Membrane-bound electron transport systems of an anammox bacterium: A complexome analysis

Almeida, Naomi M. de; Wessels, Hans; Graaf, R.M. de; Ferousi, Christina; Jetten, Mike S. M.; Keltjens, Jan T.; Kartal, Boran

doi:10.1016/j.bbabio.2016.07.006

Cited by 84 publications

(83 citation statements)

References 83 publications

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“…In some planctomycetes, the genes encoding proteins of this family are found within the operons of cyt bc complexes (Kartal et al 2011, Dibrova et al 2013. De Almeida et al (2016) have recently shown that in Ca. K. stuttgartiensis such protein complexes, which contain both the cyts b and large oxidoreductase subunits, are expressed at high levels.…”

Section: Modular Assembly Of Ancestral Cyt Bc Complexesmentioning

confidence: 99%

“…This evolutionary scenario has been recently challenged (Kao and Hunte , Ducluzeau and Nitschke ). In the view of new important data (Bergdoll et al , de Almeida et al ) and a dramatic increase in the number of sequenced genomes, we revisit here the evolutionary history of the cyt bc complexes and present an updated phylogenomic analysis of the cyt b subunits. We show that new genomic data provide further support to our earlier suggestion on the evolutionary primacy of cyt bc complexes with small cyts b .…”

Section: Introductionmentioning

confidence: 99%

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Emergence of cytochrome bc complexes in the context of photosynthesis

Dibrova

Shalaeva

Galperin

2017

Physiologia Plantarum

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The cytochrome bc (cyt bc) complexes are involved in Q‐cycling; they oxidize membrane quinols by high‐potential electron acceptors, such as cytochromes or plastocyanin, and generate transmembrane proton gradient. In several prokaryotic lineages, and also in plant chloroplasts, the catalytic core of the cyt bc complexes is built of a four‐helical cytochrome b (cyt b) that contains three hemes, a three‐helical subunit IV, and an iron‐sulfur Rieske protein (cytochrome b 6 f‐type complexes). In other prokaryotic lineages, and also in mitochondria, the cyt b subunit is fused with subunit IV, yielding a seven‐ or eight‐helical cyt b with only two hemes (cyt bc 1‐type complexes). Here we present an updated phylogenomic analysis of the cyt b subunits of cyt bc complexes. This analysis provides further support to our earlier suggestion that (1) the ancestral version of cyt bc complex contained a small four‐helical cyt b with three hemes similar to the plant cytochrome b 6 and (2) independent fusion events led to the formation of large cyts b in several lineages. In the search for a primordial function for the ancestral cyt bc complex, we address the intimate connection between the cyt bc complexes and photosynthesis. Indeed, the Q‐cycle turnover in the cyt bc complexes demands high‐potential electron acceptors. Before the Great Oxygenation Event, the biosphere had been highly reduced, so high‐potential electron acceptors could only be generated upon light‐driven charge separation. It appears that an ancestral cyt bc complex capable of Q‐cycling has emerged in conjunction with the (bacterio)chlorophyll‐based photosynthetic systems that continuously generated electron vacancies at the oxidized (bacterio)chlorophyll molecules.

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Section: Modular Assembly Of Ancestral Cyt Bc Complexesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Emergence of cytochrome bc complexes in the context of photosynthesis

Dibrova

Shalaeva

Galperin

2017

Physiologia Plantarum

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“…The resulting heat maps allow the identification of proteins forming part of protein complexes. Although introduced only relatively recently, this strategy has already added an additional degree of depth to the systematic identification of protein complexes in cells or subcellular fractions, albeit so far mainly in mammals (Heide et al ., ; Takabayashi et al ., ; Wessels et al ., ; De Almeida et al ., ; Huynen et al ., ; Müller et al ., ; Prior et al ., ; Wöhlbrand et al ., ).…”

Section: Introductionmentioning

confidence: 98%

The mitochondrial complexome of Arabidopsis thaliana

et al. 2017

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SUMMARYMitochondria are central to cellular metabolism and energy conversion. In plants they also enable photosynthesis through additional components and functional flexibility. A majority of those processes relies on the assembly of individual proteins to larger protein complexes, some of which operate as large molecular machines. There has been a strong interest in the makeup and function of mitochondrial protein complexes and protein-protein interactions in plants, but the experimental approaches used typically suffer from selectivity or bias. Here, we present a complexome profiling analysis for leaf mitochondria of the model plant Arabidopsis thaliana for the systematic characterization of protein assemblies. Purified organelle extracts were separated by 1D Blue native (BN) PAGE, a resulting gel lane was dissected into 70 slices (complexome fractions) and proteins in each slice were identified by label free quantitative shot-gun proteomics. Overall, 1359 unique proteins were identified, which were, on average, present in 17 complexome fractions each. Quantitative profiles of proteins along the BN gel lane were aligned by similarity, allowing us to visualize protein assemblies. The data allow re-annotating the subunit compositions of OXPHOS complexes, identifying assembly intermediates of OXPHOS complexes and assemblies of alternative respiratory oxidoreductases. Several protein complexes were discovered that have not yet been reported in plants, such as a 530 kDa Tat complex, 460 and 1000 kDa SAM complexes, a calcium ion uniporter complex (150 kDa) and several PPR protein complexes. We have set up a tailored online resource (https://complexomemap.de/at_mito_lea ves) to deposit the data and to allow straightforward access and custom data analyses.

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“…Recently, mass spectrometry based metaproteomic approaches are attracting particular attention for discovering microbial functions in mixed culture systems (Barr et al, 2015;Mosier et al, 2015;de Almeida et al, 2016;Salerno et al, 2016). mRNA levels can respond rapidly and sensitively to environmental conditions changes, while changes in protein abundances can be comparatively much slower (Zhu et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Evidence of differential adaptation to decreased temperature by anammox bacteria

Lin

Wang

et al. 2018

Environmental Microbiology

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Low temperature is recognized as one of the major barriers for the application of the anaerobic ammonium oxidation (anammox) process to treat mainstream wastewater. Studies are yet to reveal the underlying biological limitations and molecular mechanisms associated with the inhibition of low temperature on the anammox process. In this study, metaproteomics was used to examine proteome modulation patterns of the anammox community occurring at different temperatures. The anammox community remarkably altered their proteomes when the temperature decreased from 35 °C to 20 °C. This was especially for proteins involved in energy conversion, transcription and translation and inorganic ion transport. However, at 15 °C the anammox activities became distinctly inhibited, and there was evidence of energy limitations and severe stress in Candidatus Kuenenia and to a lesser degree in Candidatus Brocadia. Candidatus Jettenia exhibited more changes in its proteome at 15 °C. From the proteomes, at the lower temperatures there was evidence of stress caused by toxic nitrogen compounds or reactive oxygen species in the anammox bacteria. Hydroxylamine oxidoreductase (HAO)-like proteins and an oxidative stress response protein (a catalase) were in high abundance to potentially ameliorate these inhibitory effects. This study offers metaproteomic insight into the anammox community-based physiological response to decreasing temperatures.

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Membrane-bound electron transport systems of an anammox bacterium: A complexome analysis

Cited by 84 publications

References 83 publications

Emergence of cytochrome bc complexes in the context of photosynthesis

Emergence of cytochrome bc complexes in the context of photosynthesis

The mitochondrial complexome of Arabidopsis thaliana

Evidence of differential adaptation to decreased temperature by anammox bacteria

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