The “green” phylogenetic clade of Rieske/cytb complexes

Nitschke, Wolfgang; Lis, Robert van; Schoepp‐Cothenet, Barbara; Baymann, Frauke

doi:10.1007/s11120-010-9532-1

Cited by 35 publications

(45 citation statements)

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“…The Rieske/cytb complexes are energyconverting enzymes that operate between the initial electron donors and the terminal electron acceptors of respiratory chains. In halophiles, two distinct clusters of Rieske/cytb encoding genes have been described, (i) the Rieske/cytb complex cluster along with the NAR-encoding genes implied in the denitrifying chain (Martinez-Espinosa et al, 2007) and (ii) the Rieske/cytb complex cluster with a gene coding for an halocyanin followed by a cytochrome b (Nitschke et al, 2010). The implication of this second type of gene cluster in aerobic respiration seems the most likely function, where the halocyanin will work as an electron acceptor of the Rieske/ cytb complex and the donor to a cytochrome oxidase (Baymann et al, 2012).…”

Section: Inferred Metabolic and Ecological Featuresmentioning

confidence: 99%

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

et al. 2014

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We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.

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Section: Inferred Metabolic and Ecological Featuresmentioning

confidence: 99%

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

et al. 2014

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“…It has recently been found that this space in the b 6 f complex can largely be filled by a lipid and the bound chlorophyll a [25] (figure 3). The eight versus seven TMH problem in the cyt b polypeptide in energy-transducing membranes has previously been discussed in the evolutionary context of the residence of the split (four þ three) seven TMHs of b 6 f-like complexes in the 'green clade' [38]. In addition to the questions posed in [38] in the context of the finding that a lipid molecule in the b 6 f complex occupies much of the space filled by the eighth TMH in the bc 1 complex, one may ask: (i) which cyt bc complex appeared first in evolution, the respiratory or photosynthetic cyt bc complex?…”

Section: Discussionmentioning

confidence: 99%

Lipid functions in cytochrome bc complexes: an odd evolutionary transition in a membrane protein structure

Hasan

2012

Phil. Trans. R. Soc. B

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Lipid-binding sites and properties were compared in the hetero-oligomeric cytochrome (cyt) b 6 f and the yeast bc 1 complexes that function, respectively, in photosynthetic and respiratory electron transport. Seven lipid-binding sites in the monomeric unit of the dimeric cyanobacterial b 6 f complex overlap four sites in the Chlamydomonas reinhardtii algal b 6 f complex and four in the yeast bc 1 complex. The proposed lipid functions include: (i) interfacial-interhelix mediation between (a) the two 8-subunit monomers of the dimeric complex, (b) between the core domain (cyt b, subunit IV) and the six trans membrane helices of the peripheral domain (cyt f, iron-sulphur protein (ISP), and four small subunits in the boundary 'picket fence'); (ii) stabilization of the ISP domain-swapped transmembrane helix; (iii) neutralization of basic residues in the single helix of cyt f and of the ISP; (iv) a 'latch' to photosystem I provided by the b-carotene chain protruding through the 'picket fence'; (v) presence of a lipid and chlorophyll a chlorin ring in b 6 f in place of the eighth helix in the bc 1 cyt b polypeptide. The question is posed of the function of the lipid substitution in relation to the evolutionary change between the eight and seven helix structures of the cyt b polypeptide. On the basis of the known n-side activation of light harvesting complex II (LHCII) kinase by the p-side level of plastoquinol, one possibility is that the change was directed by the selective advantage of p-to n-side trans membrane signalling functions in b 6 f, with the lipid either mediating this function or substituting for the trans membrane helix of a signalling protein lost in crystallization.

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“…More recently, with expanded genome sampling, a grouping of the b-type cytochromes from cyanobacteria, chlorobi and heliobacteria was suggested, all of which share RCI-type photosystems (Nitschke et al, 2010).…”

Section: Schutz Et Al Reviewed the Evolution Of Cytochrome Bc Complexmentioning

confidence: 99%

“…Previous analyses (Schutz et al, 2000, Lebrun et al, 2006, Nitschke et al, 2010, Dibrova et al, 2013 have attempted to derive a complete phylogeny of cytochrome-b from a diverse set of prokaryotes, but they mostly focus on the comparison of cytochrome b 6 of the b 6 f complex of photosynthesis and the cytochrome bc complex of respiration. Also, in those analyses only some cytochromeb domain containing proteins were included while some other were excluded; this might skew the results, and thus the conclusions.…”

Section: Schutz Et Al Reviewed the Evolution Of Cytochrome Bc Complexmentioning

confidence: 99%

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Evolution of b-type cytochromes in prokaryotes

Koumandou

Κοσσίδα

2015

Preprint

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Abstract:Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b 6 f complex, ubiquinol and menaquinol reductases, formate dehydrogenase, Ni/Fehydrogenase, and succinate dehydrogenase). We use data from 272 species of fully sequenced bacteria and archaea, which represent the full diversity of prokaryotic lineages and multiple bioenergetic modes, to examine the distribution of these cytochromes across lineages, and ask the question of whether sequences from different species cluster by cytochrome-b family, by bioenergetic mode or by taxonomic group. Different cytochrome-b types are found in many lineages of the bacteria and archaea, and form distinct groups in phylogenetic analysis, which indicates an ancient origin for this complex, and diversification of different cytochrome-b types before the diversification of lineages. We find that species do not cluster based on bioenergetic mode. We also re-examine data from previous studies using this expanded sample of organisms spanning the full diversity of prokaryotic lineages. Concerning the b 6 f complex of photosynthetic organisms, our expanded phylogenies do not show significant bootstrap support for a "green clade" of cytochrome b 6 ; also, the split form of b 6 is not monophyletic, indicating that the split form arose independently multiple times. We also present data on the similarities between prokaryotic and eukaryotic cytochrome b561 sequences, in light of the recently reported structure of eukaryotic cytochrome b561.PeerJ PrePrints | https://doi.org/10.7287/peerj.preprints.1564v1 | CC-BY 4.0 Open Access |

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The “green” phylogenetic clade of Rieske/cytb complexes

Cited by 35 publications

References 30 publications

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

Lipid functions in cytochrome bc complexes: an odd evolutionary transition in a membrane protein structure

Evolution of b-type cytochromes in prokaryotes

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