Patent Application
20210324361
The present invention relates to the field of enzyme compositions. In particular, the invention relates to enzyme compositions for cleaving antigens, and for providing methods uses, apparatuses and systems for cleaving antigens using the compositions.
Correct matching of blood types is a central requirement of transfusion medicine since plasma of blood group A individuals contains antibodies to the B-antigen and vice versa, thus incompatible transfusions can result in activation of complement and red blood cell (RBC) lysis (Daniels 2010). These cell surface antigens are carbohydrate structures terminating in α-1,3-linked-N-acetylgalactosamine (GalNAc) or galactose (Gal) for A-type blood and B-type blood respectively. O type RBCs, on the other hand, contain neither of these terminal sugars, and may be transfused universally (Garratty 2008). Accordingly, a good supply of group O RBCs is needed in blood banks for emergency situations, where the patient's blood type is unknown or unclear. However, supplies are often limited.
The concept of enzymatic removal of the GalNAc or Gal structures from A or B RBCs as a means of converting A or B RBCs to O was first proposed and demonstrated by Goldstein (Goldstein 1982; U.S. Pat. No. 4,609,627; and CA2272925). Using an α-galactosidase from green coffee bean, B-type RBCs were converted to O and subsequent successful transfusion performed (Kruskall 2000). However, the quantities of enzyme that were needed, rendering the approach impractical. Conversion of Type A is more challenging, largely because Type A blood occurs as many subtypes that differ in their internal linkages (Clausen 1989). Similarly, α-galactosidases have been used to remove B-type antigens (for example, see EP2243793). A major advance towards practical conversions, including of Type A, was made by screening of a library of bacteria for both A and B conversion activities, using tetrasaccharide substrates. Two new families of glycosidase were found that show high antigen cleavage activity at neutral pH values: the CAZy GH109 α-N-acetylgalactosaminidases and the GH110 α-galactosidases (Liu 2007). Both enzymes converted their corresponding RBCs with complete removal of the respective antigens. However, substantial amounts of enzyme were still needed for conversion, especially of Type A (60 mg enzyme/unit of blood), limiting further development. Enzymes having greater efficiency in cleaving the carbohydrate antigens from cells would be of use.
The present invention is based in part, on the surprising discovery that the combination of a Galactosaminidase and a GalNAcDeacetylase, as described herein, are orders of magnitude more efficient than previously identified A-antigen cleaving enzymes. For example, under some conditions some of the GalNAcDeacetylase and Galactosaminidase enzymes may be capable of cleaving A-antigen at or below 1μ/ml. Furthermore, the cleavage efficiency of the enzyme combination is maintained at a pH suitable to maintain viability of the erythrocytes (i.e. pH between about 6.5 and about 7.5). Additionally, the enzymes were found to be active at temperatures between 4° C. and 37° C., which is also suitable for blood collection, washing and storage protocols. Furthermore, the efficiency of the enzymes is further improved through the addition of a crowding agent (for example, dextran). It has also been appreciated that the same two step cleavage process could be applied to donor organs. The enzymes as described herein, were tested mainly on samples with 10% hematocrit since those are better to work with and calculated the amount needed for packed red blood cell (rbc) bags (approx. 220 ml), which contains a level of around 80% hematocrit.
In some embodiments, lacking a crowding agent: 3 μg/ml 10% hemocrit, 1 h 37° C.>5.3 mg of each enzyme per packed rbc bag may be used to cleave A-antigen from erythrocytes and in other embodiments having a crowding agent: 0.5 μg/ml 10% hemocrit, 1 h 37° C.>0.9 mg of each enzyme per packed rbc bag may be used to cleave A-antigen from erythrocytes. However, it will be appreciated by a person of skill in the art that more enzyme could be used to reduce the time in which the blood may be processed or less enzyme could be used, provided that the cells are incubated longer.
In accordance with one embodiment, there is provided a composition, the composition including: (a) a purified GalNAcDeacetylase protein; and (b) a purified Galactosaminidase protein.
In accordance with one embodiment, there is provided a composition, the composition including: (a) the purified GalNAcDeacetylase protein is selected from one or more of the following: SEQ ID NO.:2; SEQ ID NO.:4; SEQ ID NO.:5; SEQ ID NO.:17; SEQ ID NO.:23; SEQ ID NO.:29; SEQ ID NO.:31; SEQ ID NO.:32; SEQ ID NO.:33; SEQ ID NO.:34; and SEQ ID NO.:35; and (b) the purified Galactosaminidase protein is selected from one or more of the following: SEQ ID NO.:7; SEQ ID NO.:9; SEQ ID NO.:10; SEQ ID NO.:19; SEQ ID NO.:21; SEQ ID NO.:36; and SEQ ID NO.:37.
In accordance with a further embodiment, there is provided a composition, the composition including: a purified enzyme having a GalNAcDeacetylase activity consisting essentially of an amino acid sequence at least 90% identical to the sequence set forth in one of SEQ ID NOs:2, 4, 5, 17, 23, 29, 31 and 32-35; and a purified enzyme having Galactosaminidase activity consisting essentially of an amino acid sequence at least 90% identical to the sequence set forth in one of SEQ ID NOs:7, 9, 10, 19, 21, 36 and 37.
In accordance with a further embodiment, there is provided a composition, the composition including: a purified enzyme having a GalNAcDeacetylase activity consisting essentially of an amino acid sequence at least 85% identical to the sequence set forth in one of SEQ ID NOs:2, 4, 5, 17, 23, 29, 31 and 32-35; and a purified enzyme having Galactosaminidase activity consisting essentially of an amino acid sequence at least 85% identical to the sequence set forth in one of SEQ ID NOs:7, 9, 10, 19, 21, 36 and 37.
In accordance with a further embodiment, there is provided a composition, the composition including: a purified enzyme having a GalNAcDeacetylase activity consisting essentially of an amino acid sequence at least 80% identical to the sequence set forth in one of SEQ ID NOs:2, 4, 5, 17, 23, 29, 31 and 32-35; and a purified enzyme having Galactosaminidase activity consisting essentially of an amino acid sequence at least 80% identical to the sequence set forth in one of SEQ ID NOs:7, 9, 10, 19, 21, 36 and 37.
In accordance with a further embodiment, there is provided a composition, the composition including: a purified enzyme having a GalNAcDeacetylase activity consisting essentially of an amino acid sequence at least 75% identical to the sequence set forth in one of SEQ ID NOs:2, 4, 5, 17, 23, 29, 31 and 32-35; and a purified enzyme having Galactosaminidase activity consisting essentially of an amino acid sequence at least 75% identical to the sequence set forth in one of SEQ ID NOs:7, 9, 10, 19, 21, 36 and 37.
In accordance with a further embodiment, there is provided a composition, the composition comprising enzymes selected from one or more of: (a) the purified GalNAcDeacetylase protein is a purified Flavonifractor plautii GalNAcDeacetylase protein of SEQ ID NO.:2, SEQ ID NO.:4 and SEQ ID NO.:5; and one or more of: (b) the purified Galactosaminidase protein is a purified Flavonifractor plautii Galactosaminidase protein of SEQ ID NO.:7, SEQ ID NO.:9 and SEQ ID NO.:10.
In accordance with a further embodiment, there is provided a composition, the composition comprising enzymes selected from one or more of: (a) the purified GalNAcDeacetylase protein of SEQ ID NO.:2, SEQ ID NO.:4, SEQ ID NO.:5, SEQ ID NO.:17 and SEQ ID NO.:32; and (b) the purified Galactosaminidase protein is a purified Flavonifractor plautii Galactosaminidase protein of SEQ ID NO.:7, SEQ ID NO.:9, SEQ ID NO.:10, SEQ ID NO.:19, SEQ ID NO.:21, SEQ ID NO.:36 and SEQ ID NO.:37.
In accordance with a further embodiment, there is provided a composition, the composition comprising enzymes selected from one or more of: (a) the purified GalNAcDeacetylase protein is a purified Clostridium tertium GalNAcDeacetylase protein of SEQ ID NO.:17 and SEQ ID NO.:32; and (b) the purified Galactosaminidase protein is a purified Clostridium tertium Galactosaminidase protein of SEQ ID NO.:19 and SEQ ID NO.:36.
The GalNAcDeacetylase and Galactosaminidase composition may be capable of cleaving A-antigen at or below 1 μg/ml. The GalNAcDeacetylase and Galactosaminidase composition may have A-antigen cleaving activity at a pH between about 6.5 and about 7.5. The GalNAcDeacetylase and Galactosaminidase composition may have A-antigen cleaving activity at a temperatures between 4° C. and 37° C.
The composition may include: (a) the purified GalNAcDeacetylase and the purified Galactosaminidase may be immobilized; (b) the purified GalNAcDeacetylase may be immobilized; or (c) the purified Galactosaminidase may be immobilized.
The immobilized enzymes may be attached to a surface, the surface may be selected from one or more of the following: (a) a bead or microsphere; (b) a container, (c) a tube; (d) a column; and (e) a matrix. The composition may further include a crowding agent. The crowding agent may be selected from one or more of: a dextran, a dextran sulfate, a dextrin, a pullulan, a poly(ethylene glycol), a Ficoll™, and an inert protein.
In accordance with a further embodiment, there is provided a purified enzyme including a Flavonifractor plautii GalNAcDeacetylase of SEQ ID NO.:2, SEQ ID NO.:4 or SEQ ID NO.:5.
In accordance with a further embodiment, there is provided a purified enzyme including a Flavonifractor plautii Galactosaminidase of SEQ ID NO.:7, SEQ ID NO.:9 or SEQ ID NO.:10.
In accordance with a further embodiment, there is provided a purified enzyme including a Clostridium tertium GalNAcDeacetylase of SEQ ID NO.:17 or SEQ ID NO.:32.
In accordance with a further embodiment, there is provided a purified enzyme including a Clostridium tertium Galactosaminidase of SEQ ID NO.:19 or SEQ ID NO.:36.
In accordance with a further embodiment, there is provided an isolated nucleic acid sequence encoding GalNAcDeacetylase selected from one or more of: SEQ ID NO.:1; SEQ ID NO.:3; SEQ ID NO.:16; SEQ ID NO.:24; SEQ ID NO.:26; SEQ ID NO.:28; and SEQ ID NO.:30.
In accordance with a further embodiment, there is provided an isolated nucleic acid sequence encoding Galactosaminidase selected from one or more of: SEQ ID NO.:6; SEQ ID NO.:8; SEQ ID NO.:18; and SEQ ID NO.:20.
In accordance with a further embodiment, there is provided a vector including the nucleic acid described herein. The vector may also include a heterologous nucleic acid sequence is selected from one or more of the following: a protein tag; and a cleavage site.
The protein tag may be selected from one or more of: Albumin-binding protein (ABP); Alkaline Phosphatase (AP); AU epitope; AU5 epitope; AviTag; Bacteriophage T7 epitope (T7-tag); Bacteriophage V5 epitope (V5-tag); Biotin-carboxy carrier protein (BCCP); Bluetongue virus tag (B-tag); single-domain camelid antibody (C-tag); Calmodulin binding peptide (CBP or Calmodulin-tag); Chloramphenicol Acetyl Transferase (CAT); Cellulose binding domain (CBP); Chitin binding domain (CBD); Choline-binding domain (CBD); Dihydrofolate reductase (DHFR); DogTag; E2 epitope; E-tag; FLAG epitope (FLAG-tag); Galactose-binding protein (GBP); Green fluorescent protein (GFP); Glu-Glu (EE-tag); Glutathione S-transferase (GST); Human influenza hemagglutinin (HA); HaloTag™; Alternating histidine and glutamine tags (HQ tag); Alternating histidine and asparagine tags (HN tag); Histidine affinity tag (HAT); Horseradish Peroxidase (HRP); HSV epitope; Isopeptag (Isopep-tag); Ketosteroid isomerase (KSI); KT3 epitope; LacZ; Luciferase; Maltose-binding protein (MBP); Myc epitope (Myc-tag); NE-tag; NusA; PDZ domain; PDZ ligand; Polyarginine (Arg-tag); Polyaspartate (Asp-tag); Polycysteine (Cys-tag); Polyglutamate (Glu-tag); Polyhistidine (His-tag); Polyphenylalanine (Phe-tag); Profinity eXact; Protein C; RhoiD4-tag; S1-tag; S-tag; Softag 1; Softag 3; SnoopTagJr; SnoopTag; Spot-tag; SpyTag (Spy-tag); Streptavadin-binding peptide (SBP); Staphylococcal protein A (Protein A); Staphylococcal protein G (Protein G); Strep-tag; Streptavadin (SBP-tag); Strep-tag II; Sdy-tag; Small Ubiquitin-like Modifier (SUMO); Tandem Affinity Purification (TAP); T7 epitope; tetracysteine tag (TC tag); Thioredoxin (Trx); TrpE; Ty tag; Ubiquitin; Universal; V5 tag; VSV-G or VSV-tag; and Xpress tag.
In accordance with a further embodiment, there is provided a method for enzymatically cleaving A-antigens from blood, erythrocytes or a donor organ, the method including: (a) combining a GalNAcDeacetylase protein and a Galactosaminidase protein with (i) blood comprising type A antigen; (ii) erythrocytes of A type or AB type; or (iii) a donor organ displaying type A antigen; (b) incubating the enzymes with the (i) the blood; (ii) the erythrocytes of an A type or AB type; or (iii) the donor organ for a period of time sufficient to allow the enzymes to cleave A-antigens from the blood, the erythrocytes or the donor organ.
The GalNAcDeacetylase may be a purified protein selected from one or more of: SEQ ID NO.:2; SEQ ID NO.:4; SEQ ID NO.:5; SEQ ID NO.:17; SEQ ID NO.:23; SEQ ID NO.:29; SEQ ID NO.:31; SEQ ID NO.:32; SEQ ID NO.:33; SEQ ID NO.:34; and SEQ ID NO.:35; and the Galactosaminidase may be a purified protein is selected from one or more of the following: SEQ ID NO.:7; SEQ ID NO.:9; SEQ ID NO.:10; SEQ ID NO.:19; SEQ ID NO.:21; SEQ ID NO.:36; and SEQ ID NO.:37.
The composition may include: a purified enzyme having a GalNAcDeacetylase activity consisting essentially of an amino acid sequence at least 90% identical to the sequence set forth in one of SEQ ID NOs:2, 4, 5, 17, 23, 29, 31 and 32-35; and a purified enzyme having Galactosaminidase activity consisting essentially of an amino acid sequence at least 90% identical to the sequence set forth in one of SEQ ID NOs:7, 9, 10, 19, 21, 36 and 37.
The GalNAcDeacetylase may be a purified Flavonifractor plautii GalNAcDeacetylase protein of SEQ ID NO.:4 or SEQ ID NO.:5 and the Galactosaminidase may be a purified Flavonifractor plautii Galactosaminidase protein of SEQ ID NO.:9 or SEQ ID NO.:10.
The method may further include adding a crowding agent. The crowding agent may be selected from one or more of: a dextran; a dextran sulfate; a dextrin; a pullulan; a poly(ethylene glycol); a Ficoll™; a hyper-branched glycerol; and an inert protein.
The method may further include washing the blood, erythrocytes or a donor organ to remove GalNAcDeacetylase, Galactosaminidase and the crowding agent.
The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 1 μg/ml. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a pH between about 6.5 and about 7.5. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a temperatures between 4° C. and 37° C.
In accordance with a further embodiment, there is provided a blood collection and storage system, including: (a) a purified GalNAcDeacetylase protein; and (b) a purified Galactosaminidase protein.
The system may further include a surface to which the enzyme is immobilized, the surface being selected from one or more of the following: (a) a bead or microsphere; (b) a container, (c) a tube; (d) a column; or (e) a matrix.
In accordance with a further embodiment, there is provided a blood collection and storage apparatus, the apparatus including: (a) a surface; (b) a purified GalNAcDeacetylase protein immobilized on the surface; and (c) a purified Galactosaminidase protein immobilized on the surface.
The apparatus surface to which the enzyme is immobilized may be selected from one or more of the following: (a) a bead or microsphere; (b) a container; (c) a tube; (d) a column; or (e) a matrix. The container may be a bag.
The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 100 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 90 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 80 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 70 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 60 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 50 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 40 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 30 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 20 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 15 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 14 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 13 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 12 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 11 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 10 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 9 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 8 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 7 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 6 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 5 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 4 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 3 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 2 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 1 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.9 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.8 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.7 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.6 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.5 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.4 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.3 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.2 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.1 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.09 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.08 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.07 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.06 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.05 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.04 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.03 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.02 μg/ml. The GalNAcDeacetylase and Galactosaminidase may be capable of cleaving A-antigen at or below 0.01 μg/ml.
The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a pH between about 6.5 and about 7.5. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a pH between about 6.0 and about 8.0. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a pH between about 6.8 and about 7.8. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a pH between about 6.9 and about 7.9. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a pH between about 6.4 and about 7.8.
The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at temperatures between 4° C. and 37° C. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at temperatures between 3° C. and 38° C. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity temperatures between 4° C. and 40° C. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at temperatures between 4° C. and 37° C. The GalNAcDeacetylase and Galactosaminidase may have A-antigen cleaving activity at a temperatures between 5° C. and 37° C.
The purified GalNAcDeacetylase and the purified Galactosaminidase may be immobilized. The purified GalNAcDeacetylase may be immobilized. The purified Galactosaminidase may be immobilized. The immobilized enzyme may be attached to a surface. The surface may be selected from one or more of the following: a bead or microsphere; a container, a tube; a column; or a matrix. The surface may be selected from one or more of the following: a container; a tube; a column; or a matrix. The container may be a bag.
In accordance with another embodiment, there is provided a purified enzyme including a Flavonifractor plautii GalNAcDeacetylase of SEQ ID NO.:2, SEQ ID NO.:4 or SEQ ID NO.:5.
In accordance with another embodiment, there is provided a purified enzyme including a Flavonifractor plautii Galactosaminidase of SEQ ID NO.:7, SEQ ID NO.:9 or SEQ ID NO.:10.
In accordance with another embodiment, there is provided a purified enzyme including a purified Clostridium tertium GalNAcDeacetylase and Galactosaminidase fusion protein of SEQ ID NO.:14.
In accordance with another embodiment, there is provided a vector including the nucleic acid as described herein and a heterologous nucleic acid sequence.
In accordance with another embodiment, the method may be carried out in vitro or ex vivo. As used herein ex vivo means that the method is carried out outside an organism. For example, ex vivo would encompass ex vivo lung perfusion (EVLP) and treatment of donated blood. As used herein, ex vivo refers to experimentation or measurements or treatments done in or on tissue or cells (for example, erythrocytes or a donor organ) from an organism in an external environment with minimal or some alterations of conditions from which the tissue or cells were under when in vivo.
The following detailed description will be better understood when read in conjunction with the appended figures. For the purpose of illustrating the invention, the figures demonstrate embodiments of the present invention. However, the invention is not limited to the precise arrangements, examples, and instrumentalities shown.
Any terms not directly defined herein shall be understood to have the meanings commonly associated with them as understood within the art of the invention.
An “immobilized enzyme” as used herein is an enzyme attached to surface, which may be an inert, insoluble material. Immobilization of enzymes can provide increased resistance to changes in conditions such as pH, temperature etc. and assist in their removal following use and for enzyme re-use.
Immobilization of an enzyme may be accomplished by various ways (for example, affinity-tag binding, surface adsorption on glass, resin, alginate beads or matrix, bead, fiber or microsphere entrapment, cross-linking to a surface or other enzymes and covalent binding to a surface).
As used herein “affinity-tag binding” refers to the immobilization of enzymes to a surface (for example, a porous material, using non-covalent or covalent protein tags). Affinity-tag binding has been used for protein purification and has more recently been used for biocatalysis applications by EziG™ (ENGINZYME AB™, Sweden—for example, PCT/US1992/010113; and PCT/SE2015/050108). Alternative systems are known in the art for attaching active enzymes to a surface (see for example, U.S. Pat. Nos. 4,088,538; 4,141,857; 4,206,259; 4,218,363; 4,229,536; 4,239,854; 4,619,897; 4,748,121; 4,749,653; 4,897,352; 4,954,444; 4,978,619; 5,154,808; 5,914,367; 5,962,279; 6,030,933; 6,291,582; 6,254,645; 10,016,490; and 10,041,055).
Protein tags are peptide sequences genetically grafted onto a recombinant protein, are often removable by chemical agents or by enzymatic means and are attached to proteins for various purposes. The protein tags set out in TABLE A are intended to be examples and are not intended to be limiting in any way. One type of protein tag is an affinity tag, which are added to proteins or peptide sequences so that they can be purified from a crude biological source using an affinity technique (for example, from expression system organisms) or to facilitate immobilization of the “tagged” protein to a surface. Some examples of affinity tags include chitin binding domain (CBD), maltose binding protein (MBP), Strep-tag, glutathione-S-transferase (GST) and the Polyhistidine (His-tag), which binds to metal matrices. Another type of protein tag is a epitope tag (for example, include V5-tag, Myc-tag, HA-tag, Spot-tag and NE-tag), which are short peptide sequences chosen for the ease of producing high-affinity antibodies and are often derived from viral gene sequences to improve immunoreactivity. Epitope tags are particularly useful for western blotting, immunofluorescence and immunoprecipitation experiments, although they also find use in purification and immobilization of proteins to a surface. Yet another type of protein tag is a chromatography tag (for example, polyanionic amino acids, such as FLAG-tag), which may be used to alter chromatographic properties of the protein to assist with separation and purification or immobilization. Yet further protein tags are solubilization tags (for example, Maltose-binding protein (MBP), Glutathione S-transferase (GST), thioredoxin (A) and poly(NANP)) and fluorescence tags (for example, Green fluorescent protein (GFP)). Protein tags may allow specific enzymatic modification, chemical modifications or to connect proteins to other components. However, depending on the type or number of tags added to a protein sequence the native function of the protein, in this case the enzymatic function, may be compromised by the tag. Accordingly, the protein tag would need to be selected to ensure that the activity of the enzyme is not compromised or alternatively, the protein tag may be cleaved from the protein before use.
The use of a protein tag is exemplified in the current application through the use of Polyhistidine protein tag (His-tag) as shown in SEQ ID NOs: 5, 10, 15, 17, 19, 21, 23, 25, 27, 29 and 31, but a person of skill in the art would readily appreciate that any number of other protein tags may be used to purify the enzymes and/or be used to attach the enzymes to a surface as described herein, depending on the purification method used and/or the surface the enzymes are attached to. Such protein tags may be selected from any one or more of the protein tags listed in TABLE A, but other such protein tags are known in the art.
Furthermore, the use of one or more cleavage sites (for example, the thrombin cleavage site as used in SEQ ID NOs: 15, 17, 19, 21, 23, 25, 27, 29 and 31) may be employed to release the protein tag from the enzyme or to otherwise cleave the enzyme. A cleavage site may be used for the removal of the N-terminal methionine, signal peptide, and/or the conversion of an inactive or non-functional protein to an active one (i.e. zymogens or proenzymes). Alternatively, a cleavage site may be used to separate two or more enzymes that were expressed in the same reading frame. Examples of enzymes that are capable of cleaving proteins or peptides and which would have sequence specific cleavage sites may be selected from one or more of the following: Arg-C proteinase; Asp-N endopeptidase; Asp-N endopeptidase+N-terminal Glu BNPS-Skatole; Caspase 1; Caspase 2; Caspase 3; Caspase 4; Caspase 5 Caspase 6; Caspase 7; Caspase 8; Caspase 9; Caspase 10; Chymotrypsin-high specificity (C-term to [FYW], not before P); Chymotrypsin-low specificity (C-term to [FYWML], not before P); Clostripain (Clostridiopeptidase B); CNBr; Enterokinase; Factor Xa; Formic acid; Glutamyl endopeptidase; GranzymeB; Hydroxylamine; Iodosobenzoic acid; LysC; LysN; NTCB (2-nitro-5-thiocyanobenzoic acid); Neutrophil elastase; Pepsin (pH1.3); Pepsin (pH>2); Proline-endopeptidase; Proteinase K; Staphylococcal peptidase I; Tobacco etch virus protease; Thermolysin; Thrombin; and Trypsin.
A person of skill in the art would appreciate that the combination of an active Galactosaminidase enzyme and an active GalNAcDeacetylase enzyme, as described herein, capable of efficiently cleaving A-antigen is of importance and that person of skill would also appreciate that the addition of one or more cleavage sites and/or one or more protein tags is optional and that such modifications may be selected based on the particular expression system, purification system and possible surface attachment strategy. Furthermore, other modifications to the Galactosaminidase and the GalNAcDeacetylase sequences are possible, provided that the activity in cleaving A-antigens is not significantly impaired. Additionally, modifications to the Galactosaminidase and the GalNAcDeacetylase enzymes is possible, provided that the A-antigen cleavage activity is not significantly impaired. The modifications to the Galactosaminidase and the GalNAcDeacetylase sequences may be a deletion, an insertion and/or a substitution. The substitution may be a conservative substitution or a neutral substitution. For example, the Galactosaminidase and the GalNAcDeacetylase sequences may share 90% or more sequence identity with the mature enzymes is possible. For example, the Galactosaminidase and the GalNAcDeacetylase sequences may share 85% or more sequence identity with the mature enzymes is possible. For example, the Galactosaminidase and the GalNAcDeacetylase sequences may share 75% or more sequence identity with the mature enzymes is possible. Alternatively, the Galactosaminidase and the GalNAcDeacetylase sequences may have modifications to 5, 10, 13, 15, 20 or up to 25%, of the amino acids.
As used herein “adsorption on glass, alginate beads or matrix” refers to the attached of an enzyme to the outside of an inert material. Generally, this type of immobilization does not result from a chemical reaction and the active site of the immobilized enzyme can be blocked by the surface to which it has absorbed, which may reduce the activity of the enzyme being absorbed.
As used herein “entrapment” refers to the trapping of an enzyme within an insoluble beads or microspheres. However, entrapment may hinder the arrival of the substrate, and the exit of products. One example, is the use of as calcium alginate beads, which may be produced by reacting a mixture of sodium alginate solution and enzyme solution with calcium chloride.
As used herein “cross-linkage” refers to the covalent bonding of enzymes to each other to create a matrix consisting of almost only enzyme. When a cross-linkage enzyme reaction is designed, the binding site ideally does not cover the enzyme's active site so that the activity of the enzyme is only affected by immobility and not by blockage of the enzyme's active site. Nevertheless, spacer molecules like poly(ethylene glycol) may be used to reduce the steric hindrance by the substrate.
As used herein “covalent bonding” refers to the bonding of an enzyme to an insoluble support or surface (for example, a silica gel) via a covalent bond. Due to the strength of the covalent bonds between the enzymes and the support or surface, there is much less likelihood of enzymes detaching from the support or surface.
As used herein “crowding agent” refers to any polymer or protein that facilitates macromolecular crowding by concentrating enzyme on the cell surface to improve activity of the enzyme. A crowding agent may for example be a dextran, a dextran sulfate, a dextrin, a pullulans, a poly(ethylene glycol), a Ficoll™, a hyper-branched glycerol and an inert protein. (Kuznetsova, I. M et al. Int J Mol Sci. (2014) “What Macromolecular Crowding Can Do to a Protein” 15(12): 23090-23140).
As used herein “dextran” refers to a polysaccharide with molecular weights ≥1,000 Daltons and having a linear backbone of α-linked d-glucopyranosyl repeating units. Dextrans may divided into 3 structural classes (i.e. classes 1-3) based on the pyranose ring structure, which contains five carbon atoms and one oxygen atom. Class 1 dextrans contain the α(1→6)-linked d-glucopyranosyl backbone modified with small side chains of d-glucose branches with α(1→2), α(1→3), and α(1→4)-linkage. The class 1 dextrans vary in their molecular weight, spatial arrangement, type and degree of branching, and length of branch chains, 3-5 depending on the microbial producing strains and cultivation conditions. Isomaltose and isomaltotriose are oligosaccharides with the class 1 dextran backbone structure. Class 2 dextrans (alternans) contain a backbone structure of alternating α(1→3) and α(1→6)-linked d-glucopyranosyl units with α(1→3)-linked branches. Class 3 dextrans (mutans) have a backbone structure of consecutive α(1→3)-linked d-glucopyranosyl units with α(1→6)-linked branches.
As used herein, “pullulans” are structural polysaccharides primarily produced from starch by the fungus Aureobasidium pullulans and are composed of repeating α(1→6)-linked maltotriose (D-glucopyranosyl-α(1→4)-D-glucopyranosyl-α(1→4)-D-glucose) units with the inclusion of occasional maltotetraose units.
As used herein, “dextrin” refers to D-glucopyranosyl units with a shorter chain lengths than dextran, which start with a single α(1→6) bond, but continue linearly with α(1→4)-linked D-glucopyranosyl units.
As used herein, “dextran sulfates” are derived from dextran via sulfation.
As used herein, “Ficoll™” is a neutral, highly branched, high-mass, hydrophilic polysaccharide, which dissolves readily in aqueous solutions.
Various alternative embodiments and examples are described herein. These embodiments and examples are illustrative and should not be construed as limiting the scope of the invention.
Chemicals and commercial enzymes used in this study were purchased from Sigma-Aldrich™ unless otherwise stated. Monosaccharide methylumbelliferyl glycosides were a generous gift from Dr. Hongming Chen and the A-antigen subtype1penta-MU was a generous gift from Dr. David Kwan (Kwan et al. 2015).
Human Feces Metagenomic Library
For the generation of the human metagenomics fosmid library human fresh fecal samples were collected from a healthy Asian male volunteer having blood group AB+. The direct DNA extraction and fosmid library creation were performed according to the procedure described in the MoE Protocol (Armstrong et al. 2017).
Fosmid Library Screening
51×384-well AB+Blood Fosmid library plates were thawed at room temperature and replicated into 384-well plates containing 50 μl screening LB-media (12.5 μg/mL chloramphenicol, 25 μg/mL kanamycin, 100 μg/mL arabinose, 0.2% (v/v) maltose, 10 mM MgSO4). Plates were incubated at 37° C. for 18 hours in a sealed container containing a reservoir of water to prevent excessive evaporation. 45 μl of the reaction mixture (100 mM NaH2PO4, pH 7.4, 2% (v/v) Triton-X 100, 100 μM GalNAc-α-MU, 100 μM Gal-α-MU) were added onto grown screening plates using the QFil™ instrument [Genetix™]. The plates were then incubated at 37° C. in a sealed container for 24 h, and the fluorescence (Ex: 365 nm Em: 435 nm, sweep-mode, gain 80) of each plate was measured at hours 1, 2, 4, 8 and 24 via a Synergy H1 plate reader [BioTek™]. For all wells a Z-score was calculated, which is given by the formula: Z-score=(Fluorescence-median value)/Standard Deviation.
All positive hits above a certain threshold, were re-arrayed in a new 384-well plate, designated the “simple substrate hit” plate and stored at −70° C. Two screening plates were replicated from the “simple substrate hit” plate and re-screened for either GalNAc-α-MU or Gal-α-MU activity to verify and deconvolute the previously detected activity.
To determine which of the hits can cleave A-antigen or B-antigen structures, their activity on 50 μM A antigen subtype 1tetra-MU or 50 μM B antigen subtype1tetra-MU was determined using a coupled enzyme assay. A version of this coupled assay was described previously by Kwan (Kwan et al. 2015). Our assay was modified to also detect cleavage of the subtype 1 A antigen, by use of BgaC (Jeong 2009) instead of BgaA (Singh 2014) as coupling enzyme. Potential α-N-acetylgalactosaminidases or α-galactosidases would cleave the terminal sugar, releasing the H antigen subtype Itri-MU. Subsequently an α-fucosidase (AfcA (Katayarna 2004)), β-galactosidase (BgaC (Jeong 2009)) and β-hexosaminidase (SpHex (Williams 2002)) will cleave the residual sugars in exo-fashion, until 4-methylumbelliferyl alcohol is released; detectable as increase of the fluorescence. To achieve this, 50 μg/mL of each enzyme was added to the reaction mixture. All positive hits above a certain threshold were re-screened in triplicate and a host cell strain containing a vector lacking any insert was used as a negative control. All verified hits were stored separately at −70° C. in LB-media (12.5 μg/mL chloramphenicol, 25 μg/mL kanamycin, 15% (v/v) glycerol, 0.2% (v/v) maltose, 10 mM MgSO4).
Fosmid Hit Sequencing
To isolate the fosmid DNA for sequencing, the positive hit fosmid glycerol stocks were used to inoculate 5 mL of TB media (12.5 μg/mL chloramphenicol, 25 μg/mL kanamycin, 100 μg/mL arabinose, 0.2% (v/v) maltose, 10 mM MgSO4), incubated overnight at 37° C. 220 rpm. Fosmid isolation was performed using the GeneJet™ plasmid miniprep kit (Thermo Fisher™). The isolated fosmids were purified from contaminating linear E. coli DNA using Plasmid-Safe™ ATP-Dependent DNase (Epicentre™), followed by another round of purification with a GeneJet™ PCR purification kit (Thermo Fisher™). Concentration was calculated with a Quant-iT™ dsDNA HS Assay Kit (Invitrogen™) on a Qbit™ fluorimeter (ThermoFisher™). Expected DNA size was validated with a 1% agarose gel. For full fosmid sequencing, 2 ng of each fosmid was sent to the UBC Sequencing Centre (Vancouver, BC, Canada). Each fosmid was individually barcoded and sequenced using an Illumina MiSeq™ system.
All Illumina MiSeq™ raw sequence data were trimmed and assembled using a python script available on GitHub™ at https://github.com/hallamlab/FabFos. Briefly, Trimmomatic was used to remove adapters and low-quality sequences from the reads (Bolger 2014). These reads were screened for vector and host sequences using BWA (L 2013) and then filtered using Samtools™ and a bam2fastq script to remove contaminants. These high-quality and purified reads were assembled by MEGAHIT with k-mer values ranging between 71 and 241, increasing by increments of 10 (Li 2015). Since these libraries often had in excess of 20,000 times coverage and to prevent the accumulation of sequencing errors interfering with proper sequence assembly, the minimum k-mer multiplicity was calculated by 1% of the estimated coverage of a fosmid. Outside of the python script assemblies, which yielded more than one contig were then scaffolded using minimus2 (Treangen 2011). Parameterized commands can be found in both documentation on the GitHub™ page and in the python script itself.
Fosmid ORF Prediction and Hit Validation
Fosmid ORFs were identified using the metagenomic version of Prodigal™ (Hyatt 2010) and compared to the CAZy™ database using BLASTP™ as part of the MetaPathways™ v2.5 software package (Konwar 2015). MetaPathways™ parameters: length >60, BLAST score >20, blast score ratio >0.4, EValue<1×10-6.
All predicted ORFs with annotations to members of a GH or CBM family (with known or suspected α-galactosidase and/or α-N-acetylgalactosaminidase activities) were cloned into pET16b plasmid using the Golden Gate™ cloning strategy (Engler 2008), the primer sequences are set out in TABLE B. The proteins were expressed in BL21(DE3), cultured in 10 mL ZY5052 auto induction media (Studier 2005) for 20 h at 37° C., 220 rpm. Cells were harvested by centrifugation (4000×g, 4° C., 10 min) and resuspended in 1 mL lysis buffer (100 mM NaH2PO4, pH 7.4, 2% (v/v) Triton-X™ 100, 1× Protease Inhibitor EDTA-free [Pierce™ ]). A coupled assay (Kwan 2015) was performed with 50 μl crude cell lysate from the candidates mixed with 50 μl assay buffer (100 mM NaH2PO4, pH 7.4, 50 μg/mL SpHex, 50 μg/mL AfcA, 50 μg/mL BgaC, 100 μM A antigen subtype 1tetra-MU or 100 μM B antigen subtype 1tetra-MU) and incubated at 37° C. All reactions were performed as triplicates in a black 96-well plate. Fluorescence (365/435 nm) was monitored continuously for 4 hours using a Synergy™ H1 plate reader [BioTek™ ]. Assays from crude extracts showing cleavage activity for A or B antigen were repeated, this time without the coupled enzymes, and the reaction product was isolated via an HF Bond Elut C18 column and analysed with LC-MS and/or TLC. TLC was performed using TLC Silica Gel 60 F254 TLC plates [EMD Millipore Corp.™, Billerica, Mass., USA].
HPAE-PAD Assay
The analysis of the enzymatic release of galactosamine was carried out on an HPAE-PAD (Dionex™) HPLC system. Cleavage activity of the different proteins was tested on the following substrates: 7.5 μg/μL mucin from porcine stomach Type II in 100 mM NaH2PO4 pH 7.4; 5 mM A antigen subtype 1penta-MU in 100 mM NaH2PO4 pH 7.4 and RBCs (50% hematocrit) from A+, B+ and O-Type Donors in 1×PBS pH 7.4. Samples containing 10 μg/mL enzyme were incubated for two hours at 37° C. then stored at −80° C. for further analysis. Small aliquots of the reaction (10 μl) were diluted in H2O (100 μl) and submitted to analysis on the HPAE-PAD instrument. Separation was performed on a CarboPAC PA200™ (150 mm) column with guard column, and detection was achieved using a disposable gold on polytetrafluoroethylene (FFE) electrode and a four-potential waveform. The separation conditions were as follows: 100 mM sodium hydroxide and a sodium acetate gradient from 70 to 300 mM over the first 10 min of the separation. The eluent was held at the final gradient conditions for 1 min and then returned to the starting conditions over the next minute. The flow rate was 1.0 ml/min and an injection was made every 27 min. A standard of the free sugars GalNAc, Gal and GalN (10 μM) was also applied to HPAE-PAD to determine the peak elution time for reference.
Kinetic Assays
All kinetic assays utilizing 4-methylumbelliferone as leaving group were performed through measurement of fluorescence. To avoid measurement errors based on the inner filter effect (Palmier 2007) standard curves were used to validate the linear range of the fluorophore.
FpGalactosaminidase
Michaelis-Menten parameter was determined for GalN antigen subtype 1penta-MU and A antigen subtype 1penta-MU in 100 mM NaH2PO4, pH 7.4 at 37° C. Reaction was performed in 100 μl with 3.4 nM FpGalactosaminidase (5.31 nM FpGalNase_truncA) and 0.1 mg/mL SpHex, AfcA, 0.2 mg/mL BgaC and varying concentrations of substrate (5 μM-2 mM). The reactions were run as a series of four with controls (no FpGalactosaminidase) as duplicates. The fluorescence signal (365/435 nm) resulting from MU release by hydrolysis was monitored by Synergy H1™ plate reader [BioTek™] and converted to concentration using MU standard concentration curves determined under identical reaction conditions. Initial rates (μM/s) were determined and plotted in Grafit 7.0™ to determine the kinetic parameters.
kcat/KM parameter was determined for GalN antigen subtype 1/2/4tetra-MU and B antigen subtype 1tetra-MU at pH 7.4 and 37° C. Reactions (total volume of 100 μL) were performed in black 96-plate wells and as coupled assays in 100 mM NaH2PO4 (pH 7.4) with 8.63 nM FpGalactosaminidase, 0.1 mg/mL SpHex, BgaC (BgaA for Subtype 2), AfcA, varying concentrations of substrate (25 μM, 20 μM, 15 μM, 10 μM, 7.5 μM, 5 μM). The reactions were run as a series of four with controls (no FpGalactosaminidase) as duplicates. The fluorescence signal (365/435 nm) resulting from MU release by hydrolysis was monitored by Synergy H1™ plate reader [BioTek™ ] and converted to concentration using MU standard concentration curves determined under identical reaction conditions. Initial rates (μM/s) were determined and plotted in Grafit 7.0™ to determine the kcat/KM (s−1*mM−1) parameters.
Michaelis-Menten parameters were determined for GalN-α-pNP in in clear 96-plate at 37° C. with 863.2 nM FpGalactosaminidase (in 100 mM NaH2PO4, pH 7.4) or 369.9 nM FpGH4 (in 50 mM Tris/HCl, pH 7.4, 100 μM NAD+, 1 mM MnCl2) with varying concentrations of substrate (10 μM-5 mM) in a volume of 100 μl. The reactions were run as a series of three with two controls (no enzyme). The absorption (at 405 nm) resulting from pNP release by hydrolysis was monitored by Synergy H1™ plate reader [BioTek™ ] and converted to concentration using p-nitrophenol standard concentration curves determined under identical reaction conditions. Initial rates (μM/s) were determined and plotted in Grafit 7.0™ to determine the kinetic parameters.
FpGalNacDeacetylase
Michaelis-Menten parameters were determined for A antigen subtype 1penta-MU in 100 mM NaH2PO4, pH 7.4 at 37° C. using the coupled assays described previously (Kwan 2015). The assay was modified to allow detection of cleavage of the subtype 1 (and later 4), by use of BgaC (Jeong 2009) instead of BgaA (Singh 2014) as β-galactosidase. In addition, since A antigen subtype 1penta-MU contains an additional galactose, the concentration of BgaC was increased to 0.2 mg/mL to compensate for its need to cleave both the Gal-β-1,3-β-GlcNAc-β-1,3-Gal-β-MU and Gal-β-MU. Further, FpGalactosaminidase was included to allow the cleavage of the galactosamine-containing intermediate. Reaction setup in 100 μl was 3 nM FpGalNacDeacetylase (4.52 nM FpGalNacDeAc_D1ext, 3.55 nM FpGalNacDeAc_D1+2) and 0.01 mg/mL FpGalactosaminidase, 0.1 mg/mL SpHex, AfcA, 0.2 mg/mL BgaC and varying concentrations of substrate (5 μM-2.5 mM). The reactions were run as a series of four with controls (no FpGalNacDeacetylase) as duplicates. The fluorescence signal (365/435 nm) resulting from MU release by hydrolysis was monitored on a Synergy H1™ plate reader (BioTek™) and converted to concentration using MU standard concentration curves determined under identical reaction conditions. Initial rates (μM/s) were determined and plotted in Grafit 7.0 to determine the kinetic parameters.
kcat/KM parameter were determined for A antigen subtype 1/2/4tetra-MU at pH 7.4 at 37° C. Reactions (total volume of 100 μL) were performed in black 96-plate wells and as coupled assays in 100 mM NaH2PO4 (pH 7.4) with 12 nM FpGalNAcDeacetylase 0.1 mg/mL SpHex, BgaC (BgaA for subtype II), AfcA, at varying concentrations of substrate (25 μM, 20 μM, 15 μM, 10 μM, 7.5 μM, 5 μM). The reactions were run as a series of four with controls (no FpGalNAcDeacetylase) as duplicates. The fluorescence signal (365/435 nm) resulting from MU release by hydrolysis was monitored on a Synergy H1™ plate reader (BioTek™) and converted to concentration using MU standard concentration curves determined under identical reaction conditions. Initial rates (μM/s) were determined and plotted in Grafit™ 7.0 to determine the kcat/KM (s-1*mM-1) parameters.
GH109 Subtype Kinetic
kcat/KM parameter was determined for A antigen subtype 1/2/4tetra-MU at pH 7.4 and 37° C. Reactions (total volume of 100 μL) were performed in black 96-plate wells and performed as coupled assays in 100 mM NaH2PO4, pH 7.4 with 86.02 nM BvGH109_1/100.49 nM EmGH109/80.52 nM BvGH109_2/87.4 nM BsGH109 and 5 μM NAD+, 0.1 mg/mL each of SpHex, BgaC (BgaA for Subtype 2), AfcA, varying concentrations of substrate (25 μM, 20 μM, 15 μM, 10 μM, 7.5 μM, 5 μM). The reactions were run as a series of four with controls (no α-N-acetylgalactosaminidase) as duplicates. The fluorescence signal (365/435 nm) resulting from MU release by hydrolysis was monitored by Synergy H1™ plate reader [BioTek™ ] and converted to concentration using MU standard concentration curves determined under identical reaction conditions. Initial rates (μM/s) were determined and plotted in Grafit 7.0™ to determine the kcat/KM (s-1*mM-1) parameters.
Crystallography
Prior to crystallization, FpGalNAcDeAc_D1ext was digested with thrombin (Novagen™) at a concentration of 1 mg/mL overnight using the manufacturer's suggested protocol. Protein was then purified by HisTrap FF column and the flow-through was collected, buffer-exchanged into 10 mM Tris pH 8.0+75 mM NaCl, and concentrated to 12 mg/mL
Crystallization
FpGalNAcDeAc_D1ext (12 mg/mL) was crystallized by use of the hanging drop diffusion method using a reservoir solution composed of 0.2 M CaCl2, 0.1 M MES pH 6, 18% PEG 4000, and 20 mM MnCl2 at a 1:1 protein:reservoir ratio. A quick bromide soak was used to derivatize crystals for phasing and was prepared by transferring the crystal to a solution of 1 M NaBr, 25% glycerol, 18% PEG4000, 20 mM CaCl¬2, and 0.1 M Mes pH for 30 seconds and flash frozen in liquid nitrogen. Crystal complexes with blood group B antigen trisaccharide (B_tri) were prepared by pre-incubating protein (12 mg/mL) with 10 mM B_tri for 2 hours before setting up drops under the same conditions as above, but omitting MnCl2. Crystals were cryoprotected with reservoir solution supplemented with 25% glycerol.
Data Collection, Phasing and Structure Determination
Datasets were collected at the Canadian Light Source™. Data were integrated using XDS (Kabsch 2010) and scaled with Aimless™ (Evans 2013). Phasing and automated structure solution was performed using CRANK2™ (Skubak 2013) in the CCP4I2™ program suite (Potterton 2018). The structure was checked and refined using alternating cycles of Coot™ (Emsley 2004) and Refmac™ (Vagin 2004). The B_tri structure complex was solved by difference Fourier and the ligand was manually built in Coot™ as were the water and metal ions. Difference density maps confirmed the presence of Mn2+ in the apo structure and Ca2+ in the liganded structure. Models were validated by Coot™ and Molprobity™ (Chen 2010). Atomic coordinates and structure factors of the apo and B_tri complex have been deposited in the Protein Data Bank (PDB) with accession numbers:
Flavonifractor plautii GalNAcDeacetylase Protein SEQ ID NO.: WP_009260926.1; and
Flavonifractor plautii Galactosaminidase Protein SEQ ID NO.: WP_044942952.1
Active-Site Mutagenesis
Based on structural information (not shown) and sequence alignment (not shown) FpGalNAcDeAc_Dimin and FpGalNase_truncA were mutated using the QuickChange™ protocol (Zhang 2004), utilizing the primers noted in TABLE B. The mutants were purified via NiNTA and HIC columns as described above. The structural integrity of all mutants was checked via CD spectroscopy; all tested enzymes were structurally similar to their wild-type. For mutants with relatively low activity, reactions were carried out under the same conditions used for full kinetic determinations; however the substrate depletion method was used for determination of kcat/KM values as has been previously described (Vocadlo 2002). In brief: at low concentrations of substrate where [Substrate]<KM (equivalent to ˜⅕- 1/10 of Km) the kcat/KM value can be approximated upon non-linear fitting of the reaction time course to a first order curve and dividing by the enzyme concentration.
GH36 Phylogenetic Mapping
Reference sequences of GH36 were downloaded from the CAZy™ database using SACCHARIS™ cazy_extract.pl script (Jones 2018). Phylogenetic-based protein profiling software, TreeSAPP™ (available at https://github.com/hallamlab/TreeSAPP), was used to both build the reference trees and map the sequences to these trees. Briefly, HMMs from dbCAN were used to extract protein family domains from all full-length sequences downloaded from CAZy™ (Yin 2012). These sequences were then clustered at 70% sequence similarity using UCLUST™ to remove redundant sequence space and decrease the size of the tree (Edgar 2010). RAxML™ version 8.2.0 was used to build the reference trees with the ‘--autoMRE’ to decide when to quit bootstrapping before 1000 replicates have been performed, and PROTGAMMAAUTO™ to select the optimal protein model (Stamatakis 2006; and Stamatakis 2008).
TreeSAPP™ was then used to map the query sequences onto these reference trees. Briefly, protein sequences were aligned to HMMs using Hmmsearch™ and the aligned regions were extracted (Eddy 1998). Hmmalign™ was used to include the new query sequences in the reference multiple alignment and then TrimA™ removed the unconserved positions from the alignment file (Capella-Gutierrez 2009). RAxML™ was used to classify the query sequences in the reference tree through insertions. Placements of each query sequence were filtered and concatenated into a single. Jplace™ file before being visualized in iTOL™ (Matsen 2012; and Letunic 2016).
RBC Assays
Whole blood from healthy consenting donors was collected into a citrate Vacutainer using a protocol approved by the clinical ethics committee of The University of British Columbia. The tube was spun at 1000×g for 4 min at RT, and RBCs were separated and washed 3 times with 1×PBS pH 7.4. For assays in the presence of dextran 40 k, washed RBCs (200 μL, 10% Hematocrit) were placed in a tube, and the supernatant was partially removed and replaced with 1×PBS pH 7.4 with and without dextran 40 k (final concentration of 300 mg/mL). In addition some assays were performed in 1×PBS pH 7.4+25% plasma or 100% plasma. RBCs were mixed carefully and placed on an orbital shaker for 30 s. Diluted enzyme solutions were then added, to a final volume of 200 μL. The tubes were vortexed very gently, and placed on an orbital shaker for defined times at set temperatures.
MTS Cards
After the reaction, RBCs were washed 3 times with an excess of 1×PBS pH 7.4 and analysed using Micro Typing System™ (MTS) cards [MTS™, Florida, USA]. RBCs (12 μl, 5% Hematocrit), suspended in diluent [MTS, Florida, USA], were added carefully to the mini gel column, leaving a space between the blood and the contents of the mini gel. The MIS cards were centrifuged at 156×g for 6 min at RT using a Beckman Coulter Allegra X-22R™ centrifuge with a modified sample holder as recommended. The extent of antigen removal from the surface of the RBC was evaluated from the location of RBCs in the mini gel after spinning, according to the manufacturer's instructions. RBCs with a high surface antigen concentration agglutinated upon interaction with the monoclonal antibody present in the gel column and could not penetrate (MTS™ score 4). RBCs with no surface antigens did not agglutinate and migrated to the bottom of the mini gel (MTS score 0). RBCs that underwent partial removal of surface antigens migrated to positions between these and were assigned scores between 0 (not present) and 4 (present) according to the manufacturer's instructions.
Agglutination Assays for H-Antigen
To analyse the conversion of A antigen to H antigen after enzymatic treatment, washed A-ECO-RBCs were mixed in equal parts with 2 μg/mL anti-H antibody (Anti-Blood Group H ab antigen antibody [97-I]: cat no. ab24213 (Abcam™)) and the appearance of agglutination within a 30 minutes time frame monitored. RBCs that underwent agglutination with the Anti-H antibody were assigned scores between 0 (no agglutination within 1800 sec) and 5 (agglutination within 120 sec).
FACS
Enzyme treated RBCs were washed 2× with 1×PBS pH 7.4 and 1% hematocrit ECO-RBCs were treated with 1/100 APC-anti-A antibody (Alexa Fluor™ 647 Mouse Anti-Human Blood Group A: cat no. 565384 (BD Pharmingen™)) and/or anti-H antibody (Anti-Blood Group H ab antigen antibody [97-I]: cat no. ab24213 (Abcam™)) for 30 minutes at RT, then washed 2× with 1×PBS pH7.4. For detection of the anti-H antibody a secondary FITC-labelled antibody (Goat F(ab′)2 Anti-Mouse IgM mu chain (FITC): cat no. ab5926 (Abcam™)) in a 1/500 concentration was used. The data were assessed after reconstitution into 1×PBS pH 7.4 (1% hematocrit) with a flow cytometer (CytoFLEX™ (Beckman Coulter™)).
Enzyme Adsorption and Antigenicity
To test whether the enzymes can be readily removed from the RBCs after treatment, potential adsorption was assessed. Pacific blue-labelled FpGalNAcDeacetylase and FpGalNase (F/P=1) were incubated with the RBC's for 1 h at 37° C. alone, and after several wash steps, and then residual fluorescence measured on a flow cytometer (CytoFLEX™ (Beckman Coulter™)).
Antigenicity was tested by incubating RBCs with 50 μg/mL of each enzyme and mixing the enzyme treated RBCs with allogeneic or autologous serum, observing potential agglutination. Additionally, to assess potential Anti-IgG,-C3d exposure the treated RBCs were tested on Anti-IgG,-C3d MTS™ cards [MTS™, Florida, USA]. Incubation time was 30 minutes at 37° C.
Antigen Subtype's Synthesis
The synthesis of the A and B antigen subtypes 1/2/4tetra-MU was a performed with a modified protocol, described in Kwan (Kwan et al. 2015).
Two-Step H Antigen Subtype 1/2/4Tri-MU Synthesis
All three synthesis were performed in scales of 20 mg GalNAc-α-MU/GlcNAc-α-MU in 10 mL 50 mM Tris/HCl, 200 mM NaCl, pH 7.4, 10 mM MnCl2, 50 U Alkaline Phosphorylase, 1.5 equivalent UDP-Gal, 1.2 equivalent GDP-Fuc (scaled on LacNAc-MU product). Depending on the desired product different glycosyl transferases in a concentration of 100 μg/mL were added; for subtype I CgtB S42 and Te2FT, for subtype II HP0826 and WbgL, for Subtype IV LgtD and Te2FT. The reaction was performed at 37° C. and the progress controlled via TLC (mobile phase, EtAc:MeOH:H2O with a ratio of 6:2:1), the 4-Methylumbelliferone was hydrolysed from the compounds via 10% H2SO4 and detected via UV (360 nm). After no further product increase could be observed the reaction was applied to a HF Bond Elut C18 column, washed with several column volumes of 5% Methanol, and product was eluted with 25% Methanol. The solvent was then removed in vacuo.
A Antigen Subtype 1/2/4tetra-MU Synthesis
The final synthesis step was performed in scale of 10 mg H antigen subtype 1/2/4tri-MU in 5 mL 50 mM Tris/HCl, 200 mM NaCl, pH 7.4, 10 mM MnCl2, 25 U Alkaline Phosphorylase, 1.5 equivalent UDP-GalNAc and 100 μg/mL BgtA at 37° C. The progress was followed via TLC, after no further product increase could be observed the reaction was applied to a HF Bond Elut C18 column, washed with several column volumes of 5% Methanol, and product was eluted with 25% Methanol. The solvent was then removed in vacuo. The final product was further purified on a 1.5×46 cm HW-40F size exclusion column and then freeze-dried.
B Antigen Subtype 1/2/4tetra-MU Synthesis
The final synthesis step was performed in scale of 10 mg H antigen subtype 1/2/4tri-MU in 5 mL 50 mM Tris/HCl, 200 mM NaCl, pH 7.4, 25 U Alkaline Phosphorylase, 1.5 equivalent UDP-Gal and 100 μg/mL BoGT6a at 37° C. The progress was followed via TLC, after no further product increase could be observed the reaction was applied to a HF Bond Elut C18 column, washed with several column volumes of 5% Methanol, and product was eluted with 25% Methanol. The solvent was then removed in vacuo. The final product was further purified on a 1.5×46 cm HW-40F size exclusion column and then freeze-dried.
GalN Antigen Subtype 1penta-MU synthesis
10 mg of A antigen subtype 1penta-MU were incubated with 1 μg/mL FpGalNAcDeacetylase in 5 mL 100 mM NaH2PO4 at 37° C. for 30 min and then stopped through addition of 1 mM EDTA. The complete conversion of the substrate was checked via TLC and the reaction applied to a HF Bond Elut C18 column, washed with several column volumes of 2% Methanol, and product was eluted with 10% Methanol. The solvent was then removed in vacuo.
Protein Purification
All proteins and there truncations were cloned via Golden Gate™ cloning (Engler 2008) or PIPE cloning (Klock 2008) into pET16b or pET28a. The primer sequences are set out in TABLE B.
The production of proteins for extended characterisation was performed in BL21(DE3) cells, cultured in 200 mL ZY5052 auto induction media (Studier 2005) for 20 h at 37° C., 220 rpm inoculated with 100 μl of an over-night LB culture. Cells were harvested by centrifugation (4000×g, 40° C., 10 min) and resuspended in 10 mL lysis buffer (50 mM Tris/HCl, 150 mM NaCl, 1% (v/v) Glycerol, 40 mM Imidazol, pH 7.4, 2 mM DT, 1× Protease Inhibitor EDTA-free (Pierce™), 2 U Benzonase (Novagen™), 0.3 mg/mL Lysozyme, 10 mM MgCl2), followed by sonification (3 min pulse time; 5 sec pulse, 10 sec pause, 35% amplitude) on ice. After removal of cell debris by centrifugation (14000×g. 4° C., 30 min), supernatant was collected and loaded on a nickel affinity chromatography column (5 mL HisTrap HP™ column (GE™)) using a peristaltic pump. The elution was performed and monitored on an AEKTApurifier™ system (GE™) with a 10-75% gradient of 50 mM Tris/HCl, 400 mM Imidazol, pH 7.4.2 mM DTT, via SDS-PAGE the fractions containing the protein were identified and then pooled. Buffer exchange into 50 mM Tris/HC, 150 mM NaCl, pH 7.4, 2 mM DTT and concentration was performed in Amicon Ultra-15 Centrifugal Filter Units™ MWCO 10 kDa (Millipore™).
FpGalNAcDeacetylase, FpGalactosaminidase and there truncations had to undergo a second round of purification, a Amicon Ultra-15 Centrifugal Filter Units™ MWCO 10 kDa (Millipore™) was used to exchange the buffers before loading the proteins on a hydrophobic interaction chromatography column (10 mL Phenyl Sepharose High Performance column (Pharmacia Biotech™)). Loading, washing and elution (gradient 0-100%) of the column was handled through an AEKTApurifier™ system (GE™), utilizing following buffer conditions: FpGalNAcDeacetylase; binding 1×PBS, 800 mM NH2PO4, pH 7.4 and elution 1×PBS, pH 7.4 and FpGalactosaminidase; binding 25 mM Tris/HCl, 1 M NaCl, pH 7.4 and elution 25 mM Tris/HCl pH 7.4. Via SDS-PAGE the fractions containing the protein were identified and then pooled. Buffer exchange into 50 mM Tris/HCl, 150 mM NaCl, pH 7.4 and concentration was performed in Amicon Ultra-15 Centrifugal Filter Units™ MWCO 10 kDa (Millipore™).
Protein Characterization
Optimum pH Value
The general pH range for activity of FpGalNAcDeacetylase and FpGalactosaminidase for A antigen subtype 1penta-MU and GalN antigen subtype 1penta-MU, respectively was determined by product occurrence on TLC plates for varying pH values. The reaction was performed in 100 μl scales at 37° C. with 50 μM substrate and 1 μg/mL enzyme in the appropriate buffer system. Buffers for pH 4 to 6 were based on a 50 mM citric acid/sodium citrate buffer, for pH 6-8 a 50 mM sodium phosphate buffer and pH 8-10 a 50 mM glycine/sodium hydroxide buffer.
To determine the optimal pH value 5 μg/mL FpGalactosaminidase was incubated in 100 μl 50 mM sodium phosphate buffer with varying pH range (5.8-8.0) and 200 μM GalN-α-pNP. The absorption (at 405 nm) resulting from pNP release was monitored by a Synergy H1™ plate reader (BioTek™) for 1 h at 37° C.
5 μg/mL FpGalNAcDeacetylase and 50 μM A antigen subtype Ipenta-MU was pre-incubated for 10 min at 37° C. in 25 mM sodium phosphate buffer with varying pH range (5.8-10.0). The reaction was quenched with 100 mM sodium phosphate buffer pH 7.5, 100 μM EDTA, 5 μg/mL FpGalactosaminidase, 50 μg/mL SpHex, 50 μg/mL AfcA and 50 μg/mL BgaC, final volume 100 μl. The fluorescence signal (365/435 nm) resulting from MU release by hydrolysis was monitored by a Synergy H1™ plate reader (BioTek™) for 30 min at 37° C.
Protein Stability
FpGalNAcDeacetylase and FpGalNase were stored in 1×PBS buffer pH 7.4 at 4° C. After 2 and 12 weeks, the activity of the enzymes were tested like described for the pH optimum against the A antigen subtype 1penta-MU in a coupled enzyme reaction for FpGalNAcDeacetylase and with GalN-α-pNP for FpGalNase.
FpGalNAcDeacetylase Inhibition
FpGalNAcDeacetylase was tested against different potential inhibitors in 96-well plate format as a coupled assay. Reaction was performed in 100 μL scale at 37° C. with 50 μM A antigen subtype 1penta-MU and 5 μg/mL FpGalNAcDeacetylase in 100 mM NaH2PO4 pH 7.4 with 10 μg/mL FpGalactosaminidase, 50 sg/mL SpHex, 50 μg/mL AfcA, 50 μg/mL BgaC. As inhibitors EDTA (1, 10, 100 μM), Marimastat (1, 10, 100, 1000 μM), DMSO (2%, 4%), Protease Inhibitor Cocktail EDTA-free (Pierce™) (1×, 2× and 4×) were tested. The Fluorescence (365/435 nm) was monitored continuously for 1 hours using a Synergy H1™ plate reader (BioTek™). Additives showing strong effects were run again without the coupled enzymes and the product formation analysed via TLC.
Limited Proteolysis
To investigate if there are smaller, stable subdomains of FpGalactosaminidase, a limited proteolysis was performed. FpGalactosaminidase was treated with Thermolysin (10:1 protein:protease mass ratio) at various temperatures (20° C., 37° C., 42° C., 50° C., and 65° C.) for 1.5 hr. Samples were then run on an SDS-PAGE gel and a stable fragment was identified running around 70 kDa (down from the initial 118 kDa) with nearly complete digestion achieved at the 50° C. incubation temperature. This fragment was sent to the UBC proteomics core facility for peptide identification and was determined to be a C-terminal truncated version of the full length protein with cleavage site between amino acids 690-700.
Glycan Array Screening
For the glycan array screening 500 μg of FpGalNAcDeAc_D2ext were labeled with Fluorescein isothiocyanate (FIC) with a F/P ratio of 1 using the Fluorotag™ FIC conjugation Kit (Sigma™). The screening was performed in the CFG's Protein-Glycan Interaction Core Facility™ with version 5.3 of the printed array, consists of 600 glycans in replicates of 6 for 5 and 50 μg/mL protein concentration. Analysis of binding motifs was performed with the webtool at Emory University (https://glycopattern.emory.edu/).
We constructed a metagenomic library that contains large (35-65 kb) fragments of DNA extracted from fecal samples provided by a male donor of AB+ blood type. Such a library contains multiple genes per bacterium, increasing the probability of expression of at least some of those genes and allowing expression of small “pathways” of multiple genes. Our library comprised ˜19,500 clones in 51×384 well plates, potentially around 800,000 genes, thus initial screening of such a library with expensive A-antigen substrates was impractical. Rather we first screened with simple, sensitive fluorogenic substrates—the methylumbelliferyl α-glycosides of galactose and N-acetyl-galactosamine (Gal-α-MU and GalNAc-α-MU). This initial screen, with a mixture of the two substrates, yielded a subset of 226 hits. These were re-screened against each individual substrate, identifying 44 with GalNAcase and 166 with galactosidase activity. A second round of screening was performed on these hits using the A-antigen and B-antigen tetrasaccharide glycoside substrates shown in
The eleven fosmids were sequenced on an Illumina MiSeq™ and ORFs therein that are present in the CAZy™ database (http://www.cazy.org/)(Lombard 2014) were identified using Metapathways™ software (Konwar 2015). Due to the considerable depth of human microbiome sequencing now available, the organisms from which all fosmids were derived could be identified. Their sequences can be grouped into five clusters since eight of the eleven derived from overlapping fragments of the genomes of just two Bacteroides sp. The only gene common to all fosmids in cluster B is a GH109 enzyme (B. vulgatus); ClusterA also contains a GH19 (B. stercoris), while a GH109 is the only CAZy gene found in the other Bacteroides-derived fosmid (B. vulgatus). Fosmid No8, from the obligate anaerobe Flavonifractor plautii (Li 2015), contains three ORFs found within CAZy: an apparent carbohydrate binding module CBM32, and two potential glycoside hydrolases—a GH36 and a GH4. Finally fosmid K05 from a Collinsella sp., probably Colinsella tanakaei, contains no CAZy related ORFs. Here the generation of a sub-library of fosmid K05 allowed the identification of the ORF with A cleaving activity, later identified as a GH36 (not shown).
The GH109 family was founded on the basis of the A-antigen-cleaving activity of several of its members. These enzymes employ an unusual NAD+¬-dependent mechanism first uncovered in enzymes from GH4 Add Yip Ref (2004) J. Amer. Chem. Soc., 126, 8354-8355 as this was the one that showed the mechanism (Varrot 2005; and Liu 2007). The three GH109 genes identified here were cloned with a His tag after removal of signal peptides and expressed in Escherichia coli BL21(DE3). These three proteins, BsGH109, BvGH109_1 and BvGH109_2 (not shown), along with the canonical GH109 from Elizabethkingia meningosepticum (EmGH109) (Liu 2007) as a standard were purified and kinetic parameters for each determined. The three new enzymes displayed similar catalytic efficiencies with each of the three A-subtype substrates tested, largely mirroring the kinetic parameters of the EmGH109 standard. By contrast, when their A-antigen removal activity was tested on A, RBCs using approved MTS cards, disappointingly only EmGH109 was significantly active. Testing was performed in the presence of Dextran 40K as a crowding agent, which we have shown to increase activity by concentrating enzyme on the cell surface (Chapanian 2014). In its absence, even at 150 ug/mL EmGH109 was ineffective, while in the presence of 300 mg/mL Dextran 40K, 15 μg/mL of enzyme was sufficient (see
The identified GH36 protein within the Fosmid K05 (named K05GH36) was active towards GalNAc-α-MU and the A antigen tetrasaccharide. This is consistent with its membership of the GH36 family, which contains primarily α-galactosidases and α-N-acetyl galactosaminidases and carries out hydrolysis via a double displacement mechanism involving a covalent β-glycosyl enzyme intermediate (Comfort 2007). Phylogenetic analysis aligned its sequence within cluster 4 of the GH36 subfamilies (Fredslund 2011). Interestingly this cluster also contains, in dose proximity, a characterized GH36 from Clostridium perfringens that is also known to cleave A antigen structures (Calcutt 2002). However, when we tested the ability of K05GH36 to remove A antigens from red blood cells its activity was disappointing, scoring only a 3, even when used in conjunction with a crowding agent.
Since these new enzymes offered no advantages, our attention turned to the No8 fosmid from F. plautii, especially since its gene products cleave both A and B-antigens. The three CAZy-related genes were cloned, their signal peptide sequences removed, expressed in E. coli BL21(DE3) and the resulting enzymes purified in yields of up to 140 mg/L. Surprisingly, when we tested the individual purified proteins against the A and B tetrasaccharide substrates the only cleavage observed was of the B-antigen by No8GH36, with no cleavage of A-antigens by any of them. We therefore tested pairwise combinations of these enzymes and were surprised to discover that the mix of No8CBM32 and No8GH36 rapidly cleaved the A-antigen tetrasaccharide. TLC analysis of reaction mixtures with the individual enzymes revealed that No8CBM32 catalysed the conversion of A-antigen to a more polar but still UV-active product, while subsequent addition of No8GH36 released a sugar product that co-migrated with galactosamine, along with H antigen trisaccharide. MS analysis of reaction mixtures demonstrated that No8CBM32 is an A-antigen de-acetylase, hence the decrease of 42 in m/z and the more polar product, while No8GH36 is a galactosaminidase, a new activity for this family (
While this pathway for degradation of the A-antigen was previously uncharacterised, fascinatingly it had been suggested over 50 years ago as an explanation for the so-called “acquired” B phenomenon wherein A-type patients infected with Clostridium tertium underwent an apparent change in blood type to type B (Gerbal 1975), as did forensic samples of human tissue that had been submerged in the river Thames (Ref Judd and Annesley https://doi.org/10.1016/S0887-7963(96)80087-3, Transfusion medicine reviews (1996) 10, 111-117). This presumably arose because the anti-B antibodies used in typing were unable to distinguish between terminal Gal and GalN.
Investigation of the third enzyme in the fosmid, the GH4, showed that while it hydrolyses Gal-α-pNP, GalN-α-pNP and GlcN-α-pNP, it does not cleave any A-antigen-based substrates. It therefore does not seem to play a direct role in conversion of A-antigen. However, these glycosaminidases do represent new activities within the GH4 family.
Closer bioinformatic analysis of this gene with Phyre2™ (Kelley 2015) indicated a ˜308 amino acid domain of previously unknown function at the N-terminus and an ˜145 amino acid CBM32 near the C-terminus, with linker regions between. Truncation analysis confirmed this basic structure since all constructs containing the intact deacetylase domain were indeed catalytically active (TABLE 2). This protein is therefore classified as the founding member of a new carbohydrate esterase family, CExx.
Acetamidosugar deacetylases have all proved to be metalloenzymes requiring divalent metal ions (Blair 2005). Consonant with this, treatment with 100 μM EDTA largely obliterated the enzyme activity, while addition of Mn2+, Co2+, Ni2+ or Zn2+ increased it. Other inhibitors of (non-metallo) amidases had no effect. The enzyme has a somewhat broad pH profile with an optimum around pH 8 (
The specificity of the CBM portion of the protein was explored using the glycan array of the Consortium for Functional Glycomics (CFG). The preferred targets were glycans with repeating N-acetyl lactosamine (LacNAc) structures, as also seen for the founding member of the CBM32 family; the N-acetylglucosaminidase from Clostridium perfringens (Ficko-Blean 2006). However, unlike that CBM, ours shows no high affinity binding to blood antigen structures. Repeating LacNAc structures are a common component of cell surfaces (Cohen 2009) as a universal component of complex and hybrid N-glycans, as well as some 0-glycans and glycolipids. In our case they presumably serve as the anchor point for attachment of the deacetylase domain. This would bring its catalytic domain into close proximity to the A-antigen without competition for its own substrate. In support of this model, removal of the domain resulted in a decreased activity on RBC's, with no effect on rates of soluble substrate cleavage (TABLE 2).
To provide structural insight into this novel enzyme activity the truncated proteins were subjected to crystallisation trials and FpGalNAcDeAc_D1ext found to produce the crystals that diffracted to the best resolution. Solution of this structure revealed a catalytic domain that adopts a 5-fold beta propeller structure with an active site harbouring a divalent metal ion coordinated by D100 and H252. Co-crystallization of the enzyme with B-antigen trisaccharide as a close analogue of the reaction product unveiled its binding mode. At the base of the active site pocket, the non-reducing end galactosyl moiety, which is the distinguishing group between A-antigen and B-antigen, makes hydrogen bonding interactions with H97, E64 and two of the metal coordinated waters. The rest of the ligand is surface-exposed and polar interactions are identified between the fucosyl group and the S61 and D121 sidechains. The C1-OH group of the reducing end galactosyl moiety is solvent exposed, thus extensions to the substrate (i.e. with GlcNAc) are readily accommodated by the enzyme. Modelling of the N-acetyl group of the A-trisaccharide onto this structure allowed us to make rational mutations of the nearby amino acids, potentially involved in substrate deacetylation. The residue E64 proved to be critical for activity since both mutants were inactive, suggesting a direct role, probably in activation of the nucleophilic water molecule (TABLE 1). The residues that coordinate the divalent metal, D100, Y315 and H252 also proved to be important, with mutation of any resulting in ˜5000-fold rate decreases, consistent with their apparent role in binding the divalent metal ions. By analogy to other acetamidosugar deacetylases we propose that FpGalNAc deacetylase carries out hydrolysis by the mechanism, wherein the metal serves to polarize the carbonyl and activate a water molecule for nucleophilic attack on the carbonyl to form the tetrahedral intermediate. Decomposition of that intermediate is facilitated by proton donation to the sugar nitrogen atom by His 100.
Phylogenetic analysis of the sequence places FpGalNase in a new subgroup (5) of the GH36 family (Fredslund 2011). The 390 amino acid catalytic domain is located in the centre of this large (1079 amino acid) protein, with a potential carbohydrate binding domain at the C terminus. Removal of this C-terminal domain had no effect on kinetic parameters of the enzyme with soluble substrates (TABLE 2), but led to reduced efficiency in cleavage of deacetylated A+ RBCs. The enzyme is specific for galactosamine-containing sugars and will not cleave GalNAc residues in any context tested. However, it has a fairly broad specificity for cleavage of de-N-acetylated galactosaminides ranging from the simple aryl glycosides GalN-α-pNP upwards. Indeed (TABLE 2) kcat/KM values for the three A subtypes tested were all similar to each other and to those of the deacetylase. Values of km/KM for cleavage of B-antigen were over 2000 times lower than for the corresponding GalN-antigen, but nonetheless were sufficient to yield a positive hit on the original screen. This specificity for de-acetylated alpha galacto-configured substrates, coupled with its pH optimum of ˜6.5-7.0 suit it well for use in blood type conversion in conjunction with the deacetylase (
Type A+, B+ and O+ RBCs were incubated with FpGalNAcDeAc and FpGalNase, individually and as a mixture and the released sugars analysed on a HPAE-PAD ion chromatogram. Neither of the enzymes used individually released any sugar products. However, when the mixture of the two was employed, galactosamine was clearly released from Type A+ RBCs but not from B+ or O+, proving a high specificity towards only the A antigen. This is very important as it shows that GalNAc is not released from the RBC surface in any other context. The truncated version of FpGalNase was also effective, but with slightly lower activity.
We then moved on to testing for antigen removal from RBCs using the industry standard MTS™ cards. These antibody-conjugated columns are loaded with RBCs and spun in a centrifuge. Antigen-free RBCs migrate to the bottom of the column and are scored as 0, while untreated RBCs bearing the corresponding antigen stick at the top and are scored as 4, with intermediate scores ranking the degree of antigen removal. Treatment with FpGalNase alone did not remove A or B antigenicity at the concentration employed (TABLE 3) consistent with its inactivity on GalNAc substrates, and its low activity on Gal. Incubation with FpGalNAcDeAc removed antigenicity due to conversion of the acetamide to an amine, compromises binding of the Anti-A antibody employed. The minimal amount of enzyme required for complete antigen de-acetylation was assessed for FpGalNAcDeAc alone and in combination with FpGalNase, both in the absence and presence of 300 mg/ml Dextran as crowding agent. Amounts of FpGalNase down to 3 μg/ml were sufficient without assistance from Dextran, while inclusion of 300 mg/ml dextran reduced the required loading to 0.5 μg/ml (TABLE 3). By comparison the best previous enzyme, EmGH109 was ineffective in the absence of Dextran, unless low salt buffers were employed, while in the presence of dextran the minimum effective concentration was 15 μg/ml, a 30-fold higher loading. Versions of FpGalNAcDeAc missing the CBM were much less effective.
Since the MTS™ card test on its does not assess the complete conversion of the A antigen and since no antibody was available to detect the GalN antigen we focused on the detection of newly formed H antigens on the treated RBC's. FpGalNase was functional at a concentration of only 5 μg/ml, leading to an increase of H-antigen level in concert with loss of A-antigen, as confirmed by FACS analysis seen in
Further characterization of the produced A-ECO RBC's may be useful to assess their full viability for usage in transfusion medicine, but the possibility to including the enzymes directly in to the blood plasma, potentially while collecting the blood donation, may allow an easy and cost efficient implementation off the process into the already existing automated routines of the blood collection and storage. In particular, the stability of the enzymes was tested as shown in TABLE 4.
In looking for similar enzymes a novel Clostridium tertium natural fusion of a Galactosaminidase and GalNAcDeacetylase connected by a CBM (GH36_domain-CBM-Deacetylation_domain) was identified. Initial testing showed that the enzyme cleaves the A antigen (same mechanism, first deacetylation then galactosamine cleavage) of red blood cells, but not as efficiently (i.e. similar to the EmGH109). The Clostridium tertium deacetylation domain is not as efficient as the F. plautii GalNAcDeacetylase, but if subsidized with the F. plautii GalNAcDeacetylase the Clostridium tertium Galactosaminidase domain shows similar activity to F. plautii Galactosaminidase on red blood cells.
Data shows that the Clostridium tertium Galactosaminidase (Ct5757_GalNAse) and Rp1021 do have comparable enzyme activity for the conversion of GalN antigen to H antigen (22nd reaction step)
Data was also collected for alternative GalNAcdeacetylase and Galactosaminidase enzymes and the alternative enzymes were compared to the Flavonifractor plautii GalNAcDeacetylase and Flavonifractor plautii Galactosaminidase. As shown in TABLE 5, the MTS scores for anti-A antibodies on treated A RBC are shown for Clostridium tertium natural fusion of a Galactosaminidase and GalNAcDeacetylase, which requires the presence of Dextran to effectively cleave A antigen, and also shows good activity Clostridium tertium GalNAcDeacetylase (Ct5757_DeAcase) when combined with Flavonifractor plautii Galactosaminidase (FpGalNase). Also in TABLE 6, the data shows that Robinsoniella peoriensis (Rp) Rp3672 and Rp3671 are able to deacetylate the A antigen on RBCs, but are less efficient then FpGalNAcDeAcase and activity was only achieved in the presence of a crowding agent (i.e. Dextran 40 k).
Although various embodiments of the invention are disclosed herein, many adaptations and modifications may be made within the scope of the invention in accordance with the common general knowledge of those skilled in this art. Such modifications include the substitution of known equivalents for any aspect of the invention in order to achieve the same result in substantially the same way. Numeric ranges are inclusive of the numbers defining the range. The word “comprising” is used herein as an open-ended term, substantially equivalent to the phrase “including, but not limited to”, and the word “comprises” has a corresponding meaning. As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a thing” includes more than one such thing. Citation of references herein is not an admission that such references are prior art to an embodiment of the present invention. The invention includes all embodiments and variations substantially as hereinbefore described and with reference to the examples and drawings.
The Flavonifractor plautii DNA sequences were modified from the naturally occurring DNA seq (GalNAcDeacetylase 2311/2319nt/Galactosaminidase 3228/3237nt). In particular, there is a difference in the length of the sequences used for protein purification, whereby the signal peptides was removed and a N-terminal HisTag was added through the vector backbone.
This application claims the benefit of U.S. Provisional Patent Application Ser. No. 62/719,272 filed on 17 Aug. 2018, entitled “ENZYMATIC COMPOSITIONS FOR CARBOHYDRATE ANTIGEN CLEAVAGE, METHODS, USES, APPARATUSES AND SYSTEMS ASSOCIATED THEREWITH”.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2019/051120 | 8/16/2019 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62719272 | Aug 2018 | US |
