The soil bacterium, Corynebacterium glutamicum, from biosynthesis of value-added products to bioremediation: A master of many trades

Recent advances in bio-based production of top platform chemical, succinic acid: an alternative to conventional chemistry

Succinic acid (SA) is one of the top platform chemicals with huge applications in diverse sectors. The presence of two carboxylic acid groups on the terminal carbon atoms makes SA a highly functional molecule that can be derivatized into a wide range of products. The biological route for SA production is a cleaner, greener, and promising technological option with huge potential to sequester the potent greenhouse gas, carbon dioxide. The recycling of renewable carbon of biomass (an indirect form of CO2), along with fixing CO2 in the form of SA, offers a carbon-negative SA manufacturing route to reduce atmospheric CO2 load. These attractive attributes compel a paradigm shift from fossil-based to microbial SA manufacturing, as evidenced by several commercial-scale bio-SA production in the last decade. The current review article scrutinizes the existing knowledge and covers SA production by the most efficient SA producers, including several bacteria and yeast strains. The review starts with the biochemistry of the major pathways accumulating SA as an end product. It discusses the SA production from a variety of pure and crude renewable sources by native as well as engineered strains with details of pathway/metabolic, evolutionary, and process engineering approaches for enhancing TYP (titer, yield, and productivity) metrics. The review is then extended to recent progress on separation technologies to recover SA from fermentation broth. Thereafter, SA derivatization opportunities via chemo-catalysis are discussed for various high-value products, which are only a few steps away. The last two sections are devoted to the current scenario of industrial production of bio-SA and associated challenges, along with the author's perspective.

Metabolic Engineering of Corynebacterium glutamicum for the Production of Flavonoids and Stilbenoids

Flavonoids and stilbenoids, crucial secondary metabolites abundant in plants and fungi, display diverse biological and pharmaceutical activities, including potent antioxidant, anti-inflammatory, and antimicrobial effects. However, conventional production methods, such as chemical synthesis and plant extraction, face challenges in sustainability and yield. Hence, there is a notable shift towards biological production using microorganisms like Escherichia coli and yeast. Yet, the drawbacks of using E. coli and yeast as hosts for these compounds persist. For instance, yeast's complex glycosylation profile can lead to intricate protein production scenarios, including hyperglycosylation issues. Consequently, Corynebacterium glutamicum emerges as a promising alternative, given its adaptability and recent advances in metabolic engineering. Although extensively used in biotechnological applications, the potential production of flavonoid and stilbenoid in engineered C. glutamicum remains largely untapped compared to E. coli. This review explores the potential of metabolic engineering in C. glutamicum for biosynthesis, highlighting its versatility as a cell factory and assessing optimization strategies for these pathways. Additionally, various metabolic engineering methods, including genomic editing and biosensors, and cofactor regeneration are evaluated, with a focus on C. glutamicum. Through comprehensive discussion, the review offers insights into future perspectives in production, aiding researchers and industry professionals in the field.

Genome sequence of PSonyx, a singleton bacteriophage infecting Corynebacterium glutamicum

PSonyx is a newly isolated phage that infects Corynebacterium glutamicum. This siphovirus was isolated from a French pond in the south of Paris by students from Paris-Saclay University. Its 80,277-bp singleton genome carries 136 protein-coding genes and 5 tRNAs.

Improving Tannery Wastewater Treatments Using an Additional Microbial Treatment with a Bacterial-Fungal Consortium

Environmental pollutants such as toxic heavy metals and oxygen-demanding solids are generated by leather manufacturing. In most tanneries, wastewaters are treated with physico-chemical methods but overly high levels of pollutants remain in surface waters. The efficiency of tanning wastewater treatment with conventional techniques was evaluated in four tanneries in Saudi Arabia. It was observed that the wastewaters contained high amounts of pollutants, needing further treatment. We isolated microorganisms from the wastewaters and carried out experiments to treat the effluents with different bacteria, fungi, and their consortia. We hypothesized that a consortium of microorganisms is more efficient than the single microorganisms in the consortium. The efficiency of five single bacterial and five fungal species from different genera was tested. In a consortium experiment, the efficiency of nine bacterial-fungal consortia was studied. The bacterium Corynebacterium glutamicum and the fungus Acremonium sp. were the most efficient in the single-microbe treatment. In the consortium treatment, the consortium of these two was the most efficient at treating the effluent. The factory wastewater treatment reduced total dissolved solids (TDS) from 1885 mg/L to 880 mg/L. C. glutamicum treatment reduced TDS to 150 mg/L and Acremonium sp. to 140 mg/L. The consortium of these two reduced TDS further to 80 mg/L. Moreover, the factory treatment reduced BOD from 943 mg/L to 440 mg/L, C. glutamicum to 75 mg/L, and Acremonium sp. 70 mg/L. The consortium reduced BOD further to 20 mg/L. The total heavy-metal concentration (Cd, Cr, Cu, Mn, and Pb) was reduced by the factory treatment from 43 μg/L to 26 μg/L and by the consortium to 0.2 μg/L. The collagen concentration that was studied using hydroxyproline assay decreased from 120 mg/L to 39 mg/L. It was shown that the consortium of the bacterium C. glutamicum and the fungus Acremonium sp. was more efficient in reducing the pollutants than the single species. The consortium reduced almost all parameters to below the environmental regulation limit for wastewater discharge to the environment in Saudi Arabia. The consortium should be studied further as an additional treatment to the existing conventional tannery wastewater treatments.

Solid-state fermentation production of L-lysine by Corynebacterium glutamicum (ATCC 13032) using agricultural by-products as substrate

To meet the growing demand for L-lysine, an essential amino acid with various applications, it is crucial to produce it on a large scale locally instead of relying solely on imports. This study aimed to evaluate the potential of using Corynebacterium glutamicum ATCC 13032 for L-lysine production from agricultural by-products such as palm kernel cake, soybean cake, groundnut cake, and rice bran. Solid-state fermentation was conducted at room temperature for 72 h, with the addition of elephant grass extract as a supplement. The results revealed that these agricultural by-products contain residual amounts of L-lysine. By employing solid-state fermentation with C. glutamicum (106 CFU/ml) in 100 g of various agricultural by-products, L-lysine production was achieved. Interestingly, the addition of elephant grass extract (1 g of elephant grass: 10 ml of water) further enhanced L-lysine production. Among the tested substrates, 100 g of groundnut cake moistened with 500 ml of elephant grass extract yielded the highest L-lysine concentration of 3.27 ± 0.02 (mg/gds). Furthermore, fermentation led to a substantial rise (p < 0.05) in soluble protein, with solid-state fermented soybean cake moistened with 500 ml of elephant grass extract exhibiting the highest amount of 7.941 ± 0.05 mg/gds. The activities of xylanase, amylase and protease were also significantly enhanced. This study demonstrates a viable biotechnological approach for locally producing L-lysine from agricultural by-products using solid-state fermentation with C. glutamicum. The findings hold potential for both health and industrial applications, providing a sustainable and economically feasible method for L-lysine production.

Structure-Guided Protein Engineering of Glyceraldehyde-3-phosphate Dehydrogenase from Corynebacterium glutamicum for Dual NAD/NADP Cofactor Specificity

Since the discovery of l-glutamate-producing Corynebacterium glutamicum, it has evolved to be an industrial workhorse. For biobased chemical production, suppling sufficient amounts of the NADPH cofactor is crucial. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme that converts glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate and produces NADH, is a major prospective solution for the cofactor imbalance issue. In this study, we determined the crystal structure of GAPDH from C. glutamicum ATCC13032 (CgGAPDH). Based on the structural information, we generated six CgGAPDH variants, CgGAPDHL36S, CgGAPDHL36S/T37K, CgGAPDHL36S/T37K/P192S, CgGAPDHL36S/T37K/F100V/P192S, CgGAPDHL36S/T37K/F100L/P192S, and CgGAPDHL36S/T37K/F100I/P192S, that can produce both NADH and NAPDH. The final CgGAPDHL36S/T37K/F100V/P192S variant showed a 212-fold increase in enzyme activity for NADP as well as 200% and 30% increased activity for the G3P substrate under NAD and NADP cofactor conditions, respectively. In addition, crystal structures of CgGAPDH variants in complex with NAD(P) permit the elucidation of differences between wild-type CgGAPDH and variants in relation to cofactor stabilization.

Robotic workflows for automated long-term adaptive laboratory evolution: improving ethanol utilization by Corynebacterium glutamicum

BACKGROUND

Adaptive laboratory evolution (ALE) is known as a powerful tool for untargeted engineering of microbial strains and genomics research. It is particularly well suited for the adaptation of microorganisms to new environmental conditions, such as alternative substrate sources. Since the probability of generating beneficial mutations increases with the frequency of DNA replication, ALE experiments are ideally free of constraints on the required duration of cell proliferation.

RESULTS

Here, we present an extended robotic workflow for performing long-term evolution experiments based on fully automated repetitive batch cultures (rbALE) in a well-controlled microbioreactor environment. Using a microtiter plate recycling approach, the number of batches and thus cell generations is technically unlimited. By applying the validated workflow in three parallel rbALE runs, ethanol utilization by Corynebacterium glutamicum ATCC 13032 (WT) was significantly improved. The evolved mutant strain WT_EtOH-Evo showed a specific ethanol uptake rate of 8.45 ± 0.12 mmolEtOH gCDW-1 h-1 and a growth rate of 0.15 ± 0.01 h-1 in lab-scale bioreactors. Genome sequencing of this strain revealed a striking single nucleotide variation (SNV) upstream of the ald gene (NCgl2698, cg3096) encoding acetaldehyde dehydrogenase (ALDH). The mutated basepair was previously predicted to be part of the binding site for the global transcriptional regulator GlxR, and re-engineering demonstrated that the identified SNV is key for enhanced ethanol assimilation. Decreased binding of GlxR leads to increased synthesis of the rate-limiting enzyme ALDH, which was confirmed by proteomics measurements.

CONCLUSIONS

The established rbALE technology is generally applicable to any microbial strain and selection pressure that fits the small-scale cultivation format. In addition, our specific results will enable improved production processes with C. glutamicum from ethanol, which is of particular interest for acetyl-CoA-derived products.

Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.

Revealing Corynebacterium glutamicum proteoforms through top-down proteomics

Corynebacterium glutamicum is a bacterium widely employed in the industrial production of amino acids as well as a broad range of other biotechnological products. The present study describes the characterization of C. glutamicum proteoforms, and their post-translational modifications (PTMs) employing top-down proteomics. Despite previous evidence of PTMs having roles in the regulation of C. glutamicum metabolism, this is the first top-down proteome analysis of this organism. We identified 1125 proteoforms from 273 proteins, with 60% of proteins presenting at least one mass shift, suggesting the presence of PTMs, including several acetylated, oxidized and formylated proteoforms. Furthermore, proteins relevant to amino acid production, protein secretion, and oxidative stress were identified with mass shifts suggesting the presence of uncharacterized PTMs and proteoforms that may affect biotechnologically relevant processes in this industrial workhorse. For instance, the membrane proteins mepB and SecG were identified as a cleaved and a formylated proteoform, respectively. While in the central metabolism, OdhI was identified as two proteoforms with potential biological relevance: a cleaved proteoform and a proteoform with PTMs corresponding to a 70 Da mass shift.

New data on microorganisms in soil and other environmental compartments

As indicated in the presentation of this Virtual Special Issue (VSI), as well as in its Call for Papers, the occurrence, fate, dynamics, effects and overall repercussions of the enormous variety of microorganisms present in soils and other environmental compartments on Earth, is of huge importance, and particularly it is fundamental to the conditioning of life and even to the time-course evolution of non-living constituents of our planet. With that in mind, shedding further light on some selected fields within this broad spectrum of research themes could be seen as an ambitious objective, but achievable when limited to progressing just a few steps forward, even if the long-term aim could be to reach a final and complete characterization and solution of all issues related to these broad lines of research and fields of knowledge. In view of this, the Editors of the Special Issue made a specific Call to receive contributions to increase the knowledge on the matter, which could stimulate future additional research. With a total number of 45 manuscripts received and 16 high-quality contributions published, we think this main objective was reached with the resulting papers now available.