Tandem clusters of membrane proteins in complete genome sequences - PubMed (original) (raw)
Comparative Study
doi: 10.1101/gr.10.6.731.
Affiliations
- PMID: 10854407
- DOI: 10.1101/gr.10.6.731
Free article
Comparative Study
Tandem clusters of membrane proteins in complete genome sequences
D Kihara et al. Genome Res. 2000 Jun.
Free article
Abstract
The distribution of genes coding for membrane proteins was investigated in 16 complete genomes: 4 archaea, 11 bacteria, and 1 eukaryote. Membrane proteins were identified by our new method of predicting transmembrane segments () after the removal of amino-terminal signal peptides. Interestingly, about half of the membrane protein genes in each genome were found to be located next to another, forming tandem clusters. Roughly 10%-30% of the tandem clusters were conserved among organisms, and most of the conserved tandem clusters belonged to one of the three functional groups, namely, transporters, the electron transport system, and cell motility. A tandem cluster sometimes contained paralogous membrane proteins, in which case the cluster size and the number of transmembrane segments could be related to a functional category, especially to transporters. In addition to the clustering of membrane proteins, the clustering of membrane proteins and ATP-binding proteins in the complete genomes was also analyzed. Although this clustering was not statistically significant, it was useful to identify candidate membrane protein partners of isolated ATP-binding protein components in the ABC transporters. Possible implications of tandem cluster organization of membrane protein genes are discussed including the complex formation and other functional coupling of protein products and the mechanism of protein translocation to the cell membrane.
Similar articles
- A comparative analysis of ABC transporters in complete microbial genomes.
Tomii K, Kanehisa M. Tomii K, et al. Genome Res. 1998 Oct;8(10):1048-59. doi: 10.1101/gr.8.10.1048. Genome Res. 1998. PMID: 9799792 - Evolution of the ATP-binding-cassette transmembrane transporters of vertebrates.
Hughes AL. Hughes AL. Mol Biol Evol. 1994 Nov;11(6):899-910. doi: 10.1093/oxfordjournals.molbev.a040163. Mol Biol Evol. 1994. PMID: 7529351 - Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping.
Fujibuchi W, Ogata H, Matsuda H, Kanehisa M. Fujibuchi W, et al. Nucleic Acids Res. 2000 Oct 15;28(20):4029-36. doi: 10.1093/nar/28.20.4029. Nucleic Acids Res. 2000. PMID: 11024184 Free PMC article. - The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis.
Braibant M, Gilot P, Content J. Braibant M, et al. FEMS Microbiol Rev. 2000 Oct;24(4):449-67. doi: 10.1111/j.1574-6976.2000.tb00550.x. FEMS Microbiol Rev. 2000. PMID: 10978546 Review. - Comparison of lantibiotic gene clusters and encoded proteins.
Siezen RJ, Kuipers OP, de Vos WM. Siezen RJ, et al. Antonie Van Leeuwenhoek. 1996 Feb;69(2):171-84. doi: 10.1007/BF00399422. Antonie Van Leeuwenhoek. 1996. PMID: 8775977 Review.
Cited by
- When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.
Cong Q, Shen J, Borek D, Robbins RK, Opler PA, Otwinowski Z, Grishin NV. Cong Q, et al. Proc Biol Sci. 2017 Feb 8;284(1848):20161735. doi: 10.1098/rspb.2016.1735. Proc Biol Sci. 2017. PMID: 28179510 Free PMC article. - Speciation in Cloudless Sulphurs Gleaned from Complete Genomes.
Cong Q, Shen J, Warren AD, Borek D, Otwinowski Z, Grishin NV. Cong Q, et al. Genome Biol Evol. 2016 Mar 30;8(3):915-31. doi: 10.1093/gbe/evw045. Genome Biol Evol. 2016. PMID: 26951782 Free PMC article. - PatchSurfers: Two methods for local molecular property-based binding ligand prediction.
Shin WH, Bures MG, Kihara D. Shin WH, et al. Methods. 2016 Jan 15;93:41-50. doi: 10.1016/j.ymeth.2015.09.026. Epub 2015 Sep 30. Methods. 2016. PMID: 26427548 Free PMC article. - Controlled Co-reconstitution of Multiple Membrane Proteins in Lipid Bilayer Nanodiscs Using DNA as a Scaffold.
Raschle T, Lin C, Jungmann R, Shih WM, Wagner G. Raschle T, et al. ACS Chem Biol. 2015 Nov 20;10(11):2448-54. doi: 10.1021/acschembio.5b00627. Epub 2015 Sep 21. ACS Chem Biol. 2015. PMID: 26356202 Free PMC article. - Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP.
Hawkins T, Chitale M, Kihara D. Hawkins T, et al. BMC Bioinformatics. 2010 May 19;11:265. doi: 10.1186/1471-2105-11-265. BMC Bioinformatics. 2010. PMID: 20482861 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources