Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

Esposti, Mauro Degli; Cortez, Diego; Lozano, Luis; Rasmussen, Simon; Nielsen, Henrik Bjørn; Martı́nez-Romero, Esperanza

doi:10.1186/s13062-016-0136-3

Cited by 24 publications

(31 citation statements)

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“…It is assumed to be involved in syntrophic oxidation of propionate (Li et al, 2014) and contains a full set of genes coding for at least one "Fe-only hydrogenase" (Pelletier et al, 2008). This "Fe-only hydrogenase, " encoded by the hymABC structural and the hydEFG accessory genes, is in fact probably a [FeFe]-hydrogenase (Degli Esposti et al, 2016), which is frequently found in anaerobic prokaryotes. "Fe-only hydrogenase" was detected so far only in Archaea (Lubitz et al, 2014) and is intimately linked to methanogenesis.…”

Section: Discussionmentioning

confidence: 99%

Microbial Community Rearrangements in Power-to-Biomethane Reactors Employing Mesophilic Biogas Digestate

et al. 2019

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The biological conversion of hydrogen (H 2) and carbon dioxide (CO 2) to methane (CH 4), is accomplished by the hydrogenotrophic methanogens (HM). HMs are difficult to cultivate in pure culture, but they are readily available in the mixed culture of effluents from the anaerobic degradation of organic matter, i.e., the fermentation effluent of biogas plants. The rate-limiting step in the work of CH 4-forming microbial communities is the low solubility of H 2 in the aqueous environment. In our approach, the simple fed-batch fermentation technique was selected to supply the gaseous substrates for the microbial community at laboratory scale and mesophilic temperature. Periodically withdrawn samples were analyzed for process parameters and the microbial communities were studied using Terminal Restriction Fragment Length Polymorphism (T-RFLP) of the mcrA gene and Ion Torrent whole metagenome DNA sequencing. The metagenome data were evaluated by both read-based and genome-centric bioinformatics tools. The rearrangements in the mixed microbial communities, triggered by switching the operating conditions to biological power-to-biomethane (bio-P2M), have been established. The production rates were 6.30 mL CH 4 L −1 h −1 during the acclimation phase and 9.21 mL CH 4 L −1 h −1 by the fully adapted community, respectively. The diversity of the anaerobic microbiota decreased as the bio-P2M process progressed. Feeding the community with H 2 apparently promoted the abundance of several genera, in particular Candidatus Cloacimonas and Herbinix. The diversity of the Archaea community decreased considerably upon daily feeding with H 2 and CO 2. The predominant Archea genus was Methanobacterium in every reactor, Methanothrix persisted for the first 4 weeks, while the initially less abundant genus Methanoculleus gained advantage during the adaptation to the sustained bio-P2M process. The accumulation of acetate indicated a strong involvement of homoacetogenic bacteria.

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Section: Discussionmentioning

confidence: 99%

Microbial Community Rearrangements in Power-to-Biomethane Reactors Employing Mesophilic Biogas Digestate

et al. 2019

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“…In return, the endosymbiont may have consumed O 2 (as proposed previously 33 ) and provided the host with an intracellular pool of biological building blocks (for example, amino acids and co-factors that the host may not have been able to synthesize that were released passively or through endosymbiont death). On the basis of the absence of host-derived (that is, archaea-related) anaerobic 2-oxoacid catabolism genes (for example, ferredoxin-dependent 2-oxoacid oxidoreductase and NiFe hydrogenases) in eukaryotes 41,42 , the host presumably lost these during evolution towards the LECA. Notably, this loss might have consequently helped to simultaneously resolve catabolic redundancy (that is, 2-oxoacid catabolism in both host and symbiont) and O 2 sensitivity (that is, O 2 inactivates these enzymes 43,44 ).…”

Section: New Insights Into Eukaryogenesismentioning

confidence: 99%

Isolation of an archaeon at the prokaryote–eukaryote interface

Imachi

Nobu

Nakahara

et al. 2020

Nature

532

493

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Setting out to isolate uncultivated deep marine sediment microorganisms, we engineered and operated a methane-fed continuous-flow bioreactor system for more than 2,000 days to enrich such organisms from anaerobic marine methane-seep sediments 15 (Supplementary Note 1). We successfully enriched many phylogenetically diverse yetto-be cultured microorganisms, including Asgard archaea members (Loki-, Heimdall-and Odinarchaeota) 15. For further enrichment and isolation, samples of the bioreactor community were inoculated in glass tubes with simple substrates and basal medium. After approximately one year, we found faint cell turbidity in a culture containing casamino acids supplemented with four bacteria-suppressing antibiotics (Supplementary Note 2) that was incubated at 20 °C. Clone librarybased small subunit (SSU) rRNA gene analysis revealed a simple community that contained Halodesulfovibrio and a small population of Lokiarchaeota (Extended Data Table 1). In pursuit of this archaeon, which we designated strain MK-D1, we repeated subcultures when MK-D1 reached maximum cell densities as measured by quantitative PCR (qPCR). This approach gradually enriched the archaeon, which has an extremely slow growth rate and low cell yield (Fig. 1a). The culture consistently had a 30-60-day lag phase and required more

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“…None of the enzymes exclusive to anaerobic metabolism in eukaryotes has clear phylogenetic affinities to alphaproteobacterial homologs [94]. A recent report that claimed an alphaproteobacterial origin for eukaryotic [Fe]-hydrogenase [95] is invalidated by the failure to include relevant non-alphaproteobacterial homologs in the analysis (see [94] for a more comprehensive analysis). For several of these enzymes, including [Fe]-hydrogenase and ASCT, eukaryotic homologs group in phylogenetic trees into multiple distinct subfamilies, each of which is most closely related to enzymes from different bacterial taxa.…”

Section: Origins Of Proteins Involved In Anaerobic Metabolism and Mrosmentioning

confidence: 99%

The Origin and Diversification of Mitochondria

2017

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Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral organelle that originated from the integration of an endosymbiotic alphaproteobacterium into a host cell related to Asgard Archaea. The transition from endosymbiotic bacterium to permanent organelle entailed a massive number of evolutionary changes including the origins of hundreds of new genes and a protein import system, insertion of membrane transporters, integration of metabolism and reproduction, genome reduction, endosymbiotic gene transfer, lateral gene transfer and the retargeting of proteins. These changes occurred incrementally as the endosymbiont and the host became integrated. Although many insights into this transition have been gained, controversy persists regarding the nature of the original endosymbiont, its initial interactions with the host and the timing of its integration relative to the origin of other features of eukaryote cells. Since the establishment of the organelle, proteins have been gained, lost, transferred and retargeted as mitochondria have specialized into the spectrum of functional types seen across the eukaryotic tree of life.

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Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

Cited by 24 publications

References 50 publications

Microbial Community Rearrangements in Power-to-Biomethane Reactors Employing Mesophilic Biogas Digestate

Microbial Community Rearrangements in Power-to-Biomethane Reactors Employing Mesophilic Biogas Digestate

Isolation of an archaeon at the prokaryote–eukaryote interface

The Origin and Diversification of Mitochondria

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