The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier

Background

Carboxysomes are polyhedral protein microcompartments found in many autotrophic bacteria; they encapsulate the CO₂ fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) within a thin protein shell and provide an environment that enhances the catalytic capabilities of the enzyme. Two types of shell protein constituents are common to carboxysomes and related microcompartments of heterotrophic bacteria, and the genes for these proteins are found in a large variety of bacteria.

Methodology/Principal Findings

We have created a Halothiobacillus neapolitanus knockout mutant that does not produce the two paralogous CsoS4 proteins thought to occupy the vertices of the icosahedral carboxysomes and related microcompartments. Biochemical and ultrastructural analyses indicated that the mutant predominantly forms carboxysomes of normal appearance, in addition to some elongated microcompartments. Despite their normal shape, purified mutant carboxysomes are functionally impaired, although the activities of the encapsulated enzymes are not negatively affected.

Conclusions/Significance

In the absence of the CsoS4 proteins the carboxysome shell loses its limited permeability to CO₂ and is no longer able to provide the catalytic advantage RubisCO derives from microcompartmentalization. This study presents direct evidence that the diffusion barrier property of the carboxysome shell contributes significantly to the biological function of the carboxysome.

Protein-based organelles in bacteria: carboxysomes and related microcompartments

Many bacteria contain intracellular microcompartments with outer shells that are composed of thousands of protein subunits and interiors that are filled with functionally related enzymes. These microcompartments serve as organelles by sequestering specific metabolic pathways in bacterial cells. The carboxysome, a prototypical bacterial microcompartment that is found in cyanobacteria and some chemoautotrophs, encapsulates ribulose-l,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase, and thereby enhances carbon fixation by elevating the levels of CO2 in the vicinity of RuBisCO. Evolutionarily related, but functionally distinct, microcompartments are present in diverse bacteria. Although bacterial microcompartments were first observed more than 40 years ago, a detailed understanding of how they function is only now beginning to emerge.

Halothiobacillus neapolitanus carboxysomes sequester heterologous and chimeric RubisCO species

BACKGROUND

The carboxysome is a bacterial microcompartment that consists of a polyhedral protein shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), the enzyme that catalyzes the first step of CO2 fixation via the Calvin-Benson-Bassham cycle.

METHODOLOGY/PRINCIPAL FINDINGS

To analyze the role of RubisCO in carboxysome biogenesis in vivo we have created a series of Halothiobacillus neapolitanus RubisCO mutants. We identified the large subunit of the enzyme as an important determinant for its sequestration into alpha-carboxysomes and found that the carboxysomes of H. neapolitanus readily incorporate chimeric and heterologous RubisCO species. Intriguingly, a mutant lacking carboxysomal RubisCO assembles empty carboxysome shells of apparently normal shape and composition.

CONCLUSIONS/SIGNIFICANCE

These results indicate that carboxysome shell architecture is not determined by the enzyme they normally sequester. Our study provides, for the first time, clear evidence that carboxysome contents can be manipulated and suggests future nanotechnological applications that are based upon engineered protein microcompartments.

CO2 fixation kinetics of Halothiobacillus neapolitanus mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for CO2

The widely accepted models for the role of carboxysomes in the carbon-concentrating mechanism of autotrophic bacteria predict the carboxysomal carbonic anhydrase to be a crucial component. The enzyme is thought to dehydrate abundant cytosolic bicarbonate and provide ribulose 1.5-bisphosphate carboxylase/oxygenase (RubisCO) sequestered within the carboxysome with sufficiently high concentrations of its substrate, CO(2), to permit its efficient fixation onto ribulose 1,5-bisphosphate. In this study, structure and function of carboxysomes purified from wild type Halothiobacillus neapolitanus and from a high CO(2)-requiring mutant that is devoid of carboxysomal carbonic anhydrase were compared. The kinetic constants for the carbon fixation reaction confirmed the importance of a functional carboxysomal carbonic anhydrase for efficient catalysis by RubisCO. Furthermore, comparisons of the reaction in intact and broken microcompartments and by purified carboxysomal RubisCO implicated the protein shell of the microcompartment as impeding diffusion of CO(2) into and out of the carboxysome interior.

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.

Characterization of the carboxysomal carbonic anhydrase CsoSCA from Halothiobacillus neapolitanus

In cyanobacteria and many chemolithotrophic bacteria, the CO(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is sequestered into polyhedral protein bodies called carboxysomes. The carboxysome is believed to function as a microcompartment that enhances the catalytic efficacy of RubisCO by providing the enzyme with its substrate, CO(2), through the action of the shell protein CsoSCA, which is a novel carbonic anhydrase. In the work reported here, the biochemical properties of purified, recombinant CsoSCA were studied, and the catalytic characteristics of the carbonic anhydrase for the CO(2) hydration and bicarbonate dehydration reactions were compared with those of intact and ruptured carboxysomes. The low apparent catalytic rates measured for CsoSCA in intact carboxysomes suggest that the protein shell acts as a barrier for the CO(2) that has been produced by CsoSCA through directional dehydration of cytoplasmic bicarbonate. This CO(2) trap provides the sequestered RubisCO with ample substrate for efficient fixation and constitutes a means by which microcompartmentalization enhances the catalytic efficiency of this enzyme.

Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography

Carboxysomes are polyhedral bodies consisting of a proteinaceous shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO). They are found in the cytoplasm of all cyanobacteria and some chemoautotrophic bacteria. Previous studies of Halothiobacillus neapolitanus and Nitrobacter agilis carboxysomes suggest that the structures are either icosahedral or dodecahedral. To determine the protein shell structure more definitively, purified H. neapolitanus carboxysomes were re-examined by cryo-electron tomography and scanning transmission electron microscopy (STEM). Due to the limited tilt angles in the electron microscope, the tomographic reconstructions are distorted. Corrections were made in the 3D orientation searching and averaging of the computationally extracted carboxysomes to minimize the missing data effects. It was found that H. neapolitanus carboxysomes vary widely in size and mass as shown by cryo-electron tomography and STEM mass measurements, respectively. We have aligned and averaged carboxysomes in several size classes from the 3D tomographic reconstruction by methods that are not model-biased. The averages reveal icosahedral symmetry of the shell, but not of the density inside it, for all the size classes.

A novel evolutionary lineage of carbonic anhydrase (epsilon class) is a component of the carboxysome shell

A significant portion of the total carbon fixed in the biosphere is attributed to the autotrophic metabolism of prokaryotes. In cyanobacteria and many chemolithoautotrophic bacteria, CO(2) fixation is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), most if not all of which is packaged in protein microcompartments called carboxysomes. These structures play an integral role in a cellular CO(2)-concentrating mechanism and are essential components for autotrophic growth. Here we report that the carboxysomal shell protein, CsoS3, from Halothiobacillus neapolitanus is a novel carbonic anhydrase (epsilon-class CA) that has an evolutionary lineage distinct from those previously recognized in animals, plants, and other prokaryotes. Functional CAs encoded by csoS3 homologues were also identified in the cyanobacteria Prochlorococcus sp. and Synechococcus sp., which dominate the oligotrophic oceans and are major contributors to primary productivity. The location of the carboxysomal CA in the shell suggests that it could supply the active sites of RuBisCO in the carboxysome with the high concentrations of CO(2) necessary for optimal RuBisCO activity and efficient carbon fixation in these prokaryotes, which are important contributors to the global carbon cycle.

Organization of carboxysome genes in the thiobacilli

The order of genes in the carboxysome gene clusters of four thiobacilli was examined and the possibility of the cluster forming an operon evaluated. Furthermore, carboxysome peptide homologs were compared with respect to similarities in primary sequence, and the unique structural features of the shell protein CsoS2 were described.

Two Copies of form I RuBisCO genes in Acidithiobacillus ferrooxidans ATCC 23270

Acidithiobacillus ferrooxidans ATCC 23270 possesses two copies of form I ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The nucleotide sequence identity between the two large and two small subunit peptides was 75% and 58%, respectively. It is proposed that the two copies resulted from lateral gene transfer.

Carboxysome genomics: a status report

Carboxysomes, microcompartments that enhance the fixation of carbon dioxide by Rubisco, are found in several chemoautotrophs and in all cyanobacteria thus far examined. The genes for Rubisco large (cbbL) and small (cbbS) subunits (cbb for Calvin-Benson-Bassham), along with the genes (csoS) for the carboxysome shell peptides, are organized in a putative operon in Halothiobacillus neapolitanus in the following order: cbbL,cbbS, csoS2, csoS3, orfA, orfB, csoS1C, csoS1A, and csoS1B. DNA sequencing has revealed essentially the same operon in three other thiobacilli, Acidithiobacillus ferrooxidans, Thiomonas intermedia, and Thiobacillus denitrificans. The carboxysome genes are also clustered inSynechococcus sp. and Synechocystis sp., although in some cases certain genes lie outside the cluster. The genes, labelled ccm for CO2 concentrating mechanism, exist in Synechococcus PCC7942 in the order ccmK, ccmL, ccmM, ccmN, and ccmO, and are located upstream of the Rubisco genes. ccmO is absent, and multiple copies of ccmK exist in some species. The ccmK/ccmO and ccmL genes are homologues of csoS1CAB andorfAB, respectively. The ccmM and ccmN genes have no apparent counterpart in the thiobacilli. More recently, the genome sequence of four additional cyanobacteria has become available. The carboxysome genes in Nostoc punctiforme are clustered like, and are similar to, the genes of the earlier mentioned cyanobacteria. However, the three marine organisms Prochlorococcus marinus MIT9313, P. marinus MED4, and Synechococcus WH8102, possess an operon nearly identical to that found in thiobacilli. Furthermore, the genes exhibit surprising sequence identity to the carboxysome genes of the thiobacilli.

Carbon cycling: the prokaryotic contribution

Although the debate continues, the concept of global warming as a consequence of the increased production of 'greenhouse gases' via human activities is now widely accepted. The role of microbes, especially the prokaryotes, in the formation, trapping and retention of 'greenhouse gases' has, for the most part, been overlooked. The future requires that we pay close attention to these organisms for possible solutions to adverse global changes.

Identification and localization of the carboxysome peptide Csos3 and its corresponding gene in Thiobacillus neapolitanus

Four genes encoding carboxysome shell peptides (csoS1A, csoS1B, csoS1C, csoS2), the genes encoding the large and small subunits of RuBisCO (cbbL, cbbS), and three unidentified ORFs constitute an operon in Thiobacillus neapolitanus. An unidentified ORF 1.54 kb in size is predicted from sequence analysis to encode a protein with a molecular mass of approximately 57 kDa. When this ORF was expressed in Escherichia coli under the control of its endogenous ribosome-binding site, no peptide product was observed. In order to correlate this ORF with a carboxysome peptide, the ORF was overexpressed in E. coli by cloning it into pProExHTb, a prokaryotic expression vector containing an E. coli ribosome binding site. When antibodies raised against the recombinant protein were used to probe an immunoblot containing carboxysome peptides, a 60-kDa peptide was recognized. The peptide was subsequently named CsoS3. CsoS3 is a minor component of the carboxysome; a peptide of this size is commonly not observed or is very faint on Coomassie blue-stained SDS-polyacrylamide gels of purified carboxysomes. Immunogold labeling established CsoS3 to be a component of the carboxysome shell.

Something from almost nothing: carbon dioxide fixation in chemoautotrophs

The last decade has seen significant advances in our understanding of the physiology, ecology, and molecular biology of chemoautotrophic bacteria. Many ecosystems are dependent on CO2 fixation by either free-living or symbiotic chemoautotrophs. CO2 fixation in the chemoautotroph occurs via the Calvin-Benson-Bassham cycle. The cycle is characterized by three unique enzymatic activities: ribulose bisphosphate carboxylase/oxygenase, phosphoribulokinase, and sedoheptulose bisphosphatase. Ribulose bisphosphate carboxylase/oxygenase is commonly found in the cytoplasm, but a number of bacteria package much of the enzyme into polyhedral organelles, the carboxysomes. The carboxysome genes are located adjacent to cbb genes, which are often, but not always, clustered in large operons. The availability of carbon and reduced substrates control the expression of cbb genes in concert with the LysR-type transcriptional regulator, CbbR. Additional regulatory proteins may also be involved. All of these, as well as related topics, are discussed in detail in this review.

Insertion mutation of the form I cbbL gene encoding ribulose bisphosphate carboxylase/oxygenase (RuBisCO) in Thiobacillus neapolitanus results in expression of form II RuBisCO, loss of carboxysomes, and an increased CO2 requirement for growth

It has been previously established that Thiobacillus neapolitanus fixes CO2 by using a form I ribulose bisphosphate carboxylase/oxygenase (RuBisCO), that much of the enzyme is sequestered into carboxysomes, and that the genes for the enzyme, cbbL and cbbS, are part of a putative carboxysome operon. In the present study, cbbL and cbbS were cloned and sequenced. Analysis of RNA showed that cbbL and cbbS are cotranscribed on a message approximately 2,000 nucleotides in size. The insertion of a kanamycin resistance cartridge into cbbL resulted in a premature termination of transcription; a polar mutant was generated. The mutant is able to fix CO2, but requires a CO2 supplement for growth. Separation of cellular proteins from both the wild type and the mutant on sucrose gradients and subsequent analysis of the RuBisCO activity in the collected fractions showed that the mutant assimilates CO2 by using a form II RuBisCO. This was confirmed by immunoblot analysis using antibodies raised against form I and form II RuBisCOs. The mutant does not possess carboxysomes. Smaller, empty inclusions are present, but biochemical analysis indicates that if they are carboxysome related, they are not functional, i.e., do not contain RuBisCO. Northern analysis showed that some of the shell components of the carboxysome are produced, which may explain the presence of these inclusions in the mutant.

Sequence homologs of the carboxysomal polypeptide CsoS1 of the thiobacilli are present in cyanobacteria and enteric bacteria that form carboxysomes - polyhedral bodies

Carboxysomes containing the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) have been demonstrated in a variety of chemoautotrophic prokaryotes and cyanobacteria. The genes in the ccm and cso operon in Synechococcus sp. PCC7942 and Thiobacillus neapolitanus, respectively, code for several carboxysome polypeptides. The polypeptides CcmK and CsoS1 exhibit a high degree of conservation, and in turn show significant homology to the CchA and PduA polypeptides of the ethanolamine and propanediol operons of enteric bacteria. Probing Southern blots of Escherichia coli genomic DNA with csoS1A showed positive hybridization indicating the presence of a csoS1-like gene. Growing Salmonella enterica and Klebsiella oxytoca with propanediol, and E.coli with ethanolamine as the energy source under anaerobic conditions resulted in the formation of polyhedral bodies in these bacteria. The DNA - deduced amino acid sequence of three additional csoS1 genes in both Thiobacillus intermedius and Thiobacillus denitrificans was determined. The nine CsoS1 polypeptides, which includes the three previously determined for T.neapolitanus, exhibited greater than 67% sequence identity. Identity and similarity comparisons and phylogenetic analysis of known polyhedral body CsoS1-like polypeptides indicate a close structural relationship between polyhedral bodies of potentially very different function.Key words: polyhedral bodies, carboxysomes, ribulose-1,5-bisphosphate carboxylase-oxygenase, cyanobacteria, thiobacilli, enteric bacteria.

Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans

The cbbL cbbS and cbbM genes of Thiobacillus denitrificans, encoding form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), respectively, were found to complement a RubisCO-negative mutant of Rhodobacter sphaeroides to autotrophic growth. Endogenous T. denitrificans promoters were shown to function in R. sphaeroides, resulting in high levels of cbbL cbbS and cbbM expression in the R. sphaeroides host. This expression system provided high levels of both T. denitrificans enzymes, each of which was highly purified. The deduced amino acid sequence of the form I enzyme indicated that the large subunit was closely homologous to previously sequenced form I RubisCO enzymes from sulfur-oxidizing bacteria. The form I T. denitrificans enzyme possessed a very low substrate specificity factor and did not exhibit fallover, and yet this enzyme showed a poor ability to recover from incubation with ribulose 1,5-bisphosphate. The deduced amino acid sequence of the form II T. denitrificans enzyme resembled those of other form II RubisCO enzymes. The substrate specificity factor was characteristically low, and the lack of fallover and the inhibition by ribulose 1,5-bisphosphate were similar to those of form II RubisCO obtained from nonsulfur purple bacteria. Both form I and form II RubisCO from T. denitrificans possessed high KCO2 values, suggesting that this organism might suffer in environments containing low levels of dissolved CO2. These studies present the initial description of the kinetic properties of form I and form II RubisCO from a chemoautotrophic bacterium that synthesizes both types of enzyme.

Expression of the cbbLcbbS and cbbM genes and distinct organization of the cbb Calvin cycle structural genes of Rhodobacter capsulatus

Rhodobacter capsulatus fixes CO2 via the Calvin reductive pentose phosphate pathway and, like some other nonsulfur purple bacteria, is known to synthesize two distinct structural forms of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Cosmid clones that hybridized to form I (cbbLcbbS) and form II (cbbM) RubisCO gene probes were isolated from a genomic library of R. capsulatus strain SB1003. Southern blotting and hybridization analysis with gene-specific probes derived from Rhodobacter sphaeroides revealed that R. capsulatus cbbM is clustered with genes encoding other enzymes of the Calvin cycle, including fructose 1,6/sedoheptulose 1,7-bisphosphatase (cbbF), phosphoribulokinase (cbbP), transketolase (cbbT), glyceraldehyde-3-phosphate dehydrogenase (cbbG), and fructose 1,6-bisphosphate aldolase (cbbA), as well as a gene (cbbR) encoding a divergently transcribed LysR-type regulatory protein. Surprisingly, a cosmid clone containing the R. capsulatus form I RubisCO genes (cbbL and cbbS) failed to hybridize to the other cbb structural gene probes, unlike the situation with the closely related organism R. sphaeroides. The form I and form II RubisCO genes were cloned into pUC-derived vectors and were expressed in Escherichia coli to yield active recombinant enzyme in each case. Complementation of a RubisCO-deletion strain of R. sphaeroides to photosynthetic growth by R. capsulatus cbbLcbbS or cbbM was achieved using the broad host-range vector, pRK415, and R. sphaeroides expression vector pRPS-1.

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.

Isolation and characterization of the replicon of a Thiobacillus intermedius plasmid

The replicon of a cryptic Thiobacillus intermedius plasmid (pTiK12) has been isolated and sequenced. Functional analysis of deletion subclones in Escherichia coli localized the replicon to a 3.5-kb region of DNA. Sequencing of this region identified a 30-bp A-T-rich potential stem-loop structure. In addition, an 11-bp direct repeat, an 11-bp inverted repeat, and a 16-bp inverted repeat were observed at the stem-loop structure. Also found in the replicon was a series of four tandem direct repeats consisting of a perfectly conserved 8-bp core. A region near the stem-loop structure is involved in the regulation of plasmid copy number. Deletion subclones lacking this region have increased copy numbers, indicating a negative regulatory role. An open reading frame capable of encoding a 320-amino-acid protein was found near the stem-loop structure. The putative amino acid sequence shares significant similarity with the two Rep proteins from the ColE2 and ColE3 replicons. Replication of the T. intermedius replicon is dependent upon DNA polymerase I. The isolation and examination of the T. intermedius plasmid replicon are initial steps toward the establishment of a genetic system in T. intermedius.

Isolation and characterization of a carboxysome shell gene from Thiobacillus neapolitanus

The gene coding for the major carboxysome shell peptide (csoS1) from Thiobacillus neapolitanus has been isolated and sequenced. Oligonucleotide primers for polymerase chain reaction (PCR) amplification of the 5' end of the gene were made possible by amino acid sequencing of the N-terminal residues of the shell peptide. A 41 bp PCR product was used as a probe to isolate the gene. The deduced amino acid composition of the 216 bp gene shows a high degree of hydrophobicity. The gene is located within a series of three repeated regions of DNA and appears to have arisen via gene duplication. The transcript of csoS1 is approximately 400 bases in length. The shell peptide shares significant homology with Synechococcus open reading frames implicated in carboxysome structure/assembly. These open reading frames and csoS1 are related and are probably members of a carboxysome gene family.

Cloning and expression of the D-ribulose-1,5-bisphosphate carboxylase/oxygenase form II gene from Thiobacillus intermedius in Escherichia coli

Both form I and II ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes were detected in Thiobacillus intermedius by heterologous hybridization using specific probes from Anacystis nidulans and Rhodobacter sphaeroides, respectively. However, only the previously reported form I enzyme could be demonstrated in cells grown under a number of different conditions. The reason(s) why the form II gene is not expressed in T. intermedius is/are not clear at this time. The form II gene was isolated from a lambda library by screening with the Rb. sphaeroides probe. A SalI fragment from this clone was ligated into pUC8 and transformed into Escherichia coli DH5 alpha. Subclones pTi20IIA and pTi20IIB representing both orientations relative to the lac promoter were isolated. Low levels of RuBisCO activity were detected in both induced and non-induced pTi20IIA indicating the probable expression from a T. intermedius promoter. Induced pTi20IIB produced much higher levels of enzyme activity. Analysis of cell-free extracts using sucrose density gradients confirmed the expression of a form II RuBisCO similar in size to that found in Rhodobacter capsulatus. Other Calvin cycle genes were not clustered with either the form I or form II genes.

Two forms of ribulose-1,5-bisphosphate carboxylase/oxygenase from Thiobacillus denitrificans

The autotrophic, sulfur-oxidizing bacterium Thiobacillus denitrificans possesses two forms of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). The form I and form II genes were isolated from a cosmid library using heterologous DNA probes. Restriction enzyme analysis indicated that the genes are within 17 kbp of each other. Other Calvin cycle enzyme genes are not present. Analysis of T. denitrificans RNA indicated that the form I genes for the large and small subunits are co-transcribed with a length of 2800 nucleotides. The transcript for the form II gene is 1900 nucleotides in length.

Nucleotide sequences of Cyanophora paradoxa cellular and cyanelle-associated 5S ribosomal RNAs: the cyanelle as a potential intermediate in plastid evolution

The 5S ribosomal RNAs from the cell cytoplasm and cyanelle (photosynthetic organelle) of Cyanophora paradoxa have been isolated and sequenced. The cellular and cyanelle 5S rRNAs were 119 and 118 nucleotides in length, respectively. Both RNAs exhibited typical 5S secondary structure, but the primary sequence of the cellular species was clearly eukaryotic in nature, while that of the organellar species was prokaryotelike. The primary sequence of the cyanellar 5S rRNA was most homologous to cyanobacterial 5S sequences, yet possessed secondary-structural features characteristic of higher-plant chloroplast 5S rRNAs. Both sequence comparison and structural analysis indicated an evolutionary position for cyanelle 5S rRNA intermediate between blue-green alga and chloroplast 5S rRNAs.

Depression of the synthesis of the intermediate and large forms of ribulose-1,5-bisphosphate carboxylase/oxygenase in Rhodopseudomonas capsulata

Rhodopseudomonas capsulata produces both an intermediate (I) and a large (L) form of ribulose-1,5-bisphosphate carboxylase/oxygenase. Both forms are derepressed under CO2-limiting conditions. The L-form of the enzyme is completely repressed when the culture is grown either photoautotrophically or photoheterotrophically with malate as the electron donor. The L-form is derepressed in the late logarithmic phase of growth when cells are grown photoheterotrophically with butyrate as the electron donor and the NaHCO3 supplement is 0.01%. The level of the I-form is increased about fivefold under latter growth conditions when compared to malate-grown cells. Analytical ultracentrifugation revealed the molecular masses of the I- and L-forms to be 300,000 and 542,000, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed the I-form to be composed of only one type subunit with a molecular weight of 64,000. The L-form possessed both large and small subunits with molecular weights of 58,000 and 10,000.

Localization of quantitation of the ornithine lipid of Thiobacillus thiooxidans

The ornithine lipid of Thiobacillus thiooxidans was found to be 1.9% of the total polar lipids. Approximately 80% of this lipid was found to be localized in the outer membrane.

Heterotrophic carbon metabolism by Beggiatoa alba

The assimilation and metabolism of CO(2) and acetate by Beggiatoa alba strain B18LD was investigated. Although B. alba was shown to require CO(2) for growth, the addition of excess CO(2) (as NaHCO(3)) to the medium in a closed system did not stimulate growth. Approximately 24 to 31% of the methyl-labeled acetate and 38 to 46% of the carboxyl-labeled acetate were oxidized to (14)CO(2) by B. alba. The apparent V(max) values for combined assimilation and oxidation of [2-(14)C]acetate by B. alba were 126 to 202 nmol min(-1) mg of protein(-1) under differing growth conditions. The V(max) values for CO(2) assimilation by heterotrophic and mixotrophic cells were 106 and 131 pmol min(-1) mg of protein(-1), respectively. The low V(max) values for CO(2) assimilation, coupled with the high V(max) values for acetate oxidation, suggested that the required CO(2) was endogenously produced from acetate. Moreover, exogenously supplied acetate was required by B. alba for the fixation of CO(2). From 61 to 73% of the [(14)C]acetate assimilated by washed trichomes was incorporated into lipid. Fifty-five percent of the assimilated [2-(14)C]acetate was incorporated into poly-beta-hydroxybutyric acid. This was consistent with chemical data showing that 56% of the heterotrophic cell dry weight was poly-beta-hydroxybutyric acid. Succinate and CO(2) were incorporated into cell wall material, proteins, lipids, nucleic acids, and amino and organic acids, but not into poly-beta-hydroxybutyric acid. Glutamate and succinate were the major stable products after short-term [1-(14)C]acetate assimilation. Glutamate and aspartate were the first stable (14)CO(2) fixation products, whereas glutamate, a phosphorylated compound, succinate, and aspartate were the major stable (14)CO(2) fixation products over a 30-min period. The CO(2) fixation enzymes isocitrate dehydrogenase (nicotinamide adenine dinucleotide phosphate; reversed) and malate dehydrogenase (nicotinamide adenine dinucleotide phosphate; decarboxylating) were found in cell-free extracts of both mixotrophically grown and heterotrophically grown cells. The data indicate that the typical autotrophic CO(2) fixation mechanisms are absent from B. alba B18LD and that the CO(2) and acetate metabolism pathways are probably linked.

Deoxyribonucleic acid in Nitrobacter carboxysomes

Carboxysomes were isolated from Nitrobacter winogradskyi and Nitrobacter agilis. The icosahedral particles contained double-stranded deoxyribonucleic acid (DNA). In the presence of ethidium bromide and cesium chloride, the particle-bound DNA had a buoyant density of rho 25 = 1.701 g/cm3. Electron microscopy revealed the DNA to be a 14-micron circular molecule.

Ribulose bisphosphate carboxylase from methanol-grown Paracoccus denitrificans

Paracoccus denitrificans grows on methanol as the sole source of energy and carbon, which it assimilates aerobically via the reductive pentose phosphate cycle. This gram-negative bacterium grew rapidly on 50 mM methanol (generation time, 7 h, 30 degrees C) in excellent yield (3 g of wet-packed cells per liter of culture). Electron microscopic studies indicated that the late-log-phase cells were coccoid, having a thick envelope surrounding a layer of more diffuse electron-dense material and a relatively electron-transparent core. Ribulose bisphosphate carboxylase in the 15,000 X g supernatant of fresh cells had specific activities (micromoles of CO2 fixed per minute per milligram of protein) of 0.026, 0.049, 0.085, 0.128, and 0.034 during the lag, early, mild-, and late log, and late stationary phases, respectively. The enzyme was purified 40-fold by pelleting at 159,000 X g, salting out, sedimentation into a 0.2 to 0.8 M linear sucrose gradient, and elution from a diethylaminoethyl-Sephadex column. The enzyme was homogeneous by the criteria of electrophoresis on polyacrylamide gels polymerized from several acrylamide concentrations and sedimentation behavior. The molecular weight of the native enzyme, as measured by gel electrophoresis and gel filtration, averaged 525,000. Sodium dodecyl sulfate dissociated the enzyme into two types of subunits with molecular weights of 55,000 and 13,600. The S20,w of the enzyme was 14.0 Km values for ribulose bisphosphate and CO2 were 0.166 and 0.051 mM, respectively, and the enzyme was inhibited to the extent of 94% by 1 mM 6-phosphogluconate.

The interpretation of the mass spectrum of an ornithine-containing lipid from Thiobacillus thiooxidans

The electron impact mass spectrum of a previously identified ornithine-containing lipid from Thiobacillus thiooxidans has been interpreted using exact mass measurements, low and high energy ionization, and defocused metastable studies. The spectrum, which did not contain a molecular ion for the intact lipid, was consistent with cyclization of the ornithine zwitterionic moiety with elimination of water to give 3[3'-(11,12-methylene-2-hydroxyoctadecanoxy)hexadecanylamine]-2-piperidone. Production of this sufficiently volatile species for mass spectral analysis was accomplished by gentle pyrolysis in the mass spectrometer source. The spectrum can be understood to arise by three primary decompositions which serve to separate the two fatty acid constituents. The remainder of the spectrum is consistent with the expected fragmentations of these constituents.

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.

Electron microscopy of the carboxysomes (polyhedral bodies) of Thiobacillus neapolitanus

The carboxysomes of Thiobacillus neapolitanus are shown, by electron microscopy, to consist of a paracrystalline array of 10-nm particles surrounded by a "membrane." The 10-nm particles have a center hole or depression and have been previously identified as ribulose diphosphate carboxylase. The membrane is a monolayer approximately 3.5-nm thick.

Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus

The polyhedral inclusions of Thiobacillus neapolitanus have been isolated; they contain ribulose diphosphate carboxylase.

Ultrastructural properties of the extra membranes of Escherichia coli O111a as revealed by freeze-fracturing and negative-staining techniques

Escherichia coli O111a is a thermosensitive strain which, when grown at 40 C, accumulates large quantities of intracellular membranes. The ultrastructure of these membranes in cells which have been chemically fixed, embedded, and examined as thin sections has been compared with that of membranes in cells negatively stained or freeze-fractured. Results indicate that the extra membranes are present in the three types of preparations examined and, therefore, clearly are not artifacts of chemical fixation. Negative staining has proved also to be a valuable tool as a rapid means of monitoring cells for the accumulation of large amounts of extra membranes. Also, examination of thin sections has shown that distinct continuities between the plasma membrane and the extra membranes exist. In general, membrane surfaces in freeze-fractured cells containing extra membranes appear smooth and lack the particles associated with the plasma membranes of many cells.

Formation and ultrastructure of extra membranes in Escherichia coli

A temperature-sensitive strain of Escherichia coli (strain 0111a(1)) was shown to accumulate membranous structures at 40 C. These "extra membranes" appeared as vesicles or whorls (or both), depending on the time of growth at 40 C. After 2 hr of growth at 40 C, only vesicles were observed in E. coli 0111a(1) cells; both vesicles and whorls were apparent after 6 hr. The number of cells which contained both types of extra membrane reached a maximum value (75%) after 10 hr of growth at 40 C. Extra membrane production was also studied by using temperature shifts. In shift-up experiments, cells grown at 30 C into early stationary phase accumulated extra membrane after a shift to 40 C. The percentage of E. coli 0111a(1) cells containing extra membrane decreased significantly after a shift from 40 to 30 C. Phase- and electron-microscopic observations indicated that E. coli 0111a(1) cells grown at 40 C were larger than E. coli 0111: B(4) cells grown at either temperature. The ratio of optical density per cell and cell measurements obtained from quantitative electron microscopy confirmed that E. coli 0111a(1) cells grown at 40 C were about twice as large. Microdensitometer traces indicated that the dimension of a single membrane of either whorls or vesicles was 5.4 nm in peak-to-peak distance (8.8 nm total thickness).

Comparative ultrastructure of the thiobacilli

The ultrastructure of seven Thiobacillus species was studied. The structure of their cell envelopes is similar, if not identical, to that found in other gram-negative bacteria. Obvious differences were noted in the middle layer of the cell envelope of the seven cultures. Polyhedral inclusion bodies were apparent in four of the organisms: T. thioparus, T. neapolitanus, T. intermedius, and T. thiooxidans. Lamellar bodies, similar to those present in certain photosynthetic bacteria were found in a few cells of T. thioparus. Structures resembling mesosomes were discovered in T. dinitrificans. A few cells of T. intermedius possessed paracrystalline bodies. Other inclusions, probably volutin and polysaccharide, were present in some of the cultures.

Isolation of an ornithine-containing lipid from Thiobacillus thiooxidans

The ornithine-containing lipid was separated from the other lipids of Thiobacillus thiooxidans by thin-layer chromatography. The aminolipid possesses both amide and ester linkages.

Phospholipids of the thiobacilli

Phosphatidyl glycerol, disphosphatidyl glycerol, and phosphatidyl ethanolamine were found in all of the Thiobacillus species studied. T. thioparus possessed only these phospholipids. T. intermedius, T. neapolitanus, and T. thiooxidans contained phosphatidyl-N-monomethylethanolamine, and T. novellus lipids contained phosphatidyl-N-monomethylethanolamine, phosphatidyl-N-N-dimethylethanolamine, and phosphatidyl choline, in addition to the three phospholipids common to all of the thiobacilli. Methionine was found to act as a methyl donor in the biosynthesis of the methylated forms of phosphatidyl ethanolamine. Phosphatidyl inositol was not detected in any of the organisms. Changing the nutrient medium did not result in a qualitative change in the phospholipid spectrum of the cultures.

Phospholipids of Thiobacillus thiooxidans

Cells and spent growth media from sulfur- and thiosulfate-grown cultures of Thiobacillus thiooxidans were analyzed. The phosphatides were examined by thinlayer chromatography, and the products of their hydrolysis by hydrochloric acid and methanolic potassium hydroxide were separated by paper chromatography. The phospholipids in both cells and spent growth media were identified as phosphatidyl ethanolamine, phosphatidyl-N-monomethylethanolamine, phosphatidyl glycerol, and diphosphatidyl glycerol. These comprised about 97% of the total lipid phosphorus. Lyso-phosphatidyl-N-monomethylethanolamine and lysophosphatidyl glycerol accounted for the remaining 3%. The percentage of the total lipid phosphorus accounted for by each phospholipid depended on the age of the culture.