Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation

Watson, G. M.; Tabita, F. Robert

doi:10.1111/j.1574-6968.1997.tb10165.x

Cited by 163 publications

(53 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the chemolithoautotrophic Proteobacteria, autotrophic carbon fixation via the Calvin-Benson cycle is an obvious target. Although the RuBisCO phylogeny, in general, differs from the traditional 16S rRNA gene-based phylogeny of autotrophic bacteria (Watson & Tabita, 1997), our analysis of the cbb genes in halophilic SOB confirms their independent deep-lineage position within the Gammaproteobacteria.…”

Section: Discussionmentioning

confidence: 48%

“…This form is mainly found in Alpha-, Beta-and Gammaproteobacteria, although a few cyanobacterial sequences also belong to form IA (Watson & Tabita, 1997). None of the obtained cbbL sequences showed high similarity to sequences in GenBank (,85 % nucleotide identity), indicating the presence of previously unknown autotrophic species.…”

Section: Detection Of Cbb Genes In Sediments Of a Hypersaline Lakementioning

confidence: 96%

“…This might be proven by finding a Thiohalospira strain that bears both cbbL genes. On the other hand, the cbbL sequences of strains HL4/HL21 cluster with the group of Allochromatium vinosum, encompassing various unrelated chemo-and photoautotrophic bacteria, and the substantial level of sequence divergence within the group might indicate lateral cbbL gene transfer (Watson & Tabita, 1997;Tourova et al, 2007Tourova et al, , 2009. Lateral cbb gene transfer might be the reason for the isolated position of Halothiobacillus neapolitanus and Thioalkalibacter halophilus among halophilic SOB on the cbbL tree.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

et al. 2010

View full text Add to dashboard Cite

The presence and diversity of the cbb genes encoding the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO) (a key enzyme of the Calvin-Benson cycle of autotrophic CO 2 assimilation) were investigated in pure cultures of seven genera of halophilic chemolithoautotrophic sulfur-oxidizing bacteria (SOB) and in sediments from a hypersaline lake in which such bacteria have been recently discovered. All of the halophilic SOB strains (with the exception of Thiohalomonas nitratireducens) possessed the cbbL gene encoding RuBisCO form I, while the cbbM gene encoding RuBisCO form II was detected only in some of the pure cultures. The general topologies of the CbbL/CbbM trees and the 16S rRNA gene tree were different, but both markers showed that the halophilic SOB genera formed independent lineages in the Gammaproteobacteria. In some cases, such as with several strains of the genus Thiohalospira and with Thioalkalibacter halophilus, the cbbL clustering was incongruent with the positions of these strains on the ribosomal tree. In the cbbM tree, the clustering of Thiohalospira and Thiohalorhabdus strains was incongruent with their branching in both cbbL and 16S rRNA gene trees. cbbL and cbbM genes related to those found in the analysed halophilic SOB were also detected in a sediment from a hypersaline lake in Kulunda Steppe (Russia). Most of the cbbL and cbbM genes belonged to members of the genus Thiohalorhabdus. In the cbbL clone library, sequences related to those of Halothiobacillus and Thiohalospira were detected as minor components. Some of the environmental cbbM sequences belonged to as yet unknown phylotypes, representing deep lineages of halophilic autotrophs.

show abstract

Section: Discussionmentioning

confidence: 48%

Section: Detection Of Cbb Genes In Sediments Of a Hypersaline Lakementioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

et al. 2010

View full text Add to dashboard Cite

show abstract

“…Form I RuBisCOs have been divided into red or green types with reference to their presence in red algae or chlorophytes respectively (Delwiche & Palmer, 1996). Both types, and the two major subgroups of each, contain examples from prokaryotes (Watson & Tabita, 1997). The partial sequences of RuBisCO large subunits predicted from cbbL gene fragments of Sulfobacillus strain NMW-6 (Holden & Brown, 1993) and Sulfobacillus acidophilus (Clark, 1995) were reported as most similar to sequences of those proteobacteria, such as Ralstonia eutropha, that have redtype RuBisCOs.…”

Section: Introductionmentioning

confidence: 99%

Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

2007

View full text Add to dashboard Cite

The Calvin-Benson-Bassham (CBB) cycle has been extensively studied in proteobacteria, cyanobacteria, algae and plants, but hardly at all in Gram-positive bacteria. Some characteristics of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) and a cluster of potential CBB cycle genes in a Gram-positive bacterium are described in this study with two species of Sulfobacillus (Gram-positive, facultatively autotrophic, mineral sulfide-oxidizing acidophiles). In contrast to the Gram-negative, iron-oxidizing acidophile Acidithiobacillus ferrooxidans, Sulfobacillus thermosulfidooxidans grew poorly autotrophically unless the CO 2 concentration was enhanced over that in air. However, the RuBisCO of each organism showed similar affinities for CO 2 and for ribulose 1,5-bisphosphate, and similar apparent derepression of activity under CO 2 limitation. The red-type, form I RuBisCO of Sulfobacillus acidophilus was confirmed as closely related to that of the anoxygenic phototroph Oscillochloris trichoides. Eight genes potentially involved in the CBB cycle in S. acidophilus were clustered in the order cbbA, cbbP, cbbE, cbbL, cbbS, cbbX, cbbG and cbbT.

show abstract

“…The most important enzyme in the CBB cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco: EC 4.1.1.39) (1,2). Rubisco is responsible for the single carbon dioxidefixing step of the cycle, in which ribulose-1,5-bisphosphate reacts with CO 2 and H 2 O to form two molecules of 3-phosphoglycerate.…”

mentioning

confidence: 99%

Structure-based Catalytic Optimization of a Type III Rubisco from a Hyperthermophile

Nishitani

Yoshida

Fujihashi

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

The Calvin-Benson-Bassham cycle is responsible for carbon dioxide fixation in all plants, algae, and cyanobacteria. The enzyme that catalyzes the carbon dioxide-fixing reaction is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) belongs to the type III group, and shows high activity at high temperatures. We have previously found that replacement of the entire ␣-helix 6 of Tk-Rubisco with the corresponding region of the spinach enzyme (SP6 mutant) results in an improvement of catalytic performance at mesophilic temperatures, both in vivo and in vitro, whereas the former and latter half-replacements of the ␣-helix 6 (SP4 and SP5 mutants) do not yield such improvement. We report here the crystal structures of the wild-type Tk-Rubisco and the mutants SP4 and SP6, and discuss the relationships between their structures and enzymatic activities. A comparison among these structures shows the movement and the increase of temperature factors of ␣-helix 6 induced by four essential factors. We thus supposed that an increase in the flexibility of the ␣-helix 6 and loop 6 regions was important to increase the catalytic activity of Tk-Rubisco at ambient temperatures. Based on this structural information, we constructed a new mutant, SP5-V330T, which was designed to have significantly greater flexibility in the above region, and it proved to exhibit the highest activity among all mutants examined to date. The thermostability of the SP5-V330T mutant was lower than that of wild-type Tk-Rubisco, providing further support on the relationship between flexibility and activity at ambient temperatures.The Calvin-Benson-Bassham (CBB) 4 cycle contributes to the fixation of carbon for all plants, algae, and cyanobacteria. The most important enzyme in the CBB cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco: EC 4.1.1.39) (1, 2). Rubisco is responsible for the single carbon dioxidefixing step of the cycle, in which ribulose-1,5-bisphosphate reacts with CO 2 and H 2 O to form two molecules of 3-phosphoglycerate. However, it also catalyzes a competitive oxygenase reaction, by which ribulose-1,5-bisphosphate reacts with O 2 to form one molecule of 3-phosphoglycerate and one molecule of 2-phosphoglycolate (3, 4). Moreover, a typical Rubisco is able to fix only three carbon dioxide molecules/s, an extremely low turnover rate for an enzyme (3). Rubisco is thus considered to be the rate-limiting enzyme of the CBB pathway, and has been an important target for protein engineering (3).From sequence alignment, Rubiscos can be classified into four groups, types I, II, III, and IV (5). The classical type I and II Rubiscos function in the CBB cycle. Type I Rubisco is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L 8 S 8 ) (6). Type II Rubisco is usually composed of only two L subunits (L 2 ) (7, 8). In both cases, the L 2 dimer is the catalytic unit of Rubisco, generating two catalytic...

show abstract

Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation

Cited by 163 publications

References 31 publications

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

Structure-based Catalytic Optimization of a Type III Rubisco from a Hyperthermophile

Contact Info

Product

Resources

About