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.
Highlights
Bacteria of the family Methylophilaceae are ubiquitous in natural environments, with the exception of extreme environments, and are found in fresh and saline waters, soils, air, industrial waste-water treatment reactors etc., pointing to the environmental importance of this group (Chistoserdova, 2011a)
Expression of xoxF genes suggests different regulation and different roles for multiple homologs We have previously noted that multiple homologs of xoxF genes were present in the genomes of the three organisms, and more recently we have reported on the phenotypes of xoxF mutants in M. mobilis JLW8 that suggested these genes must encode enzymes involved in methanol oxidation, even though methanol dehydrogenase activity could not be measured in this organism (Mustakhimov et al, 2013)
We found that the fae subtype that has been previously determined as a novel subtype in M. mobilis based on phylogenetic analysis (Kalyuzhnaya et al, 2008) was overexpressed in sediment samples in both M. mobilis JLW8 and M. versatilis 301, while this type was not encoded by M. glucosotrophus SIP3-4 (Fig. 4B)
Summary
Bacteria of the family Methylophilaceae are ubiquitous in natural environments, with the exception of extreme environments, and are found in fresh and saline waters, soils, air, industrial waste-water treatment reactors etc., pointing to the environmental importance of this group (Chistoserdova, 2011a). Some Methylophilaceae are very easy to cultivate, and these (mostly Methylophilus and Methylobacillus species) have served for decades as models for studying the biology of methylotrophs utilizing the ribulose monophosphate pathway (RuMP) for formaldehyde assimilation (Anthony, 1982) Based on these studies, Methylophilaceae have been assumed to be fast growers tolerating high concentrations of C1 substrates (i.e., substrates not containing carbon-carbon bonds), typically methanol and methylamine, resulting in high biomass yields (Baev et al, 1992). Abundant unclassified marine Methylophilaceae represented by strain HTCC2181 demonstrate extremely slow growth and are inhibited by millimolar concentrations of C1 substrates (Halsey, Carter & Giovannoni, 2012) The genomes of these organisms encode neither MDH nor MADH (Giovannoni et al, 2008; Huggett, Hayakawa & Rappe, 2012).
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
