Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T

Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, et al. (2017)
SCIENTIFIC REPORTS 7: 3682.

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Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum Y-T, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum Y-T having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by 'ancient' CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after -550 generations, the strain exhibited the mutation rate of >= 1.3 x 10(-8) single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G: C to A: T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum Y-T variants from geographically distant populations.
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SCIENTIFIC REPORTS
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3682
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Golyshina OV, Tran H, Reva ON, et al. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T. SCIENTIFIC REPORTS. 2017;7: 3682.
Golyshina, O. V., Tran, H., Reva, O. N., Lemak, S., Yakunin, A. F., Goesmann, A., Nechitaylo, T. Y., et al. (2017). Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T. SCIENTIFIC REPORTS, 7, 3682. doi:10.1038/s41598-017-03904-5
Golyshina, O. V., Tran, H., Reva, O. N., Lemak, S., Yakunin, A. F., Goesmann, A., Nechitaylo, T. Y., LaCono, V., Smedile, F., Slesarev, A., et al. (2017). Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T. SCIENTIFIC REPORTS 7:3682.
Golyshina, O.V., et al., 2017. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T. SCIENTIFIC REPORTS, 7: 3682.
O.V. Golyshina, et al., “Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T”, SCIENTIFIC REPORTS, vol. 7, 2017, : 3682.
Golyshina, O.V., Tran, H., Reva, O.N., Lemak, S., Yakunin, A.F., Goesmann, A., Nechitaylo, T.Y., LaCono, V., Smedile, F., Slesarev, A., Rojo, D., Barbas, C., Ferrer, M., Yakimov, M.M., Golyshin, P.N.: Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T. SCIENTIFIC REPORTS. 7, : 3682 (2017).
Golyshina, Olga V., Tran, Hai, Reva, Oleg N., Lemak, Sofia, Yakunin, Alexander F., Goesmann, Alexander, Nechitaylo, Taras Y., LaCono, Violetta, Smedile, Francesco, Slesarev, Alexei, Rojo, David, Barbas, Coral, Ferrer, Manuel, Yakimov, Michail M., and Golyshin, Peter N. “Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y-T”. SCIENTIFIC REPORTS 7 (2017): 3682.

2 Zitationen in Europe PMC

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Cuniculiplasmataceae, their ecogenomic and metabolic patterns, and interactions with 'ARMAN'.
Golyshina OV, Bargiela R, Golyshin PN., Extremophiles 23(1), 2019
PMID: 30499003
Co-culture of a Novel Fermentative Bacterium, Lucifera butyrica gen. nov. sp. nov., With the Sulfur Reducer Desulfurella amilsii for Enhanced Sulfidogenesis.
Sánchez-Andrea I, Florentino AP, Semerel J, Strepis N, Sousa DZ, Stams AJM., Front Microbiol 9(), 2018
PMID: 30631314

68 References

Daten bereitgestellt von Europe PubMed Central.

Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea.
Golyshina OV, Pivovarova TA, Karavaiko GI, Kondrateva TF, Moore ER, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM, Golyshin PN., Int. J. Syst. Evol. Microbiol. 50 Pt 3(), 2000
PMID: 10843038
Community structure and metabolism through reconstruction of microbial genomes from the environment.
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF., Nature 428(6978), 2004
PMID: 14961025
Proteogenomic approaches for the molecular characterization of natural microbial communities.
Banfield JF, Verberkmoes NC, Hettich RL, Thelen MP., OMICS 9(4), 2005
PMID: 16402891
The 'pH optimum anomaly' of intracellular enzymes of Ferroplasma acidiphilum.
Golyshina OV, Golyshin PN, Timmis KN, Ferrer M., Environ. Microbiol. 8(3), 2006
PMID: 16478448
The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated.
Ferrer M, Golyshina OV, Beloqui A, Golyshin PN, Timmis KN., Nature 445(7123), 2007
PMID: 17203061
A purple acidophilic di-ferric DNA ligase from Ferroplasma.
Ferrer M, Golyshina OV, Beloqui A, Bottger LH, Andreu JM, Polaina J, De Lacey AL, Trautwein AX, Timmis KN, Golyshin PN., Proc. Natl. Acad. Sci. U.S.A. 105(26), 2008
PMID: 18577594
Genome dynamics in a natural archaeal population.
Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF., Proc. Natl. Acad. Sci. U.S.A. 104(6), 2007
PMID: 17267615
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM., Int. J. Syst. Evol. Microbiol. 57(Pt 1), 2007
PMID: 17220447
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M., BMC Bioinformatics 14(), 2013
PMID: 23432962
GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'.
Menigaud S, Mallet L, Picord G, Churlaud C, Borrel A, Deschavanne P., Bioinformatics 28(9), 2012
PMID: 22426345

AUTHOR UNKNOWN, 0
Insertion sequence diversity in archaea.
Filee J, Siguier P, Chandler M., Microbiol. Mol. Biol. Rev. 71(1), 2007
PMID: 17347521
RecA family proteins in archaea: RadA and its cousins.
Haldenby S, White MF, Allers T., Biochem. Soc. Trans. 37(Pt 1), 2009
PMID: 19143611
Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
Tyson GW, Banfield JF., 2008
No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales.
Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV., ISME J 9(9), 2015
PMID: 25710183
Evolution and classification of the CRISPR-Cas systems.
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV., Nat. Rev. Microbiol. 9(6), 2011
PMID: 21552286
A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus.
Deng L, Garrett RA, Shah SA, Peng X, She Q., Mol. Microbiol. 87(5), 2013
PMID: 23320564
RNA-guided genetic silencing systems in bacteria and archaea.
Wiedenheft B, Sternberg SH, Doudna JA., Nature 482(7385), 2012
PMID: 22337052
Rate, molecular spectrum, and consequences of human mutation.
Lynch M., Proc. Natl. Acad. Sci. U.S.A. 107(3), 2010
PMID: 20080596
Drift-barrier hypothesis and mutation-rate evolution.
Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M., Proc. Natl. Acad. Sci. U.S.A. 109(45), 2012
PMID: 23077252
Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli.
Tompkins JD, Nelson JL, Hazel JC, Leugers SL, Stumpf JD, Foster PL., J. Bacteriol. 185(11), 2003
PMID: 12754247
The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum: A membrane-bound complex oxidizing ferrous iron.
Castelle CJ, Roger M, Bauzan M, Brugna M, Lignon S, Nimtz M, Golyshina OV, Giudici-Orticoni MT, Guiral M., Biochim. Biophys. Acta 1847(8), 2015
PMID: 25896560
Genome sequence of Picrophilus torridus and its implications for life around pH 0.
Futterer O, Angelov A, Liesegang H, Gottschalk G, Schleper C, Schepers B, Dock C, Antranikian G, Liebl W., Proc. Natl. Acad. Sci. U.S.A. 101(24), 2004
PMID: 15184674
Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments
Golyshina OV., 2016
Regulation of Gene Expression in Halobacterium salinarum: The arcrACB Gene Cluster and the TATA box-binding protein
Soppa J, Vatter P, zur A, Link T, Ruepp A., 1998
Evolution of arginine deiminase (ADI) pathway genes.
Zuniga M, Perez G, Gonzalez-Candelas F., Mol. Phylogenet. Evol. 25(3), 2002
PMID: 12450748
A bioinformatics classifier and database for heme-copper oxygen reductases.
Sousa FL, Alves RJ, Pereira-Leal JB, Teixeira M, Pereira MM., PLoS ONE 6(4), 2011
PMID: 21559461
One step beyond a ribosome: The ancient anaerobic core.
Sousa FL, Nelson-Sathi S, Martin WF., Biochim. Biophys. Acta 1857(8), 2016
PMID: 27150504
The origin of membrane bioenergetics.
Lane N, Martin WF., Cell 151(7), 2012
PMID: 23260134
Genome sequence of Halobacterium species NRC-1.
Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S., Proc. Natl. Acad. Sci. U.S.A. 97(22), 2000
PMID: 11016950
Hydrogenobacter thermophilus gen. nov., sp. nov., an extremely thermophilic, aerobic, hydrogen-oxidizing bacterium
Kawasumi T, Igarashi Y, Kodama T, Minoda Y., 1984
Carboxylation reaction catalyzed by 2-oxoglutarate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus.
Yamamoto M, Ikeda T, Arai H, Ishii M, Igarashi Y., Extremophiles 14(1), 2009
PMID: 19894084
Metabolism of methanogens.
Blaut M., Antonie Van Leeuwenhoek 66(1-3), 1994
PMID: 7747931
Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.
Baker-Austin C, Potrykus J, Wexler M, Bond PL, Dopson M., Extremophiles 14(6), 2010
PMID: 20835877

AUTHOR UNKNOWN, 0
Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea.
Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Goker M, Klenk HP, Bajic V, Stingl U., Sci Rep 6(), 2016
PMID: 26758088
[Phenotypic features of Ferroplasma acidiphilum strains Yt and Y-2].
Pivovarova TA, Kondrat'eva TF, Batrakov SG, Esipov SE, Sheichenko VI, Bykova SA, Lysenko AM, Karavaiko GI., Mikrobiologiia 71(6), 2002
PMID: 12526203
Major facilitator superfamily.
Pao SS, Paulsen IT, Saier MH Jr., Microbiol. Mol. Biol. Rev. 62(1), 1998
PMID: 9529885
The role of tricorn protease and its aminopeptidase-interacting factors in cellular protein degradation.
Tamura N, Lottspeich F, Baumeister W, Tamura T., Cell 95(5), 1998
PMID: 9845366
On the Origin of Heterotrophy.
Schonheit P, Buckel W, Martin WF., Trends Microbiol. 24(1), 2015
PMID: 26578093
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Ewing B, Hillier L, Wendl MC, Green P., Genome Res. 8(3), 1998
PMID: 9521921

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Finishing ‘Working Draft’ BAC projects by directed sequencing with ThermoFidelase and Fimers
Malykh A, Malykh O, Polushin N, Kozyavkin S, Slesarev A., 2004
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.
Schattner P, Brooks AN, Lowe TM., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980563
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
Grissa I, Vergnaud G, Pourcel C., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17537822
Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice.
Marco ML, Bongers RS, de Vos WM, Kleerebezem M., Appl. Environ. Microbiol. 73(1), 2006
PMID: 17071785

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