The use of gene clusters to infer functional coupling.
Previously, we presented evidence that it is possible to predict functional coupling between genes based on conservation of gene clusters between genomes. With the rapid increase in the availability of prokaryotic sequence data, it has become possible to verify and apply the technique. In this paper, we extend our characterization of the parameters that determine the utility of the approach, and we generalize the approach in a way that supports detection of common classes of functionally coupled genes (e.g., transport and signal transduction clusters). Now that the analysis includes over 30 complete or nearly complete genomes, it has become clear that this approach will play a significant role in supporting efforts to assign functionality to the remaining uncharacterized genes in sequenced genomes.
19 references, click to expand
-
Bacillus subtilis pur operon expression and regulation.J Bacteriol. 1989 Apr;171(4):2136-41 PMID: 2495272
-
Nucleotide sequence analysis of the purEK operon encoding 5'-phosphoribosyl-5-aminoimidazole carboxylase of Escherichia coli K-12.J Bacteriol. 1989 Jan;171(1):205-12 PMID: 2464576
-
Molecular cloning and nucleotide sequence of the gene for pyruvate kinase of Bacillus stearothermophilus and the production of the enzyme in Escherichia coli. Evidence that the genes for phosphofructokinase and pyruvate kinase constitute an operon.Eur J Biochem. 1993 Feb 1;211(3):851-9 PMID: 8436141
-
Cloning and nucleotide sequences of the genes encoding triose phosphate isomerase, phosphoglycerate mutase, and enolase from Bacillus subtilis.J Bacteriol. 1994 Jul;176(13):3903-10 PMID: 8021172
-
The genes for phosphofructokinase and pyruvate kinase of Lactobacillus delbrueckii subsp. bulgaricus constitute an operon.J Bacteriol. 1996 Aug;178(15):4727-30 PMID: 8755908
-
Enzymes of nucleotide synthesis.Curr Opin Struct Biol. 1995 Dec;5(6):752-7 PMID: 8749362
-
Selfish operons: horizontal transfer may drive the evolution of gene clusters.Genetics. 1996 Aug;143(4):1843-60 PMID: 8844169
-
The RDP (Ribosomal Database Project).Nucleic Acids Res. 1997 Jan 1;25(1):109-11 PMID: 9016515
-
Genome organization, natural genetic engineering and adaptive mutation.Trends Genet. 1997 Mar;13(3):98-104 PMID: 9066268
-
Glycolytic enzyme operon of Borrelia burgdorferi: characterization and evolutionary implications.Gene. 1997 Apr 1;188(2):221-8 PMID: 9133595
-
Representation of function: the next step.Gene. 1997 May 20;191(1):GC1-GC9 PMID: 9210599
-
Selfish operons and speciation by gene transfer.Trends Microbiol. 1997 Sep;5(9):355-9 PMID: 9294891
-
A genomic perspective on protein families.Science. 1997 Oct 24;278(5338):631-7 PMID: 9381173
-
Cloning, sequence, and expression of the phosphofructokinase gene of Clostridium acetobutylicum ATCC 824 in Escherichia coli.Curr Microbiol. 1998 Jul;37(1):17-22 PMID: 9625784
-
Yeast "operons".Microb Comp Genomics. 1998;3(2):133-40 PMID: 9697097
-
Gene clusters and polycistronic transcription in eukaryotes.Bioessays. 1998 Jun;20(6):480-7 PMID: 9699460
-
Operon hypothesis: new evidence from the "constant proportion" group of the Embden-Meyerhof pathway.Nature. 1966 Mar 5;209(5027):1022-3 PMID: 5927508
-
Identification and sequence analysis of Escherichia coli purE and purK genes encoding 5'-phosphoribosyl-5-amino-4-imidazole carboxylase for de novo purine biosynthesis.J Bacteriol. 1989 Jan;171(1):198-204 PMID: 2644189
-
De novo purine nucleotide biosynthesis.Prog Nucleic Acid Res Mol Biol. 1992;42:259-87 PMID: 1574589
Contact
No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong
Qilu Normal University · Genelibs Bioinformatics Lab
750 Shunhua Rd, Jinan
2F, Bldg F, University Science Park
Tel: 0531-88819269
WeChat Official Account
Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.
Business Email
E-mail: [email protected]
Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2
