Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss. Pawlowski, K., Wibberg, D., Mehrabi, S., Obaid, N. B., Patyi, A., Berckx, F., Nguyen, H., Hagen, M., Lundin, D., Brachmann, A., Blom, J., Herrera-Belaroussi, A., Abrouk, D., Pujic, P., Hahlin, A., Kalinowski, J., Normand, P., & Sellstedt, A. FEMS Microbiology Ecology, October, 2024. ![Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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 et al. (2016); 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 1h and group 3b are not.
@article{pawlowski_frankia_2024,
title = {Frankia [{NiFe}] uptake hydrogenases and genome reduction: different lineages of loss},
issn = {0168-6496},
shorttitle = {Frankia [{NiFe}] uptake hydrogenases and genome reduction},
url = {https://doi.org/10.1093/femsec/fiae147},
doi = {10.1093/femsec/fiae147},
abstract = {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 et al. (2016); 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 1h and group 3b are not.},
urldate = {2024-11-01},
journal = {FEMS Microbiology Ecology},
author = {Pawlowski, Katharina and Wibberg, Daniel and Mehrabi, Sara and Obaid, Nadia Binte and Patyi, András and Berckx, Fede and Nguyen, Han and Hagen, Michelle and Lundin, Daniel and Brachmann, Andreas and Blom, Jochen and Herrera-Belaroussi, Aude and Abrouk, Danis and Pujic, Petar and Hahlin, Ann-Sofi and Kalinowski, Jörn and Normand, Philippe and Sellstedt, Anita},
month = oct,
year = {2024},
pages = {fiae147},
}
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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 et al. (2016); 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 1h and group 3b are not.","urldate":"2024-11-01","journal":"FEMS Microbiology Ecology","author":[{"propositions":[],"lastnames":["Pawlowski"],"firstnames":["Katharina"],"suffixes":[]},{"propositions":[],"lastnames":["Wibberg"],"firstnames":["Daniel"],"suffixes":[]},{"propositions":[],"lastnames":["Mehrabi"],"firstnames":["Sara"],"suffixes":[]},{"propositions":[],"lastnames":["Obaid"],"firstnames":["Nadia","Binte"],"suffixes":[]},{"propositions":[],"lastnames":["Patyi"],"firstnames":["András"],"suffixes":[]},{"propositions":[],"lastnames":["Berckx"],"firstnames":["Fede"],"suffixes":[]},{"propositions":[],"lastnames":["Nguyen"],"firstnames":["Han"],"suffixes":[]},{"propositions":[],"lastnames":["Hagen"],"firstnames":["Michelle"],"suffixes":[]},{"propositions":[],"lastnames":["Lundin"],"firstnames":["Daniel"],"suffixes":[]},{"propositions":[],"lastnames":["Brachmann"],"firstnames":["Andreas"],"suffixes":[]},{"propositions":[],"lastnames":["Blom"],"firstnames":["Jochen"],"suffixes":[]},{"propositions":[],"lastnames":["Herrera-Belaroussi"],"firstnames":["Aude"],"suffixes":[]},{"propositions":[],"lastnames":["Abrouk"],"firstnames":["Danis"],"suffixes":[]},{"propositions":[],"lastnames":["Pujic"],"firstnames":["Petar"],"suffixes":[]},{"propositions":[],"lastnames":["Hahlin"],"firstnames":["Ann-Sofi"],"suffixes":[]},{"propositions":[],"lastnames":["Kalinowski"],"firstnames":["Jörn"],"suffixes":[]},{"propositions":[],"lastnames":["Normand"],"firstnames":["Philippe"],"suffixes":[]},{"propositions":[],"lastnames":["Sellstedt"],"firstnames":["Anita"],"suffixes":[]}],"month":"October","year":"2024","pages":"fiae147","bibtex":"@article{pawlowski_frankia_2024,\n\ttitle = {Frankia [{NiFe}] uptake hydrogenases and genome reduction: different lineages of loss},\n\tissn = {0168-6496},\n\tshorttitle = {Frankia [{NiFe}] uptake hydrogenases and genome reduction},\n\turl = {https://doi.org/10.1093/femsec/fiae147},\n\tdoi = {10.1093/femsec/fiae147},\n\tabstract = {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 et al. (2016); 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 1h and group 3b are not.},\n\turldate = {2024-11-01},\n\tjournal = {FEMS Microbiology Ecology},\n\tauthor = {Pawlowski, Katharina and Wibberg, Daniel and Mehrabi, Sara and Obaid, Nadia Binte and Patyi, András and Berckx, Fede and Nguyen, Han and Hagen, Michelle and Lundin, Daniel and Brachmann, Andreas and Blom, Jochen and Herrera-Belaroussi, Aude and Abrouk, Danis and Pujic, Petar and Hahlin, Ann-Sofi and Kalinowski, Jörn and Normand, Philippe and Sellstedt, Anita},\n\tmonth = oct,\n\tyear = {2024},\n\tpages = {fiae147},\n}\n\n\n\n\n\n\n\n\n\n\n\n","author_short":["Pawlowski, K.","Wibberg, D.","Mehrabi, S.","Obaid, N. 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