Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation.
Bacillus subtilis
genome mining
genomic phylostratigraphy
sporulation
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
01 06 2020
01 06 2020
Historique:
pubmed:
16
2
2020
medline:
2
4
2021
entrez:
16
2
2020
Statut:
ppublish
Résumé
Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.
Identifiants
pubmed: 32061128
pii: 5736554
doi: 10.1093/molbev/msaa035
pmc: PMC7426031
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1667-1678Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
PLoS Comput Biol. 2013;9(8):e1003118
pubmed: 23950696
J Mol Biol. 2003 Apr 11;327(5):945-72
pubmed: 12662922
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Microbiol Mol Biol Rev. 2004 Jun;68(2):234-62
pubmed: 15187183
Trends Genet. 2007 Nov;23(11):533-9
pubmed: 18029048
Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):6406-6411
pubmed: 28484005
Mol Microbiol. 2014 Aug;93(4):587-98
pubmed: 24988880
Nucleic Acids Res. 2011 Jan;39(2):414-28
pubmed: 20817675
Appl Environ Microbiol. 2004 Nov;70(11):6809-15
pubmed: 15528548
Mol Cell Proteomics. 2014 Aug;13(8):1965-78
pubmed: 24390483
Nucleic Acids Res. 2014 Jan;42(Database issue):D685-91
pubmed: 24170806
Trends Genet. 2018 Jan;34(1):11-20
pubmed: 29061469
Appl Environ Microbiol. 2011 Dec;77(23):8249-58
pubmed: 21965392
Gene. 1999 Feb 4;227(1):101-10
pubmed: 9931458
Mol Syst Biol. 2015 Nov 17;11(11):839
pubmed: 26577401
Nature. 2010 Dec 9;468(7325):815-8
pubmed: 21150997
Cell Rep. 2016 Oct 11;17(3):917-928
pubmed: 27732864
J Bacteriol. 2013 Jan;195(2):253-60
pubmed: 23123912
Sci Rep. 2018 Nov 22;8(1):17246
pubmed: 30467398
Front Zool. 2013 Apr 12;10(1):18
pubmed: 23587066
Nucleic Acids Res. 2018 Jan 4;46(D1):D743-D748
pubmed: 29788229
Nat Rev Microbiol. 2013 Jan;11(1):33-44
pubmed: 23202530
Cell. 2013 Oct 24;155(3):647-58
pubmed: 24243021
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nat Protoc. 2010 Apr;5(4):725-38
pubmed: 20360767
PLoS Genet. 2014 Oct 09;10(10):e1004636
pubmed: 25299644
PLoS Biol. 2016 Jan 06;14(1):e1002341
pubmed: 26735940
J Mol Biol. 1998 Nov 13;283(5):907-12
pubmed: 9799632
J Bacteriol. 1994 Apr;176(7):2003-12
pubmed: 8144469
Microbiology. 2005 Feb;151(Pt 2):399-420
pubmed: 15699190
Microbiology. 2003 Oct;149(Pt 10):3011-3021
pubmed: 14523132
J Biol Eng. 2013 Dec 02;7(1):29
pubmed: 24295448
Proteomics. 2011 Aug;11(15):2981-91
pubmed: 21630458
J Bacteriol. 1996 Jun;178(12):3486-95
pubmed: 8655545
Microbiol Mol Biol Rev. 1999 Mar;63(1):1-20
pubmed: 10066829
Nat Genet. 2002 Jul;31(3):255-65
pubmed: 12089522
Trends Genet. 2013 Nov;29(11):659-68
pubmed: 23915718
Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21027-34
pubmed: 19995980
Mol Microbiol. 2013 Jun;88(5):921-35
pubmed: 23634894
Science. 2012 Mar 2;335(6072):1103-6
pubmed: 22383849
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
J Bacteriol. 1971 Mar;105(3):1110-8
pubmed: 4994032