Differential accumulation of form I RubisCO in Rhodopseudomonas palustris CGA010 under Photoheterotrophic growth conditions with reduced carbon sources

The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

The purple non-sulfur bacterium Rhodopseudomonas palustris is recognized as a critical microorganism in the nitrogen and carbon cycle and one of the most common members in wastewater treatment communities. This bacterium is metabolically extremely versatile. It is capable of heterotrophic growth under aerobic and anaerobic conditions, but also able to grow photoautotrophically as well as mixotrophically. Therefore R. palustris can adapt to multiple environments and establish commensal relationships with other organisms, expressing various enzymes supporting degradation of amino acids, carbohydrates, nucleotides, and complex polymers. Moreover, R. palustris can degrade a wide range of pollutants under anaerobic conditions, e.g., aromatic compounds such as benzoate and caffeate, enabling it to thrive in chemically contaminated environments. However, many metabolic mechanisms employed by R. palustris to breakdown and assimilate different carbon and nitrogen sources under chemoheterotrophic or photoheterotrophic conditions remain unknown. Systems biology approaches, such as metabolic modeling, have been employed extensively to unravel complex mechanisms of metabolism. Previously, metabolic models have been reconstructed to study selected capabilities of R. palustris under limited experimental conditions. Here, we developed a comprehensive metabolic model (M-model) for R. palustris Bis A53 (iDT1294) consisting of 2,721 reactions, 2,123 metabolites, and comprising 1,294 genes. We validated the model using high-throughput phenotypic, physiological, and kinetic data, testing over 350 growth conditions. iDT1294 achieved a prediction accuracy of 90% for growth with various carbon and nitrogen sources and close to 80% for assimilation of aromatic compounds. Moreover, the M-model accurately predicts dynamic changes of growth and substrate consumption rates over time under nine chemoheterotrophic conditions and demonstrated high precision in predicting metabolic changes between photoheterotrophic and photoautotrophic conditions. This comprehensive M-model will help to elucidate metabolic processes associated with the assimilation of multiple carbon and nitrogen sources, anoxygenic photosynthesis, aromatic compound degradation, as well as production of molecular hydrogen and polyhydroxybutyrate.

CO2 improves the anaerobic biodegradation intensity and selectivity of heterocyclic hydrocarbons in heavy oil

Heterocyclic hydrocarbons pollution generated by oil spills and oilfield wastewater discharges threatens the ecological environment and human health. Here we described a strategy that combines the greenhouse gas CO₂ reduction with microbial remediation. In the presence of nitrate, CO₂ can improve the biodegradation efficiency of the resins and asphaltenes in heavy oil, particularly the biodegradation selectivity of the polar heterocyclic compounds by the newly isolated Klebsiella michiganensis. This strain encoded 80 genes for the xenobiotic biodegradation and metabolism, and can efficiently utilize CO₂ when degrading heavy oil. The total abundance of resins and asphaltenes decreased significantly with CO₂, from 40.816% to 26.909%, to 28.873% with O₂, and to 36.985% with N₂. The transcripts per million (TPM) value of accA gene was 57.81 under CO₂ condition, while respectively 8.86 and 21.23 under O₂ and N₂ conditions. Under CO₂ condition, the total relative percentage of N1-type heterocyclic compounds was selectively decreased from 32.25% to 22.78%, resulting in the heavy oil viscosity decreased by 46.29%. These results demonstrated a novel anaerobic degradation mechanism that CO₂ can promote the anaerobic biodegradation of heterocyclic hydrocarbons in heavy oil, which provides a promising biotreatment technology for the oil-contaminated water.

Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 through a Genome-Scale Metabolic and Expression Model

Rhodopseudomonas palustris CGA009 is a Gram-negative purple nonsulfur bacterium that grows phototrophically by fixing carbon dioxide and nitrogen or chemotrophically by fixing or catabolizing a wide array of substrates, including lignin breakdown products for its carbon and fixing nitrogen for its nitrogen requirements. It can grow aerobically or anaerobically and can use light, inorganic, and organic compounds for energy production. Due to its ability to convert different carbon sources into useful products during anaerobic growth, this study reconstructed a metabolic and expression (ME) model of R. palustris to investigate its anaerobic-photoheterotrophic growth. Unlike metabolic (M) models, ME models include transcription and translation reactions along with macromolecules synthesis and couple these reactions with growth rate. This unique feature of the ME model led to nonlinear growth curve predictions, which matched closely with experimental growth rate data. At the theoretical maximum growth rate, the ME model suggested a diminishing rate of carbon fixation and predicted malate dehydrogenase and glycerol-3 phosphate dehydrogenase as alternate electron sinks. Moreover, the ME model also identified ferredoxin as a key regulator in distributing electrons between major redox balancing pathways. Because ME models include the turnover rate for each metabolic reaction, it was used to successfully capture experimentally observed temperature regulation of different nitrogenases. Overall, these unique features of the ME model demonstrated the influence of nitrogenases and rubiscos on R. palustris growth and predicted a key regulator in distributing electrons between major redox balancing pathways, thus establishing a platform for in silico investigation of R. palustris metabolism from a multiomics perspective. IMPORTANCE In this work, we reconstructed the first ME model for a purple nonsulfur bacterium (PNSB). Using the ME model, different aspects of R. palustris metabolism were examined. First, the ME model was used to analyze how reducing power entering the R. palustris cell through organic carbon sources gets partitioned into biomass, carbon dioxide fixation, and nitrogen fixation. Furthermore, the ME model predicted electron flux through ferredoxin as a major bottleneck in distributing electrons to nitrogenase enzymes. Next, the ME model characterized different nitrogenase enzymes and successfully recapitulated experimentally observed temperature regulations of those enzymes. Identifying the bottleneck responsible for transferring an electron to nitrogenase enzymes and recapitulating the temperature regulation of different nitrogenase enzymes can have profound implications in metabolic engineering, such as hydrogen production from R. palustris. Another interesting application of this ME model can be to take advantage of its redox balancing strategy to gain an understanding of the regulatory mechanism of biodegradable plastic production precursors, such as polyhydroxybutyrate (PHB).

Rhodopseudomonas palustris: A biotechnology chassis

Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.

TCA Cycle Replenishing Pathways in Photosynthetic Purple Non-Sulfur Bacteria Growing with Acetate

Purple non-sulfur bacteria (PNSB) are anoxygenic photosynthetic bacteria harnessing simple organic acids as electron donors. PNSB produce a-aminolevulinic acid, polyhydroxyalcanoates, bacteriochlorophylls a and b, ubiquinones, and other valuable compounds. They are highly promising producers of molecular hydrogen. PNSB can be cultivated in organic waste waters, such as wastes after fermentation. In most cases, wastes mainly contain acetic acid. Therefore, understanding the anaplerotic pathways in PNSB is crucial for their potential application as producers of biofuels. The present review addresses the recent data on presence and diversity of anaplerotic pathways in PNSB and describes different classifications of these pathways.

Construction of engineered RuBisCO Kluyveromyces marxianus for a dual microbial bioethanol production system

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes play important roles in CO₂ fixation and redox balancing in photosynthetic bacteria. In the present study, the kefir yeast Kluyveromyces marxianus 4G5 was used as host for the transformation of form I and form II RubisCO genes derived from the nonsulfur purple bacterium Rhodopseudomonas palustris using the Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO) method. Hungateiclostridium thermocellum ATCC 27405, a well-known bacterium for its efficient solubilization of recalcitrant lignocellulosic biomass, was used to degrade Napier grass and rice straw to generate soluble fermentable sugars. The resultant Napier grass and rice straw broths were used as growth media for the engineered K. marxianus. In the dual microbial system, H. thermocellum degraded the biomass feedstock to produce both C₅ and C₆ sugars. As the bacterium only used hexose sugars, the remaining pentose sugars could be metabolized by K. marxianus to produce ethanol. The transformant RubisCO K. marxianus strains grew well in hydrolyzed Napier grass and rice straw broths and produced bioethanol more efficiently than the wild type. Therefore, these engineered K. marxianus strains could be used with H. thermocellum in a bacterium-yeast coculture system for ethanol production directly from biomass feedstocks.

Regulatory components of carbon concentrating mechanisms in aquatic unicellular photosynthetic organisms

This review provides an insight into the regulation of the carbon concentrating mechanisms (CCMs) in lower organisms like cyanobacteria, proteobacteria, and algae. CCMs evolved as a mechanism to concentrate CO₂ at the site of primary carboxylating enzyme Ribulose-1, 5-bisphosphate carboxylase oxygenase (Rubisco), so that the enzyme could overcome its affinity towards O₂ which leads to wasteful processes like photorespiration. A diverse set of CCMs exist in nature, i.e., carboxysomes in cyanobacteria and proteobacteria; pyrenoids in algae and diatoms, the C₄ system, and Crassulacean acid metabolism in higher plants. Prime regulators of CCM in most of the photosynthetic autotrophs belong to the LysR family of transcriptional regulators, which regulate the activity of the components of CCM depending upon the ambient CO₂ concentrations. Major targets of these regulators are carbonic anhydrase and inorganic carbon uptake systems (CO₂ and HCO₃^- transporters) whose activities are modulated either at transcriptional level or by changes in the levels of their co-regulatory metabolites. The article provides information on the localization of the CCM components as well as their function and participation in the development of an efficient CCM. Signal transduction cascades leading to activation/inactivation of inducible CCM components on perception of low/high CO₂ stimuli have also been brought into picture. A detailed study of the regulatory components can aid in identifying the unraveled aspects of these mechanisms and hence provide information on key molecules that need to be explored to further provide a clear understanding of the mechanism under study.

Skatole remediation potential of Rhodopseudomonas palustris WKU-KDNS3 isolated from an animal waste lagoon

Skatole (3MI) is a major contributor to the malodor emission resulting from ruminant and human faeces. The remediation of malodor has been a major challenge for the animal production industry. In this investigation, a pure culture of purple nonsulphur bacterium capable of degrading 3MI was isolated from a swine waste lagoon using an enrichment technique and identified as Rhodopseudomonas palustris WKU-KDNS3 based on 16S rRNA analysis and UV-visible spectroscopy. The cell structure of the organism was confirmed by transmission electron microscopy. Growth profile and 3MI removal pattern were determined using media supplemented with 0.1 μmol 3MI under short-term and long-term aerobic growth conditions. The organism grew on 3MI media as luxuriantly as control (without 3MI). Growth of R. palustris WKU-KDNS3 demonstrated a significant reduction in the level of 3MI (>48%) in 72 h. The level of 3MI dropped further by >93% of the total concentration present in the medium in 21 days. Skatole remediation potential of R. palustris WKU-KDNS3 can be judiciously utilized in various animal and industrial waste treatment systems.

SIGNIFICANCE AND IMPACT OF THE STUDY

Odour pollution is a serious environmental problem, particularly in the agriculture industry, and technologies based on chemical remediation are less effective and cost prohibitive. In this study, the newly isolated Rhodopseudomonas palustris strain WKU-KDNS3 causes biodegradation of 3-methylindole (skatole), which is one of the most offensive odorants present in wastewater lagoons. Aerobic degradation of this widely spread aromatic pollutant by Rhodopseudomonas strain is a significant finding that enhances the present understanding about metabolic versatility of purple photosynthetic nonsulphur bacteria. The remediation potential of R. palustris WKU-KDNS3 can also be gainfully utilized in various waste treatment facilities.

A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.

Biohydrogen, biomethane and bioelectricity as crucial components of biorefinery of organic wastes: a review

Biohydrogen is a sustainable form of energy as it can be produced from organic waste through fermentation processes involving dark fermentation and photofermentation. Very often biohydrogen is included as a part of biorefinery approaches, which reclaim organic wastes that are abundant sources of renewable and low cost substrate that can be efficiently fermented by microorganisms. The aim of this work was to critically assess selected bioenergy alternatives from organic solid waste, such as biohydrogen and bioelectricity, to evaluate their relative advantages and disadvantages in the context of biorefineries, and finally to indicate the trends for future research and development. Biorefining is the sustainable processing of biomass into a spectrum of marketable products, which means: energy, materials, chemicals, food and feed. Dark fermentation of organic wastes could be the beach-head of complete biorefineries that generate biohydrogen as a first step and could significantly influence the future of solid waste management. Series systems show a better efficiency than one-stage process regarding substrate conversion to hydrogen and bioenergy. The dark fermentation also produces fermented by-products (fatty acids and solvents), so there is an opportunity for further combining with other processes that yield more bioenergy. Photoheterotrophic fermentation is one of them: photosynthetic heterotrophs, such as non-sulfur purple bacteria, can thrive on the simple organic substances produced in dark fermentation and light, to give more H2. Effluents from photoheterotrophic fermentation and digestates can be processed in microbial fuel cells for bioelectricity production and methanogenic digestion for methane generation, thus integrating a diverse block of bioenergies. Several digestates from bioenergies could be used for bioproducts generation, such as cellulolytic enzymes and saccharification processes, leading to ethanol fermentation (another bioenergy), thus completing the inverse cascade. Finally, biohydrogen, biomethane and bioelectricity could contribute to significant improvements for solid organic waste management in agricultural regions, as well as in urban areas.

Maintaining photosynthetic CO2 fixation via protein remodelling: the Rubisco activases

The key photosynthetic, CO2-fixing enzyme Rubisco forms inactivated complexes with its substrate ribulose 1,5-bisphosphate (RuBP) and other sugar phosphate inhibitors. The independently evolved AAA+ proteins Rubisco activase and CbbX harness energy from ATP hydrolysis to remodel Rubisco complexes, facilitating release of these inhibitors. Here, we discuss recent structural and mechanistic advances towards the understanding of protein-mediated Rubisco activation. Both activating proteins appear to form ring-shaped hexameric arrangements typical for AAA+ ATPases in their functional form, but display very different regulatory and biochemical properties. Considering the thermolability of the plant enzyme, an improved understanding of the mechanism for Rubisco activation may help in developing heat-resistant plants adapted to the challenge of global warming.

Regulatory twist and synergistic role of metabolic coinducer- and response regulator-mediated CbbR-cbbI interactions in Rhodopseudomonas palustris CGA010

Rhodopseudomonas palustris assimilates CO2 by the Calvin-Benson-Bassham (CBB) reductive pentose phosphate pathway. Most genes required for a functional CBB pathway are clustered into the cbbI and cbbII operons, with the cbbI operon subject to control by a LysR transcriptional activator, CbbR, encoded by cbbR, which is divergently transcribed from the cbbLS genes (encoding form I RubisCO) of the cbbI operon. Juxtaposed between the genes encoding CbbR and CbbLS are genes that encode a three-protein two-component system (CbbRRS system) that functions to modify the ability of CbbR to regulate cbbLS expression. Previous studies indicated that the response regulators, as well as various coinducers (effectors), specifically influence CbbR-promoter interactions. In the current study, it was shown via several experimental approaches that the response regulators and coinducers act synergistically on CbbR to influence cbbLS transcription. Synergistic effects on the formation of specific CbbR-DNA complexes were quantified using surface plasmon resonance (SPR) procedures. Gel mobility shift and DNA footprint analyses further indicated structural changes in the DNA arising from the presence of response regulators and coinducer molecules binding to CbbR. Based on previous studies, and especially emphasized by the current investigation, it is clear that protein complexes influence promoter activity and the cbbLS transcription machinery.

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.

Further unraveling the regulatory twist by elucidating metabolic coinducer-mediated CbbR-cbbI promoter interactions in Rhodopseudomonas palustris CGA010

The cbb(I) region of Rhodopseudomonas palustris (Rp. palustris) contains the cbbLS genes encoding form I ribulose-1,5-bisphosphate (RuBP) carboxylase oxygenase (RubisCO) along with a divergently transcribed regulator gene, cbbR. Juxtaposed between cbbR and cbbLS are the cbbRRS genes, encoding an unusual three-protein two-component (CbbRRS) system that modulates the ability of CbbR to influence cbbLS expression. The nature of the metabolic signals that Rp. palustris CbbR perceives to regulate cbbLS transcription is not known. Thus, in this study, the CbbR binding region was first mapped within the cbbLS promoter by the use of gel mobility shift assays and DNase I footprinting. In addition, potential metabolic coinducers (metabolites) were tested for their ability to alter the cbbLS promoter binding properties of CbbR. Gel mobility shift assays and surface plasmon resonance analyses together indicated that biosynthetic intermediates such as RuBP, ATP, fructose 1,6-bisphosphate, and NADPH enhanced DNA binding by CbbR. These coinducers did not yield identical CbbR-dependent DNase I footprints, indicating that the coinducers caused significant changes in DNA structure. These in vitro studies suggest that cellular signals such as fluctuating metabolite concentrations are perceived by and transduced to the cbbLS promoter via the master regulator CbbR.

Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach

Background

Rhodopseudomonas palustris (R. palustris) is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin–Benson–Bassham (CBB) cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach.

Methodology/Principal Findings

By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM) but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC) strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain.

Conclusions/Significance

Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth through both common and divergent metabolic mechanisms.

The poor growth of Rhodospirillum rubrum mutants lacking RubisCO is due to the accumulation of ribulose-1,5-bisphosphate

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the first step of CO(2) fixation in the Calvin-Benson-Bassham (CBB) cycle. Besides its function in fixing CO(2) to support photoautotrophic growth, the CBB cycle is also important under photoheterotrophic growth conditions in purple nonsulfur photosynthetic bacteria. It has been assumed that the poor photoheterotrophic growth of RubisCO-deficient strains was due to the accumulation of excess intracellular reductant, which implied that the CBB cycle is important for maintaining the redox balance under these conditions. However, we present analyses of cbbM mutants in Rhodospirillum rubrum that indicate that toxicity is the result of an elevated intracellular pool of ribulose-1,5-bisphosphate (RuBP). There is a redox effect on growth, but it is apparently an indirect effect on the accumulation of RuBP, perhaps by the regulation of the activities of enzymes involved in RuBP regeneration. Our studies also show that the CBB cycle is not essential for R. rubrum to grow under photoheterotrophic conditions and that its role in controlling the redox balance needs to be further elucidated. Finally, we also show that CbbR is a positive transcriptional regulator of the cbb operon (cbbEFPT) in R. rubrum, as seen with related organisms, and define the transcriptional organization of the cbb genes.

Unravelling the regulatory twist--regulation of CO2 fixation in Rhodopseudomonas palustris CGA010 mediated by atypical response regulator(s)

In Rhodopseudomonas palustris CGA010, the LysR type regulator, CbbR, specifically controls transcription of the cbbLS genes encoding form I RubisCO. Previous genetic and physiological studies had indicated that a unique two-component (CbbRRS) system influences CbbR-mediated cbbLS transcription under conditions where CO(2) is the sole carbon source. In this study, we have established direct protein-protein interactions between the response regulators of the CbbRRS system and CbbR, using a variety of techniques. The bacterial two-hybrid system established a specific interaction between CbbR and CbbRR1 (response regulator 1 of the CbbRRS system), confirmed in vitro by chemical cross-linking. In addition, both response regulators (CbbRR1 and CbbRR2) played distinct roles in influencing the CbbR-cbbLS promoter interactions in gel mobility shift assays. CbbRR1 increased the binding affinity of CbbR at the cbb(I) promoter three- to fivefold while CbbRR2 appeared to stabilize CbbR binding. Specific interactions were further supported by surface plasmon resonance (SPR) analyses. In total, the results suggested that both response regulators, with no discernible DNA-binding domains, must interact with CbbR to influence cbbLS expression. Thus the CbbRRS system provides an additional level of transcriptional control beyond CbbR alone, and appears to be significant for potentially fine-tuning cbbLS expression in Rps. palustris.

Ecological aspects of the distribution of different autotrophic CO2 fixation pathways

Autotrophic CO(2) fixation represents the most important biosynthetic process in biology. Besides the well-known Calvin-Benson cycle, five other totally different autotrophic mechanisms are known today. This minireview discusses the factors determining their distribution. As will be made clear, the observed diversity reflects the variety of the organisms and the ecological niches existing in nature.