XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments

Abstract

). (2015) XoxFencoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environmental Microbiology, 17 (10). pp. 3937-3948. Permanent WRAP URL:http://wrap.warwick.ac.uk/67990 Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement:"This is the peer reviewed version of the following article: which has been published in final form at http://dx.doi.org/10.1111/1462-2920.12896 This article may be used for noncommercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving." A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. Abstract 22The xoxF gene, encoding a pyrroloquinoline quinone-dependent methanol dehydrogenase, is found in all 23 known proteobacterial methylotrophs. In several newly discovered methylotrophs, XoxF is the active methanol 24 dehydrogenase, catalysing the oxidation of methanol to formaldehyde. Apart from that, its potential role in 25 methylotrophy and carbon cycling is unknown. So far, the diversity of xoxF in the environment has received 26 little attention. We designed PCR primer sets targeting clades of the xoxF gene, and used 454 pyrosequencing 27 of PCR amplicons obtained from DNA of four coastal marine environments for a unique assessment of the 28 diversity of xoxF in these habitats. Phylogenetic analysis of the data obtained revealed a high diversity of xoxF 29 genes from two of the investigated clades, and substantial differences in sequence composition between 30 environments. Sequences were classified as being related to a wide range of both methylotrophs and non-31 methylotrophs from Alpha-, Beta-and Gammaproteobacteria. The most prominent sequences detected were 32 related to the family Rhodobacteraceae, the genus Methylotenera and the OM43 clade of Methylophilales, 33 and are thus related to organisms that employ XoxF for methanol oxidation. Furthermore, our analyses 34 revealed a high degree of so far undescribed sequences, suggesting a high number of unknown species in 35 these habitats. 36

Quantitative Transcriptomics Reveals the Growth- and Nutrient-Dependent Response of a Streamlined Marine Methylotroph to Methanol and Naturally Occurring Dissolved Organic Matter

“…The initial step in C1 metabolism is methanol oxidation to formaldehyde via an xoxF -type methanol dehydrogenase (32, 33), and in our experiments, xoxF was often the most highly transcribed gene, with tens to hundreds of transcripts cell −1 (Fig. 5, box 1A).…”

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

“…The MDH proteins represented in the proteome were aligned with sequences from the literature (Taubert et al, 2015) and a tree was built, resulting in the clustering of the proteins by phylum. The Rokubacteria XoxF sequences formed a distinct branch in the MDH protein tree (XoxF and MxaF families) and the Gemmatimonadetes sequences formed a new clade with the XoxF sequences from various Proteobacteria (Taubert et al, 2015) (Fig. 3) The Gemmatimonadetes PQQ-MDH proteins were generally more abundant than those from Rokubacteria (as shown in the heat map on the right side of Fig.…”

Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440

“…Phylogenetic analysis of available sequence information suggests that lanthanide dependency is an ancestral feature of PQQ-ADHs and that these enzymes are more abundant than their Ca 2+ -dependent counterparts (15, 34). In addition, a very recent publication described the first lanthanide-dependent ethanol dehydrogenase in Methylobacterium extorquens AM1 (16).…”