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The phylogeny of uptake hydrogenases in Frankia
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Microbial Ecology, UMR 5557, CNRS, University Lyon 1, Villeurbanne, France.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0002-0536-903X
2009 (English)In: International Microbiology, ISSN 1139-6709, E-ISSN 1618-1905, Vol. 12, no 1, 23-28 p.Article in journal (Refereed) Published
Abstract [en]

Uptake hydrogenase is an enzyme that is beneficial for nitrogen fixation in bacteria. Recent studies have shown that Frankia sp. has two sets of uptake hydrogenase genes, organized in synton 1 and synton 2. In the present study, phylogenetic analysis of the structural subunits of hydrogenase syntons 1 and 2 showed a distinct clustering pattern between the proteins of Frankia strains that were isolated from different host plants and non-Frankia organisms. The structural subunits of hydrogenase synton 1 of Frankia sp. CpI1, Frankia alni ACN14a, and F. alni AvCI1 were grouped together while those of Frankia spp. CcI3, KB5, UGL140104, and UGL011102 formed another group. The structural subunits of hydrogenase synton 2 of F. alni ACN14a and Frankia spp. CcI3 and BCU110501 grouped together, but those of Frankia spp. KB5 and CpI1, F. alni ArI3, and F. alniAvCI1 comprised a separate group. The structural subunits of hydrogenase syntons 1 and 2 of Frankia sp. EAN1pec were more closely related to those of non-Frankia bacteria, i.e., Streptomyces avermitilis and Anaeromyxobacter sp., respectively, than to those of other Frankia strains, suggesting the occurrence of lateral gene transfer between these organisms. In addition, the accessory Hyp proteins of hydrogenase syntons 1 and 2 of F. alni ACN14a and Frankia sp. CcI3 were shown to be phylogenetically more related to each other than to those of Frankia EAN1pec.

Place, publisher, year, edition, pages
2009. Vol. 12, no 1, 23-28 p.
Keyword [en]
Frankia cluster, lateral gene transfer, hydrogenase syntons
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:umu:diva-23628DOI: 10.2436/20.1501.01.78PubMedID: 19440980OAI: oai:DiVA.org:umu-23628DiVA: diva2:225505
Available from: 2009-06-29 Created: 2009-06-29 Last updated: 2017-12-13Bibliographically approved
In thesis
1. The Biodiversity of Hydrogenases in Frankia: Characterization, regulation and phylogeny
Open this publication in new window or tab >>The Biodiversity of Hydrogenases in Frankia: Characterization, regulation and phylogeny
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

All the eighteen Frankia strains isolated from ten different actinorhizal host plants showed uptake hydrogenase activity. The activity of this enzyme is further increased by addition of nickel. Nickel also enhanced the degree of hydrogenase transfer into the membranes of Frankia, indicating the role of this metal in the processing of this enzyme. The uptake hydrogenase of Frankia is most probably a Ni-Fe hydrogenase.

Genome characterization revealed the presence of two hydrogenase genes (syntons) in Frankia, which are distinctively separated in all the three available Frankia genomes. Both hydrogenase syntons are also commonly found in other Frankia strains. The structural, regulatory and accessory genes of both hydrogenase synton #1 and #2 are arranged closely together, but in a clearly contrasting organization. Hydrogenase synton #1 and #2 of Frankia are phylogenetically divergent and that hydrogenase synton #1 is probably ancestral among the actinobacteria. Hydrogenase synton #1 (or synton #2) of Frankia sp. CcI3 and F. alni ACN14a are similar in gene arrangement, content and orientation, while the syntons are both reduced and rearranged in Frankia sp. EANpec. The hydrogenases of Frankia sp. CcI3 and F. alni ACN14a are phylogenetically grouped together but never with the Frankia sp. EAN1pec, which is more closely related to the non-Frankia bacteria than Frankia itself. The tree topology is indicative of a probable gene transfer to or from Frankia that occurred before the emergence of Frankia. All of the available evidence points to hydrogenase gene duplication having occurred long before development of the three Frankia lineages. The uptake hydrogenase synton #1 of Frankia is more expressed under free-living conditions whereas hydrogenases synton #2 is mainly involved in symbiotic interactions. The uptake hydrogenase of Frankia can also be manipulated to play a larger role in increasing the efficiency of nitrogen fixation in the root nodules of the host plants, there by minimizing the need for environmentally unfriendly and costly fertilizers.

The hydrogen-evolving hydrogenase activity was recorded in only four Frankia strains: F. alni UGL011101, UGL140102, Frankia sp. CcI3 and R43. After addition of 15mM Nicl2, activity was also detected in F. alni UGL011103, Frankia sp. UGL020602, UGL020603 and 013105. Nickel also increased the activity of hydrogen-evolving hydrogenases in Frankia, indicating that Frankia may have different types of hydrogen-evolving hydrogenases, or that the hydrogen-evolving hydrogenases may at least be regulated differently in different Frankia strains. The fact that Frankia can produce hydrogen is reported only recently. The knowledge of the molecular biology of Frankia hydrogenase is, therefore, of a paramount importance to optimize the system in favor of hydrogen production. Frankia is an attractive candidate in search for an organism efficient in biological hydrogen production since it can produce a considerable amount of hydrogen.

Place, publisher, year, edition, pages
Umeå: Fysiologisk botanik, 2007. 63 p.
Keyword
Biodiversity, Frankia, immunoblotting, gene expression, uptake hydrogenase, hydrogen-evolving hydrogenase, nickel, phylogeny
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-1435 (URN)978-91-7264-444-1 (ISBN)
Public defence
2007-12-07, KB3A9, KBC, Umeå University, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2007-11-16 Created: 2007-11-16 Last updated: 2011-03-14Bibliographically approved

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