In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle

Frontiers in Microbiology
Xian ZhangXueduan Liu

Abstract

The coinage "pan-genome" was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species' basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species' core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, an...Continue Reading

References

Sep 1, 1990·Applied and Environmental Microbiology·E DrobnerK O Stetter
Apr 1, 1993·FEMS Microbiology Reviews·L F Wu, M A Mandrand
Jan 1, 1996·Annual Review of Microbiology·S Silver, L T Phung
Jan 16, 1997·Biochimica Et Biophysica Acta·S P AlbrachtP de Jong
Nov 5, 1997·Advances in Microbial Physiology·J T Lin, V Stewart
Aug 29, 2001·FEMS Microbiology Reviews·P M VignaisJ Meyer
Oct 5, 2001·Trends in Genetics : TIG·A MiraN A Moran
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Nov 1, 1951·Journal of Bacteriology·K L TEMPLE, A R COLMER
Jun 1, 2004·Journal of Bioenergetics and Biomembranes·Reiner Hedderich
Aug 13, 2004·Environmental Microbiology·Hanno TeelingFrank Oliver Glöckner
Dec 15, 2004·Proceedings of the National Academy of Sciences of the United States of America·G Dean PriceLoraine Tucker
Feb 8, 2005·Genome Biology·Alexis DufresneFrédéric Partensky
Sep 16, 2005·Nature·Kevin R Arrigo
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hervé TettelinClaire M Fraser
Sep 28, 2005·Current Opinion in Genetics & Development·Duccio MediniRino Rappuoli
Jul 1, 1991·Applied and Environmental Microbiology·J T PronkJ G Kuenen
Dec 31, 2005·Nucleic Acids Research·P SiguierM Chandler
Jan 16, 2007·International Journal of Systematic and Evolutionary Microbiology·Johan GorisJames M Tiedje
Jan 16, 2007·Environmental Microbiology·Víctor ParroElena González-Toril
May 29, 2007·Nucleic Acids Research·Yuki MoriyaMinoru Kanehisa
Oct 19, 2007·Nature·Mark J Pallen, Brendan W Wren
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Apr 2, 2008·Annals of the New York Academy of Sciences·Francis E Jenney, Michael W W Adams
Jun 5, 2008·BMC Microbiology·Mária TakácsKornél L Kovács
Dec 18, 2008·Current Opinion in Microbiology·Hervé TettelinDuccio Medini
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Oct 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Michael Richter, Ramon Rosselló-Móra
Sep 17, 2010·Nature·Yun Jae KimSung Gyun Kang
Feb 1, 2011·Bioinformatics·Mitchell J SullivanScott A Beatson
Feb 10, 2011·Standards in Genomic Sciences·Lars Snipen, David W Ussery
Jun 28, 2011·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Xiao-Yan YouShuang-Jiang Liu
Nov 5, 2011·Environmental Microbiology·Violaine Bonnefoy, David S Holmes
Dec 4, 2012·Nucleic Acids Research·Andrea FranceschiniLars J Jensen
Feb 26, 2013·Biotechnology and Bioengineering·Roberto A Bobadilla FazziniPilar Parada
Mar 1, 2013·Mobile Genetic Elements·Jodi A LindsayAlex J McCarthy

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Citations

Nov 24, 2019·Journal of Industrial Microbiology & Biotechnology·Shoushuai FengHailin Yang
Aug 30, 2019·Applied Microbiology and Biotechnology·Lei YangLei Yan
Jan 29, 2019·Frontiers in Microbiology·Rui WangLin-Xu Chen
Jan 12, 2020·The Science of the Total Environment·Xian ZhangMengshi Chen
Jul 22, 2021·Microbiology Spectrum·Krzysztof FiedorukIzabela Swiecicka

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Datasets Mentioned

BETA
LZYI00000000

Software Mentioned

NGS QC Toolkit
shapiro
BLAST
ClustalX
Pan
CVTree3
EasyFig
MUMmer
DNAMAN
Velvet

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