Roles of RubisCO and the RubisCO-Like Protein in 5-Methylthioadenosine Metabolism in the Nonsulfur Purple Bacterium
            <i>Rhodospirillum rubrum</i>

Singh, Jaya; Tabita, F. Robert

doi:10.1128/jb.01442-09

Cited by 21 publications

(45 citation statements)

References 25 publications

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“…Numerous species of Actinomycetales were reported to be cold adapted and could grow at or below 0°C and were observed in Antarctic soils (Babalola et al 2009). Rhizobiales consisted of Bradyrhizobium, Starkeya, Rhizobium, and Mesorhizobium which were reported to degrade diverse organic matters and are typical symbiotic rhizobia that establish an N 2 -fixing symbiosis with its legume host soybean (Borodina et al 2005;Gourion et al 2011;Singh and Tabita 2010). Burkholderiales consisted of Variovorax paradoxus and Rubrivivax gelatinosus are capable of degrading diverse organic carbons including starch, cellulose, gelatin, chitin, and humic acids (Han et al 2011;Nagashima et al 2012;Satola et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

Guo

Kong

Wang

et al. 2015

Appl Microbiol Biotechnol

112

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Soil microbial autotrophs play a significant role in CO 2 fixation in terrestrial ecosystem, particularly in vegetation-constrained ecosystems with environmental stresses, such as the Tibetan Plateau characterized by low temperature and high UV. However, soil microbial autotrophic communities and their driving factors remain less appreciated. We investigated the structure and shift of microbial autotrophic communities and their driving factors along an elevation gradient (4400-5100 m above sea level) in alpine grassland soils on the Tibetan Plateau. The autotrophic microbial communities were characterized by quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning/ sequencing of cbbL genes, encoding the large subunit for the CO 2 fixation protein ribulose-1,5-bisphosphate carboxylase/ oxygenase (RubisCO). High cbbL gene abundance and high RubisCO enzyme activity were observed and both significantly increased with increasing elevations. Path analysis identified that soil RubisCO enzyme causally originated from microbial autotrophs, and its activity was indirectly driven by soil water content, temperature, and NH 4 + content. Soil autotrophic microbial community structure dramatically shifted along the elevation and was jointly driven by soil temperature, water content, nutrients, and plant types. The autotrophic microbial communities were dominated by bacterial autotrophs, which were affiliated with Rhizobiales, Burkholderiales, and Actinomycetales. These autotrophs have been well documented to degrade organic matters; thus, metabolic versatility could be a key strategy for microbial autotrophs to survive in the harsh environments. Our results demonstrated high abundance of microbial autotrophs and high CO 2 fixation potential in alpine grassland soils and provided a novel model to identify dominant drivers of soil microbial communities and their ecological functions.

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Section: Discussionmentioning

confidence: 99%

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

Guo

Kong

Wang

et al. 2015

Appl Microbiol Biotechnol

112

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“…Form IV is a recently discovered, diverse group of enzymes referred to as Rubisco‐like proteins (RLPs). These enzymes are found within many diverse clades of organisms (including the Proteobacteria, Firmicutes, Chlorobia, Clostridia, Chloroflexi non‐methanogenic euryarchaeota, and the unicellular green alga O. tauri ), lack the active‐site residues of canonically characterized Rubisco, and are not known to carry out the carboxylase/oxygenase activity; the full range of metabolic functions of the RLPs have not been explored but at least some are involved in sulfur metabolism (Singh & Tabita, 2010; Tabita et al., 2007). …”

Section: Introductionmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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Ribulose 1,5‐bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen‐sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem‐bearing, oxygen‐evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen‐sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

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“…RLPs are structural homologs of RubisCO that are unable to catalyze CO 2 fixation (59). They form six deeply branching subclades, only two of which have defined biochemical functions, participating in methionine salvage pathways (60,61). Another clade (form IV-Photo) has an unknown role during growth using thiosulfate as an electron donor (62).…”

Section: Biocathode Metagenomementioning

confidence: 99%

A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO ₂ -Fixing Constituent in a Self-Regenerating Biocathode

Wang

Leary

Malanoski

et al. 2015

Appl Environ Microbiol

151

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Biocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O 2 reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortia in situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (؉310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O 2 , and presumably fixing CO 2 for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided between Alpha-and Gammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, with Marinobacter, Chromatiaceae, and Labrenzia the most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified from Chromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed for Chromatiaceae. These findings represent the first description of putative EET and CO 2 fixation mechanisms for a selfregenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics. Bioelectrochemical systems (BES) use microorganisms as catalysts to drive complex electrochemical reactions, such as electricity generation by microbial fuel cells (MFCs) (1), wastewater treatment (2), and microbial electrosynthesis (3-6), that would not be possible without living cells. The term "biocathode" refers to a biofilm, constituted of a single organism or microbial consortium, that has formed on the cathode of a BES and consumes electrons (e Ϫ ). Cathodes hold great potential as a stable electron source to drive microbial metabolism (7); however, little is known about the underlying extracellular electron transfer (EET) pathways that could be exploited for biocathode functional engineering. Although biocathode EET has been demonstrated for a variety of microorganisms, including acetogens (5) and a methanogenic archaeon (6), studies aimed at identifying EET conduits from the electrode to cells have mostly been confined to the model organisms Geobacter (8) and Shewanella (9), due to the massive effort put forth to understand how these iron-reducing bacteria are able to catalyze EET at bioanodes (10-12). The ability of iron-...

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Roles of RubisCO and the RubisCO-Like Protein in 5-Methylthioadenosine Metabolism in the Nonsulfur Purple Bacterium Rhodospirillum rubrum

Cited by 21 publications

References 25 publications

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO ₂ -Fixing Constituent in a Self-Regenerating Biocathode

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Roles of RubisCO and the RubisCO-Like Protein in 5-Methylthioadenosine Metabolism in the Nonsulfur Purple Bacterium Rhodospirillum rubrum

Cited by 21 publications

References 25 publications

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO 2 -Fixing Constituent in a Self-Regenerating Biocathode

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A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO ₂ -Fixing Constituent in a Self-Regenerating Biocathode