Nucleic Acids Research, 2003, Vol. 31, No. 1 418-420
© 2003 Oxford University Press
REBASE: restriction enzymes and methyltransferases
New England BioLabs, Inc., 32 Tozer Road, Beverly, MA 01915, USA
*To whom correspondence should be addressed. Tel: +1 978 927 3382; Fax: +1 978 921 1527; Email: roberts{at}neb.com
Received September 23, 2002; Accepted September 27, 2002
ABSTRACT
REBASE contains comprehensive information about restriction enzymes, DNA methyltransferases and related proteins such as nicking enzymes, specificity subunits and control proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, crystal and sequence data. Homing endonucleases are also included. REBASE contains the most complete and up-to-date information about the methylation sensitivity of restriction endonucleases. In addition, there is extensive information about the known and putative restriction-modification (R-M) systems in more than 100 sequenced bacterial and archaeal genomes. The data is available on the web (http://rebase.neb.com/rebase/rebase.html), through ftp (ftp.neb.com) and as monthly updates via email.
INTRODUCTION
REBASE has undergone considerable growth since the 2001 NAR Database Issue (1). In addition to restriction enzymes, methyltransferases and homing endonucleases, REBASE also includes information about other types of related proteins: nicking enzymes, specificity subunits of the Type I enzymes, control proteins and methyl-directed restriction enzymes. From biochemical screening, it seemed that perhaps 20–25% of all bacterial strains possessed restriction enzymes. However, with the advent of massive DNA sequencing efforts and the large number of complete and survey sequences now available for bacterial and archaeal genome sequences, it is clear that restriction-modification (R-M) systems are much common than had once seemed likely. These potential systems are now included within REBASE. The deduced DNA methyltransferases and restriction enzymes are given names that resemble those of normal restriction enzymes (using the conventions of reference 2), but with the suffix ‘P’ added to indicate their putative status. The REBASE web site (http://rebase.neb.com/rebase/rebase.html) provides a summary of information known about every restriction enzyme and their associated proteins—such as commercial availability, sequence data, crystal structures, cleavage sites, recognition sequences, isoschizomers, growth temperatures and methylation sensitivity. A major focus is now on the genes that encode restriction systems and we provide both schematic illustrations of the organization of these systems and their nearest neighbours. We also provide tools (REBASE tools) that are useful in conjunction with restriction enzymes and BLAST searches can be run against all known restriction enzyme and methylase genes from the home page.
There are currently 3576 biochemically-characterized restriction enzymes in REBASE. These include twelve new Type II specificities discovered since the last review (1). Of the 3516 Type II restriction enzymes, 588 are commercially available, including 211 distinct specificities from a total of 240 total specificities known. In addition, 15 DNA methyltransferases, 5 homing endonucleases and 3 nicking enzymes are commercially available. From sequence analysis of Genbank entries and other web sites such as JGI-DOE, TIGR and the Sanger Institute, there are 1411 putative genes that could be components of R-M systems. We currently have 6838 references in REBASE (journal and book publications, patents, and unpublished observations). These are complete with abstracts and with full text links, when available. References are provided for every enzyme and each fact about that enzyme is documented.
REBASE has its own dedicated web server (http://rebase.neb.com/rebase/rebase.html) and can be searched extensively. From the REBASE Lists icon on the home page, a number of tables of specialized information can be accessed. This include crystal data, cloned/sequenced genes, enzymes listed by cleavage properties and other useful compilations. Suggestions for new lists are always welcomed. An extensive effort has gone into checking and recompiling information about the sensitivity of restriction enzymes to methylation. Previous compilations (3,4) had numerous errors and each item now listed within REBASE has been checked rigorously for its accuracy. In the case of unpublished observations from those earlier compilations, individual authors have been contacted to verify the observations. In addition, all published literature has been scanned and much new information is now available. These data can be accessed both from an enzyme's main page as well as from the ‘REBASE Methylation Sensitivity’ icon on the home page. Importantly, the data is shown in double-strand format so that the effects of hemi-methylation and double-strand methylation are clearly differentiated.
The analysis of sequenced genomes has been a major focus and entries can be found from the REBASE Genomes icon. More than 120 complete or shotgun genomes have been analyzed and the results are presented in several formats. The analysis of Bacillus halodurans C-125 (GenBank # NC_002570) is shown in Figure 1. Two complete R-M systems are present, encoding BhaI (recognition sequence: GCATC) and BhaII (recognition sequence: GGCC). In addition, an aminomethyltransferase gene is present, but none of the surrounding open reading frames show similarity to known restriction enzyme genes. This is either a solitary enzyme or the associated restriction enzyme gene is dissimilar to any known gene.
|
The REBASE files icon brings up the growing list of currently available monthly data formats. Click on any of the numbered choices for their descriptions or to download these files. Click on the SUBSCRIBE TO REBASE icon to receive monthly email updates. Users who prefer retrieving REBASE data via anonymous FTP may continue to do so at ftp.neb.com (cd/pub/rebase). We also continue to maintain a monthly emailing list.
ACKNOWLEDGEMENTS
Special thanks are due to the many individuals who have so kindly contributed their unpublished results for inclusion in this compilation and to the REBASE users who continue to steer our efforts with their helpful comments. We are especially grateful to Karen Otto for secretarial help. This database is supported by the National Library of Medicine (LM04971).
REFERENCES
- Roberts,R.J. and Macelis,D. (2001) REBASE—restriction enzymes and methylases. Nucleic Acids Res., 29, 268–269.
[Abstract/Free Full Text] - Smith,H.O. and Nathans,D.J. (1973) A suggested nomenclature for bacterial host modification and restriction systems and their enzymes. J. Mol. Biol., 81, 419–423.[CrossRef][Web of Science][Medline]
- McClelland,M., Nelson,M. and Raschke,E. (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res., 22, 3640–3659.
[Abstract/Free Full Text] - Nelson,M., Raschke,E. and McClelland,M. (1993) Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res., 21, 3139–3154.
[Free Full Text] - Posfai,J., Bhagwat,A.S., Posfai,G. and Roberts,R.J. (1989) Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res., 17, 2421–2435.
[Abstract/Free Full Text] - Klimasauskas,S., Timinskas,A., Menkevicius,S., Butkiene,D., Butkus,V. and Janulaitis,A.A. (1989) Sequence motifs characteristic of DNA [cytosine-N4] methylases: similarity to adenine and cytosine-C5 DNA-methylases. Nucleic Acids Res., 17, 9823–9832.
[Abstract/Free Full Text]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Watanabe, H. Yuzawa, N. Handa, and I. Kobayashi Hyperthermophilic DNA Methyltransferase M.PabI from the Archaeon Pyrococcus abyssi Appl. Envir. Microbiol., August 1, 2006; 72(8): 5367 - 5375. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. E. Erova, L. Pillai, A. A. Fadl, J. Sha, S. Wang, C. L. Galindo, and A. K. Chopra DNA Adenine Methyltransferase Influences the Virulence of Aeromonas hydrophila Infect. Immun., January 1, 2006; 74(1): 410 - 424. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Armalyte, J. M. Bujnicki, J. Giedriene, G. Gasiunas, J. Kosinski, and A. Lubys Mva1269I: A Monomeric Type IIS Restriction Endonuclease from Micrococcus Varians with Two EcoRI- and FokI-like Catalytic Domains J. Biol. Chem., December 16, 2005; 280(50): 41584 - 41594. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Gromek and T. Kaczorowski DNA Sequencing by Indexer Walking Clin. Chem., September 1, 2005; 51(9): 1612 - 1618. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Grote, K. Hiller, M. Scheer, R. Munch, B. Nortemann, D. C. Hempel, and D. Jahn JCat: a novel tool to adapt codon usage of a target gene to its potential expression host Nucleic Acids Res., July 1, 2005; 33(suppl_2): W526 - W531. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. A. Chmiel, M. Radlinska, S. D. Pawlak, D. Krowarsch, J. M. Bujnicki, and K. J. Skowronek A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy Protein Eng. Des. Sel., April 1, 2005; 18(4): 181 - 189. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Ponger and W.-H. Li Evolutionary Diversification of DNA Methyltransferases in Eukaryotic Genomes Mol. Biol. Evol., April 1, 2005; 22(4): 1119 - 1128. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Pingoud, A. Sudina, H. Geyer, J. M. Bujnicki, R. Lurz, G. Luder, R. Morgan, E. Kubareva, and A. Pingoud Specificity Changes in the Evolution of Type II Restriction Endonucleases: A BIOCHEMICAL AND BIOINFORMATIC ANALYSIS OF RESTRICTION ENZYMES THAT RECOGNIZE UNRELATED SEQUENCES J. Biol. Chem., February 11, 2005; 280(6): 4289 - 4298. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. G. Miller, B. M. Pearson, J. M. Wells, C. T. Parker, V. V. Kapitonov, and R. E. Mandrell Diversity within the Campylobacter jejuni type I restriction-modification loci Microbiology, February 1, 2005; 151(2): 337 - 351. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. J. Roberts, T. Vincze, J. Posfai, and D. Macelis REBASE--restriction enzymes and DNA methyltransferases Nucleic Acids Res., January 1, 2005; 33(suppl_1): D230 - D232. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Rudd, H. Schoof, and K. Mayer PlantMarkers--a database of predicted molecular markers from plants Nucleic Acids Res., January 1, 2005; 33(suppl_1): D628 - D632. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zheng, R. J. Roberts, and S. Kasif Identification of genes with fast-evolving regions in microbial genomes Nucleic Acids Res., December 2, 2004; 32(21): 6347 - 6357. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-h. Chan, Z. Zhu, J. L. Van Etten, and S.-y. Xu Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification Nucleic Acids Res., November 29, 2004; 32(21): 6187 - 6199. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Keatch, T.-J. Su, and D. T. F. Dryden Alleviation of restriction by DNA condensation and non-specific DNA binding ligands Nucleic Acids Res., November 1, 2004; 32(19): 5841 - 5850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Chin, V. Valinluck, S. Magaki, and J. Ryu KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system Nucleic Acids Res., October 8, 2004; 32(18): e138 - e138. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Iyer, K. S. Makarova, E. V. Koonin, and L. Aravind Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging Nucleic Acids Res., October 5, 2004; 32(17): 5260 - 5279. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. O'Driscoll, F. Glynn, O. Cahalane, M. O'Connell-Motherway, G. F. Fitzgerald, and D. van Sinderen Lactococcal Plasmid pNP40 Encodes a Novel, Temperature-Sensitive Restriction-Modification System Appl. Envir. Microbiol., September 1, 2004; 70(9): 5546 - 5556. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. W. J. van Passel, A. Bart, R. J. A. Waaijer, A. C. M. Luyf, A. H. C. van Kampen, and A. van der Ende An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes Nucleic Acids Res., August 10, 2004; 32(14): e114 - e114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Samuelson, Z. Zhu, and S.-y. Xu The isolation of strand-specific nicking endonucleases from a randomized SapI expression library Nucleic Acids Res., July 9, 2004; 32(12): 3661 - 3671. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Doi, S. Kumadaki, Y. Oishi, N. Matsumura, and H. Yanagawa In vitro selection of restriction endonucleases by in vitro compartmentalization Nucleic Acids Res., July 6, 2004; 32(12): e95 - e95. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. P. So, R. F. B. Turner, and C. A. Haynes Increasing the efficiency of SAGE adaptor ligation bydirected ligation chemistry Nucleic Acids Res., July 6, 2004; 32(12): e96 - e96. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Dong, P. Stothard, I. J. Forsythe, and D. S. Wishart PlasMapper: a web server for drawing and auto-annotating plasmid maps Nucleic Acids Res., July 1, 2004; 32(suppl_2): W660 - W664. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Gowers, S. R.W. Bellamy, and S. E. Halford One recognition sequence, seven restriction enzymes, five reaction mechanisms Nucleic Acids Res., June 29, 2004; 32(11): 3469 - 3479. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. K. A. Kasarjian, M. Hidaka, T. Horiuchi, M. Iida, and J. Ryu The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI Nucleic Acids Res., June 15, 2004; 32(10): e82 - e82. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. G. Kossykh and R. S. Lloyd A DNA Adenine Methyltransferase of Escherichia coli That Is Cell Cycle Regulated and Essential for Viability J. Bacteriol., April 1, 2004; 186(7): 2061 - 2067. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T.-L. Lin, C.-T. Shun, K.-C. Chang, and J.-T. Wang Isolation and Characterization of a HpyC1I Restriction-Modification System in Helicobacter pylori J. Biol. Chem., March 19, 2004; 279(12): 11156 - 11162. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Callow, S. Drmanac, and R. Drmanac Selective DNA amplification from complex genomes using universal double-sided adapters Nucleic Acids Res., January 28, 2004; 32(2): e21 - e21. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. L. Christensen and J. Josephsen The Methyltransferase from the LlaDII Restriction-Modification System Influences the Level of Expression of Its Own Gene J. Bacteriol., January 15, 2004; 186(2): 287 - 295. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. M. Cohen, D. S. Tawfik, and A. D. Griffiths Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization Protein Eng. Des. Sel., January 1, 2004; 17(1): 3 - 11. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. A. M. Loenen Tracking EcoKI and DNA fifty years on: a golden story full of surprises Nucleic Acids Res., December 15, 2003; 31(24): 7059 - 7069. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Adamczyk-Poplawska, A. Kondrzycka, K. Urbanek, and A. Piekarowicz Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems Microbiology, November 1, 2003; 149(11): 3311 - 3319. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Mruk, M. Cichowicz, and T. Kaczorowski Characterization of the LlaCI methyltransferase from Lactococcus lactis subsp. cremoris W15 provides new insights into the biology of type II restriction-modification systems Microbiology, November 1, 2003; 149(11): 3331 - 3341. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. J. Kingston, N. A. Gormley, and S. E. Halford DNA supercoiling enables the Type IIS restriction enzyme BspMI to recognise the relative orientation of two DNA sequences Nucleic Acids Res., September 15, 2003; 31(18): 5221 - 5228. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Osipiuk, M. A. Walsh, and A. Joachimiak Crystal structure of MboIIA methyltransferase Nucleic Acids Res., September 15, 2003; 31(18): 5440 - 5448. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. M. Skowron, J. Majewski, A. Zylicz-Stachula, S. M. Rutkowska, I. Jaworowska, and R. I. Harasimowicz-Slowinska A new Thermus sp. class-IIS enzyme sub-family: isolation of a 'twin' endonuclease TspDTI with a novel specificity 5'-ATGAA(N11/9)-3', related to TspGWI, TaqII and Tth111II Nucleic Acids Res., July 15, 2003; 31(14): e74 - e74. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Vincze, J. Posfai, and R. J. Roberts NEBcutter: a program to cleave DNA with restriction enzymes Nucleic Acids Res., July 1, 2003; 31(13): 3688 - 3691. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. J. Roberts, M. Belfort, T. Bestor, A. S. Bhagwat, T. A. Bickle, J. Bitinaite, R. M. Blumenthal, S. Kh. Degtyarev, D. T. F. Dryden, K. Dybvig, et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes Nucleic Acids Res., April 1, 2003; 31(7): 1805 - 1812. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||