D-Ribulose-1,5-bisphosphate carboxylase and polyhedral inclusion bodies in Thiobacillus intermedius

Organization, structure, and assembly of alpha-carboxysomes determined by electron cryotomography of intact cells

Carboxysomes are polyhedral inclusion bodies that play a key role in autotrophic metabolism in many bacteria. Using electron cryotomography, we examined carboxysomes in their native states within intact cells of three chemolithoautotrophic bacteria. We found that carboxysomes generally cluster into distinct groups within the cytoplasm, often in the immediate vicinity of polyphosphate granules, and a regular lattice of density frequently connects granules to nearby carboxysomes. Small granular bodies were also seen within carboxysomes. These observations suggest a functional relationship between carboxysomes and polyphosphate granules. Carboxysomes exhibited greater size, shape, and compositional variability in cells than in purified preparations. Finally, we observed carboxysomes in various stages of assembly, as well as filamentous structures that we attribute to misassembled shell protein. Surprisingly, no more than one partial carboxysome was ever observed per cell. Based on these observations, we propose a model for carboxysome assembly in which the shell and the internal RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) lattice form simultaneously, likely guided by specific interactions between shell proteins and RuBisCOs.

Transcript analysis of the Halothiobacillus neapolitanus cso operon

Carboxysomes are polyhedral microcompartments that sequester the CO(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase in many autotrophic bacteria. Their protein constituents are encoded by a set of tightly clustered genes that are thought to form an operon (the cso operon). This study is the first to systematically address transcriptional regulation of carboxysome protein expression. Quantification of transcript levels derived from the cso operon of Halothiobacillus neapolitanus, the sulfur oxidizer that has emerged as the model organism for carboxysome structural and functional studies, indicated that all cso genes are transcribed, albeit at different levels. Combined with comparative genomic evidence, this study supports the premise that the cso gene cluster constitutes an operon. Characterization of transcript 5'- and 3'-ends and examination of likely regulatory sequences and secondary structure elements within the operon suggested potential strategies by which the vastly different levels of individual carboxysome proteins in the microcompartment could have arisen.

Thiovirga sulfuroxydans gen. nov., sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium isolated from a microaerobic waste-water biofilm

A novel mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain SO07(T), was isolated from a microaerobic waste-water biofilm. Chemolithoautotrophic growth was observed with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Anaerobic and heterotrophic growth were not observed. Nitrate was not used as a terminal electron acceptor. The optimum pH and temperature for growth were pH 7.5 and 30 degrees C, respectively. The major isoprenoid quinone was Q-8. The DNA G + C content of strain SO07(T) was 47.1 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain SO07(T) formed a monophyletic group in the gamma-Proteobacteria with only 89 % similarity to members of the genus Halothiobacillus, its nearest phylogenetic neighbours. In addition, the isolate differed from members of the genus Halothiobacillus in its requirement for and tolerance of NaCl; strain SO07(T) was unable to grow in NaCl concentrations of more than 180 mM. On the basis of phylogenetic, chemotaxonomic and physiological data, it is proposed that isolate SO07(T) (=JCM 12417(T) = ATCC BAA-1033(T)) represents the type strain of a novel species in a new genus, Thiovirga sulfuroxydans gen. nov., sp. nov.

Proteomic analysis of the CO2-concentrating mechanism in the open-ocean cyanobacterium Synechococcus WH8102

The open-ocean cyanobacterium Synechococcus WH8102 has recently been sequenced, making high-throughput mass spectrometry(MS)-based proteomics studies possible. Here, we used 1D and 2D gel electrophoresis, matrix-assisted laser desorption–ionization – time-of-flight (MALDI-TOF) MS, and two-hybrid analysis to study the composition and protein interactions within the carboxysome, a protein-rich polyhedral body involved in the CO2-concentrating mechanism. We identified the Rubisco large and small subunits and CsoS1 and CsoS2 in the carboxysome-rich particulate fraction and thus conclude the proteins were solely associated with the carboxysome. We also determined that the carboxysome fraction contained numerous membrane-associated proteins, consistent with the presence of membrane contamination. Two-hybrid analysis indicated that CsoS2 and OrfA strongly interacted. They formed dimers and interacted with each other. To our knowledge, this is the first indication of OrfA being biochemically linked to the carboxysome. The ε-class carbonic anhydrase CsoS3 did not interact with other carboxysome components in a binary manner. CsoS3 may not interact, or it may only bind, in fully formed multiprotein complexes. Finally, growth rates and protein expression were unchanged between 100 and 750 µL·L–1 CO2.Key words: proteomics, CO2-concentrating mechanism, carboxysome, cyanobacteria, Synechococcus.

Organization and regulation of cbb CO2 assimilation genes in autotrophic bacteria

The Calvin-Benson-Bassham cycle constitutes the principal route of CO2 assimilation in aerobic chemoautotrophic and in anaerobic phototrophic purple bacteria. Most of the enzymes of the cycle are found to be encoded by cbb genes. Despite some conservation of the internal gene arrangement cbb gene clusters of the various organisms differ in size and operon organization. The cbb operons of facultative autotrophs are more strictly regulated than those of obligate autotrophs. The major control is exerted by the cbbR gene, which codes for a transcriptional activator of the LysR family. This gene is typically located immediately upstream of and in divergent orientation to the regulated cbb operon, forming a control region for both transcriptional units. Recent studies suggest that additional protein factors are involved in the regulation. Although the metabolic signal(s) received by the regulatory components of the operons is (are) still unknown, the redox state of the cell is believed to play a key role. It is proposed that the control of the cbb operon expression is integrated into a regulatory network.

Use of Electroporation To Generate a Thiobacillus neapolitanus Carboxysome Mutant

Two cloning vectors designed for use in Escherichia coli and the thiobacilli were constructed by combining a Thiobacillus intermedius plasmid replicon with a multicloning site, lacZ(prm1), and either a kanamycin or a streptomycin resistance gene. Conditions necessary for the introduction of DNA into T. intermedius and T. neapolitanus via electroporation were examined and optimized. By using optimal electroporation conditions, the gene encoding a carboxysome shell protein, csoS1A, was insertionally inactivated in T. neapolitanus. The mutant showed a reduced number of carboxysomes and an increased level of CO(inf2) necessary for growth.

Mixotrophic and Autotrophic Growth of Thiobacillus acidophilus on Glucose and Thiosulfate

Mixotrophic growth of the facultatively autotrophic acidophile Thiobacillus acidophilus on mixtures of glucose and thiosulfate or tetrathionate was studied in substrate-limited chemostat cultures. Growth yields in mixotrophic cultures were higher than the sum of the heterotrophic and autotrophic growth yields. Pulse experiments with thiosulfate indicated that tetrathionate is an intermediate during thiosulfate oxidation by cell suspensions of T. acidophilus . From mixotrophic growth studies, the energetic value of thiosulfate and tetrathionate redox equivalents was estimated to be 50% of that of redox equivalents derived from glucose oxidation. Ribulose 1,5-bisphosphate carboxylase (RuBPCase) activities in cell extracts and rates of sulfur compound oxidation by cell suspensions increased with increasing thiosulfate/glucose ratios in the influent medium of the mixotrophic cultures. Significant RuBPCase and sulfur compound-oxidizing activities were detected in heterotrophically grown T. acidophilus . Polyhedral inclusion bodies (carboxysomes) could be observed at low frequencies in thin sections of cells grown in heterotrophic, glucose-limited chemostat cultures. Highest RuBPCase activities and carboxysome abundancy were observed in cells from autotrophic, CO 2 -limited chemostat cultures. The maximum growth rate at which thiosulfate was still completely oxidized was increased when glucose was utilized simultaneously. This, together with the fact that even during heterotrophic growth the organism exhibited significant activities of enzymes involved in autotrophic metabolism, indicates that T. acidophilus is well adapted to a mixotrophic lifestyle. In this respect, T. acidophilus may have a competitive advantage over autotrophic acidophiles with respect to the sulfur compound oxidation in environments in which organic compounds are present.

Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms

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Ribulose 1,5-bisphosphate carboxylase and polyhedral bodies of Chlorogloeopsis fritschii

Ribulose 1,5-bisphosphate (RuBP) carboxylase (EC 4.1.1.39) activity was approximately equally distributed between supernatant and pellet fractions produced by differential centrifugation of disrupted cells of Chlorogloeopsis fritschii. Low ionic strength buffer favoured the recovery of particulate RuBP carboxylase. Density gradient centrifugation of resuspended cell-free particulate material produced a single band of RuBP carboxylase activity, which was associated with the polyhedral body fraction, rather than with the thylakoids or other observable particles. Isolated polyhedral body stability was improved by density gradient centrifugation through gradients of Percoll plus sucrose in buffer, which yielded apparently intact polyhedral bodies. These were 100 to 150 nm in diameter and contained ring-shaped, 12 nm diameter particles. It is inferred that the C. fritschii polyhedral bodies are carboxysomes. Sodium dodecyl sulphate (SDS) polyacrylamide gel electrophoresis of SDS-dissociated polyhedral bodies revealed 8 major polypeptides. The most abundant, with molecular weights of 52,000 and 13,000, correspond with the large and small subunits, respectively, of RuBP carboxylase.

Presence of two subunit types in ribulose 1,5-bisphosphate carboxylase from Thiobacillus intermedius

Ribulose bisphosphate carboxylase (EC 4.1.1.39) has been purified to homogeneity from glutamate-CO2-thiosulfate-grown Thiobacillus intermedius by pelleting the protein from the 93,000 X g supernatant fluid followed by ammonium sulfate fractionation and sedimentation into a discontinuous sucrose density gradient. The molecular weight of the native protein approximated that of the higher plant enzyme (550,000) based on its relative electrophoretic mobility in polyacrylamide disc gels compared with that of standards of known molecular weight, including crystalline tobacco ribulose bisphosphate carboxylase. Sodium dodecyl sulfate electrophoresis in 12% polyacrylamide disc gels and Sephadex G-100 chromatography in the presence of sodium dodecyl sulfate indicated that the purified Thiobacillus protein, like the tobacco enzyme, consisted of two types of nonidentical subunits. The molecular weights of the large and small subunits were estimated to be about 55,000 and 13,000, respectively, by means of sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The carboxylase activity of the protein purified from spinach leaves and T. intermedius responded similarly to the effectors reduced nicotinamide adenine dinucleotide phosphate and 6-phosphogluconate. Contrary to a previous report (K. Purohit, B. A. McFadden, and A. L. Cohen, J. Bacteriol. 127:505-515, 1976), these results indicate that ribulose bisphosphate carboxylase purified from Thiobacillus intermedius closely resembles the higher plant enzyme with respect to quaternary structure, molecular weight, and regulatory properties.

Icosahedral inclusions (carboxysomes) of Nitrobacter agilis

The icosahedral bodies of Nitrobacter agilis are about 120 nm in diameter and, as viewed by electron microscopy, consist of an outer shell enclosing 10-nm particles. The inner 10-nm particle is the enzyme D-ribulose 1,5-bisphosphate carboxylase. The bodies isolated from cells incubated 1 month without nitrite had a specific activity for the enzyme of 0.54 mu mol of CO2 fixed per min per mg of protein.

Morphogenesis and differentiation in Rhodomicrobium vannielii and other budding and prosthecate bacteria

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Micromorphology of Gram-negative hydrogen bacteria. II. Cell envelope, membranes, and cytoplasmic inclusions

The fine structure of the cell envelope, of membrane systems and of cytoplasmic inclusions of Gram-negative aerobic hydrogen bacteria has been studied. The results have been tabulated, and three main groups could be recognized: Group 1: Alcaligenes eutrophus, A.paradoxus, A.ruhlandii, Pseudomonas facilis, P.flava, P.pseudoflava, P.palleronii, and Aquaspirillum autotrophicum; Group 2: "Corynebacterium" autotrophicum and strains MA 2 and SA 35; Group 3: Paracoccus denitrificans. Special structures related to the chemoautotrophic way of life of the hydrogen bacteria were not observed.

Oxalate, formate, formamide, and methanol metabolism in Thiobacillus novellus

Thiobacillus novellus was able to grow with oxalate, formate, formamide, and methanol as sole sources of carbon and energy. Extensive growth on methanol required yeast extract or vitamins. Glyoxylate carboligase was detected in extracts of oxalate-grown cells. Ribulose bisphosphate carboxylase was found in extracts of cells grown on formate, formamide, and thiosulfate. These data indicate that oxalate is utilized heterotrophically in the glycerate pathway, and formate and formamide are utilized autotrophically in the ribulose bisphosphate pathway. Nicotinamide adenine dinucleotide-linked formate dehydrogenase was present in extracts of oxalate-, formate-, formamide-, and methanol-grown cells but was absent in thiosulfate- and acetate-grown cells.

Purification, quaternary structure, composition, and properties of D-ribulose-1,5-bisphosphate carboxylase from Thiobacillus intermedius

D-Ribulose-1,5-bisphosphate (RuBP) carboxylase has been purified from glutamate-CO2-S2O3(2)-grown Thiobacillus intermedius by pelleting the enzyme from the high-speed supernatant and by intermediary crystallization followed by sedimentation into a discontinuous 0.2 to 0.8 M sucrose gradient. The enzyme was homogeneous by the criteria of electrophoresis on polyacrylamide gels of several acrylamide concentrations, sedimentation velocity and equilibrium measurements, and electron microscopic observations of negatively stained preparations. The molecular weights of the enzyme determined by sedimentation equilibrium and light-scattering measurements averaged 462,500 +/- 13,000. The enzyme consisted of closely similar or identical polypeptide chains of a molecular weight of 54,500 +/- 5,450 determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The S(0)20,w of the enzyme was 18.07S +/- 0.22. Electron microscopic examination suggested that the octomeric enzyme (inferred from the molecular measurements mentioned) had a cubical structure. The specific activity of the enzyme was 2.76 mumol of RuBP-dependent CO2 fixed/min per mg of protein (at pH 8 and 30 C), and the turnover number in terms of moles of CO2 fixed per mole of catalytic site per second was 2.6. The enzyme was stable for 3 months at -20 C and at least 4 weeks at 0 C. The apparent Km for CO2 was 0.75 mM, and Km values for RuBP and Mg2+ were 0.076 and 3.6 mM, respectively. Dialyzed enzyme could be fully reactivated by the addition of 20 mM Mg2+ and partially reactivated by 20 mM Co2+, but Cd2+, Mn2+, Ca2+, and Zn2+ had no effect. The compound 6-phosphogluconate was a linear competitive inhibitor with respect to RuBP when it had been preincubated with enzyme, Mg2+, and HCO3-.