Exploitation of gene context

Current Opinion in Structural Biology

Volumn 10, Issue 3, 2000, Pages 366-370

  Huynen, Martijn ^a,b   Snel, Berend ^a   Lathe III, Warren ^a,b   Bork, Peer ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

DNA REPLICATION; GENE FUSION; GENE SEQUENCE; HUMAN; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS);

EID: 0034072743     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(00)00098-1     Document Type: Review

References (36)

1. Marcotte E.M., Pellegrini M., Ng H., Rice W.D., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999;751-753. The authors introduce the idea of inferring functional interactions among genes on the basis of their fused occurrence. The paper only considers homologous relations. The paper shows that metabolic pathways are reflected in gene fusion events.
2. •], this method distinguishes between orthologs and paralogs, and uses a manual check of the functional interactions.
3. Dandekar T., Snel B., Huynen M., Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 23:1998;324-328. A comparison of three sets of three genomes shows that genes whose order is conserved within the genome tend to code for proteins that physically interact with each other. The paper predicts interactions for some hypothetical proteins on the basis of conserved gene order.
4. •].
5. Huynen M.A., Bork P. Measuring genome evolution. Proc Natl Acad Sci USA. 95:1998;5849-5856. The first large-scale analysis comparing the rates of evolution of various aspects of the genome. The authors introduce the idea of detecting functional interactions among genes from their co-occurrence in genomes.
6. Pellegrini M., Marcotte E.M., Thompson J.M., Eisenberg D., Yeats T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA. 96:1999;4285-4288. A large-scale implementation of the idea that genes that have the same phylogenetic distribution are functionally related. The paper includes some functional predictions, one of which was shown to be correct, and analyses of correlations in the phylogenetic distribution of proteins that functionally interact.
7. Snel B., Bork P., Huynen M. Genome evolution: gene fusion versus gene fission. Trends Genet. 16:2000;9-11.
8. Blumenthal T. Gene clusters and polycistronic transcription in eukaryotes. Bioessays. 20:1998;480-487.
9. Nassau P., Martin S.L., Brown R., Weston A., Monsey D., McNeil M., Duncan K. Galactofuranose biosynthesis in Escherichia coli K-12: identification and cloning of UDP-galactopyranose mutase. J Bacteriol. 178:1996;1047-1052.
10. Huynen M.A., Snel B. Gene and context: towards an integrative approach to genome analysis. Bork P. Analysis of Amino Acid Sequences, vol 10. 2000;345-379 Academic Press, San Diego.
11. Tamames J., Casari G., Ouzounis C., Valencia A. Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol. 44:1997;66-73.
12. Mushegian A.R., Koonin E.V. Gene order is not conserved in bacterial evolution. Trends Genet. 12:1996;289-290.
13. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D., Maltsev, N.: Use of contiguity on the chromosome to predict functional coupling. In Silico Biology 1998, 1:9. [URL: http://www.bioinfo.de/isb/1998/01/0009/ ].
14. Gaasterland T., Ragan M.A. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb Comp Genomics. 3:1998;199-217.
15. Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., Yuan Y. Predicting function: from genes to genomes and back. J Mol Biol. 283:1998;707-725.
16. Selkov E., Grechkin Y., Mikhailova N., Selkov E. MPW: The Metabolic Pathways Database. Nucleic Acids Res. 26:1998;43-45.
17. Xenarios I., Rice D.W., Salwinski L., Baron M.K., Marcotte E.M., Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Res. 28:2000;289-291.
18. Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., Zhao Q.et al. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 282:1998;754-759.
19. Huynen M.A., Dandekar T., Bork P. Variation and evolution of the citric acid cycle: a genomic perspective. Trends Microbiol. 7:1999;281-291. Comparative analysis of the citric acid cycle via the gene content of the published genomes. By including the gene context and other information about the species compared, the authors solve some of the pitfalls in orthology prediction to predict pathways. The authors reconstruct the evolution of the citric acid cycle in archaea.
20. Tatusov R., Galperin M.Y., Natale D., Koonin E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:2000;33-36. The latest article describing clusters of orthologous groups (COGs). This paper shows the uses of COGs not only for conventional genome annotation, but also points out how 'phylogenetic patterns of COG distribution' can be used for more advanced analysis. The COG web page ( http://www.ncbi.nlm.nih.gov ) allows the automatic extraction of groups of orthologous genes with a similar COG distribution pattern.
21. Schultz J., Copley R., Doerks T., Ponting C.P., Bork P. Smart: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28:2000;231-234.
22. Bateman A., Birney E., Durbin R., Eddy S.R., Howe K.L., Sonnhammer E.L. The pfam protein families database. Nucleic Acids Res. 28:2000;263-266.
23. Marcotte E., Pellegrini M., Thompson M., Yeates T., Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature. 402:1999;83-86. The authors describe an approach that combines different methods to predict functional links among proteins. Using this combination, high coverage and increased confidence can be attained. All the computational predictions rely on homologs. Potential biologically relevant links for several proteins are described.
24. Heim S., Kunkel A., Thauer R.K., Hedderich R. Thiol:fumarate reductase (tfr) from Methanobacterium thermoautotrophicum - identification of the catalytic sites for fumarate reduction and thiol oxidation. Eur J Biochem. 253:1998;292-299.
25. Janssen S., Schafer G., Anemuller S., Moll R. A succinate dehydrogenase with novel structure and properties from the hyperthermophilic archaeon Sulfolobus acidocaldarius: genetic and biophysical characterization. J Bacteriol. 179:1997;5560-5569.
26. Kromer W., Arndt E. Halobacterial S9 operon. Three ribosomal protein genes are cotranscribed with genes encoding a tRNA(Leu), the enolase, and a putative membrane protein in the Archaebacterium haloarcula (halobacterium) marismortui. J Biol Chem. 266:1991;24573-24579.
27. Tornow J., Santangelo G.M. Efficient expression of the Saccharomyces cerevisiae glycolytic gene ADH1 is dependent upon a cis-acting regulatory element (UASRPG) found initially in genes encoding ribosomal proteins. Gene. 90:1990;79-85.
28. Snel B., Bork P., Huynen M. Genome phylogeny based on gene content. Nat Genet. 21:1999;108-110.
29. Huynen M.A., Snel B., Bork P. Lateral gene transfer, genome surveys and the phylogeny of prokaryotes. Science. 286:1999;1441. a.
30. Galperin M., Koonin E.V. Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis. Mol Microbiol. 24:1997;443-445.
31. Kruglyak S., Tang H. Regulation of adjacent yeast genes. Trends Genet. 16:2000;109-111.
32. Gelfand M., Koonin E.V., Mironov A.A. Prediction of transcription regulatory sites in archaea by a comparative genomic approach. Nucleic Acids Res. 28:2000;695-705. The authors attempt to detect regulatory sites in archaea using profiles of known sites and comparative genomics. Their method proves to be able to predict new members for several regulons.
33. Doolittle R.F. Do you dig my groove? Nat Genet. 23:1999;6-8.
34. Sali A. Functional links between proteins. Nature. 402:1999;23-24.
35. Karzai A., Susskind M.M., Sauer R.T. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of Ssra (tmRNA). EMBO J. 18:1999;3793-3799.
36. Britton R., Lupski J.R. Isolation and characterization of suppressors of two Escherichia coli dnaG mutations, dnaG2903 and parB. Genetics. 145:1997;867-875.