Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen

• Published in: The ISME Journal 2018-05, Vol.12 (5), p.1225-1236
• Main Authors: Adam, Nicole, Perner, Mirjam
• Format: Article
• Language: English
• Subjects: 631/158/2452; 631/1647; 631/208/212/2142; 704/158/2445; Bacteria - enzymology; Bacteria - genetics; Biomedical and Life Sciences; Cell culture; Deep sea; Ecology; Enzymes; Evolutionary Biology; Hydrogen; Hydrogen - metabolism; Hydrogenase; Hydrogenase - genetics; Hydrothermal plumes; Hydrothermal Vents - microbiology; Inserts; Life Sciences; Markov chains; Membrane proteins; Metabolism; Metagenome; Metagenomics; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microorganisms; Molecular chains; Oxidation; Protons
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/s41396-017-0040-6

Hydrogen is one of the most common elements on Earth. The enzymes converting molecular hydrogen into protons and electrons are the hydrogenases. Hydrogenases are ubiquitously distributed in all three domains of life where they play a central role in cell metabolism. So far, the recovery of hydrogenases has been restricted to culture-dependent and sequence-based approaches. We have recently developed the only activity-based screen for seeking H 2 -uptake enzymes from metagenomes without having to rely on enrichment and isolation of hydrogen-oxidizing microorganisms or prior metagenomic sequencing. When screening 14,400 fosmid clones from three hydrothermal vent metagenomes using this solely activity-based approach, four clones with H 2 -uptake activity were identified with specific activities of up to 258 ± 19 nmol H 2 /min/mg protein of partially purified membrane fractions. The respective metagenomic fragments exhibited mostly very low or no similarities to sequences in the public databases. A search with hidden Markov models for different hydrogenase groups showed no hits for three of the four metagenomic inserts, indicating that they do not encode for classical hydrogenases. Our activity-based screen serves as a powerful tool for the discovery of (novel) hydrogenases which would not have been identified by the currently available techniques. This screen can be ideally combined with culture- and sequence-based approaches to investigate the tremendous hydrogen-converting potential in the environment.