# Patent

## Title
Single stranded DNA binding proteins from archaea

## Abstract

The invention provides ssDNA-binding proteins from three species of archaeons, Methanococcus jannaschii, Methanobacter theromoautotrophicum, and Archaeoglobus fulgidus, as well as the ability to identify ssDNA-binding proteins from other archaeons. The proteins help render DNA more accessible to DNA polymerase and are robust reagents for a variety of biotechnical processes, including PCR. The invention further provides nucleic acids encoding such proteins, vectors for transfecting host cells, host cells comprising the vectors, and methods of using the proteins.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims priority from U.S. Provisional Application No. 60/147,680, filed Aug. 6, 1999, which is hereby incorporated by reference.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
This invention was made with government support under grant number AI-18987 awarded by the National Institutes of Health. The government has certain rights in the invention.


BACKGROUND OF THE INVENTION
Single stranded (ss) DNA-binding proteins are essential to virtually all aspects of DNA metabolism. These proteins, typified by the Escherichia coli ssDNA-binding protein (SSB) in Bacteria (Sancar, A., et al., Proc. Natl. Acad. Sci. USA 78, 4274-4278 (1981), Lohman, T. M. et al., Annu. Rev. Biochem. 63, 527-570 (1994)) and the human replication protein-A (RPA) complex in Eucarya (Fairman, M. P. et al., Embo J 7, 1211-1218 (1988); Wold, M. S. et al., Proc. Natl. Acad. Sci. USA 85, 2523-2527 (1988); and Wold, M. S., Annu. Rev. Biochem. 66, 61-92 (1997)), are required for in vitro DNA replication and are key components in DNA recombination and repair. Although functionally equivalent, SSB protein and RPA have very different protein structures. Bacterial SSB proteins are encoded by a single gene, although the active form is a homotetramer of SSB where each monomer contributes one ssDNA-binding domain. By contrast, the RPA complex is composed of three distinct subunits.
The large subunit of RPA, RPA70, has several-domains, each associated with a given function (Gomes, X. V., J. Biol. Chem. 270, 4534-4543 (1995), Gomes, X. V. Biochemistry 35, 10558-10568 (1996)). The N-terminal region of RPA70 mediates interactions between RPA and many cellular or viral proteins, whereas the central region contains two functional, homologous, ssDNA-binding sites that are arranged in tandem. The C-terminal region of RPA70 is involved in the assembly of the heterotrimeric complex. The intermediate subunit of RPA, RPA32, which carries a third functional ssDNA-binding site (Bochkareva, E., et al., J. Biol. Chem. 273, 3932-3947 (1998)), is phosphorylated in a cell-cycle dependent manner, although no specific role is attributed to this modification (Henricksen, L. A., Nucleic Acids Res. 24, 3107-3112 (1996)). Finally, the small subunit (RPA14) carries an additional putative ssDNA-binding motif; however, but no direct evidence for DNA binding by this subunit exists.
Interestingly, the four ssDNA-binding motifs of RPA and the motif of SSB protein show a significant degree of homology Philipova, D. et al. Genes Dev. 10, 2222-2233 (1996)). Moreover, there is striking structural conservation among the ssDNA-binding domains of RPA, and members of both the prokaryotic SSB protein family and the phage-encoded SSB proteins (Bochkarev, A., Nature 385, 176-181 (1997)). These findings suggest that RPA and SSB protein originated from a common ancestral ssDNA-binding protein and then diverged through evolution by a combination of duplications, deletions, and additions.
While ssDNA binding proteins have been known for Bacteria and for Eucarya, the art has not identified a counterpart of a ssDNA binding protein for the third domain of life, the Archaea.
SUMMARY OF THE INVENTION
We have discovered a novel type of ssDNA-binding protein in the genomes of several archaeons. These proteins possess four conserved DNA binding sites within a single polypeptide or, in one case, two polypeptides. Because members of the Archaea exist in extreme conditions of pH, salt concentrations, and low and high temperatures, the ssDNA binding proteins of these archaeons are especially robust reagents for use in biotechnical applications involving DNA, such as PCR.
The invention provides isolated nucleic acid sequences encoding an ssDNA-binding protein from an Archaeon. In particular, the Archaeon is selected from the group consisting of Methanococcus jannaschii, Methanobacter theromoautotrophicum, and Archaeoglobus filgidus. The nucleic acid sequence can have, for example, 70% or more sequence identity to a nucleic acid selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:7, and SEQ ID NO:8, or can be selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:7, and SEQ ID NO:8.
The invention further provides recombinant expression vectors containing any of the nucleic acid sequences described above, as well as cells containing one or more of these recombinant expression vectors. In some preferred embodiments, the recombinant expression vectors are in E. coli cells.
Additionally, the invention provides isolated ssDNA-binding proteins. In particular, the invention provides an isolated ssDNA-binding protein wherein the ssDNA-binding protein is isolated from an Archaeon selected from the group consisting of Methanococcus jannaschii, Methanobacter theromoautotrophicum, and Archaeoglobus fulgidus. The ssDNA-binding protein can have 70% or more sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS:1, 5, 6, 9, and 10, or can be selected from the group consisting of SEQ ID NOS:1, 5, 6, 9, and 10.
The invention further provides a method of performing polymerase chain reaction, comprising using a ssDNA-binding protein isolated from an archaeon. The method can conveniently be performed using an ssDNA-binding protein of an archaeon selected from the group consisting of Methanococcus jannaschii, Methanobacter theromoautotrophicum, and Archaeoglobus fulgidus. In particular, the method can use ssDNA binding proteins having 70% or more sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOS:1, 5, 6, 9, and 10, or can be selected from the group consisting of SEQ ID NOS:1, 5, 6, 9, and 10



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1: A. Alignment of residues 80 to 297 of MJ1159 with the RPA70 subunit of a variety of eukaryotes and the Escherichia coli (Ec) ssDNA-binding protein (SSB). Residues that are conserved between MJ1159 and its RPA70 counterparts are shown in bold font; conservative substitutions are shown in italics. The corresponding residues in SSB protein are also indicated. Dots represent gaps in the alignment. The boxed residues in human RPA70 are known to contact DNA (Bochkarev, A., Nature 385, 176-181 (1997)). The sequence numbering relates to MJ1159. All alignments and consensus building were performed using the Multalin version 5.3.3 program (available at on the internet by entering “www.” followed by “toulouse.inra.fr/multalin.html”) and the Wisconsin Package Version 9.1 (Genetics Computer Group (GCG), Madison, Wis.). B. Alignment of the four putative ssDNA-binding domains in MJ1159. The fonts are as in A.; additional conservative substitutions between two binding domains are underlined. Dashes represent gaps in the alignment. The consensus sequence derived from the four MJ1159 domains is shown, as is a eukaryotic ssDNA-binding domain A consensus derived from the sequences shown in A. Upper case indicates highly conserved residues, lower case indicates less conserved residues; asterisks indicate a lack of consensus. Two dots between the consensus sequences indicate identical residues; one dot indicates conserved substitutions. Three residues were omitted from the eukaryotic consensus in order to allow a better alignment; these are shown below the alignment. Cf, Crithidia fasciculata; Dm, Drosophila melanogaster; Hs, Homo sapiens; Sp, Schizosaccharomyces pombe; Sc, Saccharomyces cerevisiae; Xl, Xenopus laevis. 
FIG. 2: Structure of the ssDNA-binding domain A. A. Human RPA70 ssDNA-binding domain A. B. Methanococcus jannaschii MJ1159 ssDNA-binding domain A (residues 80-162) modeled using the structure of human RPA70 domain A as a guide. The modeling was carried out by the Swiss model server using the ProModII and Gromos96 programs (available on the internet by entering “www.” followed by “expasy.ch/swissmod/SWISS-MODEL.html”) for comparative protein modeling and energy minimization, respectively. The structures are shown so that the axis of the channel in which DNA binds is perpendicular to the figure (the position of DNA is shown as a circle).
FIG. 3: Alignment of the zinc-finger domains of eukaryotic RPA70s (SEQ ID NOS:26-31) and residues 524-595 of MJ1159 (SEQ ID NO:25). Conserved residues are shown in bold; conservative substitutions are shown in italics. Cysteine residues thought to be part of a zinc-finger domain are indicated by asterisks. Abbreviations: Cf, Crithidia fasciculata; Dm, Drosophila melanogaster; Hs, Homo sapiens; Sp, Schizosaccharomyces pombe; Sc, Saccharomyces cerevisiae; XI, Xenopus laevis. 
FIG. 4: A. Comparison of the structures of ssDNA-binding proteins in Bacteria, Eukarya and Archaea. The ssDNA-binding domains are indicated by letters, putative zinc-finger domains are indicated by the letters “Zn” over the domain, the protein-protein interaction domain is indicated by text over the domain. B. Model for the evolution of ssDNA-binding proteins. B′ and D′ indicate products of homologous recombination. RPA, replication protein A; SSB, prokaryotic ssDNA-binding protein. Indications for the ssDNA-binding domains and zinc finger domains are as for FIG. 4A.



DETAILED DESCRIPTION
I. Uses of the ssDNA-Binding Proteins of the Invention
Members of the Archaea typically live in conditions of extreme heat, pH, or salt concentrations. Thus, they offer a source of enzymes which can be useful reagents in assays and other commercial reactions. We have identified nucleic acid sequences encoding ssDNA-binding proteins in the archaeons Methanococcus jannaschii, Methanobacter thermoautotrophicum and Archaeoglobus fulgidus. All three organisms are thermophiles, and their DNA replication accordingly takes place at high temperature. M. jannaschii, for example, grows near deep ocean thermal vents under conditions of 200 atm and a temperature range of 48° to 94° C. (see, e.g., Bult, C. J. et al., Science 273:1058-1073 (1996)). The ssDNA-binding proteins of these organisms are therefore robust reagents useful for a variety of biotechnical applications. For example, the proteins are especially useful in applications in which functioning under high temperature conditions is desirable, such as the temperatures usually associated with the polymerase chain reaction (PCR).
ssDNA-binding proteins are known to be involved in eliminating DNA secondary structure, and in DNA recombination. The ssDNA-binding proteins of the invention are therefore useful reagents for genetic engineering and other procedures involving DNA recombination, as well as in performing PCR.
During PCR, the activity of ssDNA-binding proteins in eliminating secondary structure permits DNA polymerase to replicate more of the DNA template strand in each PCR cycle than would be replicated in the absence of the protein, thereby increasing yield. Moreover, temperature-resistant ssDNA-binding proteins are not inactivated by the temperature cycling which is part of the PCR process, and thus do not have to be replaced before the next reaction can proceed. This enhances the ability to automate the procedures. Thus, use of heat-resistant ssDNA-binding proteins, like the ones provided here, not only increases the yield of each PCR cycle, but also permits automation of the overall process and the speed with which cycles can be conducted.
PCR reactions generally benefit from the use of between about 0.05 μg to about 1 μg of ssDNA-binding protein of the invention. Higher yields of PCR product have been obtained, for example, by using 0.2 to 0.6 μg of M. jannaschii ssDNA-binding protein in a 50 μL PCR reaction containing 1 unit of Taq polymerase and 50 μg of DNA. Using these amounts as guidelines, persons of skill in the art can readily determine and optimize the amounts to use for any given volume of PCR reactants or amount of DNA. Accordingly, among other advantages, the invention has significant benefits in the practice of PCR.
II. Discovery of the ssDNA-Binding Protein of Methanococcus jannaschii 
A. Search for the Gene
In a major feat, which made the cover of Science, the genome of an entire autotrophic archaeon, Methanococcus jannaschii, was sequenced in 1996. (Bult, C. J. et al., Science 273:1058-1073 (1996)). According to the news article accompanying the research report, the study's forty co-authors searched the existing databases of bacterial and eukaryotic genomes for homologs. Morell, V., Science, 273:1043-1045 (1996). The team found matches for only 44% of the genes, id., and only 38% of the genes could be assigned a putative cellular role with any confidence. Bult, et al., supra. The majority of the genes could not be identified.
We have now been able to identify the function of one of the genes to which Bult et al. could not assign a function. Briefly, we searched the M. jannaschii genome for a protein with homology to the Saccharomyces cerevisiae RFA1 gene, which encodes the RPA70 subunit, using the Grasta program (available at http://www.tigr.org) and a low cutoff score. Several putative candidates were retrieved and were subsequently used as queries in Blast or PSI-Blast searches (available on the internet by entering “www.” followed by “ncbi.nlm.nih.gov”). One of these M. jannaschii sequences, ORF MJ1159, retrieved the Crithidia fasciculata RFA1 gene product. The MJ1159 protein (SEQ ID NO:1) is 645 amino acids in length and, interestingly, one of the regions of similarity detected by Blast corresponds to the ssDNA-binding domain A of C. fasciculata RPA70. MJ1159 is one of the genes for which Bult et al. could not determine a function. The entire sequence of the protein is publicly available, and can be accessed on the Internet at the National Center for Biotechnology Information (“NCBI”) website (by entering “WWW.” followed by “ncbi.nlm.nih.gov”). It can be found using the NCBI's Entrez browser under accession number F64444. The gene sequence (SEQ ID NO:2) is available at the website of The Institute for Genomic Research (TIGR by entering “www.” followed by “tigr.org”, in the microbial database, and can be searched simply by entering MJ1159 in the locus search once one is in the M. jannaschii section of the database.
To extend the analysis, we performed multiple alignments of the MJ1159 sequence with sequences of known members of the RPA70 family (FIG. 1A). Residues 80-297 of MJ1159 display a significant degree of similarity to the residues encompassing ssDNA-binding domains A and B of RPA70 from a variety of organisms: this similarity ranged from 39.4% (for residues comprising the domain A of RPA70 from S. cerevisiae) to 48.6% (for residues comprising domain A of human RPA70). Therefore, it appears that MJ1159 has two homologous ssDNA-binding domains, named A and B (by analogy with RPA70), which are arranged in tandem.
Interestingly, most of the amino acids that contact DNA in the human RPA70 subunit (boxed residues in FIG. 1A) are conserved in MJ1159: in ssDNA-binding domain A, which makes most of the contacts with DNA (Bochkarev, A., Nature 385, 176-181 (1997)), all but one of the DNA-contacting residues are conserved. Homology-dependent structure modeling [which has a high degree of success in predicting the structure of OB-fold family members (A. Edwards, personal communication)] of the archaeal ssDNA-binding domain A (residues 80 to 162) indicates that it shows striking similarity to the equivalent human RPA70 domain (FIG. 2). Both the observed and predicted structures form a channel in which DNA binds, and the residues known to interact with DNA are found along the surface of this channel.
In addition to the homology identified in ssDNA-binding domains A and B, a second region of homology was detected by Blast searches. This region corresponds to residues 400-595 of MJ1159 and shares 29.3 and 35.4% similarity with the C-terminal region of the RPA70 proteins of C. fasciculata and S. cerevisiae, respectively. Furthermore, a strongly conserved zinc-finger domain, which was recently shown to be important for RPA function (Lin, Y.-L. et al., J. Biol. Chem. 273, 1453-1461 (1996)), is located within this region. The four cysteine residues (marked by asterisks in FIG. 3) of this putative zinc-finger are strictly conserved and correctly spaced. The sequences that border this domain also share a significant degree of similarity.
Portions of the discussion herein were published by us in Chedin et al., TIBS 23:273-277 (1998), which is hereby incorporated by reference.
B. Structure of the Gene
Unexpectedly, alignment of either of the MJ1159 ssDNA-binding domain identified (A or B) with the entire MJ1159 open reading frame revealed two additional homologous regions (called C and D) were revealed. Pairwise comparisons showed that the degree of sequence similarity shared by the four domains ranges from 46% (C-D) to 53% (A-B). When we compared a consensus derived by aligning these four domains with one obtained by aligning the ssDNA-binding domains A of several RPA70 subunits, we found that many residues are conserved between the M. jannaschii MJ1159 protein and eukaryotic RPA70 subunits (FIG. 1B). Because the RPA70 ssDNA-binding domain A also shows similarity to E. coli SSB protein (Philipova, D. et al., Genes Dev. 10, 2222-2233 (1996)) (FIG. 1A), we conclude that Archaea, Bacteria and Eucarya share a common ssDNA-binding motif. The architecture of the archaeal protein—specifically, its four ssDNA-binding motifs and the zinc-finger domain-, is particularly striking, however, and invites speculation about the evolution of ssDNA-binding proteins.
E. coli SSB protein binds to DNA as a homotetramer and each monomer contains one DNA-binding motif. Our analysis shows that the protein identified in M. jannaschii possesses four conserved putative DNA-binding domains, but that these are present in a single polypeptide chain. This finding might imply that the archaeal RPA functions as a single subunit that does not require multimerization, or, as is the case in eukaryotic RPA, association with other subunits. The fact that searches of the M. jannaschii genome using either the middle or small subunits of the eukaryotic RPA did not retrieve any genes that shared significant homology with these proteins supports this hypothesis. However, as elaborated below, the genome of another archaeon reveals a different genetic structure.
C. Discovery of Two Additional Archeaon ssDNA-Binding Proteins
The genome sequences of two archaeons, Methanobacter thermoautotrophicum and Archaeoglobus fulgidus, were recently released (Klenk, H. P. et al., Nature 390, 364-370 (1996), Shamoo, Y. et al., Nature 376, 362-366 (1996)). This allowed us to determine whether or not the findings reported here for M. jannaschii hold true for other members of the Archaea. We searched the M. thermoautotrophicum genome using MJ1159 as a query and retrieved a 622-residue protein that shares substantial homology with MJ1159 (44% similarity over 410 residues). This protein, MTH1385, also possesses four putative DNA-binding motifs that are arranged in tandem but lacks the zinc-finger domain. However, a second, partially overlapping, gene, MTH1384, lies downstream of MTH1385. The former encodes a protein that shares homology with the C-terminus of MJ1159 and that contains a region that is homologous to the zinc-finger motif described above. It appears that a frameshift was introduced during the sequence and therefore erroneously suggested the existence of two distinct genes—a possibility that was in fact raised by the authors (Klenk, H. P. et al., Nature 390, 364-370 (1996)). Thus, it appears that the nucleic acid sequence originally identified as two genes, MTH1384 and MTH1385, actually constitute one continuous gene, and the organization we have described for M. jannaschii MJ1159 therefore holds true for a protein in a second archaeon.
The nucleotide sequences of MTH1384 and MTH1385 are set forth as SEQ ID NOS:3 and 4, respectively. The amino acid sequences of MTH1384 and MTH1385 are set forth as SEQ ID NOS:5 and 6, respectively. Given this information, a person of skill in the art has all the information necessary to compare the two sequences, determine the frameshift error, if present, and determine the sequence of the gene and the sequence of the protein it encodes.
In A. fulgidus, our initial search identified a gene encoding a 236-residue protein, AF0382, that shares homology with the N-terminus of MJ1159 (46.6% similarity over 236 residues) and contains two DNA-binding domains. Interestingly, a second search revealed a gene encoding a 312-residue, AF0780, that shares homology with the C-terminus of MJ1159 (40% similarity over 312 residues) and contains two DNA-binding domains, in addition to the putative zinc-finger region. However, the first AF0780 DNA-binding domain appears to be shorter than a typical ssDNA-binding domain (as defined in FIG. 1A) and only three cysteine residues (compared to the four that are found typically) are present in the zinc-finger region. Thus, it appears that the A. fulgidus ssDNA-binding protein is split into two pieces. The nucleotide sequences of AF0382 and AF0780 are set forth as SEQ ID NOS:7 and 8, respectively. The amino acid sequences of AF0382 and AF0780 are set forth as SEQ ID NOS:9 and 10, respectively.
Thus, identifying the function of the M. jannaschii MJ1159 gene has permitted us to identify the function of genes from two other archaeons. It is expected that persons of skill in the art will now be able to examine the genome of other archaeons as they are sequenced, find their ssDNA-binding proteins by virtue of their homology to these genes and by virtue of the similarity of their structure to the genes taught herein. It is expected that such comparisons can be readily made for other members of the same genuses, families and orders, as the three archaeons discussed herein, and very likely for other archaeons as well. Finally, the function of the genes can then be confirmed by expressing the encoded proteins and testing them by well known assays for their function as ssDNA-binding proteins.
As noted, the nucleic acid sequences for the ssDNA binding protein genes from M. thermoautotrophicum and A. fulgidus and the amino acid sequences of the proteins themselves are set forth in the sequence listing. This information is also available in publicly accessible databases. The nucleic acid sequences of the genes encoding the A. fulgidus proteins are available on the TIGR website in the microbial database under the name of the organism, at locus search AF0780 and AF0382. The amino acid sequence of the M thermoautotrophicum protein is available on the internet by entering “www.” followed by genomecorp.com/genesequences/methanobacter/abstract.html (which can be reached by hyperlink from the microbial database of the TIGR website); the gene sequences for both MT1385 and MT1384 can be found in GenBank at locus AE000901.
D. Modifications of the Genes and of the ssDNA-Binding Proteins.
1. Definitions
As used herein, the term “ssDNA-binding protein” means an archaeon protein which binds single-stranded DNA, or a protein with 70% or more sequence identity to one of the exemplary archaeon ssDNA-binding proteins described herein. ssDNA-binding proteins generally do not bind double-stranded DNA, or do so at a relatively low level compared with its binding of single-stranded DNA. The proteins usually comprise four DNA binding domains and typically comprise one or more zinc-containing domains which, due to their conformation, are known in the art as “zinc-fingers.” Typically, ssDNA-binding proteins are 200 to 900 amino acids in length and more commonly are 500 to 800 amino acid residues in length. Archaeon ssDNA-binding proteins can be a multimer comprising two or more subunits, or can comprise a single polypeptide chain.
The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. When percentage of sequence identity is used in reference to proteins or peptides, it is recognized that residue positions that are not identical often differ by conservative amino acid substitutions, where amino acids residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated according to, e.g., the algorithm of Meyers & Miller, Computer Applic. Biol. Sci. 4:11-17 (1988), e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif., USA).
As to amino acid sequences, one of skill will recognize that individual substitutions, in a nucleic acid, peptide, polypeptide, or protein sequence which alters a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. The following six groups each contain amino acids that are conservative substitutions for one another:

    
    
        1) Alanine (A), Serine (S), Threonine (T);
        2) Aspartic acid (D), Glutamic acid (E);
        3) Asparagine (N), Glutamine (Q);
        4) Arginine (R), Lysine (K);
        5) Isoleucine (1), Leucine (L), Methionine (M), Valine (V); and
        6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).
        (see, e.g., Creighton, Proteins (W. H. Freeman & Co., New York, N.Y. 1984)).
    
    


The phrase “substantially identical,” in the context of two nucleic acids or polypeptides, refers to sequences or subsequences that have at least 60%, preferably 70%, more preferably 80%, even more preferably 90% and most preferably 95% or more nucleotide or amino acid residue identity when aligned for maximum correspondence over a comparison window as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. With respect to nucleic acids, this definition also refers to the complement of a test sequence, which has substantial sequence or subsequence complementarity when the test sequence has substantial identity to a reference sequence.
One of skill in the art will recognize that two polypeptides can also be “substantially identical” if the two polypeptides are immunologically similar. Thus, overall protein structure may be similar while the primary structure of the two polypeptides display significant variation. Therefore a method to measure whether two polypeptides are substantially identical involves measuring the binding of monoclonal or polyclonal antibodies to each polypeptide. Two polypeptides are substantially identical if the antibodies specific for a first polypeptide bind to a second polypeptide with an affinity of at least one third of the affinity for the first polypeptide.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally, Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).
Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (whose website can be found on the internet by entering “www.” followed by “ncbi.nlm.nlm.gov/”). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Porc. Natl. Acad. Sci. USA 89:10915 (1989)). 
In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
“Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein or incorporated herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.
Another indication that two nucleic acid sequences are substantially identical is that one of the two sequences hybridizes to the complement of the other under stringent conditions, as described below.
The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).
The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, highly stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Lower stringency conditions are generally selected to be about 15-30° C. below the Tm. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 times background hybridization.
Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. In the present invention, genomic DNA or cDNA comprising nucleic acids of the invention can be identified in standard Southern blots under stringent conditions using the nucleic acid sequences disclosed here. For the purposes of this disclosure, suitable stringent conditions for such hybridizations are those which include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and at least one wash in 0.2×SSC at a temperature of at least about 50° C., usually about 55° C. to about 60° C., for 20 minutes, or equivalent conditions. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.
A further indication that two polynucleotides are substantially identical is if the reference sequence, amplified by a pair of oligonucleotide primers, can then be used as a probe under stringent hybridization conditions to isolate the test sequence from a cDNA or genomic library, or to identify the test sequence in, e.g., an RNA gel or DNA gel blot hybridization analysis.
It is anticipated that conservative substitutions can be made in the nucleic acids taught herein which will permit expression of ssDNA-binding proteins functionally identical to those of the invention. It is further anticipated that conservative substitutions can be made in the amino acid sequence of the ssDNA-binding proteins themselves which still result in proteins of the desired robustness for use in PCR and other applications. These minor variations are fairly encompassed in the invention as described herein.
2. Nucleotide Sequences and Proteins with Sequence Identity to the Sequences Identified Herein
Persons of skill in the art will recognize that the nucleotide sequences and protein sequences of the archaeon ssDNA-binding proteins identified herein can undergo substantial variation and still function as ssDNA-binding proteins. First, it will be recognized that, due to the degeneracy of the genetic code, the ssDNA-binding proteins identified herein can be encoded by large number of other nucleic acid sequences than the sequences determined from the genomes of the archaeons. Second, amino acid substitutions, and especially conservative substitutions, can be made in the proteins themselves without eliminating their ability to function as ssDNA-binding proteins. Third, persons of skill may wish to change the sequence of the protein to improve properties of the proteins, such as solubility, stability or DNA-binding, or to change the sequence of the nucleotides to improve, for example, yield of the protein when expressed in bacteria.
In general, nucleic acid sequences which encode ssDNA-binding proteins and having at least 70% sequence identity to SEQ ID NOS:2, 3, 4, 7, or 8 are encompassed by the present invention. More preferably, the nucleic acid sequences have 75%, 80%, or 85% sequence identity to SEQ ID NOS:2, 3, 4, 7, or 8, respectively. Even more preferably, the nucleic acid sequences have 90%, or 95% or even higher sequence identity to SEQ ID NOS:2, 3, 4, 7, or 8, respectively.
Similarly, ssDNA-binding proteins which have at least 70% sequence identity to SEQ ID NOS:1, 5, 6, 9, or 10, respectively, are encompassed by the present invention. More preferably, the proteins have 75%, 80%, or 85% sequence identity to SEQ ID NOS:1, 5, 6, 9, or 10, respectively. Even more preferably, the proteins have 90%, or 95% or even higher sequence identity to SEQ ID NOS:1, 5, 6, 9, or 10, respectively.
Any particular protein, such as the protein encoded by any particular nucleic acid, can be tested by standard assays to determine whether it functions as an ssDNA binding protein. Proteins which do not bind to ssDNA, and nucleic acid sequences encoding such proteins, are not within the scope of the present invention.
As noted, determinations of whether a particular protein binds DNA can be made by standard assays. Conveniently, such determinations can be made, for example, by agarose gel mobility shift assays with radioactively labeled single-stranded deoxythymidine-containing oligonucleotides. The oligonucleotides are incubated with increasing concentrations of a single-stranded DNA binding protein and then subjected to electrophoresis in an agarose gel to separate any protein-oligonucleotide complexes from free oligonucleotide. If the resulting bands show decreased mobility of oligonucleotides incubated with a higher concentration of the protein when compared to bands of oligonucleotides incubated with a lower concentration of protein, it indicates that a complex has formed between the oligonucleotide and the protein and thus that the protein has functioned as an ssDNA-binding protein. Details of performing such assays are taught, for example, by Kim et al., Biochemistry, 33:14197-206 (1994) and Kim et al., Mol. Cell Biol., 12:3050-3059.
If desired or necessary, binding competition studies can be conducted to confirm that the DNA binding protein binds single-stranded, not double-stranded, DNA. Conveniently, such assays can be performed by incubating reaction mixtures containing fixed amounts of the DNA binding protein and a radiolabeled deoxythymidine (dT) oligonucleotide with increasing concentrations of unlabeled single- or double-stranded DNA, such as M13. In the absence of sufficient amounts of the unlabeled DNA, most of the radiolabeled dT will form protein-DNA complexes. If the DNA binding protein binds single-stranded DNA, it will take significantly more double-stranded DNA to reduce the fraction of the radiolabeled dT in protein-DNA complexes by 50%. If the DNA binding protein binds double-stranded DNA, the reverse will be true. The assay can thus determine the relative affinity of the protein for each form of DNA.
E. Vectors, Host Cells Comprising Vectors, and Production of ssDNA Binding Proteins
The ssDNA binding proteins of the invention can be prepared by cloning techniques. Examples of appropriate cloning and sequencing techniques, and instructions sufficient to direct persons of skill through many cloning exercises are found in Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL (2ND ED.), VOLS. 1-3, Cold Spring Harbor Laboratory (1989)), Berger and Kimmel (eds.), GUIDE TO MOLECULAR CLONING TECHNIQUES, Academic Press, Inc., San Diego Calif. (1987)), or Ausubel, et al. (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Greene Publishing and Wiley-Interscience, NY (1987). Product information from manufacturers of biological reagents and experimental equipment also provide useful information. Such manufacturers include the SIGMA chemical company (Saint Louis, Mo.), R&D systems (Minneapolis, Minn.), Pharmacia LKB Biotechnology (Piscataway, N.J.), CLONTECH Laboratories, Inc. (Palo Alto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee, Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc. (Gaithersburg, Md.), Fluka Chemica-Biochemika Analytika (Fluka Chemie AG, Buchs, Switzerland), Invitrogen, San Diego, Calif., and Applied Biosystems (Foster City, Calif.), as well as many other commercial sources known to one of skill.
Nucleic acids encoding an ssDNA binding protein can be amplified by in vitro methods. Amplification methods include the polymerase chain reaction (PCR), the ligase chain reaction (LCR), the transcription-based amplification system (TAS), the self-sustained sequence replication system (3SR). A wide variety of cloning methods, host cells, and in vitro amplification methodologies are well known to persons of skill.
In a preferred embodiment, an ssDNA binding protein is prepared by inserting the cDNA which encodes it into a vector. The insertion is made so that the an ssDNA binding protein are read in frame, that is, in one continuous polypeptide.
In addition to recombinant methods, ssDNA binding proteins can also be constructed in whole or in part using standard peptide synthesis. Solid phase synthesis of polypeptides of the present invention of less than about 50 amino acids in length may be accomplished by attaching the C-terminal amino acid of the sequence to an insoluble support followed by sequential addition of the remaining amino acids in the sequence. Techniques for solid phase synthesis are described by Barany & Merrifield, THE PEPTIDES: ANALYSIS, SYNTHESIS, BIOLOGY. VOL. 2: SPECIAL METHODS IN PEPTIDE SYNTHESIS, PART A. pp. 3-284; Merrifield, et al. J. Am. Chem. Soc. 85:2149-2156 (1963), and Stewart, et al, SOLID PHASE PEPTIDE SYNTHESIS, 2ND ED., Pierce Chem. Co., Rockford, Ill. (1984). Proteins of greater length may be synthesized by condensation of the amino and carboxyl termini of shorter fragments. Methods of forming peptide bonds by activation of a carboxyl terminal end (e.g., by the use of the coupling reagent N, N′-dicycylohexylcarbodiimide) are known to those of skill.
Once the nucleic acids encoding an ssDNA binding protein of the present invention are isolated and cloned, one may express the desired protein in a recombinantly engineered cell such as bacteria, plant, yeast, insect and mammalian cells. It is expected that those of skill in the art are knowledgeable in the numerous expression systems available for expression of proteins including E. coli, other bacterial hosts, such as Bacillus or Pseudomonas, yeast, and various higher eukaryotic cells such as the COS, CHO, HeLa and myeloma cell lines. No attempt to describe in detail the various methods known for the expression of proteins in prokaryotes or eukaryotes will be made.
In brief, the expression of natural or synthetic nucleic acids encoding the isolated proteins of the invention will typically be achieved by operably linking the DNA or cDNA to a promoter (which is either constitutive or inducible), followed by incorporation into an expression cassette. The cassettes can be suitable for replication and integration in either prokaryotes or eukaryotes. Typical expression cassettes contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the DNA encoding the protein. To obtain high level expression of a cloned gene, it is desirable to construct expression cassettes which contain, at the minimum, a strong promoter to direct transcription, a ribosome binding site for translational initiation, and a transcription/translation terminator. For E. coli this includes a promoter such as the T7, trp, lac, or lambda promoters, a ribosome binding site and preferably a transcription termination signal. For eukaryotic cells, the control sequences can include a promoter and preferably an enhancer derived from immunoglobulin genes, SV40, cytomegalovirus, and a polyadenylation sequence, and may include splice donor and acceptor sequences. The cassettes of the invention can be transferred into the chosen host cell by well-known methods such as calcium chloride transformation or electroporation for E. coli and calcium phosphate treatment, electroporation or lipofection for mammalian cells. Cells transformed by the cassettes can be selected by resistance to antibiotics conferred by genes contained in the cassettes, such as the amp, gpt, neo and hyg genes. Expression of the proteins in prokaryotic cells, such as E. coli, is preferred.
F. An Evolutionary Model for ssDNA-Binding Proteins.
Alignment of the prokaryotic, archaeal and eukaryotic proteins that contain DNA-binding domain A reveals several features that are relevant to the evolution of ssDNA-binding proteins (see FIG. 4A). The N-terminal region of RPA70, which is involved in protein-protein interactions, is 100 residues longer than that of Methanococcus RPA. This is expected, if we assume that a specific protein-protein-interaction domain was acquired late in evolution. The putative zinc-finger domain in RPA70 is also present in the archaeal protein, which argues for an early appearance of this motif. A zinc-finger is also found in the bacteriophage T4 ssDNA-binding protein, gene 32 protein, which shares little sequence homology with other ssDNA-binding proteins but retains considerable structural similarity (Smith, D. R et al. J. Bacteriol. 179, 7135-7155 (1996)).
The structure of the archaeal protein offers some insights into a plausible succession of events linking the prokaryotic SSBs to their archaeal and eukaryotic counterparts. Gene amplification of a prokaryotic gene may have generated a protein that had several DNA-binding domains—as is the case for M. jannaschii and M. thermoautotrophicum (FIG. 4B). The N-terminal domain (which is involved in specific protein-protein interactions) and the C-terminal domain (which contains the zinc-finger motif) could have been acquired by gene fusion. Recombination between the partially homologous domains B and D would then produce a protein that was essentially similar to the RPA70 subunit, in that it had two DNA-binding domains and a conserved C-terminal region (FIG. 4B). This proposition is supported by the fact that the human RPA70 domain B shares the greatest degree of homology with the M. jannaschii MJ1159 domain D, while the RPA70 domain A is more similar to the MJ1159 domain A—thus reinforcing the idea that domains B and C were lost from RPA70.
If recombination between domains B and D was intramolecular and reciprocal, the reciprocal fragment could have been re-inserted into the genome by illegitimate recombination and therefore kept four ssDNA-binding sites available. Interestingly, such an organization corresponds closely to that described above for AF0382 and AF0780 in A. fulgidus, and could represent an intermediate gene organization that led ultimately to the emergence of eukaryotic RPAs. The RPA32 and RPA14 subunits would then have arisen after a final step of gene separation (FIG. 4B).
Note that although the pathway depicted in FIG. 4B starts with the prokaryotic SSB, we do not imply that bacterial SSBs correspond to the ancestral protein; it is equally plausible that the bacterial proteins arose from an ancestor rooted in the archaeal tree, by a process that is the reverse of the first step shown in FIG. 4B.
Together, these data strongly suggest that ssDNA-binding proteins in the Archaea belong to a class of previously undescribed DNA-binding proteins whose architecture might represent the missing evolutionary link between the prokaryotic and the eukaryotic SSB proteins. The presence of RPA-related proteins in archaeal organisms indicates that, despite the extreme environmental conditions typical of their natural habitats (e.g., high temperatures), their chromosomal DNA is likely to be stabilized in a double-stranded form and, hence, that the need for such proteins has been conserved. Archaeal RPA homologues, like their bacterial and eukaryotic counterparts, are probably involved in maintaining DNA in a transient single-stranded form, protecting this single-stranded DNA from nucleases and promoting important protein-protein contacts.
All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

## Claims

1. A complex of (a) an isolated single stranded (ss) DNA-binding protein, wherein the ssDNA-binding protein has at least 90% sequence identity to the full-length of an amino acid sequence selected from the group consisting of SEQ ID NOS:1, 5, and 6, which protein is an oligonucleotide/oligosaccharide binding (OB)-fold protein which:
(i) comprises four ssDNA-binding protein domains, said domains having a channel so sized as to permit binding of ssDNA along the channel; 
(ii) comprises at least one zinc finger domain in the carboxyl portion of the protein, which zinc finger domain comprises at least four cysteines; and 
(iii) binds single stranded DNA, and 
(b) an ssDNA.

2. A complex of (a) an isolated single stranded (ss) DNA-binding protein, wherein the ssDNA binding protein has at least 90% sequence identity to amino acid of SEQ ID NO:1, and (b) an ssDNA.

3. A complex of (a) an isolated single stranded (ss) DNA binding protein, wherein the ssDNA binding protein has at least 95% sequence identity to SEQ ID NO:1 and which binds (b) a single stranded DNA.

4. A complex of (a) an isolated single stranded (ss) DNA-binding protein, wherein the ssDNA-binding protein has the amino acid sequence of SEQ ID NO:1, and (b) a ssDNA.

5. An isolated ssDNA binding protein wherein the ssDNA-binding protein has at least 90% sequence identity to the full length of each of SEQ ID NO:5 and 6.

6. An isolated single stranded (ss) DNA-binding protein complex comprised of a first peptide chain and a second peptide chain, wherein said first peptide chain has at least 90% sequence identity to SEQ ID NO:9 and said second peptide chain has at least 90% sequence identity to SEQ ID NO:10, which protein complex:
(a) comprises a total of four ss DNA-binding protein domains of an oligonucleotide/oligosaccharide binding (OB)-fold protein, each of said domains having a channel so sized as to permit binding of ssDNA along the channel; 
(b) comprises at least one zinc finger domain in a carboxyl portion of one of the peptide chains, which zinc finger domain comprises at least three cysteines; and 
(c) binds single stranded DNA.

7. An isolated ssDNA-binding protein complex of claim 6, wherein one peptide chain of the ssDNA-binding protein complex has the sequence of SEQ ID NO:9 and one peptide chain has the sequence of SEQ ID NO:10.

8. An isolated ssDNA binding protein of claim 5, wherein the ssDNA binding protein has at least 95% sequence identity to the sequence of each of SEQ ID NOS:5 and 6.