Function, Structure, and Evolution of the RubisCO-Like Proteins and Their RubisCO Homologs

Tabita, F. Robert; Hanson, Thomas E.; Li, Huiying; Satagopan, Sriram; Singh, Jaya; Chan, Sammy

doi:10.1128/mmbr.00015-07

Cited by 332 publications

(375 citation statements)

References 78 publications

Supporting

Mentioning

364

Contrasting

Unclassified

Order By: Relevance

“…indicating their functionality in vivo (Tabita et al, 2007). However, other experiments have shown that type III RuBisCO enzymes are involved in adenosine monophosphate metabolism (Sato et al, 2007).…”

Section: Op5mentioning

confidence: 99%

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

et al. 2010

View full text Add to dashboard Cite

Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium inside a hyper-mesophilic (that is, between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified b-oxidation to H 2 /CO 2 and acetate. These intermediates are converted to CH 4 /CO 2 by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to CO 2 /H 2 and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H 2 -producing syntroph-methanogen partnership that may serve to improve community stability. The ISME Journal (2011) 5, 122-130; doi:10.1038/ismej.2010; published online 5 August 2010Subject Category: integrated genomics and post-genomics approaches in microbial ecology Keywords: metagenomics; methanogenesis; syntroph; microbial diversity; carbon cycling Introduction Terephthalate (TA) is used as the raw material for the manufacture of numerous plastic products (for example, polyethylene TA bottles and textile fibers). During its production, TA-containing wastewater is discharged in large volumes (as high as 300 million m 3 per year) and high concentration (up to 20 kg COD (chemical oxygen demand) m À3 ) (Razo-Flores et al., 2006). This wastewater is generally treated by anaerobic biological processes under mesophilic conditions (B35 1C). However, anaerobic processes operated at hyper-mesophilic (46-50 1C) and thermophilic (B55 1C) temperatures may be preferable because of the ability to achieve higher loading rate (van Lier et al., 1997;Chen et al., 2004), which reduces the reactor volume. Moreover, TA wastewater is usually generated at 54-60 1C, and does not require additional energy input for maintaining reactor temperature (Chen et al., 2004). The microbial biomass usually occurs in the form of granules or biofilms attaching on the surface of porous media. Under such environments, TA degradation has been hypothesized (Kleerebezem et al., 1999) to be based on a syntrophic microbial relationship whereby fermentative H 2 -producing bacteria (syntrophs) convert TA through benzoate to acetate and H 2 /CO 2 , and acetoclastic and hydrogenotrophic methanogens further convert the intermediates to methane by physically positioning themselves close to the syntrophs to overcome the www.nature.com/ismej thermodynamic barrier (Stams, 1994;Conrad, 1999;Dolfing, 2001).In practice, the complexities of TA-degrading communities are not...

show abstract

Section: Op5mentioning

confidence: 99%

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

et al. 2010

View full text Add to dashboard Cite

show abstract

“…Trace amounts of RubisCO activity and the lack of phosphoribulokinase activity do not support the operation of the Calvin-Bassham-Benson cycle. Possible functions of the archaeal RubisCO have been discussed (Tabita et al, 2007;Sato et al, 2007;Ashida et al, 2008). P. fumarii is a representative of the family Pyrodictiaceae (Desulfurococcales).…”

Section: Enzyme Activities In P Fumariimentioning

confidence: 99%

Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota

et al. 2010

View full text Add to dashboard Cite

Two new autotrophic carbon fixation cycles have been recently described in Crenarchaeota. The 3-hydroxypropionate/4-hydroxybutyrate cycle using acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme has been identified for (micro)aerobic members of the Sulfolobales. The dicarboxylate/4-hydroxybutyrate cycle using oxygen-sensitive pyruvate synthase and phosphoenolpyruvate carboxylase as carboxylating enzymes has been found in members of the anaerobic Desulfurococcales and Thermoproteales. However, Sulfolobales include anaerobic and Desulfurococcales aerobic autotrophic representatives, raising the question of which of the two cycles they use. We studied the mechanisms of autotrophic CO 2 fixation in the strictly anaerobic Stygiolobus azoricus (Sulfolobales) and in the facultatively aerobic Pyrolobus fumarii (Desulfurococcales). The activities of all enzymes of the 3-hydroxypropionate/4-hydroxybutyrate cycle were found in the anaerobic S. azoricus. In contrast, the aerobic or denitrifying P. fumarii possesses all enzyme activities of the dicarboxylate/4-hydroxybutyrate cycle. We conclude that autotrophic Crenarchaeota use one of the two cycles, and that their distribution correlates with the 16S rRNA-based phylogeny of this group, rather than with the aerobic or anaerobic lifestyle.

show abstract

“…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

View full text Add to dashboard Cite

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.

show abstract

Function, Structure, and Evolution of the RubisCO-Like Proteins and Their RubisCO Homologs

Cited by 332 publications

References 78 publications

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota

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

Contact Info

Product

Resources

About