Relaxed control of sugar utilization in Parageobacillus thermoglucosidasius DSM 2542

An Initial Genome Editing Toolset for Caldimonas thermodepolymerans, the First Model of Thermophilic Polyhydroxyalkanoates Producer

The limited number of well-characterised model bacteria cannot address all the challenges in a circular bioeconomy. Therefore, there is a growing demand for new production strains with enhanced resistance to extreme conditions, versatile metabolic capabilities and the ability to utilise cost-effective renewable resources while efficiently generating attractive biobased products. Particular thermophilic microorganisms fulfil these requirements. Non-virulent Gram-negative Caldimonas thermodepolymerans DSM15344 is one such attractive thermophile that efficiently converts a spectrum of plant biomass sugars into high quantities of polyhydroxyalkanoates (PHA)-a fully biodegradable substitutes for synthetic plastics. However, to enhance its biotechnological potential, the bacterium needs to be 'domesticated'. In this study, we established effective homologous recombination and transposon-based genome editing systems for C. thermodepolymerans. By optimising the electroporation protocol and refining counterselection methods, we achieved significant improvements in genetic manipulation and constructed the AI01 chassis strain with improved transformation efficiency and a ΔphaC mutant that will be used to study the importance of PHA synthesis in Caldimonas. The advances described herein highlight the need for tailored approaches when working with thermophilic bacteria and provide a springboard for further genetic and metabolic engineering of C. thermodepolymerans, which can be considered the first model of thermophilic PHA producer.

Development of a xylose-inducible and glucose-insensitive expression system for Parageobacillus thermoglucosidasius

Inducible expression systems are pivotal for governing gene expression in strain engineering and synthetic biotechnological applications. Therefore, a critical need persists for the development of versatile and efficient inducible expression mechanisms. In this study, the xylose-responsive promoter xylA5p and its transcriptional regulator XylR were identified in Parageobacillus thermoglucosidasius DSM 2542. By combining promoter xylA5p with its regulator XylR, fine-tuning the expression strength of XylR, and reducing the glucose catabolite repression on xylose uptake, we successfully devised a xylose-inducible and glucose-insensitive expression system, denoted as IExyl*. This system exhibited diverse promoter strengths upon induction with xylose at varying concentrations and remained unhindered in the presence of glucose. Moreover, we showed the applicability of IExyl* in P. thermoglucosidasius by redirecting metabolic flux towards riboflavin biosynthesis, culminating in a 2.8-fold increase in riboflavin production compared to that of the starting strain. This glucose-insensitive and xylose-responsive expression system provides valuable tools for designing optimized biosynthetic pathways for high-value products and facilitates future synthetic biology investigations in Parageobacillus. KEY POINTS: • A xylose-inducible and glucose-insensitive expression system IExyl* was developed. • IExyl* was applied to enhance the riboflavin production in P. thermoglucosidasius • A tool for metabolic engineering and synthetic biology research in Parageobacillus strains.

The effects of synthesis gas feedstocks and oxygen perturbation on hydrogen production by Parageobacillus thermoglucosidasius

BACKGROUND

The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen gas (H2) through the water-gas shift (WGS) reaction. To date this process has been evaluated under controlled conditions, with gas feedstocks comprising carbon monoxide and variable proportions of air, nitrogen and hydrogen. Ultimately, an economically viable hydrogenogenic system would make use of industrial waste/synthesis gases that contain high levels of carbon monoxide, but which may also contain contaminants such as H2, oxygen (O2) and other impurities, which may be toxic to P. thermoglucosidasius.

RESULTS

We evaluated the effects of synthesis gas (syngas) mimetic feedstocks on WGS reaction-driven H2 gas production by P. thermoglucosidasius DSM 6285 in small-scale fermentations. Improved H2 gas production yields and faster onset towards hydrogen production were observed when anaerobic synthetic syngas feedstocks were used, at the expense of biomass accumulation. Furthermore, as the WGS reaction is an anoxygenic process, we evaluated the influence of O2 perturbation on P. thermoglucosidasius hydrogenogenesis. O2 supplementation improved biomass accumulation, but reduced hydrogen yields in accordance with the level of oxygen supplied. However, H2 gas production was observed at low O2 levels. Supplementation also induced rapid acetate consumption, likely to sustain growth.

CONCLUSION

The utilisation of anaerobic syngas mimetic gas feedstocks to produce H2 and the relative flexibility of the P. thermoglucosidasius WGS reaction system following O2 perturbation further supports its applicability towards more robust and continuous hydrogenogenic operation.

Parageobacillus thermoglucosidasius as an emerging thermophilic cell factory

Parageobacillus thermoglucosidasius is a thermophilic and facultatively anaerobic microbe, which is emerging as one of the most promising thermophilic model organisms for metabolic engineering. The use of thermophilic microorganisms for industrial bioprocesses provides the advantages of increased reaction rates and reduced cooling costs for bioreactors compared to their mesophilic counterparts. Moreover, it enables starch or lignocellulose degradation and fermentation to occur at the same temperature in a Simultaneous Saccharification and Fermentation (SSF) or Consolidated Bioprocessing (CBP) approach. Its natural hemicellulolytic capabilities and its ability to convert CO to metabolic energy make P. thermoglucosidasius a potentially attractive host for bio-based processes. It can effectively degrade hemicellulose due to a number of hydrolytic enzymes, carbohydrate transporters, and regulatory elements coded from a genomic cluster named Hemicellulose Utilization (HUS) locus. The growing availability of effective genetic engineering tools in P. thermoglucosidasius further starts to open up its potential as a versatile thermophilic cell factory. A number of strain engineering examples showcasing the potential of P. thermoglucosidasius as a microbial chassis for the production of bulk and fine chemicals are presented along with current research bottlenecks. Ultimately, this review provides a holistic overview of the distinct metabolic characteristics of P. thermoglucosidasius and discusses research focused on expanding the native metabolic boundaries for the development of industrially relevant strains.

Metabolic engineering of Geobacillus thermoglucosidasius for polymer-grade lactic acid production at high temperature

The production and application of biodegradable polylactic acid are still severely hindered by the cost of its polymer-grade lactic acid monomers. High-temperature biomanufacturing has emerged as an increasingly attractive approach to enable low-cost and high-efficiency bulk chemical production. In this study, thermophilic Geobacillus thermoglucosidasius was reprogrammed to obtain optically pure l-lactic acid- and d-lactic acid-producing strains, G. thermoglucosidasius GTD17 and GTD7, by using rational metabolic engineering strategies including pathway construction, by-product elimination, and production enhancing. Moreover, semi-rational adaptive evolution was carried out to further improve their lactic acid synthesis performance. The final strains GTD17-55 and GTD7-144 produce 151.1 g/L of l-lactic acid and 153.1 g/L of d-lactic acid at 60 °C, respectively. In consideration of the high temperature, productive performance of these strains is superior compared to the state-of-the-art industrial strains. This study lays the foundation for the low-cost and efficient production of biodegradable plastic polylactic acid.

Optimization and biochemical characterization of a thermotolerant processive cellulase, PtCel1, of Parageobacillus thermoglucosidasius NBCB1

Vermicomposting involves enrichment of microorganisms that are able to resist higher temperatures and perform simultaneous degradation of lignocellulose, and therefore, such microbial communities are a potential source of cellulolytic enzymes. This study aimed to optimize the production of a processive cellulase by Parageobacillus thermoglucosidasius NBCB1 isolated from vermicompost, under submerged fermentation of rice straw and to characterize the purified enzyme for industrial suitability. Cellulase production in basal medium (7.27 IU/mg) was enhanced to 61 IU/mg by One Factor At a Time approach, which was further improved to 78.46 IU/mg by genetic algorithm based artificial neural networking. The cellulase PtCel1 purified from bacterial culture showed a molecular weight of ≈33 kD, had activity on both crystalline (305 IU/mg) and amorphous (184 IU/mg) cellulose as substrates. It had pH and temperature optima of 5.5°C and 60°C, respectively, and retained 100% activity upon preincubation at 60°C for 1 h indicating thermostability. PtCel1 was tolerant to sodium dodecyl sulfate, glucose and mannose; and the various metal chlorides, such as sodium, magnesium, calcium and zinc, acted as inducers giving 77.54%, 45.15%, 61.10%, and 169.14% augmentation of activity, respectively. Its efficiency on cellulosic substrates and robustness against aforementioned chemical and thermal environment makes it suitable for industrial applications.

Macroalgal biomass as a potential resource for lactic acid fermentation

Lactic acid is an essential platform chemical with various applications in the chemicals, food, pharmaceutical, and cosmetic industries. Currently, the demand for lactic acid is driven by the role of lactic acid as the starting material for the production of bioplastic polylactide. Microbial fermentation for lactic acid production is favored due to the production of enantiomerically pure lactic acid required for polylactide synthesis, as opposed to the racemic mixture obtained via chemical synthesis. The utilization of first-generation feedstock for commercial lactic acid production is challenged by feedstock costs and sustainability issues. Macroalgae are photosynthetic benthic aquatic plants that contribute tremendously towards carbon capture with subsequent carbon-rich biomass production. Macroalgae are commercially cultivated to extract hydrocolloids, and recent studies have focused on applying biomass as a fermentation feedstock. This review provides comprehensive information on the design and development of sustainable and cost-effective, algae-based lactic acid production. The central carbon regulation in lactic acid bacteria and the metabolism of seaweed-derived sugars are described. An exhaustive compilation of lactic acid fermentation of macroalgae hydrolysates revealed that lactic acid bacteria can effectively ferment the mixture of sugars present in the hydrolysate with comparable yields. The environmental impacts and economic prospects of macroalgal lactic acid are analyzed. Valorization of the vast amounts of spent macroalgal biomass residue post hydrocolloid extraction in a biorefinery is a viable strategy for cost-effective lactic acid production.

Removing carbon catabolite repression in Parageobacillus thermoglucosidasius DSM 2542

Parageobacillus thermoglucosidasius is a thermophilic bacterium of interest for lignocellulosic biomass fermentation. However, carbon catabolite repression (CCR) hinders co-utilization of pentoses and hexoses in the biomass substrate. Hence, to optimize the fermentation process, it is critical to remove CCR in the fermentation strains with minimal fitness cost. In this study, we investigated whether CCR could be removed from P. thermoglucosidasius DSM 2542 by mutating the Ser46 regulatory sites on HPr and Crh to a non-reactive alanine residue. It was found that neither the ptsH1 (HPr-S46A) nor the crh1 (Crh-S46A) mutation individually eliminated CCR in P. thermoglucosidasius DSM 2542. However, it was not possible to generate a ptsH1 crh1 double mutant. While the Crh-S46A mutation had no obvious fitness effect in DSM 2542, the ptsH1 mutation had a negative impact on cell growth and sugar utilization under fermentative conditions. Under these conditions, the ptsH1 mutation was associated with the production of a brown pigment, believed to arise from methylglyoxal production, which is harmful to cells. Subsequently, a less directed adaptive evolution approach was employed, in which DSM 2542 was grown in a mixture of 2-deoxy-D-glucose(2-DG) and xylose. This successfully removed CCR from P. thermoglucosidasius DSM 2542. Two selection strategies were applied to optimize the phenotypes of evolved strains. Genome sequencing identified key mutations affecting the PTS components PtsI and PtsG, the ribose operon repressor RbsR and adenine phosphoribosyltransferase APRT. Genetic complementation and bioinformatics analysis revealed that the presence of wild type rbsR and apt inhibited xylose uptake or utilization, while ptsI and ptsG might play a role in the regulation of CCR in P. thermoglucosidasius DSM 2542.