Metagenomic sequencing unravels gene fragments with phylogenetic signatures of O2-tolerant NiFe membrane-bound hydrogenases in lacustrine sediment

Couto, J. M., Ijaz, U. Z. , Phoenix, V. R. , Schirmer, M. and Sloan, W. T. (2015) Metagenomic sequencing unravels gene fragments with phylogenetic signatures of O2-tolerant NiFe membrane-bound hydrogenases in lacustrine sediment. Current Microbiology, 71(2), pp. 296-302. (doi:10.1007/s00284-015-0846-2) (PMID:26044993) (PMCID:PMC4486115)

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Abstract

Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Couto, Dr Jillian and Phoenix, Dr Vernon and Sloan, Professor William and Ijaz, Dr Umer Zeeshan
Authors: Couto, J. M., Ijaz, U. Z., Phoenix, V. R., Schirmer, M., and Sloan, W. T.
College/School:College of Science and Engineering > School of Engineering > Infrastructure and Environment
College of Science and Engineering > School of Geographical and Earth Sciences
Journal Name:Current Microbiology
Publisher:Springer US
ISSN:0343-8651
ISSN (Online):1432-0991
Copyright Holders:Copyright © 2015 The Authors
First Published:First published in Current Microbiology 71(2):296-302
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
402264The Supergen Biological Fuel Cells ConsortiumWilliam SloanEngineering & Physical Sciences Research Council (EPSRC)EP/H019480/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR
642321Sustainable and resilient water systems for small communities.William SloanEngineering & Physical Sciences Research Council (EPSRC)EP/K038885/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR
652771Understanding microbial community through in situ environmental 'omic data synthesisUmer IjazNatural Environment Research Council (NERC)NE/L011956/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR