Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2017 Feb 16

PMID 28201618

Citations 4

Authors

Vandana Viswanathan

Anushree Narjala

Aravind Ravichandran

Suvratha Jayaprasad

Shivakumara Siddaramappa

Affiliations

Soon will be listed here.

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Phylogenetic insights into the diversity of species.

Siddaramappa S, Narjala A, Viswanathan V, Maliye C, Lakshminarayanan R Access Microbiol. 2020; 1(3):e000019.

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Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents.

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References

Zuo G, Hao B . CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. Genomics Proteomics Bioinformatics. 2015; 13(5):321-31. PMC: 4678791. DOI: 10.1016/j.gpb.2015.08.004. View

LWOFF A . Lysogeny. Bacteriol Rev. 1953; 17(4):269-337. PMC: 180777. DOI: 10.1128/br.17.4.269-337.1953. View

Singh P, Kim Y, Hoang V, Farh M, Yang D . Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng. Antonie Van Leeuwenhoek. 2015; 108(3):711-20. DOI: 10.1007/s10482-015-0527-y. View

Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H . Prophage genomics. Microbiol Mol Biol Rev. 2003; 67(2):238-76, table of contents. PMC: 156470. DOI: 10.1128/MMBR.67.2.238-276.2003. View

Shaw F, Elliott K, Kinch L, Fuell C, Phillips M, Michael A . Evolution and multifarious horizontal transfer of an alternative biosynthetic pathway for the alternative polyamine sym-homospermidine. J Biol Chem. 2010; 285(19):14711-23. PMC: 2863184. DOI: 10.1074/jbc.M110.107219. View

Zheng Q, Lin W, Liu Y, Chen C, Jiao N . A Comparison of 14 Erythrobacter Genomes Provides Insights into the Genomic Divergence and Scattered Distribution of Phototrophs. Front Microbiol. 2016; 7:984. PMC: 4919336. DOI: 10.3389/fmicb.2016.00984. View

El Hamel C, Chevalier S, De E, Orange N, Molle G . Isolation and characterisation of the major outer membrane protein of Erwinia carotovora. Biochim Biophys Acta. 2001; 1515(1):12-22. DOI: 10.1016/s0005-2736(01)00387-x. View

Nikaido H, Vaara M . Molecular basis of bacterial outer membrane permeability. Microbiol Rev. 1985; 49(1):1-32. PMC: 373015. DOI: 10.1128/mr.49.1.1-32.1985. View

Kosako Y, Yabuuchi E, Naka T, Fujiwara N, Kobayashi K . Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and.... Microbiol Immunol. 2000; 44(7):563-75. DOI: 10.1111/j.1348-0421.2000.tb02535.x. View

10.

Arndt D, Grant J, Marcu A, Sajed T, Pon A, Liang Y . PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016; 44(W1):W16-21. PMC: 4987931. DOI: 10.1093/nar/gkw387. View

11.

Singh A, Lal R . Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil. Int J Syst Evol Microbiol. 2009; 59(Pt 1):162-6. DOI: 10.1099/ijs.0.65712-0. View

12.

Bobay L, Touchon M, Rocha E . Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci U S A. 2014; 111(33):12127-32. PMC: 4143005. DOI: 10.1073/pnas.1405336111. View

13.

Bobay L, Rocha E, Touchon M . The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol. 2012; 30(4):737-51. PMC: 3603311. DOI: 10.1093/molbev/mss279. View

14.

Aylward F, McDonald B, Adams S, Valenzuela A, Schmidt R, Goodwin L . Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol. 2013; 79(12):3724-33. PMC: 3675938. DOI: 10.1128/AEM.00518-13. View

15.

Garcia-Romero I, Perez-Pulido A, Gonzalez-Flores Y, Reyes-Ramirez F, Santero E, Floriano B . Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA. BMC Genomics. 2016; 17:93. PMC: 4741004. DOI: 10.1186/s12864-016-2411-1. View

16.

Zheng Q, Zhang R, Xu Y, White 3rd R, Wang Y, Luo T . A marine inducible prophage vB_CibM-P1 isolated from the aerobic anoxygenic phototrophic bacterium Citromicrobium bathyomarinum JL354. Sci Rep. 2014; 4:7118. PMC: 4236739. DOI: 10.1038/srep07118. View

17.

TABOR C, Tabor H . Polyamines in microorganisms. Microbiol Rev. 1985; 49(1):81-99. PMC: 373019. DOI: 10.1128/mr.49.1.81-99.1985. View

18.

Woese C . Bacterial evolution. Microbiol Rev. 1987; 51(2):221-71. PMC: 373105. DOI: 10.1128/mr.51.2.221-271.1987. View

19.

Takeuchi M, Sawada H, Oyaizu H, Yokota A . Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria. Int J Syst Bacteriol. 1994; 44(2):308-14. DOI: 10.1099/00207713-44-2-308. View

20.

Tamm L, Hong H, Liang B . Folding and assembly of beta-barrel membrane proteins. Biochim Biophys Acta. 2004; 1666(1-2):250-63. DOI: 10.1016/j.bbamem.2004.06.011. View