Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis

The energy metabolism of Cupriavidus necator in different trophic conditions

The "knallgas" bacterium Cupriavidus necator is attracting interest due to its extremely versatile metabolism. C. necator can use hydrogen or formic acid as an energy source, fixes CO2 via the Calvin-Benson-Bassham (CBB) cycle, and grows on organic acids and sugars. Its tripartite genome is notable for its size and duplications of key genes (CBB cycle, hydrogenases, and nitrate reductases). Little is known about which of these isoenzymes and their cofactors are actually utilized for growth on different substrates. Here, we investigated the energy metabolism of C. necator H16 by growing a barcoded transposon knockout library on succinate, fructose, hydrogen (H2/CO2), and formic acid. The fitness contribution of each gene was determined from enrichment or depletion of the corresponding mutants. Fitness analysis revealed that (i) some, but not all, molybdenum cofactor biosynthesis genes were essential for growth on formate and nitrate respiration. (ii) Soluble formate dehydrogenase (FDH) was the dominant enzyme for formate oxidation, not membrane-bound FDH. (iii) For hydrogenases, both soluble and membrane-bound enzymes were utilized for lithoautotrophic growth. (iv) Of the six terminal respiratory complexes in C. necator H16, only some are utilized, and utilization depends on the energy source. (v) Deletion of hydrogenase-related genes boosted heterotrophic growth, and we show that the relief from associated protein cost is responsible for this phenomenon. This study evaluates the contribution of each of C. necator's genes to fitness in biotechnologically relevant growth regimes. Our results illustrate the genomic redundancy of this generalist bacterium and inspire future engineering strategies.IMPORTANCEThe soil bacterium Cupriavidus necator can grow on gas mixtures of CO2, H2, and O2. It also consumes formic acid as carbon and energy source and various other substrates. This metabolic flexibility comes at a price, for example, a comparatively large genome (6.6 Mb) and a significant background expression of lowly utilized genes. In this study, we mutated every non-essential gene in C. necator using barcoded transposons in order to determine their effect on fitness. We grew the mutant library in various trophic conditions including hydrogen and formate as the sole energy source. Fitness analysis revealed which of the various energy-generating iso-enzymes are actually utilized in which condition. For example, only a few of the six terminal respiratory complexes are used, and utilization depends on the substrate. We also show that the protein cost for the various lowly utilized enzymes represents a significant growth disadvantage in specific conditions, offering a route to rational engineering of the genome. All fitness data are available in an interactive app at https://m-jahn.shinyapps.io/ShinyLib/.

Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches

Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.

Toward a synthetic hydrogen sensor in cyanobacteria: Functional production of an oxygen-tolerant regulatory hydrogenase in Synechocystis sp. PCC 6803

Cyanobacteria have raised great interest in biotechnology, e.g., for the sustainable production of molecular hydrogen (H₂) using electrons from water oxidation. However, this is hampered by various constraints. For example, H₂-producing enzymes compete with primary metabolism for electrons and are usually inhibited by molecular oxygen (O₂). In addition, there are a number of other constraints, some of which are unknown, requiring unbiased screening and systematic engineering approaches to improve the H₂ yield. Here, we introduced the regulatory [NiFe]-hydrogenase (RH) of Cupriavidus necator (formerly Ralstonia eutropha) H16 into the cyanobacterial model strain Synechocystis sp. PCC 6803. In its natural host, the RH serves as a molecular H₂ sensor initiating a signal cascade to express hydrogenase-related genes when no additional energy source other than H₂ is available. Unlike most hydrogenases, the C. necator enzymes are O₂-tolerant, allowing their efficient utilization in an oxygenic phototroph. Similar to C. necator, the RH produced in Synechocystis showed distinct H₂ oxidation activity, confirming that it can be properly matured and assembled under photoautotrophic, i.e., oxygen-evolving conditions. Although the functional H₂-sensing cascade has not yet been established in Synechocystis yet, we utilized the associated two-component system consisting of a histidine kinase and a response regulator to drive and modulate the expression of a superfolder gfp gene in Escherichia coli. This demonstrates that all components of the H₂-dependent signal cascade can be functionally implemented in heterologous hosts. Thus, this work provides the basis for the development of an intrinsic H₂ biosensor within a cyanobacterial cell that could be used to probe the effects of random mutagenesis and systematically identify promising genetic configurations to enable continuous and high-yield production of H₂ via oxygenic photosynthesis.

Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering

Conversion of CO₂ to value-added products presents an opportunity to reduce GHG emissions while generating revenue. Formate, which can be generated by the electrochemical reduction of CO₂, has been proposed as a promising intermediate compound for microbial upgrading. Here we present progress towards improving the soil bacterium Cupriavidus necator H16, which is capable of growing on formate as its sole source of carbon and energy using the Calvin-Benson-Bassham (CBB) cycle, as a host for formate utilization. Using adaptive laboratory evolution, we generated several isolates that exhibited faster growth rates on formate. The genomes of these isolates were sequenced, and resulting mutations were systematically reintroduced by metabolic engineering, to identify those that improved growth. The metabolic impact of several mutations was investigated further using RNA-seq transcriptomics. We found that deletion of a transcriptional regulator implicated in quorum sensing, PhcA, reduced expression of several operons and led to improved growth on formate. Growth was also improved by deleting large genomic regions present on the extrachromosomal megaplasmid pHG1, particularly two hydrogenase operons and the megaplasmid CBB operon, one of two copies present in the genome. Based on these findings, we generated a rationally engineered ΔphcA and megaplasmid-deficient strain that exhibited a 24% faster maximum growth rate on formate. Moreover, this strain achieved a 7% growth rate improvement on succinate and a 19% increase on fructose, demonstrating the broad utility of microbial genome reduction. This strain has the potential to serve as an improved microbial chassis for biological conversion of formate to value-added products.

Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opacus DSM 43205

Hydrogen oxidizing autotrophic bacteria are promising hosts for conversion of CO₂ into chemicals. In this work, we engineered the metabolically versatile lithoautotrophic bacterium R. opacus strain DSM 43205 for synthesis of polymer precursors. Aspartate decarboxylase (panD) or lactate dehydrogenase (ldh) were expressed for beta-alanine or L-lactic acid production, respectively. The heterotrophic cultivations on glucose produced 25 mg L⁻¹ beta-alanine and 742 mg L⁻¹ L-lactic acid, while autotrophic cultivations with CO₂, H₂, and O₂ resulted in the production of 1.8 mg L⁻¹ beta-alanine and 146 mg L⁻¹ L-lactic acid. Beta-alanine was also produced at 345 μg L⁻¹ from CO₂ in electrobioreactors, where H₂ and O₂ were provided by water electrolysis. This work demonstrates that R. opacus DSM 43205 can be engineered to produce chemicals from CO₂ and provides a base for its further metabolic engineering.

Hydrogen-oxidizing bacteria and their applications in resource recovery and pollutant removal

Hydrogen oxidizing bacteria (HOB), a type of chemoautotroph, are a group of bacteria from different genera that share the ability to oxidize H₂ and fix CO₂ to provide energy and synthesize cellular material. Recently, HOB have received growing attention due to their potential for CO₂ capture and waste recovery. This review provides a comprehensive overview of the biological characteristics of HOB and their application in resource recovery and pollutant removal. Firstly, the enzymes, genes and corresponding regulation systems responsible for the key metabolic processes of HOB are discussed in detail. Then, the enrichment and cultivation methods including the coupled water splitting-biosynthetic system cultivation, mixed cultivation and two-stage cultivation strategies for HOB are summarized, which is the critical prerequisite for their application. On the basis, recent advances of HOB application in the recovery of high-value products and the removal of pollutants are presented. Finally, the key points for future investigation are proposed that more attention should be paid to the main limitations in the large-scale industrial application of HOB, including the mass transfer rate of the gases, the safety of the production processes and products, and the commercial value of the products.

The Carbon Source Effect on the Production of Ralstonia eutropha H16 and Proteomic Response Underlying Targeting the Bioconversion with Solar Fuels

Chemoautotrophic bacterium Ralstonia eutropha H16 can fix CO₂ to bioplastic and is potentially useful for CO₂ neutralization. Targeting the solar fuel-based plastic biomanufactory, the polyhydroxybutyrate (PHB) production between heterotrophy and chemoautotrophy conditions was evaluated and the proteomic responses of the R. eutropha H16 cells to different carbon and energy sources were investigated. The results show that the chemoautotrophic mode hardly affected the cellular PHB accumulation capacity. Benefited from the high coverage proteome data, the global response of R. eutropha H16 to different carbon and energy sources was presented with a 95% KEGG pathway annotation, and the genome-wide location-related protein expression pattern was also identified. PHB depolymerase Q0K9H3 was found as a key protein responding to the low carbon input while CO₂ and H₂ were used, and will be a new regulation target for further high PHB production based on solar fuels.

A Review on Biological Synthesis of the Biodegradable Polymers Polyhydroxyalkanoates and the Development of Multiple Applications

Polyhydroxyalkanoates, or PHAs, belong to a class of biopolyesters where the biodegradable PHA polymer is accumulated by microorganisms as intracellular granules known as carbonosomes. Microorganisms can accumulate PHA using a wide variety of substrates under specific inorganic nutrient limiting conditions, with many of the carbon-containing substrates coming from waste or low-value sources. PHAs are universally thermoplastic, with PHB and PHB copolymers having similar characteristics to conventional fossil-based polymers such as polypropylene. PHA properties are dependent on the composition of its monomers, meaning PHAs can have a diverse range of properties and, thus, functionalities within this biopolyester family. This diversity in functionality results in a wide array of applications in sectors such as food-packaging and biomedical industries. In order for PHAs to compete with the conventional plastic industry in terms of applications and economics, the scale of PHA production needs to grow from its current low base. Similar to all new polymers, PHAs need continuous technological developments in their production and material science developments to grow their market opportunities. The setup of end-of-life management (biodegradability, recyclability) system infrastructure is also critical to ensure that PHA and other biobased biodegradable polymers can be marketed with maximum benefits to society. The biobased nature and the biodegradability of PHAs mean they can be a key polymer in the materials sector of the future. The worldwide scale of plastic waste pollution demands a reformation of the current polymer industry, or humankind will face the consequences of having plastic in every step of the food chain and beyond. This review will discuss the aforementioned points in more detail, hoping to provide information that sheds light on how PHAs can be polymers of the future.

Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes

Macrolides are broad-spectrum antibiotics used to treat a range of infections. Resistance to macrolides is often conferred by mobile resistance genes encoding Erm methyltransferases or Mph phosphotransferases. New erm and mph genes keep being discovered in clinical settings but their origins remain unknown, as is the type of macrolide resistance genes that will appear in the future. In this study, we used optimized hidden Markov models to characterize the macrolide resistome. Over 16 terabases of genomic and metagenomic data, representing a large taxonomic diversity (11 030 species) and diverse environments (1944 metagenomic samples), were searched for the presence of erm and mph genes. From this data, we predicted 28 340 macrolide resistance genes encoding 2892 unique protein sequences, which were clustered into 663 gene families (<70 % amino acid identity), of which 619 (94 %) were previously uncharacterized. This included six new resistance gene families, which were located on mobile genetic elements in pathogens. The function of ten predicted new resistance genes were experimentally validated in Escherichia coli using a growth assay. Among the ten tested genes, seven conferred increased resistance to erythromycin, with five genes additionally conferring increased resistance to azithromycin, showing that our models can be used to predict new functional resistance genes. Our analysis also showed that macrolide resistance genes have diverse origins and have transferred horizontally over large phylogenetic distances into human pathogens. This study expands the known macrolide resistome more than ten-fold, provides insights into its evolution, and demonstrates how computational screening can identify new resistance genes before they become a significant clinical problem.

What makes a megaplasmid?

Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids—known as megaplasmids—are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements.

This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

Investigation of the robustness of Cupriavidus necator engineered strains during fed-batch cultures

It is of major interest to ensure stable and performant microbial bioprocesses, therefore maintaining high strain robustness is one of the major future challenges in industrial microbiology. Strain robustness can be defined as the persistence of genotypic and/or phenotypic traits in a system. In this work, robustness of an engineered strain is defined as plasmid expression stability, cultivability, membrane integrity and macroscopic cell behavior and was assessed in response to implementations of sugar feeding strategies (pulses and continuous) and two plasmid stabilization systems (kanamycin resistance and Post-Segregational Killing hok/sok). Fed-batch bioreactor cultures, relevant mode to reach high cell densities and higher cell generation number, were implemented to investigate the robustness of C. necator engineered strains. Host cells bore a recombinant plasmid encoding for a plasmid expression level monitoring system, based on eGFP fluorescence quantified by flow cytometry. We first showed that well-controlled continuous feeding in comparison to a pulse-based feeding allowed a better carbon use for protein synthesis (avoiding organic acid excretion), a lower heterogeneity of the plasmid expression and a lower cell permeabilization. Moreover, the plasmid stabilization system Post-Segregational Killing hok/sok, an autonomous system independent on external addition of compounds, showed the best ability to maintain plasmid expression level stability insuring a greater population homogeneity in the culture. Therefore, in the case of engineered C. necator, the PSK system hok/sok appears to be a relevant and an efficient alternative to antibiotic resistance system for selection pressure, especially, in the case of bioprocess development for economic and environmental reasons.

Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO2 valorization

BACKGROUND

CO₂ valorization is one of the effective methods to solve current environmental and energy problems, in which microbial electrosynthesis (MES) system has proved feasible and efficient. Cupriviadus necator (Ralstonia eutropha) H16, a model chemolithoautotroph, is a microbe of choice for CO₂ conversion, especially with the ability to be employed in MES due to the presence of genes encoding [NiFe]-hydrogenases and all the Calvin-Benson-Basham cycle enzymes. The CO₂ valorization strategy will make sense because the required hydrogen can be produced from renewable electricity independently of fossil fuels.

MAIN BODY

In this review, synthetic biology toolkit for C. necator H16, including genetic engineering vectors, heterologous gene expression elements, platform strain and genome engineering, and transformation strategies, is firstly summarized. Then, the review discusses how to apply these tools to make C. necator H16 an efficient cell factory for converting CO₂ to value-added products, with the examples of alcohols, fatty acids, and terpenoids. The review is concluded with the limitation of current genetic tools and perspectives on the development of more efficient and convenient methods as well as the extensive applications of C. necator H16.

CONCLUSIONS

Great progress has been made on genetic engineering toolkit and synthetic biology applications of C. necator H16. Nevertheless, more efforts are expected in the near future to engineer C. necator H16 as efficient cell factories for the conversion of CO₂ to value-added products.

The over-expression of phasin and regulator genes promoting the synthesis of polyhydroxybutyrate in Cupriavidus necator H16 under non-stress conditions

Cupriavidus necator H16 is an ideal strain for polyhydroxybutyrate (PHB) production from CO₂. Low-oxygen-stress can induce PHB synthesis in C. necator H16 while reducing bacterial growth under chemoautotrophic culture. The optimum growth and PHB synthesis of C. necator H16 cannot be achieved simultaneously, which restricts PHB production. The present study was initiated to address the issue through comparative transcriptome and gene function analysis. Firstly, the comparative transcriptome of C. necator H16 chemoautotrophically cultured under low-oxygen-stress and non-stress conditions was studied. Three types of transcription different genes were discovered: PHB enzymatic synthesis, PHB granulation, and regulators. Under low-oxygen-stress condition, acetoacetyl-CoA reductase gene phaB2, PHB synthase gene phaC2, phasins genes phaP1 and phaP2, regulators genes uspA and rpoN were up-regulated 3.0, 2.5, 1.8, 2.7, 3.5, 1.6 folds, respectively. Secondly, the functions of up-regulated genes and their applications in PHB synthesis were further studied. It was found that the over-expression of phaP1, phaP2, uspA, and rpoN can induce PHB synthesis under non-stress condition, while phaB2 and phaC2 have no significant effect. Under the optimum condition, PHB percentage content in C. necator H16 was respectively increased by 37.2%, 28.4%, 15.8%, and 41.0% with the over-expression of phaP1, phaP2, uspA, and rpoN, and the corresponding PHB production increased by 49.8%, 42.9%, 47.0%, and 77.5% under non-stress chemoautotrophic conditions. Similar promotion by phaP1, phaP2, uspA, and rpoN was observed in heterotrophically cultured C. necator H16. The PHB percentage content and PHB production were respectively increased by 54.4% and 103.1% with the over-expression of rpoN under non-stress heterotrophic conditions. Importance Microbial fixation of CO₂ is an effective way to reduce greenhouse gases. Some microbes such as C. necator H16 usually accumulate PHB when they grow under stress. Low-oxygen-stress can induce PHB synthesis when C. necator H16 is autotrophically cultured with CO₂, H₂, and O₂, while under stress, growth is restricted and total PHB yield is reduced. Achieving the optimal bacterial growth and PHB synthesis at the same time is an ideal condition for transforming CO₂ into PHB by C. necator H16. The present study was initiated to clarify the molecular basis of low-oxygen-stress promoting PHB accumulation and to realize the optimal PHB production by C. necator H16. Genes up-regulated under non-stress conditions were identified through comparative transcriptome analysis and over-expression of phasin and regulator genes were demonstrated to promote PHB synthesis in C. necator H16.

Cupriavidus metallidurans CH34, a historical perspective on its discovery, characterization and metal resistance

Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its isolation in 1976. This minireview describes the early research and legacy tools used to study its metal resistance determinants, characteristic megaplasmids, ecological niches and environmental applications.

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes

Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO₂ to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO₂ emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO₂ to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO₂. Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO₂.

Engineering the Calvin-Benson-Bassham cycle and hydrogen utilization pathway of Ralstonia eutropha for improved autotrophic growth and polyhydroxybutyrate production

Background

CO₂ is fixed by all living organisms with an autotrophic metabolism, among which the Calvin–Benson–Bassham (CBB) cycle is the most important and widespread carbon fixation pathway. Thus, studying and engineering the CBB cycle with the associated energy providing pathways to increase the CO₂ fixation efficiency of cells is an important subject of biological research with significant application potential.

Results

In this work, the autotrophic microbe Ralstonia eutropha (Cupriavidus necator) was selected as a research platform for CBB cycle optimization engineering. By knocking out either CBB operon genes on the operon or mega-plasmid of R. eutropha, we found that both CBB operons were active and contributed almost equally to the carbon fixation process. With similar knock-out experiments, we found both soluble and membrane-bound hydrogenases (SH and MBH), belonging to the energy providing hydrogenase module, were functional during autotrophic growth of R. eutropha. SH played a more significant role. By introducing a heterologous cyanobacterial RuBisCO with the endogenous GroES/EL chaperone system(A quality control systems for proteins consisting of molecular chaperones and proteases, which prevent protein aggregation by either refolding or degrading misfolded proteins) and RbcX(A chaperone in the folding of Rubisco), the culture OD₆₀₀ of engineered strain increased 89.2% after 72 h of autotrophic growth, although the difference was decreased at 96 h, indicating cyanobacterial RuBisCO with a higher activity was functional in R. eutropha and lead to improved growth in comparison to the host specific enzyme. Meanwhile, expression of hydrogenases was optimized by modulating the expression of MBH and SH, which could further increase the R. eutropha H16 culture OD₆₀₀ to 93.4% at 72 h. Moreover, the autotrophic yield of its major industrially relevant product, polyhydroxybutyrate (PHB), was increased by 99.7%.

Conclusions

To our best knowledge, this is the first report of successfully engineering the CBB pathway and hydrogenases of R. eutropha for improved activity, and is one of only a few cases where the efficiency of CO₂ assimilation pathway was improved. Our work demonstrates that R. eutropha is a useful platform for studying and engineering the CBB for applications.

Metabolic pathway analysis for in silico design of efficient autotrophic production of advanced biofuels

Herein, autotrophic metabolism of Cupriavidus necator H16 growing on CO2, H2 and O2 gas mixture was analyzed by metabolic pathway analysis tools, specifically elementary mode analysis (EMA) and flux balance analysis (FBA). As case studies, recombinant strains of C. necator H16 for the production of short-chain (isobutanol) and long-chain (hexadecanol) alcohols were constructed and examined by a combined tools of EMA and FBA to comprehensively identify the cell’s metabolic flux profiles and its phenotypic spaces for the autotrophic production of recombinant products. The effect of genetic perturbations via gene deletion and overexpression on phenotypic space of the organism was simulated to improve strain performance for efficient bioconversion of CO2 to products at high yield and high productivity. EMA identified multiple gene deletion together with controlling gas input composition to limit phenotypic space and push metabolic fluxes towards high product yield, while FBA identified target gene overexpression to debottleneck rate-limiting fluxes, hence pulling more fluxes to enhance production rate of the products. A combination of gene deletion and overexpression resulted in designed mutant strains with a predicted yield of 0.21–0.42 g/g for isobutanol and 0.20–0.34 g/g for hexadecanol from CO2. The in silico-designed mutants were also predicted to show high productivity of up to 38.4 mmol/cell-h for isobutanol and 9.1 mmol/cell-h for hexadecanol under autotrophic cultivation. The metabolic modeling and analysis presented in this study could potentially serve as a valuable guidance for future metabolic engineering of C. necator H16 for an efficient CO2-to-biofuels conversion.

Exploiting Hydrogenophaga pseudoflava for aerobic syngas-based production of chemicals

Gasification is a suitable technology to generate energy-rich synthesis gas (syngas) from biomass or waste streams, which can be utilized in bacterial fermentation processes for the production of chemicals and fuels. Established microbial processes currently rely on acetogenic bacteria which perform an energetically inefficient anaerobic CO oxidation and acetogenesis potentially hampering the biosynthesis of complex and ATP-intensive products. Since aerobic oxidation of CO is energetically more favorable, we exploit in this study the Gram-negative β-proteobacterium Hydrogenophaga pseudoflava DSM1084 as novel host for the production of chemicals from syngas. We sequenced and annotated the genome of H. pseudoflava and established a genetic engineering toolbox, which allows markerless chromosomal modification via the pk19mobsacB system and heterologous gene expression on pBBRMCS2-based plasmids. The toolbox was extended by identifying strong endogenous promotors such as P_gapA2 which proved to yield high expression under heterotrophic and autotrophic conditions. H. pseudoflava showed relatively fast heterotrophic growth in complex and minimal medium with sugars and organic acids which allows convenient handling in lab routines. In autotrophic bioreactor cultivations with syngas, H. pseudoflava exhibited a growth rate of 0.06 h^-1 and biomass specific uptakes rates of 14.2 ± 0.3 mmol H₂ g_CDW^-1 h^-1, 73.9 ± 1.8 mmol CO g_CDW^-1 h^-1, and 31.4 ± 0.3 mmol O₂ g_CDW^-1 h^-1. As proof of concept, we engineered the carboxydotrophic bacterium for the aerobic production of the C₁₅ sesquiterpene (E)-α-bisabolene from the C₁ carbon source syngas by heterologous expression of the (E)-α-bisabolene synthase gene agBIS. The resulting strain H. pseudoflava (pOCEx1:agBIS) produced 59 ± 8 μg (E)-α-bisabolene L^-1 with a volumetric productivity Q_p of 1.2 ± 0.2 μg L^-1 h^-1 and a biomass-specific productivity q_p of 13.1 ± 0.6 μg g_CDW^-1 h^-1. The intrinsic properties and the genetic repertoire of H. pseudoflava make this carboxydotrophic bacterium a promising candidate for future aerobic production processes to synthesize more complex or ATP-intensive chemicals from syngas.

Efficient biochemical production of acetoin from carbon dioxide using Cupriavidus necator H16

BACKGROUND

Cupriavidus necator is the best-studied knallgas (also termed hydrogen oxidizing) bacterium and provides a model organism for studying the production of the storage polymer polyhydroxybutyrate (PHB). Genetically engineered strains could be applied for the autotrophic production of valuable chemicals. Nevertheless, the efficiency of the catalyzed processes is generally believed to be lower than with acetogenic bacteria. Experimental data on the potential efficiency of autotrophic production with C. necator are sparse. Hence, this study aimed at developing a strain for the production of the bulk chemical acetoin from carbon dioxide and to analyze the carbon and electron yield in detail.

RESULTS

We developed a constitutive promoter system based on the natural PHB promoter of this organism. Codon-optimized versions of the acetolactate dehydrogenase (alsS) and acetolactate decarboxylase (alsD) from Bacillus subtilis were cloned under control of the PHB promoter in order to produce acetoin from pyruvate. The production process's efficiency could be significantly increased by deleting the PHB synthase phaC2. Further deletion of the other PHB synthase encoded in the genome (phaC1) led to a strain that produced acetoin with > 100% carbon efficiency. This increase in efficiency is most probably due to a minor amount of cell lysis. Using a variation in hydrogen and oxygen gas mixtures, we observed that the optimal oxygen concentration for the process was between 15 and 20%.

CONCLUSION

To the best of our knowledge, this study describes for the first time a highly efficient process for the chemolithoautotrophic production of the platform chemical acetoin.

Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

BACKGROUND

Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism. Yet, numerous experiments have underlined XCL-2's inability to consume hydrogen under the tested conditions. A recent study showed that the closely related strain SP-41 contains a homolog of the XCL-2 hydrogenase (a group 1b [NiFe]-hydrogenase), but that it can indeed use hydrogen. Hence, the question remained unresolved, why SP-41 is capable of using hydrogen, while XCL-2 is not.

RESULTS

Here, we present the genome sequence of the SP-41 strain and compare it to that of the XCL-2 strain. We show that the chromosome of SP-41 codes for a further hydrogenase gene cluster, including two additional hydrogenases: the first appears to be a group 1d periplasmic membrane-anchored hydrogenase, and the second a group 2b sensory hydrogenase. The region where these genes are located was likely acquired horizontally and exhibits similarity to other Hydrogenovibrio species (H. thermophilus MA2-6 and H. marinus MH-110 T) and other hydrogen oxidizing Proteobacteria (Cupriavidus necator H16 and Ghiorsea bivora TAG-1 T). The genomes of XCL-2 and SP-41 show a strong conservation in gene order. However, several short genomic regions are not contained in the genome of the other strain. These exclusive regions are often associated with signs of DNA mobility, such as genes coding for transposases. They code for transport systems and/or extend the metabolic potential of the strains.

CONCLUSIONS

Our results suggest that horizontal gene transfer plays an important role in shaping the genomes of these strains, as a likely mechanism for habitat adaptation, including, but not limited to the transfer of the hydrogen conversion ability.

Comparative genome analysis of completely sequenced Cupriavidus genomes provides insights into the biosynthetic potential and versatile applications of Cupriavidus alkaliphilus ASC-732

The genome analysis of microorganisms provides valuable information to endorse more extensive research on their potential applications. In this paper, the genome of Cupriavidus alkaliphilus ASC-732, isolated from agave rhizosphere in northeastern Mexico, was analyzed and compared with the genomes of other Cupriavidus species to gain better insight into the parts in the genetic makeup responsible for essential metabolic pathways and others of biotechnological importance. Here, the key genes related to glycolysis, pentose phosphate, and the Entner-Doudoroff and tricarboxylic acid cycle pathways were predicted. Comparative genome analysis revealed that the key genes for hydrogenotrophic growth and carbon fixation pathway, i.e., those coding for hydrogenase and enzymes Calvin-Benson-Bassham cycle, are absent in C. alkaliphilus ASC-732. Furthermore, capabilities for producing polyhydroxyalkanoates and extracellular polysaccharide matrix and degrading xenobiotics were found, and the related pathways are explained. Moreover, biofilm formation and the production of exopolysaccharides and polyhydroxyalkanoates were corroborated with crystal violet staining, calcofluor, and Nile red fluorochromes, confirming the presence of the products of the active genes in these pathways and their related metabolic routes, respectively. Additionally, a large group of genes essential for the resistance and detoxification of several heavy metals were also found. Thus, the present study demonstrates that this strain can respond to various environmental signals, such as energy source, nutrient limitations, virulence, and extreme metals concentration, indicating the possibility to foster C. alkaliphilus ASC-732 in diverse biotechnological applications.

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.

Development of an autotrophic fermentation technique for the production of fatty acids using an engineered Ralstonia eutropha cell factory

Massive emission of CO₂ into atmosphere from consumption of carbon deposit is causing climate change. Researchers have applied metabolic engineering and synthetic biology techniques for improving CO₂ fixation efficiency in many species. One solution might be the utilization of autotrophic bacteria, which have great potential to be engineered into microbial cell factories for CO₂ fixation and the production of chemicals, independent of fossil resources. In this work, several pathways of Ralstonia eutropha H16 were modulated by manipulation of heterologous and endogenous genes related to fatty acid synthesis. The resulting strain B2(pCT, pFP) was able to produce 124.48 mg/g (cell dry weight) free fatty acids with fructose as carbon source, a fourfold increase over the parent strain H16. To develop a truly autotrophic fermentation technique with H₂, CO₂ and O₂ as substrates, we assembled a relatively safe, continuous, lab-scale gas fermentation system using micro-fermentation tanks, H₂ supplied by a hydrogen generator, and keeping the H₂ to O₂ ratio at 7:1. The system was equipped with a H₂ gas alarm, rid of heat sources and placed into a fume hood to further improve the safety. With this system, the best strain B2(pCT, pFP) produced 60.64 mg free fatty acids per g biomass within 48 h, growing in minimal medium supplemented with 9 × 10³ mL/L/h hydrogen gas. Thus, an autotrophic fermentation technique to produce fatty acids was successfully established, which might inspire further research on autotrophic gas fermentation with a safe, lab-scale setup, and provides an alternative solution for environmental and energy problems.

Contribution of the Cpx envelope stress system to metabolism and virulence regulation in Salmonella enterica serovar Typhimurium

The Cpx-envelope stress system regulates the expression of virulence factors in many Gram-negative pathogens. In Salmonella enterica serovar Typhimurium deletion of the sensor kinase CpxA but not of the response regulator CpxR results in the down regulation of the key regulator for invasion, HilA encoded by the Salmonella pathogenicity island 1 (SPI-1). Here, we provide evidence that cpxA deletion interferes with dephosphorylation of CpxR resulting in increased levels of active CpxR and consequently in misregulation of target genes. 14 potential operons were identified to be under direct control of CpxR. These include the virulence determinants ecotin, the omptin PgtE, and the SPI-2 regulator SsrB. The Tat-system and the PocR regulator that together promote anaerobic respiration of tetrathionate on 1,2-propanediol are also under direct CpxR control. Notably, 1,2-propanediol represses hilA expression. Thus, our work demonstrates for the first time the involvement of the Cpx system in a complex network mediating metabolism and virulence function.

The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16

BACKGROUND

3-Hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this study, the native 3-HP metabolism of Cupriavidus necator was investigated and manipulated as it represents a promising chassis for the production of 3-HP and other fatty acid derivatives from CO₂ and H₂.

RESULTS

When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy, a highly undesirable trait in the context of biological 3-HP production which required elimination. Inactivation of the methylcitrate pathway needed for propionate utilisation did not affect the organism's ability to grow on 3-HP. Putative genes involved in 3-HP degradation were identified by bioinformatics means and confirmed by transcriptomic analyses, the latter revealing considerably increased expression in the presence of 3-HP. Genes identified in this manner encoded three putative (methyl)malonate semialdehyde dehydrogenases (mmsA1, mmsA2 and mmsA3) and two putative dehydrogenases (hpdH and hbdH). These genes, which are part of three separate mmsA operons, were inactivated through deletion of the entire coding region, either singly or in various combinations, to engineer strains unable to grow on 3-HP. Whilst inactivation of single genes or double deletions could only delay but not abolish growth, a triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain was unable utilise 3-HP as the sole source of carbon and energy. Under the used conditions this strain was also unable to co-metabolise 3-HP alongside other carbon and energy sources such as fructose and CO₂/H₂. Further analysis suggested primary roles for the different mmsA operons in the utilisation of β-alanine generating substrates (mmsA1), degradation of 3-HP (mmsA2), and breakdown of valine (mmsA3).

CONCLUSIONS

Three different (methyl)malonate semialdehyde dehydrogenases contribute to 3-HP breakdown in C. necator H16. The created triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain represents an ideal chassis for autotrophic 3-HP production.

Environmental strains potentially contribute to the proliferation and maintenance of antibiotic resistance in drinking water: A case study of Cupriavidus metallidurans

Fitness costs of antibiotic resistance detrimentally affect the fate of resistance carriers. Intriguingly, numerous antibiotic resistant bacteria (ARB) have been detected despite the low concentration of antibiotics in drinking water. To reveal the causes of this discrepancy, we investigated the fitness cost of antimicrobial resistance in strain Cupriavidus metallidurans CR2 which was isolated from a drinking water filter. Pure culture and 1:1 competitive experiments were established at different nutrient levels. The growth rates of strain C. metallidurans CR2 significantly decreased when pure cultured under poor nutrient conditions, however, the multi-resistance and the resistance megaplasmids were well maintained. Competitiveness costs were observed in C. metallidurans when separately co-cultured with environmentally-isolated Flectobacillus BS1 and Pseudomonas sp. S3, while C. metallidurans was outnumbered by the rivals with a decrease of 1-2 logs. But the majority of C. metallidurans retained the plasmids under oligotrophic conditions even after 144 h (1.99 and 0.199 mg C/L). Additionally, C. metallidurans CR2 has a higher tolerance to chlorine and chloramine, which potentially could become prevalent in the subsequent distribution systems other than drinking water treatment plant. As a potential pathogen, the prevalence of Cupriavidus metallidurans in drinking water would also pose certain threats to human health.

Algae induce siderophore biosynthesis in the freshwater bacterium Cupriavidus necator H16

Cupriachelin is a photoreactive lipopeptide siderophore produced by the freshwater bacterium Cupriavidus necator H16. In the presence of sunlight, the iron-loaded siderophore undergoes photolytic cleavage, thereby releasing solubilized iron into the environment. This iron is not only available to the siderophore producer, but also to the surrounding microbial community. In this study, the cupriachelin-based interaction between C. necator H16 and the freshwater diatom Navicula pelliculosa was investigated. A reporter strain of the bacterium was constructed to study differential expression levels of the cupriachelin biosynthesis gene cucJ in response to varying environmental conditions. Not only iron starvation, but also culture supernatants of N. pelliculosa were found to induce cupriachelin biosynthesis. The transcription factors involved in this differential gene expression were identified using DNA-protein pulldown assays. Besides the well-characterized ferric uptake regulator, a two-component system was found to tune the expression of cupriachelin biosynthesis genes in the presence of diatom supernatants.

Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes

Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.

Sequential processing with fermentative Caldicellulosiruptor kronotskyensis and chemolithoautotrophic Cupriavidus necator for converting rice straw and CO2 to polyhydroxybutyrate

Unpretreated rice straw was fermented by the extremely thermophilic bacterium Caldicellulosiruptor kronotskyensis, generating solubilized carbohydrates, organic acids, lignin-derived aromatics, H₂ , and CO₂ , which were subsequently used to produce polyhydroxybutyrate (PHB) by the chemolithoautotrophic bacterium Cupriavidus necator. The fermented liquid significantly enhanced the growth of C. necator, leading to a five-fold cell biomass yield, and a nine-fold PHB yield compared to what was obtained from conventional mineral media. This integrated process utilized all products of lignocellulose fermentation without H (electron) loss and carbon emission, while concomitantly enhancing CO₂ fixation by C. necator for PHB production. The sequential coupling of C. kronotskyensis and C. necator provides not only a new biorefinery paradigm characterized by reduced pretreatment and saccharification requirements but also an efficient way for enhancing CO₂ fixation.

13C-assisted metabolic flux analysis to investigate heterotrophic and mixotrophic metabolism in Cupriavidus necator H16

INTRODUCTION

Cupriavidus necator H16 is a gram-negative bacterium, capable of lithoautotrophic growth by utilizing hydrogen as an energy source and fixing carbon dioxide (CO2) through Calvin-Benson-Bassham (CBB) cycle. The potential to utilize synthesis gas (Syngas) and the prospects of rerouting carbon from polyhydroxybutyrate synthesis to value-added compounds makes C. necator an excellent chassis for industrial application.

OBJECTIVES

In the context of lack of sufficient quantitative information of the metabolic pathways and to advance in rational metabolic engineering for optimized product synthesis in C. necator H16, we carried out a metabolic flux analysis based on steady-state 13C-labelling.

METHODS

In this study, steady-state carbon labelling experiments, using either d-[1-13C]fructose or [1,2-13C]glycerol, were undertaken to investigate the carbon flux through the central carbon metabolism in C. necator H16 under heterotrophic and mixotrophic growth conditions, respectively.

RESULTS

We found that the CBB cycle is active even under heterotrophic condition, and growth is indeed mixotrophic. While Entner-Doudoroff (ED) pathway is shown to be the major route for sugar degradation, tricarboxylic acid (TCA) cycle is highly active in mixotrophic condition. Enhanced flux is observed in reductive pentose phosphate pathway (redPPP) under the mixotrophic condition to supplement the precursor requirement for CBB cycle. The flux distribution was compared to the mRNA abundance of genes encoding enzymes involved in key enzymatic reactions of the central carbon metabolism.

CONCLUSION

This study leads the way to establishing 13C-based quantitative fluxomics for rational pathway engineering in C. necator H16.

Minimal Influence of [NiFe] Hydrogenase on Hydrogen Isotope Fractionation in H2-Oxidizing Cupriavidus necator

Fatty acids produced by H₂-metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons for such a depletion are not known, but are often assumed to involve the strong D-depletion of H₂. Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H₂-consuming, chemoautotrophic conditions and measured the isotopic compositions of its fatty acids. In parallel with the wild type, two mutants of this strain, each lacking one of two key hydrogenase enzymes, were also grown and measured. In all three strains, fractionations between fatty acids and water ranged from -173‰ to -235‰, and averaged -217‰, -196‰, and -226‰, respectively, for the wild type, SH^- mutant, and MBH^- mutant. There was a modest increase in δD as a result of loss of the soluble hydrogenase enzyme. Fractionation curves for all three strains were constructed by growing parallel cultures in waters with δD_water values of approximately -25‰, 520‰, and 1100‰. These curves indicate that at least 90% of the hydrogen in fatty acids is derived from water, not H₂. Published details of the biochemistry of the soluble and membrane-bound hydrogenases confirm that these enzymes transfer electrons rather than intact hydride (H^-) ions, providing no direct mechanism to connect the isotopic composition of H₂ to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H₂ plays little or no direct role in controlling lipid δD values. The observed fractionations must instead result from isotope effects in the reduction of NAD(P)H by reductases with flavin prosthetic groups, which transfer two electrons and acquire H⁺ (or D⁺) from solution. Parallels to NADPH reduction in photosynthesis may explain why D/H fractionations in C. necator are nearly identical to those in many photoautotrophic algae and bacteria. We conclude that strong D-depletion is not a diagnostic feature of chemoautotrophy.

Polyhydroxyalkanoate-associated phasins as phylogenetically heterogeneous, multipurpose proteins

Polyhydroxyalkanoates (PHAs) are natural polyesters of increasing biotechnological importance that are synthesized by many prokaryotic organisms as carbon and energy storage compounds in limiting growth conditions. PHAs accumulate intracellularly in form of inclusion bodies that are covered with a proteinaceous surface layer (granule-associated proteins or GAPs) conforming a network-like surface of structural, metabolic and regulatory polypeptides, and configuring the PHA granules as complex and well-organized subcellular structures that have been designated as 'carbonosomes'. GAPs include several enzymes related to PHA metabolism (synthases, depolymerases and hydroxylases) together with the so-called phasins, an heterogeneous group of small-size proteins that cover most of the PHA granule and that are devoid of catalytic functions but nevertheless play an essential role in granule structure and PHA metabolism. Structurally, phasins are amphiphilic proteins that shield the hydrophobic polymer from the cytoplasm. Here, we summarize the characteristics of the different phasins identified so far from PHA producer organisms and highlight the diverse opportunities that they offer in the Biotechnology field.

The Molecular Level Characterization of Biodegradable Polymers Originated from Polyethylene Using Non-Oxygenated Polyethylene Wax as a Carbon Source for Polyhydroxyalkanoate Production

There is an increasing demand for bio-based polymers that are developed from recycled materials. The production of biodegradable polymers can include bio-technological (utilizing microorganisms or enzymes) or chemical synthesis procedures. This report demonstrates the corroboration of the molecular structure of polyhydroxyalkanoates (PHAs) obtained by the conversion of waste polyethylene (PE) via non-oxygenated PE wax (N-PEW) as an additional carbon source for a bacterial species. The N-PEW, obtained from a PE pyrolysis reaction, has been found to be a beneficial carbon source for PHA production with Cupriavidus necator H16. The production of the N-PEW is an alternative to oxidized polyethylene wax (O-PEW) (that has been used as a carbon source previously) as it is less time consuming to manufacture and offers fewer industrial applications. A range of molecular structural analytical techniques were performed on the PHAs obtained; which included nuclear magnetic resonance (NMR) and electrospray ionisation tandem mass spectrometry (ESI-MS/MS). Our study showed that the PHA formed from N-PEW contained 3-hydroxybutyrate (HB) with 11 mol% of 3-hydroxyvalerate (HV) units.

Growth medium and electrolyte-How to combine the different requirements on the reaction solution in bioelectrochemical systems using Cupriavidus necator

Microbial electrosynthesis is a relatively new research field where microbial carbon dioxide fixation based on the energy supplied by a cathode is investigated. Reaction media used in such bioelectrochemical systems have to fulfill requirements of classical biotechnology as well as electrochemistry. The design and characterization of a medium that enables fast electroautotrophic growth of Cupriavidus necator in microbial electrosynthesis was investigated in detail. The identified chloride-free medium mainly consists of low buffer concentration and is supplied with trace elements. Biotechnologically relevant parameters, such as high-specific growth rates and short lag phases, were determined for growth characterization. Fast growth under all conditions tested, i.e. heterotrophic, autotrophic and electroautotrophic was achieved. The lag phase was shortened by increasing the FeSO₄ concentration. Additionally, electrochemical robustness of the reaction media was proven. Under reductive conditions, no deposits on electrodes or precipitations in the media were observed and no detectable hydrogen peroxide evolved. In the bioelectrochemical system, no lag phase occurred and specific growth rate of C. necator was 0.09 h⁻¹. Using this medium shortens seed train drastically and enables fast electrobiotechnological production processes based on C. necator.

Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates

Synthesis of poly-[3-hydroxybutyrate] (PHB) by Cupriavidus necator H16 in batch cultures was evaluated using three biodiesel-derived by-products as the sole carbon sources: waste glycerol (REG-80, refined to 80 % purity with negligible free fatty acids); glycerol bottom (REG-GB, with up to 65 % glycerol and 35 % free fatty acids), and free fatty acids (REG-FFA, with up to 75 % FFA and no glycerol). All the three substrates supported growth and PHB production by C. necator, with polymer accumulation ranging from 9 to 84 % cell dry weight (cdw), depending on the carbon source. To help understand these differences, proteomic analysis indicated that although C. necator H16 was able to accumulate PHB during growth on all three biodiesel by-products, no changes in the levels of PHB synthesis enzymes were observed. However, significant changes in the levels of expression were observed for two Phasin proteins involved with PHB accumulation, and for a number of gene products in the fatty acid β-oxidation pathway, the Glyoxylate Shunt, and the hydrogen (H2) synthesis pathways in C. necator cells cultured with different substrates. The glycerol transport protein (GlpF) was induced in REG-GB and REG-80 glycerol cultures only. Cupriavidus necator cells cultured with REG-GB and REG-FFA showed up-regulation of β-oxidation and Glyoxylate Shunt pathways proteins at 24 h pi, but H2 synthesis pathways enzymes were significantly down-regulated, compared with cells cultured with waste glycerol. Our data confirmed earlier observations of constitutive expression of PHB synthesis proteins, but further suggested that C. necator H16 cells growing on biodiesel-derived glycerol were under oxidative stress.

Construction and use of a Cupriavidus necator H16 soluble hydrogenase promoter (PSH) fusion to gfp (green fluorescent protein)

Hydrogenases are metalloenzymes that reversibly catalyse the oxidation or production of molecular hydrogen (H₂). Amongst a number of promising candidates for application in the oxidation of H₂ is a soluble [Ni–Fe] uptake hydrogenase (SH) produced by Cupriavidus necator H16. In the present study, molecular characterisation of the SH operon, responsible for functional SH synthesis, was investigated by developing a green fluorescent protein (GFP) reporter system to characterise P_SH promoter activity using several gene cloning approaches. A P_SH promoter-gfp fusion was successfully constructed and inducible GFP expression driven by the P_SH promoter under de-repressing conditions in heterotrophic growth media was demonstrated in the recombinant C. necator H16 cells. Here we report the first successful fluorescent reporter system to study P_SH promoter activity in C. necator H16. The fusion construct allowed for the design of a simple screening assay to evaluate P_SH activity. Furthermore, the constructed reporter system can serve as a model to develop a rapid fluorescent based reporter for subsequent small-scale process optimisation experiments for SH expression.

Plasmid-Mediated Tolerance Toward Environmental Pollutants

The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.

Atmospheric hydrogen scavenging: from enzymes to ecosystems

We have known for 40 years that soils can consume the trace amounts of molecular hydrogen (H2) found in the Earth’s atmosphere.This process is predicted to be the most significant term in the global hydrogen cycle. However, the organisms and enzymes responsible for this process were only recently identified. Pure culture experiments demonstrated that several species of Actinobacteria, including streptomycetes and mycobacteria, can couple the oxidation of atmospheric H2 to the reduction of ambient O2. A combination of genetic, biochemical, and phenotypic studies suggest that these organisms primarily use this fuel source to sustain electron input into the respiratory chain during energy starvation. This process is mediated by a specialized enzyme, the group 5 [NiFe]-hydrogenase, which is unusual for its high affinity, oxygen insensitivity, and thermostability. Atmospheric hydrogen scavenging is a particularly dependable mode of energy generation, given both the ubiquity of the substrate and the stress tolerance of its catalyst. This minireview summarizes the recent progress in understanding how and why certain organisms scavenge atmospheric H2. In addition, it provides insight into the wider significance of hydrogen scavenging in global H2 cycling and soil microbial ecology.