Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss.

Autor: Pawlowski K; Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden., Wibberg D; Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany., Mehrabi S; Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden.; Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden., Obaid NB; Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden., Patyi A; Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden., Berckx F; Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden.; Department of Crop Production Ecology, Swedish University of Agricultural Sciences, 75651 Uppsala, Sweden., Nguyen H; Department of Plant Physiology, UPSC, Umeå University, 90187 Umeå, Sweden., Hagen M; Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden., Lundin D; Department of Biology and Environmental Science, Linnaeus University, 39182 Kalmar, Sweden., Brachmann A; Biocenter of the LMU Munich, Genetics Section, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany., Blom J; Bioinformatics and Systems Biology, Justus-Liebig Universität Giessen, 35392 Giessen, Germany., Herrera-Belaroussi A; Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France., Abrouk D; Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France., Pujic P; Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France., Hahlin AS; Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden., Kalinowski J; Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany., Normand P; Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France., Sellstedt A; Department of Plant Physiology, UPSC, Umeå University, 90187 Umeå, Sweden.
Jazyk: angličtina
Zdroj: FEMS microbiology ecology [FEMS Microbiol Ecol] 2024 Nov 23; Vol. 100 (12).
DOI: 10.1093/femsec/fiae147
Abstrakt: Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup-, while only one Hup-  Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a, and 3b according to Søndergaard, Pedersen, and Greening (HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016;6:34212. https://doi.org/10.1038/srep34212.); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h, and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1 h and group 3b are not.
(© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)
Databáze: MEDLINE
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