Systems for categorizing functions of gene products

Current Opinion in Structural Biology

Volumn 8, Issue 3, 1998, Pages 388-392

  Riley, Monica ^a  

^a MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT;

DNA SEQUENCE; GENE FUNCTION; PRIORITY JOURNAL; SHORT SURVEY;

EID: 0032102745     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80074-2     Document Type: Article

References (28)

1. Bachmann BJ. Linkage map of Escherichia K-12, edition 8. Microbiol Rev. 54:1990;130-197.
2. Berlyn MKB, Low KB, Rudd KE, Singer M. Linkage map of Escherichia coli K-12, edition 9. Neidhardt FN, Curtiss R III, Lin ECC, Ingraham JL, Low KB, Magasanik B, Reznikoff W, Riley M, Schaechter M, Umbarger E. edn 2 Escherichia coli and Salmonella: Cellular and Molecular Biology. 1996;1715-1902 American Society for Microbiology Press, Washington, DC.
3. Ingraham JL, Maaloe O, Neidhardt FC. Appendix B. Growth of the Bacterial Cell. 1983;391-403 Sinauer Associates Incorporated, Sunderland, Massachusetts.
4. Riley M. Functions of the gene products of E. coli. Microbiol Rev. 57:1993;862-952.
5. Riley M, Labedan B. E. coli gene products: physiological functions and common ancestries. of special interest Neidhardt FN, Curtiss R III, Lin ECC, Ingraham JL, Low KB, Magasanik B, Reznikoff W, Riley M, Schaechter M, Umbarger E. edn 2 Escherichia coli and Salmonella: Cellular and Molecular Biology. 1996;2118-2202 ASM Press, Washington, DC, The basic scheme for organizing E. coli cellular functions - connecting gene products and genes.
6. Karp P, Riley M, Paley SM, Pellegrini-Toole A, Krummenacker M. EcoCyc: encyclopedia of Escherichia genes and metabolism. Nucleic Acids Res. 26:1998;50-53. [URL: http://www.ecocyc.PangeaSystems.com/ecocyc/ecocyc.html].
7. Riley M. Genes and proteins of Escherichia coli K-12 (GenProtEC). Nucleic Acids Res. 26:1998;54. [URL: http://mbl.edu/html/ecoli.html].
8. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb J-F, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
9. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, klenk HP, Gill S, Dougherty BA, et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 388:1997;539-547. [URL: http://www.tigr.org/tdb/mdb/hpdb/hpdb.html].
10. Riley M, Labedan B. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J Mol Biol. 268:1997;857-868.
11. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 390:1997;249-256. [URL: http://www.pasteur.fr/Bio/SubtiList/help/classif-search.html].
12. Mewes HW, Albermann K, Heumann K, Liebl S, Pfeiffer F. MIPS: a database for protein sequences, complete genomes. of special interest Nucleic Acid Res. 25:1998;28-30 This database provides several 'catalogs' which are ways of viewing gene products in different ways. In the functional catalog, sometimes useful pictures explain the inter-relationship of reactions and protein interactions. Pathway catalogs are under construction. Information provided includes prosite motifs, EC numbers, types of proteins, protein complexes (with links to documentation).
13. Hodges PE, Payne WE, Garrels JI. Yeast protein database (YPD): a curated proteome database for Saccharomyces cerevisiae. of special interest Nucleic Acid Res. 25:1998;68-72 This database organizes gene products under several banners: localization, molecular environment, post-translational modification and gene location on chromosomes.
14. Drosophila functions available by FTP from: ftp.ebi.ac.uk/pub/databases/edgp/misc/ashburner/fly_function_tree. An incredibly detailed listing of Drosophila functions from Michael Ashburner. A first attempt at classifying functions of gene products for a higher organism. The next step is to populate the list with genes and proteins.
15. Carper D, Nishimura C, Shinohara T, Dietzchold B, Wistow G, Craft C, Kador P, Kinoshita JH. Aldose reductase and p-crystallin belong to the same protein superfamily as aldehyde reductase. FEBS Lett. 220:1987;209-213.
16. Timchenko T, Bailone A, Devoret R. Btcd, a mouse protein that binds to curved DNA can substitute in Escherichia coli for H-NS, a bacterial nucleoid protein. of special interest EMBO J. 15:1996;3986-3992 Mouse and E. coli both have proteins that bind to DNA. The trick is to recognize their similarity by taking care when describing the functions of the gene products in databases.
17. On World Wide Web URL: http://info.gdb.org/Letovsky/provence.html. This site begins the discussion on correlating information on gene products by developing a common vocabulary.
18. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew G, et al. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1462. [URL: http://www.genetics.wisc.edu/html/k12.html].
19. Goto S, Bono H, Ogata H, Fujibuchi W, N shioka T, Sato K, Kanehisa M. Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput. 1997;175-186. [URL: http://www.genome.ad.jp/kegg/docs/intro.html].
20. Selkov E Jr, Grechkin Y, Milhailova N, Selkov E. MPW: the metabolic pathways database. Nucleic Acids Res. 26:1998;43-45. [URL: http://www.mcs.anl.gov/home/compbio/WIT/wit.html].
21. Proforma controlled vocabularies on World Wide Web URL: http://www.ebi.ac.uk:7081/docs/flydocs/flybase/controlled-vocabularies.txt. An early attempt at a controlled vocabulary. The site includes components of the gross anatomy (body parts) of the fruit fly, only the metabolism is shared by lower organisms.
22. Webb EC. Enzyme Nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. 1992;Academic Press, New York.
23. Paulsen IT, Sliwinski MK, Saier MH Jr. Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. J Mol Biol. 277:1998;573-592.
24. Gerloff DL, Cohen FE, Korostensky C, Turcotte M, Gonnet GH, Benner SA. A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family. of special interest Proteins. 27:1997;450-458 The approach used here has been successful in predicting secondary structures of many proteins - this is just one example.
25. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. of special interest J Mol Biol. 247:1995;536-540 An indispensable reference resource. It offers a BLAST search for similar proteins whose structures are known.
26. Orengo CA, Micnie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure. 5:1997;1093-1108.
27. Dodge C, Schneider R, Sander C. The HSSP database of protein structure-sequence alignments and family profiles. of special interest Nucleic Acids Res. 26:1998;313-315 This is a comprehensive collection of data on protein families and relationships between structure and sequence alignments. Wandering around this site gives ore a sense of how the field stands today and where it is going tomorrow.
28. Holm L, Sander C. Touring protein fold space with Dali/FSSP. of special interest Nucleic Acids Res. 26:1998;319-319 Emphasis is on the folds that appear in various combinations in proteins. Many useful database connections are provided.