title: Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation.
abstract: We carried out whole transcriptome analysis of three species of Methylophilaceae, Methylotenera mobilis, Methylotenera versatilis and Methylovorus glucosotrophus, in order to determine which metabolic pathways are actively transcribed in cultures grown in laboratory on C1 substrates and how metabolism changes under semi-in situ conditions. Comparative analyses of the transcriptomes were used to probe the metabolic strategies utilized by each of the organisms in the environment. Our analysis of transcript abundance data focused on changes in expression of methylotrophy metabolic modules, as well as on identifying any functional modules with pronounced response to in situ conditions compared to a limited set of laboratory conditions, highlighting their potential role in environmental adaptation. We demonstrate that transcriptional responses to environmental conditions involved both methylotrophy and non-methylotrophy metabolic modules as well as modules responsible for functions not directly connected to central metabolism. Our results further highlight the importance of XoxF enzymes that were previously demonstrated to be highly expressed in situ and proposed to be involved in metabolism of methanol by Methylophilaceae. At the same time, it appears that different species employ different homologous Xox systems as major metabolic modules. This study also reinforces prior observations of the apparent importance of the methylcitric acid cycle in the Methylotenera species and its role in environmental adaptation. High transcription from the respective gene clusters and pronounced response to in situ conditions, along with the reverse expression pattern for the ribulose monophosphate pathway that is the major pathway for carbon assimilation in laboratory conditions suggest that a switch in central metabolism of Methylotenera takes place in response to in situ conditions. The nature of the metabolite(s) processed via this pathway still remains unknown. Of the functions not related to central metabolism, flagellum and fimbria synthesis functions appeared to be of significance for environmental adaptation, based on their high abundance and differential expression. Our data demonstrate that, besides shared strategies, the organisms employed in this study also utilize strategies unique to each species, suggesting that the genomic divergence plays a role in environmental adaptation.
authors.affiliation: Department of Chemical Engineering, University of Washington , Seattle, WA , USA.
authors.forename: Alexey
authors.initials: A
authors.lastname: Vorobev
authors.forename: David A C
authors.initials: DA
authors.lastname: Beck
authors.forename: Marina G
authors.initials: MG
authors.lastname: Kalyuzhnaya
authors.forename: Mary E
authors.initials: ME
authors.lastname: Lidstrom
authors.forename: Ludmila
authors.initials: L
authors.lastname: Chistoserdova
keywords: Lake sediment; Methylophilaceae; Methylotenera; Methylotrophy; Methylovorus; Transcriptomics
references.citation: Microb Ecol. 2004 Nov;48(4):463-72
references.pmid: 15696380
references.citation: Environ Microbiol. 2011 Oct;13(10):2603-22
references.pmid: 21443740
references.citation: J Bacteriol. 2010 Oct;192(19):4859-67
references.pmid: 20639322
references.citation: Microbiology (Reading). 1997 Mar;143 ( Pt 3):793-801
references.pmid: 9084163
references.citation: Biotechnol Bioeng. 1992 Mar 15;39(6):688-95
references.pmid: 18600999
references.citation: Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):903-906
references.pmid: 15774683
references.citation: Mol Microbiol. 2010 Jan;75(2):426-39
references.pmid: 19943898
references.citation: Microbiol Mol Biol Rev. 2013 Mar;77(1):1-52
references.pmid: 23471616
references.citation: Environ Microbiol Rep. 2009 Oct;1(5):385-92
references.pmid: 23765891
references.citation: OMICS. 2007 Winter;11(4):325-40
references.pmid: 18092906
references.citation: ISME J. 2010 Mar;4(3):388-98
references.pmid: 19924155
references.citation: Nat Biotechnol. 2008 Sep;26(9):1029-34
references.pmid: 18711340
references.citation: J Bacteriol. 2011 Aug;193(15):3757-64
references.pmid: 21622745
references.citation: Res Microbiol. 2013 Jul-Aug;164(6):545-55
references.pmid: 23542426
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: J Bacteriol. 2013 May;195(10):2207-11
references.pmid: 23475964
references.citation: Environ Microbiol. 2012 Mar;14(3):630-40
references.pmid: 21981742
references.citation: Antonie Van Leeuwenhoek. 1991 Aug;60(2):101-7
references.pmid: 1804027
references.citation: Environ Microbiol. 2008 Jul;10(7):1771-82
references.pmid: 18393994
references.citation: Philos Trans R Soc Lond B Biol Sci. 2012 Apr 19;367(1592):1073-87
references.pmid: 22411979
references.citation: Appl Environ Microbiol. 2011 Jul;77(14):4705-11
references.pmid: 21622781
references.citation: PeerJ. 2013 Feb 19;1:e23
references.pmid: 23638358
references.citation: J Bacteriol. 2011 Sep;193(18):4758-65
references.pmid: 21764938
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Microbiol Mol Biol Rev. 2012 Dec;76(4):740-72
references.pmid: 23204365
references.citation: Int J Syst Evol Microbiol. 2006 Dec;56(Pt 12):2819-2823
references.pmid: 17158982
references.citation: J Bacteriol. 2000 Dec;182(23):6645-50
references.pmid: 11073907
references.citation: Int J Syst Evol Microbiol. 2012 Jan;62(Pt 1):106-111
references.pmid: 21335496
references.citation: Stand Genomic Sci. 2012 Mar 19;6(1):11-20
references.pmid: 22675594
references.citation: J Bacteriol. 1994 Jul;176(13):4052-65
references.pmid: 8021187