (Errington, 1986, Journal of General Microbiology 132: 2953-2961) was used as a vector for constructing the chromosomal bank. pSGMU2 was isolated as follows. Cells of E. coli JJC 128F′, containing pSGMU2, were grown in 4 ml of 2×YT medium (Sambrook et al., 1989, supra) overnight. The cell pellet was resuspended in 100 μl of 50 mM glucose, 25 mM Tris/HCl pH 8.0, 10 mM EDTA solution (TE). Then a 100 μl volume of 10 mg/ml lysozyme was added. After 30 minutes 400 μl of 1% (w/v) SDS, 0.2 M NaOH were added. After cell lysis, 300 μl of 3 M sodium acetate pH 4.8, was added. After 30 minutes on ice, tubes were centrifuged at 13,000 rpm (5000×g) for 1 hour and 0.6 ml of isopropanol was added to the supernatant. After centrifugation as before for 10 minutes, the pellet was dissolved in 100 μl of water and then 100 μl of 9 M lithium chloride was added. After 1 hour at −20° C., tubes were centrifuged at 13,000 rpm (5000×g) for 10 minutes. The pellet was discarded and 500 μl of absolute ethanol was added to the supernatant. The pellet was redissolved in 300 μl of 0.3 M sodium acetate pH 4.8 and precipitated again. After dissolving the pellet in 100 μl of TE, the plasmid preparation was sufficiently pure for fluorescent sequencing.
A library with insert sizes in the range from 1 to 2 kb, was constructed by using pSGMU2. A 20 μg quantity of Bacillus clausii chromosomal DNA was sonicated using a VibraCell 72408 sonicator (Bioblock Scientific) at minimal amplitude for 10 seconds. The sonication was performed in 300 μl of Bal31 buffer (600 mM NaCl, 20 mM Tris-HCl pH 8.0, 12 mM CaCl2, 12 mM MgCl2, 1 mM EDTA) in a 1.5 ml Eppendorf tube. After sonication the chromosomal DNA was treated with Bal31 exonuclease (New England Biolabs, Inc., Beverly, Mass.) for 5 minutes at 25° C. After water-saturated phenol extraction and ethanol precipitation the DNA was treated by Klenow fragment of DNA polymerase I under the following conditions: 10 mM Tris HCl pH 7.6, 10 mM MgCl2, 0.2 mM each dNTP, at 37° C. for 1 hour. After water-saturated phenol extraction and ethanol precipitation, the DNA was ligated with SmaI-digested pSGMU2 and treated with bacterial alkaline phosphatase. The ligation was performed in 10 mM Tris HCl pH 7.6, 10 mM MgCl2, 1 mM DTT, 1 mM ATP at 10° C. for 6 hours. DNA from the ligation mixture was precipitated with ethanol in the presence of 1 mM glycogen at −20° C.
The DNA was then electroporated into E. coli JJC128F′ cells using 2.5kV and 25 mF. The cells were plated on LB agar medium containing 50 μg/ml of ampicillin for selection of transformants and 20 μg/ml of 5-bromo-4-chloro-3-indolyl beta-D-galactopyranoside (XGAL) and 20 μg/ml of isopropyl beta-D-thiogalactopyranoside (IPTG) for selection of inserts. The ratio of white to blue colonies in a successful experiment was 4 to 1. A total of 6.554 plasmids were extracted from the white colonies and were sequenced by forward (M13-21) primer using a Perkin-Elmer Applied Biosystems Model 377 XL Automatic DNA Sequencer, Perkin-Elmer Applied Biosystems, Inc., Foster City, Calif.) with successful sequencing rate of about 90%. The sequencing produced 3,191.401 bp. The total accumulated nonredundant contig length was 2.022.840 bp in 2.232 contigs randomly distributed over the chromosome.
Oligonucleotides were synthesized using a DNA Synthesizer “Oligo 1000” (Beckman-Coulter, Fullerton, Calif.). Primers used for Long Accurate PCR were 20-22-mers, chosen to contain 12 GC-bases.
The overall results are summarized in Table 2.
Nucleotide sequence data were scrutinized for quality, and samples giving improper spacing or ambiguity levels exceeding 2% were discarded or re-run. Vector sequences were removed with the crossmatch program from the Phred/Phrap package (Ewing and Green, 1998, Genome Research 8: 186-194). The sequences were assembled with Phrap also from the Phred/Phrap package.
Annotation of a gene means assignment of a function to a given sequence. The protein encoded genes were found and annotated the following way: The assembled sequences were searched with BLASTX (Pearson and Lipman, 1988, Proceedings of the National Academy of Science USA 85: 2444-2448; Pearson, 1990, Methods in Enzymology 183: 63-98) against a customized database consisting of protein sequences from SWISSPROT, SWISSPROTNEW, TREMBL, TREMBLNEW, REMTREMBL, PDB and GeneSeqP. The matrix used was BL50. The start and stop position of each hit and the score of the hit where temporarily marked in the sequence. All open reading frames starting with ATG, GTG or TTG where temporarily marked with the start and stop position and a score. The score of the ORF was calculated as 0.5 times the length of the ORF for ORF starting with ATG and 0.25 times the length of the ORF for ORFs starting with GTG or TTG. A non overlapping set of regions with maximal score larger than 100 was found from the temporarily marked sequence. Each region represents a gene. The best hit for each gene is shown in Appendix 2. Functional category assignment was done by fastx homology search against clusters of orthologous genes from ncbi. In Appendix 2, the assignment to a particular functional category is represented by a single letter. “C” means energy production and conversion. “D” means cell division and chromosome partitioning. “E” means amino acid transport and metabolism. “F” means nucleotide transport and metabolism. “G” means carbohydrate transport and metabolism. “H” means coenzyme metabolism. “I” means lipid metabolism. “J” means translation, ribosomal structure and biogenesis. “K” means transcription. “L” means DNA replication, recombination and repair. “M” means cell envelope biogenesis, outer membrane. “N” means cell motility and secretion. “O” means posttranslational modification, protein turnover, chaperones. “P” means inorganic ion transport and metabolism. “Q” means secondary metabolites biosynthesis, transport and catabolism. “R” means general function prediction only. “S” means function unknown. “T” means signal transduction mechanisms.
Structural RNA encoding genes were found by homology (blastn) to tRNA and rRNA genes in Bacillus subtilis.
The Bacillus clausii GST sequences, which encode proteins are designated SEQ ID NOs. 4449-8481. An “N” in a nucleic acid sequence means that the nucleotide is an A, C, G, or T.
Details of the construction of a typical microarrayer can be found on the world wide web site of Professor Patrick Brown of Stanford University. Scanners and computer software for analysis of DNA microarrays are available from several commercial sources such as General Scanning Inc. (Watertown, Mass.), or Axon Instruments (Foster City, Calif.).
Individual Bacillus GST clones were purified as plasmid minipreps using Qiagen Biorobot 9600 (QIAGEN, Inc., Valencia, Calif.). The plasmid minipreps were precipitated with isopropanol, aliquoted and stored as described on the web site of Professor Patrick Brown of Stanford University.
The amplified GST targets prepared in this manner were spotted individually onto polylysine-coated glass slides using a microarrayer device as described by DeRisi et al. (1997, Science 278: 680-686). The microarrays were probed with fluorescently labeled cDNA prepared by reverse transcription of polyadenylated mRNA (DeRisi et al., 1997, supra) extracted from Bacillus cells (Example 2 or Example 4). Conditions for pretreatment of the microarrays, hybridization and washing conditions have been described previously (DeRisi et al., 1997, supra.
To increase the reliability with which changes in expression levels could be discerned, probes prepared from induced or treated cells were labeled with the red fluorescent dye, Cy5 (Amersham Corporation, Arlington Heights, Ill.), and mixed with probes from uninduced, untreated, or “reference” cells were labeled with a green fluorescent dye, Cy3 (Amersham Corporation, Arlington Heights, Ill.) The relative ratio of fluorescence intensity measured for the Cy3 and Cy5 fluorophors corresponding to each GST target in the arrays was determined using ScanAlyze software. This provides a reliable measure of the relative abundance of the corresponding mRNA in the two cell populations (e.g., treated cells versus reference cells).
The invention described and claimed herein is not to be limited in scope by the specific embodiments herein disclosed, since these embodiments are intended as illustrations of several aspects of the invention. Any equivalent embodiments are intended to be within the scope of this invention. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. In the case of conflict, the present disclosure including definitions will control.
Various references are cited herein, the disclosures of which are incorporated by reference in their entireties.
Appendix 1: Bacillus licheniformis Annotation and Divisions Into Functional Categories
Information Storage and Processing
Staphylococcus aureus mutant P10B2 virulence gene product.
Corynebacterium thermoaminogenes acn protein.
Bacillus subtilis ypgA clade protein.
Corynebacterium thermoaminogenes acn protein.
Arabidopsis aldehyde dehydrogenase (ALDH)-1.
Corynebacterium glutamicum MCT protein SEQ ID NO: 544.
Neisseria meningitidis ORF 567 protein sequence SEQ ID NO: 16
Arabidopsis thaliana protein fragment SEQ ID NO: 42012.
B. subtilis AnsB homologue.
Bacillus subtilis metalloprotease YurH.
Bacillus subtilis Class II EPSPS.
B. subtilis hydrolase protein YTMA.
Neisseria gonorrheae ORF 705 protein sequence SEQ ID NO: 2358
Arabidopsis thaliana protein fragment SEQ ID NO: 18888.
Arabidopsis thaliana protein fragment SEQ ID NO: 12719.
Staphylococcus aureus mutant P7C18 virulence gene product.
B. subtilis acetohydroxyacid synthetase subunit, IlvB.
B. subtilis IlvE homologue #1.
B. subtilis oppD ATPase.
B. subtilis oppA ligand binding protein.
B. subtilis oppB membrane protein.
B. subtilis oppA ligand binding protein.
Pyrococcus horikoshii thermophilic dehydrogenase.
Corynebacterium glutamicum MP protein sequence SEQ ID NO: 948
Zea mays protein fragment SEQ ID NO: 40074.
Corynebacterium glutamicum MP protein sequence SEQ ID NO: 998
Bacillus species alpha-glucosidase.
Bacillus sp. exo-alpha-1,4-glucosidase, AMY1084
Bacillus subtilis araN gene product.
B. licheniformis acid stable and thermostable alpha-amylase.
Bacillus sp. OC187 4(R)-hydroxy-2-ketoglutaric acid aldolase
B. subtilis cysteine protease CP3 protein sequence.
Bacillus subtilis L-arabinose isomerase.
S. pneumoniae derived protein #352.
Enterococcus faecalis protein EF092.
Enterococcus faecalis protein EF092.
S. pneumoniae cellobiose phosphotransferase system celA.
B. subtilis rib operon protein translated from reading frame
B. subtilis pantothenate kinase, CoaA#1.
B. subtilis pantothenate synthetase.
Synechocystis sp. 6803 DXP synthase protein sequence.
Bacillus subtilis DXP synthase protein sequence.
Synechocystis sp. 6803 DXP synthase protein sequence.
B. subtilis hydrolase protein YTPA.
Streptococcus pneumoniae glycyl tRNA synthetase alpha.
B. subtilis novel pantothenate kinase encoded by the gene co
L. lactis HsdM subunit #2.
Staphylococcus aureus CcrB1 protein sequence SEQ ID NO: 8.
L. lactis HsdM subunit #1.
B. subtilis yaeL polypeptide.
B. subtilis glycosyl transferase catalytic domain.
Bacillus subtilis IFO 3336 PGA synthesising enzyme.
B. subtilis hexulose phosphate isomerase.
Staphylococcus aureus ica A protein.
B. subtilis secretion factor SecDF.
Bacillus subtilis protein secretion chaperone FtsY.
B. subtilis FtsH protein.
Bacillus megaterium HSP (Bmehsp70).
Bacillus megaterium HSP (Bmehsp70).
Bacillus carlsberg alkaline elastase.
Arabidopsis thaliana protein fragment SEQ ID NO: 56671.
Staphylococcus aureus glycoprotease (gcp) protein.
Bacillus megaterium HSP (Bmehsp70).
S. pneumoniae phosphate transport ATP-binding protein.
B. subtilis hydrolase protein YJCH.
B. subtilis hydrolase protein YJCH.
S. xylosus DltA protein.
H. ghilianii/B. megaterium fusion protein Tridegin/GlcDH.
B. subtilis hydrolase protein YODH.
Bacillus subtilis inositol dehydrogenase.
Bacillus subtilis yihA family member polypeptide sequence.
Bacillus subtilis serine protease SP3 (YITV).
B. subtilis hydrolase protein YUII.
B. subtilis hydrolase protein YCGS.
B. subtilis nitroreductase Bs YrwO.
Bacillus subtilis metalloprotease YhaA.
Bacillus licheniformis Pectin lyase III.
Bacillus licheniformis endo-beta-1,4-glucanase.
Bacillus licheniformis endo-beta-1,4-glucanase.
Bacillus licheniformis Pectate lyase I.
Bacillus sp. transglutaminase.
S. pneumoniae derived protein #146.
Bacillus subtilis prenyl diphosphate synthetase subunit.
B. subtilis hydrolase protein YQJL.
Bacillus subtilis IFO 3336 PGA synthesising enzyme.
Thermotoga maritima endoglucanase.
Sorangium cellulosum protein Orf 4.
Chlamydia pneumoniae lipoprotein sequence.
Porphorymonas gingivalis protein PG22.
Bacillus licheniformis (BLC) RP-II protease.
Arabidopsis thaliana protein fragment SEQ ID NO: 48115.
M. tuberculosis SYNEC protein.
Streptococcus pneumoniae encoded polypeptide.
Arabidopsis thaliana protein fragment SEQ ID NO: 22242.
Streptococcus pneumoniae spo/rel protein sequence.
Staphylococcus aureus response regulator protein.
Appendix 2: Bacillus clausii Annotation and Divisions Into Functional Categories
Information Storage and Processing
Staphylococcus aureus respiratory nitrate reductase alpha su
Staphylococcus carnosus nitrate reductase biogenesis protein
Staphylococcus aureus respiratory nitrate reductase alpha su
Staphylococcus carnosus nitrate reductase NarJ subunit.
Arabidopsis thaliana protein fragment SEQ ID NO: 8020.
Corynebacterium glutamicum MP protein sequence SEQ ID NO: 338
S. pneumoniae phospho-2-dehydro-3-deoxyheptonate aldolase.
T. vaginalis homocysteinase # 2.
H. pylori cytoplasmic protein 04ge10816orf2.
B. subtilis oppC membrane protein.
Enterococcus faecalis antigenic polypeptide fragment EF045.
Corynebacterium glutamicum MCT protein SEQ ID NO: 522.
Arabidopsis thaliana protein fragment SEQ ID NO: 1993.
S. pneumoniae adenylosuccinate lyase.
E. coli cytosine-deaminase.
Arabidopsis thaliana protein fragment SEQ ID NO: 43508.
Paenibacillus pabuli 2,6-beta-D-fructan hydrolase.
Streptococcus pneumoniae photomutase yhxB.
S. pneumoniae derived protein #253.
Enterococcus faecalis protein EF048.
S. pneumoniae derived protein #302.
Streptococcus pneumoniae type 4 protein sequence #56.
Streptococcus pneumoniae type 4 protein sequence #18.
B. subtilis hexulose phosphate synthase.
S. pneumoniae derived protein #253.
Streptococcus pneumoniae SP0014 protein.
Streptococcus pneumoniae type 4 protein sequence #55.
S. carnosus nitrate reductase molybdenum cofactor MoeB.
E. coli proliferation associated protein sequence SEQ ID NO:
Streptococcus pneumoniae prfC protein sequence.
H. pylori GHPO 728 protein.
Arabidopsis thaliana protein fragment SEQ ID NO: 29871.
Brevibacterium lactofermentum aspC protein.
Staphylococcus aureus regulator protein.
Streptomyces globisporus C-1027 gene cluster ORF −1.
S. fradiae tylosin biosynthetic pathway D-alanine carboxypep
S. aureus MurB protein #1.
B. subtilis hexulose phosphate synthase.
S. aureus gidB protein sequence.
B. stearothermophilus alanine racemase.
Racillus subtilis teichoic acid polymerase.
Racillus subtilis teichoic acid polymerase.
S. pneumoniae derived protein #264.
Staphylococcus aureus protein SEQ ID #5196.
S. aureus gidB protein sequence.
S. aureus MurB protein SEQ ID 1.
Bacilus megaterium YkoY protein.
Staphylococcus carnosus nitrate reductase NarH subunit.
Corynebacterium glutamicum MCT protein SEQ ID NO: 566.
B. subtilis hydrolase protein YFHM.
Neisseria meningitidis strain A antigen encoded by ORF6.
Bacillus subtilis metalloprotease YhaA.
Bacillus subtilis metalloprotease YmfH.
Staphylococcal ABC transporter protein.
Ammonifex degensii KC4 alkaline phosphatase (3A1A = 3A2A).
Staphylococcus aureus protein homologous to hypothetical pro
E. coli proliferation associated protein sequence SEQ ID NO:
Streptococcus pneumoniae polypeptide.
STREPTOCOCCAL HEMAGGLUTININ.
M. tuberculosis polypeptide sequence comprising Mtb-81 antig
Staphylococcus aureus protein homologous to subunit fmdE.
Staphylococcus aureus protein homologous to hypothetical pro
Streptococcus pneumoniae encoded polypeptide.
S. pneumoniae derived protein #199.
Staphylococcus aureus histidine kinase polypeptide sequence.
Staphylococcus aureus protein of unknown function.
Streptococcus pneumoniae encoded polypeptide.
S. pneumoniae 30S ribosomal protein S2.
Corynebacterium glutamicum SMP protein sequence SEQ ID NO: 50
Staphylococcus aureus protein of unknown function.
Bacillus clausii NN049095 BXM20 beta-1,4-mannanase precursor
S. pneumoniae diacylglycerol kinase.
Streptococcus pneumoniae encoded polypeptide.
Streptococcus pneumoniae type 4 protein sequence #75.
Staphylococcus aureus protein of unknown function.
E. coli aspartokinase III variant No. 169 (T352I, S369F).
Streptococcus pneumoniae SP0014 protein.
Synechocystis sp phytochrome-related gene Cph1.
Streptococcus pneumoniae encoded polypeptide.
Chlamydia pneumoniae lipoprotein sequence.
Chlamydia pneumoniae lipoprotein sequence.
Streptococcus pneumoniae encoded polypeptide.
Chlamydia pneumoniae lipoprotein sequence.
Staphylococcus aureus protein homologous to subunit fmdE.
Chlamydia pneumoniae lipoprotein sequence.
Mycobacterium bovis regX3 protein.
Staphylococcus aureus protein SEQ ID #5239.
This application contains 2 copies of the Sequence Listing on compact disk, which are incorporated herein by reference. Copy 1 is made with an Intel x86 machine format, with Windows XP operating system compatibility, and one file was saved as 10085.510-U.S. SEQLIST, and is 7,179 kb bytes, and was created on Nov. 1, 2005, Copy 2 is identical to Copy 1.
This application is a divisional of U.S. application Ser. No. 09/974,300 filed on Oct. 5, 2001, which is a continuation-in-part of U.S. application Ser. No. 09/680,598 filed on Oct. 6, 2000, now abandoned, and claims priority from U.S. provisional application Ser. No. 60/279,526 filed on Mar. 27, 2001, which applications are fully incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 20070015168 A1 | Jan 2007 | US |
| Number | Date | Country | |
|---|---|---|---|
| 60279217 | Mar 2001 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 09974300 | Oct 2001 | US |
| Child | 11203606 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 09680598 | Oct 2000 | US |
| Child | 09974300 | US |
