Reductive Pentose Phosphate Cycle Research Articles

Analysis of diversity and function of epiphytic bacterial communities associated with macrophytes using a metagenomic approach

Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3–1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.

Effect of soil flooding and drying on the metabolic pathways of CO2 fixing microorganisms along an elevation gradient in the Three Gorges Reservoir drawdown area

AbstractThe construction of dams and subsequent water level fluctuations significantly alters the environmental conditions of reservoir ecosystems, affecting the metabolic pathways of CO2 fixing microorganisms (CFMs) and carbon storage in drawdown areas. We investigated the response of soil bacterial communities and carbon fixation pathways to periodic flooding and drying at different elevations by collecting surface soil samples (0–10 cm) in the drawdown area of the Three Gorges Reservoir. The results show that periodic flooding and drying increased the complexity of bacterial co‐occurrence networks. We identified the reductive citrate cycle (rTCA cycle), dicarboxylate‐hydroxybutyrate cycle (DC/4‐HB cycle), 3‐Hydroxypropionate cycle (3‐HP cycle) and reductive pentose phosphate cycle (Calvin cycle) as the main carbon fixation pathways. Notably, as the inundation duration increased, the abundance of the Calvin cycle and its key gene (cbbL) gradually decreased. We also found that soil moisture, pH and the different organic carbon components affected the composition of bacterial communities and the abundance of carbon fixation pathways. These findings elucidate evolutionary trends bacterial communities and the impacts of water level fluctuations on microbial‐mediated carbon cycling processes because of dam construction.

Adapting from Low to High: An Update to CO2-Concentrating Mechanisms of Cyanobacteria and Microalgae.

The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.

Site Specialization of Human Oral Veillonella Species.

Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.

Metabolic pathways of CO2 fixing microorganisms determined C-fixation rates in grassland soils along the precipitation gradient

CO2 fixing microorganisms (CFMs) play a crucial role in carbon (C) sequestration in vegetation restricted areas, e.g., under semiarid and arid conditions. The factors controlling the underlying pathways of the CO2 fixation by microorganisms living in soils remain unclear. Here, almost all genes responsible for the eight CO2 fixation pathways in semiarid soil CFMs communities were identified using metagenomic analysis: including the reductive citrate cycle (rTCA), dicarboxylate-hydroxybutyrate cycle (DC/4-HB), reductive pentose phosphate cycle (Calvin), 3-hydroxypropionate bicycle (3-HP), 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB), C4-dicarboxylic acid, CAM cycle, and reductive acetyl-CoA pathway (Wood-Ljungdahl pathway). By tracing the CO2 fixation flux via 13C labeling, it was shown that the CO2 fixation rates increased along the precipitation gradient. The rTCA and 3-HP pathways for CO2 fixing microorganisms were closely associated with 13C incorporation into the soil organic matter under high mean annual precipitation (MAP) (400–600 mm), whereas the Calvin cycle played a vital role in soils under low MAP (<400 mm) conditions. The abundance of the key genes within the C fixing pathways showed that the microbial C accumulation in soils was mainly influenced by the MAP. In semi-arid to semi-humid grassland soils, where CO2 fixation by CFMs provided about 8.1–27 mg C m−2 day−1 input into the ecosystem, we demonstrated that the rTCA, Calvin, and 3-HP cycle were vital to this essential pathway of C sequestration.

Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes.

Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.

Biogeography of soil bacterial populations in the Jutulsessen and Ahlmannryggen of Western Dronning Maud Land, Antarctica

Soils of continental Antarctic nunataks represent unusual ecosystems with concomitant unique bacterial community profiles which have not been assessed for the vast majority of Antarctic nunataks. This study focussed on the previously uncharacterised inland nunataks of the Jutulsessen and Ahlmannryggen ranges in Dronning Maud Land. As with many oligotrophic soils in Antarctica, bacteria from the phyla Acidobacteria, Actinobacteria and Proteobacteria were prevalent. High relative abundances of Bacteroidetes and Chloroflexi were also observed in these soils. Potential phototrophic capabilities of these bacterial populations were indicated by the presence of genes involved in the Calvin–Benson reductive pentose phosphate cycle as well as that of aerobic phototrophic bacteriochlorophyll. Clear spatial patterns of bacterial biodiversity between nunataks in this study were observed, particularly between the Jutulsessen and Ahlmannryggen nunataks which are geographically separated by the Jutulstraumen glacier. Not unexpectedly, the bacterial community profiles found in these nunataks were distinct from those found in alternate biogeographic regions (e.g. Dry Valleys, Peninsula and Larsemann Hills). Despite belonging to the same bioregion (i.e. Dronning Maud Land), however, the clear differentiation of bacterial communities between the Jutulsessen/Ahlmannryggen and that of Sor Rondane suggests that, based on bacterial phylogeography, the Dronning Maud Land bioregion can be divided into sub-bioregions.

Phytochrome B-dependent regulation of reductive phase of photosynthetic carbon assimilation

The experiments were conducted with 10-day-old seedlings of wheat (Triticum aestivum L). Phytochrome B was activated using an array of light diodes emitting light in the red spectral region (RL) and inactivated by an array of light diodes emitting far-red light (FRL). At the end of the night dark period (8 h), activity of the chloroplastic GAP-dehydrogenase complex (the sequence of reactions: 3-PGA → 1,3-PGA → 3-GAP) was 1.0−1.2 μmol of oxidized NADPH/(min g fr wt of the leaf). When the leaves of intact plants were exposed to a maximal dose of RL (20 min at 17.5 kJ/m2), enzyme activity rose by 100–120%. Longer exposure to RL (30 and 40 min) did not cause further activation. Successive exposure to RL and FRL (20 min at 3.0 kJ/m2) completely negated a stimulatory effect of RL. It was shown that as little as 5-min-long exposure to RL increased the rate of 3-GAP formation by 20–25%, and enzyme activity rose linearly when radiation dose was elevated. Determination of the lifetime of RL-activated state by its decrease in plants placed in darkness showed that decay occurred with τ1/2 of 50−60 min when RL was switched off. Thus, a phytochrome B-induced regulation of reducing enzyme complex governing the reductive pentose phosphate cycle was discovered. Judging from the kinetics of attenuation of the activated state, phytochrome B apparently does not affect de novo synthesis of the enzyme. Since the investigated metabolic process consists of two coupled reactions controlled by kinase and dehydrogenase, the place and mechanism of action of the phytochrome system remain unknown.

Variations in microbial carbon sources and cycling in the deep continental subsurface

Deep continental subsurface fracture water systems, ranging from 1.1 to 3.3km below land surface (kmbls), were investigated to characterize the indigenous microorganisms and elucidate microbial carbon sources and their cycling. Analysis of phospholipid fatty acid (PLFA) abundances and direct cell counts detected varying biomass that was not correlated with depth. Compound-specific carbon isotope analyses (δ13C and Δ14C) of the phospholipid fatty acids (PLFAs) and carbon substrates combined with genomic analyses did identify, however, distinct carbon sources and cycles between the two depth ranges studied.In the shallower boreholes at circa 1kmbls, isotopic evidence indicated microbial incorporation of biogenic CH4 by the in situ microbial community. At the shallowest site, 1.05kmbls in Driefontein mine, this process clearly dominated the isotopic signal. At slightly deeper depths, 1.34kmbls in Beatrix mine, the isotopic data indicated the incorporation of both biogenic CH4 and dissolved inorganic carbon (DIC) derived from CH4 oxidation. In both of these cases, molecular genetic analysis indicated that methanogenic and methanotrophic organisms together comprised a small component (<5%) of the microbial community. Thus, it appears that a relatively minor component of the prokaryotic community is supporting a much larger overall bacterial community in these samples.In the samples collected from >3kmbls in Tau Tona mine (TT107, TT109 Bh2), the CH4 had an isotopic signature suggesting a predominantly abiogenic origin with minor inputs from microbial methanogenesis. In these samples, the isotopic enrichments (δ13C and Δ14C) of the PLFAs relative to CH4 were consistent with little incorporation of CH4 into the biomass. The most 13C-enriched PLFAs were observed in TT107 where the dominant CO2-fixation pathway was the acetyl-CoA pathway by non-acetogenic bacteria. The differences in the δ13C of the PLFAs and the DIC and DOC for TT109 Bh2 were ∼−24‰ and 0‰, respectively. The dominant CO2-fixation pathways were 3-HP/4-HB cycle>acetyl-CoA pathway>reductive pentose phosphate cycle.

Benson-Bassham-Calvin cycle contribution to the organic life on our planet

The review is devoted to the outstanding contributions to the path of carbon in photosynthesis by Professor Emeritus Andrew A. Benson, on the occasion of his death at the age of 97, on January 16, 2015. Benson is the legendary co-discoverer of the photosynthetic reductive pentose phosphate cycle, known to every student of photosynthesis as the Benson-Bassham-Calvin cycle. This pathway evolved into the dominant assimilation mechanism for atmospheric carbon into metabolites. The fundamental ecological and biochemical optimization and evolutionary stability of this mechanism unfolded elegantly in Benson’s hands, as he was the first to recognize the building blocks for the synthesis of essential organic compounds that satisfy the energetic needs and demands of most life forms. Photosynthetic carbon metabolism together with other energy and oxidative reactions and secondary biosynthetic processes are critical for the formation of organic matter; and, thereby, the Benson-Bassham-Calvin cycle ensures maintenance of the biosphere.

A survey of carbon fixation pathways through a quantitative lens

While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures of yet unknown carbon fixation pathways are suggested and discussed.

Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii

To clarify the oil biosynthetic routes of the oil-producing green alga Botryococcus braunii, here the race-specific gene expression patterns were examined using representative strains of race A and race B producing fatty acid- and triterpene-derived hydrocarbon oils, respectively. The strain-specific gene expression patterns in the BOT-88-2 strain (race A) and the BOT-22 strain (race B) were revealed by transcriptome comparison and real-time PCR quantification. For race A, it was inferred from the gene expression patterns that the fatty acid elongation in the acyl-carrier-protein (acp)-bound form followed by further elongation in the coenzyme A (CoA)-bound form is the major route of oil biosynthesis. The fatty acids may be desaturated in both acp- and CoA-bound forms and once metabolized into glycerolipids prior to further elongation. For race B, relatively direct entry of photosynthetic products from the reductive pentose phosphate cycle into the mevalonate-independent triterpene biosynthesis was implicated.

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. In the extant biosphere the reductive pentose phosphate (Calvin-Benson) cycle is the predominant mechanism by which many prokaryotes and all plants fix CO(2) into biomass. However, the fact that five alternative autotrophic pathways exist in prokaryotes is often neglected. This bias may lead to serious misjudgments in models of the global carbon cycle, in hypotheses on the evolution of metabolism, and in interpretations of geological records. Here, I review these alternative pathways that differ fundamentally from the Calvin-Benson cycle. Revealingly, these five alternative pathways pivot on acetyl-coenzyme A, the turntable of metabolism, demanding a gluconeogenic pathway starting from acetyl-coenzyme A and CO(2). It appears that the formation of an activated acetic acid from inorganic carbon represents the initial step toward metabolism. Consequently, biosyntheses likely started from activated acetic acid and gluconeogenesis preceded glycolysis.

Starch-related cytosolic heteroglycans in roots from Arabidopsis thaliana

Both photoautotrophic and heterotrophic plant cells are capable of accumulating starch inside the plastid. However, depending on the metabolic state of the respective cell the starch-related carbon fluxes are different. The vast majority of the transitory starch biosynthesis relies on the hexose phosphate pools derived from the reductive pentose phosphate cycle and, therefore, is restricted to ongoing photosynthesis. Transitory starch is usually degraded in the subsequent dark period and mainly results in the formation of neutral sugars, such as glucose and maltose, that both are exported into the cytosol. The cytosolic metabolism of the two carbohydrates includes reversible glucosyl transfer reactions to a heteroglycan that are mediated by two glucosyl transferases, DPE2 and PHS2 (or, in all other species, Pho2). In heterotrophic cells, accumulation of starch mostly depends on the long distance transport of reduced carbon compounds from source to sink organs and, therefore, includes as an essential step the import of carbohydrates from the cytosol into the starch forming plastids. In this communication, we focus on starch metabolism in heterotrophic tissues from Arabidopsis thaliana wild type plants (and in various starch-related mutants as well). By using hydroponically grown A. thaliana plants, we were able to analyse starch-related biochemical processes in leaves and roots from the same plants. Within the roots we determined starch levels and the morphology of native starch granules. Cytosolic and apoplastic heteroglycans were analysed in roots and compared with those from leaves of the same plants. A. thaliana mutants lacking functional enzymes either inside the plastid (such as phosphoglucomutase) or in the cytosol (disproportionating isoenzyme 2 or the phosphorylase isozyme, PHS2) were included in this study. In roots and leaves from the three mutants (and from the respective wild type organ as well), starch and heteroglycans as well as enzyme patterns were analysed.

Acetate-dependent photoheterotrophic growth and the differential requirement for the Calvin–Benson–Bassham reductive pentose phosphate cycle in Rhodobacter sphaeroides and Rhodopseudomonas palustris

Rhodobacter sphaeroides ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-deletion strain 16 was capable of photoheterotrophic growth with acetate, while Rhodopseudomonas palustris RubisCO-deletion strain 2040 could not grow under these conditions. The reason for this difference lies in the fact that Rba. sphaeroides and Rps. palustris use different pathways for acetate assimilation, the ethylmalonyl-CoA pathway, and glyoxylate-bypass cycle, respectively. The ethylmalonyl-CoA pathway is distinct from the glyoxylate cycle as one molecule of CO(2) and one molecule of HCO(3) (-) per three molecules of acetyl-CoA are co-assimilated to form two malate molecules. The glyoxylate cycle directly converts two acetyl-CoA molecules to malate. Each pathway, therefore, also dictates at what point, CO(2) and reductant are consumed, thereby determining the requirement for the Calvin-Benson-Bassham reductive pentose phosphate cycle.

Draft Genome Sequence of the Anoxygenic Filamentous Phototrophic Bacterium Oscillochloris trichoides subsp. DG-6

Oscillochloris trichoides is a mesophilic, filamentous, photoautotrophic, nonsulfur, diazotrophic bacterium which is capable of carbon dioxide fixation via the reductive pentose phosphate cycle and possesses no assimilative sulfate reduction. Here, we present the draft genome sequence of Oscillochloris trichoides subsp. DG-6, the type strain of the species, which has permitted the prediction of genes for carbon and nitrogen metabolism and for the light-harvesting apparatus.

Expression and regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in Mycobacterium sp. strain JC1 DSM 3803

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. Two sets of structural genes (cbbLS-1 and -2) for form I RubisCO have been previously identified in the Mycobacterium sp. strain JC1, which is able to grow on carbon monoxide (CO) or methanol as sole sources of carbon and energy. Northern blot and reverse transcriptase PCR showed that the cbbLS-1 and -2 genes are expressed in cells grown on either carbon monoxide (CO) or methanol, but not in cells grown in nutrient broth. A promoter assay revealed that the cbbLS-2 promoter has a higher activity than the cbbLS-1 promoter in both CO- and methanol-grown cells, and that the activities of both promoters were higher in CO-grown cells than in methanol-grown cells. A gel mobility shift assay and footprinting assays showed that CbbR expressed in Escherichia coli from a cbbR gene, which is located downstream of cbbLS-1 and transcribed in the same orientation as that of the cbbLS genes, specifically bound to the promoter regions of the cbbLS-1 and -2 genes containing inverted repeat sequence. A DNase I footprinting assay revealed that CbbR protected positions -59 to -3 and -119 to -78 of the cbbLS-1 and -2 promoters, respectively. Overexpression of CbbR induced the transcription of RubisCO genes in Mycobacterium sp. strain JC1 grown in nutrient broth. Our results suggest that the CbbR product from a single cbbR gene may positively regulate two cbbLS operons in the Mycobacterium sp. strain JC1 as is the case for Rhodobacter sphaeroides and Cupriavidus necator.

Gene Organization and CO&lt;sub&gt;2&lt;/sub&gt;-Responsive Expression of Four &lt;i&gt;cbb&lt;/i&gt; Operons in the Biomining Bacterium &lt;i&gt;Acidithiobacillus Ferrooxidans&lt;/i&gt;

Acidithiobacillus ferrooxidans is an obligately chemolithoautotrophic, -proteobacterium that fixes CO2 by the Calvin-Benson-Bassham (CBB) reductive pentose phosphate cycle. Our objective is to identify genes potentially involved in CO2 fixation and to advance our understanding of how they might be regulated in response to environmental signals. Bioinformatic analyses, based on the complete genome sequence of the type strain ATCC 23270, identified five cbb gene clusters four of which we show experimentally to be operons. These operons are predicted to encode: (i) the components of the carboxysome and one copy of form I RubisCO (cbb1 operon), (ii) a second copy of form I RubisCO (cbb2 operon), (iii) enzymes of central carbon metabolism (cbb3 operon), (iv) a phosphoribulokinase and enzymes of sulfur metabolism (cbb4 operon) and RubisCO form II (cbb5 gene cluster). In addition, the gene for a LysR-type transcriptional regulator CbbR was identified immediately upstream and in divergent orientation to the cbb1 operon and another associated with the cbb5 gene cluster. A. ferrooxidans was grown under different concentrations of CO2 (2.5 to 20% [v/v]), and levels of mRNA and protein were evaluated by qPCR and Western blotting, respectively. CbbR binding to predicted promoter regions of operons cbb1-4 was assayed by EMSA This information permitted the formulation of models explaining how these operons might be regulated by environmental CO2 concentrations. These models were evaluated in vivo in a heterologous host, using cloned A. ferrooxidans cbbR to complement a mutant of the facultative chemoautotroph Ralstonia eutropha H16 lacking a functional cbbR. Cloned copies of A. ferrooxidans promoter regions were also introduced into R. eutropha to evaluate their ability to drive reporter gene expression. This work lays the framework for further studies that should result in a more comprehensive picture of how CO2 fixation is regulated in A. ferrooxidans.

Presence of duplicate genes encoding a phylogenetically new subgroup of form I ribulose 1,5-bisphosphate carboxylase/oxygenase in Mycobacterium sp. strain JC1 DSM 3803

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. Two sets of the structural genes for form I RubisCO were identified in Mycobacterium sp. strain JC1. The genes were clustered on the chromosome in the transcriptional order of cbbL– cbbS. Cloned cbbL-1 and cbbS-1 and cbbL-2 and cbbS-2 have open reading frames of 1431, 426, 1428, and 426 nucleotides, respectively. Primer extension analysis revealed that transcriptional start sites of cbbLS-1 and -2 genes were the nucleotides T and G located 99 and 41 bp upstream of the cbbL start codons, respectively. CbbLS-1 and CbbLS-2 that were expressed in Escherichia coli exhibited RubisCO activity. A phylogeny of CbbL amino acid sequences revealed that the two enzymes in Mycobacterium sp. strain JC1 may form a new phylogenetic subgroup, type IE, in the ‘red-like’ group of the form I RubisCO family.

Metabolic Engineering Towards the Enhancement of Photosynthesis†

Photosynthetic capacity is a promising target for metabolic engineering of crop plants towards higher productivity. Crop photosynthesis is limited by multiple factors dependent on the environmental conditions. This includes photosynthetic electron transport, regeneration of CO2 acceptor molecules in the reductive pentose phosphate cycle, the activity and substrate specificity of the CO2-fixing enzyme Ribulose-1,5-bisphosphate carboxylase/oxygenase, and the associated flow through the photorespiratory pathway. All these aspects of the photosynthetic network have been the subject of recently published metabolic engineering approaches in model species. Together, the novel results raise hopes that engineering of photosynthesis in crop species can significantly increase agricultural productivity.