COGcollator: a Web Server for Analysis of Distant Relationships Between Homologous Protein Families

Overview

Journal Biol Direct

Publisher Biomed Central

Specialty Biology

Date 2017 Dec 1

PMID 29187234

Citations 7

Authors

Daria V Dibrova

Kirill A Konovalov

Vadim V Perekhvatov

Konstantin V Skulachev

Armen Y Mulkidjanian

Affiliations

Soon will be listed here.

Abstract

Background: The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs.

Aim: We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server.

Results: Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis. We demonstrate the utility of this tool by identifying the COGs that contain distant homologs of (i) the catalytic subunit of bacterial rotary membrane ATP synthases and (ii) the DNA/RNA helicases of the superfamily 1.

Reviewers: This article was reviewed by Drs. Igor N. Berezovsky, Igor Zhulin and Yuri Wolf.

Citing Articles

The Leptospira interrogans proteome's response to zinc highlights the potential involvement of this metal in translational-machinery and virulence.

Hecktheuer A, Santos C, Ferreira F, Barbosa A, Isaac L, Marques M Biometals. 2024; 37(6):1677-1698.

PMID: 39305434 DOI: 10.1007/s10534-024-00634-w.

Common Mechanism of Activated Catalysis in P-loop Fold Nucleoside Triphosphatases-United in Diversity.

Kozlova M, Shalaeva D, Dibrova D, Mulkidjanian A Biomolecules. 2022; 12(10).

PMID: 36291556 PMC: 9599734. DOI: 10.3390/biom12101346.

Profiling Signal Transduction in Global Marine Biofilms.

Wang R, Zhang W, Ding W, Liang Z, Long L, Wong W Front Microbiol. 2022; 12:768926.

PMID: 35069473 PMC: 8776716. DOI: 10.3389/fmicb.2021.768926.

Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes.

Sanchez-Osuna M, Cortes P, Lee M, Smith A, Barbe J, Erill I Nucleic Acids Res. 2021; 49(19):11050-11066.

PMID: 34614190 PMC: 8565304. DOI: 10.1093/nar/gkab773.

Chained Structure of Dimeric F-like ATPase in Mycoplasma mobile Gliding Machinery.

Toyonaga T, Kato T, Kawamoto A, Kodera N, Hamaguchi T, Tahara Y mBio. 2021; 12(4):e0141421.

PMID: 34281395 PMC: 8406192. DOI: 10.1128/mBio.01414-21.

References

Soontharapirakkul K, Promden W, Yamada N, Kageyama H, Incharoensakdi A, Iwamoto-Kihara A . Halotolerant cyanobacterium Aphanothece halophytica contains an Na+-dependent F1F0-ATP synthase with a potential role in salt-stress tolerance. J Biol Chem. 2011; 286(12):10169-76. PMC: 3060469. DOI: 10.1074/jbc.M110.208892. View

Saitou N, Nei M . The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4(4):406-25. DOI: 10.1093/oxfordjournals.molbev.a040454. View

Mazhab-Jafari M, Rubinstein J . Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases. Sci Adv. 2016; 2(7):e1600725. PMC: 4985227. DOI: 10.1126/sciadv.1600725. View

Mulkidjanian A, Makarova K, Galperin M, Koonin E . Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nat Rev Microbiol. 2007; 5(11):892-9. DOI: 10.1038/nrmicro1767. View

Klimchuk O, Konovalov K, Perekhvatov V, Skulachev K, Dibrova D, Mulkidjanian A . COGNAT: a web server for comparative analysis of genomic neighborhoods. Biol Direct. 2017; 12(1):26. PMC: 5700660. DOI: 10.1186/s13062-017-0196-z. View

Edgar R . MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004; 5:113. PMC: 517706. DOI: 10.1186/1471-2105-5-113. View

Imada K, Minamino T, Uchida Y, Kinoshita M, Namba K . Insight into the flagella type III export revealed by the complex structure of the type III ATPase and its regulator. Proc Natl Acad Sci U S A. 2016; 113(13):3633-8. PMC: 4822572. DOI: 10.1073/pnas.1524025113. View

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S . MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28(10):2731-9. PMC: 3203626. DOI: 10.1093/molbev/msr121. View

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

10.

Jones D, Taylor W, Thornton J . The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992; 8(3):275-82. DOI: 10.1093/bioinformatics/8.3.275. View

11.

Marcotte E, Pellegrini M, Ng H, Rice D, Yeates T, Eisenberg D . Detecting protein function and protein-protein interactions from genome sequences. Science. 1999; 285(5428):751-3. DOI: 10.1126/science.285.5428.751. View

12.

Dimroth P . Primary sodium ion translocating enzymes. Biochim Biophys Acta. 1997; 1318(1-2):11-51. DOI: 10.1016/s0005-2728(96)00127-2. View

13.

Koonin E . Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol. 2004; 1(2):127-36. DOI: 10.1038/nrmicro751. View

14.

BOYER P . The ATP synthase--a splendid molecular machine. Annu Rev Biochem. 1997; 66:717-49. DOI: 10.1146/annurev.biochem.66.1.717. View

15.

Kristensen D, Kannan L, Coleman M, Wolf Y, Sorokin A, Koonin E . A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics. 2010; 26(12):1481-7. PMC: 2881409. DOI: 10.1093/bioinformatics/btq229. View

16.

Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki C, Lu S . CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2016; 45(D1):D200-D203. PMC: 5210587. DOI: 10.1093/nar/gkw1129. View

17.

Dibrova D, Galperin M, Koonin E, Mulkidjanian A . Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics. Biochemistry (Mosc). 2015; 80(5):495-516. PMC: 5898217. DOI: 10.1134/S0006297915050016. View

18.

Mulkidjanian A, Dibrov P, Galperin M . The past and present of sodium energetics: may the sodium-motive force be with you. Biochim Biophys Acta. 2008; 1777(7-8):985-92. PMC: 2695506. DOI: 10.1016/j.bbabio.2008.04.028. View

19.

Finn R, Clements J, Eddy S . HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011; 39(Web Server issue):W29-37. PMC: 3125773. DOI: 10.1093/nar/gkr367. View

20.

Walker J . The ATP synthase: the understood, the uncertain and the unknown. Biochem Soc Trans. 2013; 41(1):1-16. DOI: 10.1042/BST20110773. View