Developing a Riboswitch-Mediated Regulatory System for Metabolic Flux Control in Thermophilic Bacillus methanolicus

Bacillus methanolicus: an emerging chassis for low-carbon biomanufacturing

Bacillus methanolicus is a thermophilic methylotrophic bacterium that grows quickly on methanol in sea water-based media. It has been engineered for chemical bioproduction from methanol, but its efficiency needs improvement for industrialization. Synthetic biology approaches such as metabolic modeling and genome editing can reprogram B. methanolicus for low-carbon biomanufacturing.

Identification and characterization of a novel formaldehyde dehydrogenase in Bacillus subtilis

Formaldehyde is a known toxic compound, and functional formaldehyde detoxification is crucial for the survival of all living cells. Such detoxification systems are of particular importance for methylotrophic microorganisms that rely on formaldehyde as a central metabolite in their one-carbon metabolism. Understanding formaldehyde dissimilation pathways in non-methylotrophic industrial microorganisms is necessary for ongoing research aiming at engineering methylotrophy into their metabolism (synthetic methylotrophy). There is a variety of formaldehyde dissimilation pathways across microorganisms, often based on the activity of formaldehyde dehydrogenases. In this study, we investigated the role of the yycR gene of Bacillus subtilis putatively encoding a novel, uncharacterized zinc-type alcohol dehydrogenase-like protein. We showed that the B. subtilis ΔyycR mutant displayed a reduced formaldehyde tolerance level and confirmed the enzymatic activity of recombinantly produced and purified YycR as formaldehyde dehydrogenase in vitro. Biochemical analyses demonstrated that YycR activity is optimal at 40°C, with the highest measured activity at pH 9.5, formaldehyde is the preferred substrate, and the kinetic constants are Km of 0.19 ± 0.05 mM and Vmax of 2.24 ± 0.05 nmol min-1. Altogether, we showed that YycR is a novel formaldehyde dehydrogenase with a role in formaldehyde detoxification in B. subtilis, providing valuable insights for future research on synthetic methylotrophy in this organism.

IMPORTANCE

Formaldehyde is a key metabolite in methanol assimilation for many methylotrophic microorganisms, and at the same time, it is toxic to all living cells, which means its intracellular concentrations must be tightly controlled. An in-depth understanding of methanol detoxification systems in industrially relevant microorganisms is a prerequisite for the introduction of methanol utilization pathways into their metabolism (synthetic methylotrophy). Bacillus subtilis, an industrial workhorse conventionally used for the production of enzymes, is known to possess two formaldehyde detoxification pathways. Here, we identify a novel formaldehyde dehydrogenase in this bacterium as a path towards creating innovative prospect strategies for strain engineering towards synthetic methylotrophy.

Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology

Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.

Metabolic engineering of thermophilic Bacillus methanolicus for riboflavin overproduction from methanol

The growing need of next generation feedstocks for biotechnology spurs an intensification of research on the utilization of methanol as carbon and energy source for biotechnological processes. In this paper, we introduced the methanol-based overproduction of riboflavin into metabolically engineered Bacillus methanolicus MGA3. First, we showed that B. methanolicus naturally produces small amounts of riboflavin. Then, we created B. methanolicus strains overexpressing either homologous or heterologous gene clusters encoding the riboflavin biosynthesis pathway, resulting in riboflavin overproduction. Our results revealed that the supplementation of growth media with sublethal levels of chloramphenicol contributes to a higher plasmid-based riboflavin production titre, presumably due to an increase in plasmid copy number and thus biosynthetic gene dosage. Based on this, we proved that riboflavin production can be increased by exchanging a low copy number plasmid with a high copy number plasmid leading to a final riboflavin titre of about 523 mg L^-1 in methanol fed-batch fermentation. The findings of this study showcase the potential of B. methanolicus as a promising host for methanol-based overproduction of extracellular riboflavin and serve as basis for metabolic engineering of next generations of riboflavin overproducing strains.

Riboswitch-mediated regulation of riboflavin biosynthesis genes in prokaryotes

Prokaryotic organisms frequently use riboswitches to quantify intracellular metabolite concentration via high-affinity metabolite receptors. Riboswitches possess a metabolite-sensing system that controls gene regulation in a cis-acting fashion at the initiation of transcriptional/translational level by binding with a specific metabolite and controlling various biochemical pathways. Riboswitch binds with flavin mononucleotide (FMN), a phosphorylated form of riboflavin and controls gene expression involved in riboflavin biosynthesis and transport pathway. The first step of the riboflavin biosynthesis pathway is initiated by the conversion of guanine nucleotide triphosphate (GTP), which is an intermediate of the purine biosynthesis pathway. An alternative pentose phosphate pathway of riboflavin biosynthesis includes the enzymatic conversion of ribulose-5-phosphate into 3, 4 dihydroxy-2-butanone-4-phosphates by DHBP synthase. The product of ribAB interferes with both GTP cyclohydrolase II as well as DHBP synthase activities, which catalyze the cleavage of GTP and converts DHBP Ribu5P in the initial steps of both riboflavin biosynthesis branches. Riboswitches are located in the 5' untranslated region (5' UTR) of messenger RNAs and contain an aptamer domain (highly conserved in sequence) where metabolite binding leads to a conformational change in an aptamer domain, which modulate the regulation of gene expression located on bacterial mRNA. In this review, we focus on how riboswitch regulates the riboflavin biosynthesis pathway in Bacillus subtilis and Lactobacillus plantarum.

Efficient cell factories for the production of N-methylated amino acids and for methanol-based amino acid production

The growing world needs commodity amino acids such as L-glutamate and L-lysine for use as food and feed, and specialty amino acids for dedicated applications. To meet the supply a paradigm shift regarding their production is required. On the one hand, the use of sustainable and cheap raw materials is necessary to sustain low production cost and decrease detrimental effects of sugar-based feedstock on soil health and food security caused by competing uses of crops in the feed and food industries. On the other hand, the biotechnological methods to produce functionalized amino acids need to be developed further, and titres enhanced to become competitive with chemical synthesis methods. In the current review, we present successful strain mutagenesis and rational metabolic engineering examples leading to the construction of recombinant bacterial strains for the production of amino acids such as L-glutamate, L-lysine, L-threonine and their derivatives from methanol as sole carbon source. In addition, the fermentative routes for bioproduction of N-methylated amino acids are highlighted, with focus on three strategies: partial transfer of methylamine catabolism, S-adenosyl-L-methionine dependent alkylation and reductive methylamination of 2-oxoacids.

The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes

Riboswitches are regulatory noncoding RNAs found in bacteria, fungi and plants, that modulate gene expressions through structural changes in response to ligand binding. Understanding how ligands interact with riboswitches in solution can shed light on the molecular mechanisms of this ancient regulators. Previous studies showed that riboswitches undergo global conformation changes in response to ligand binding to relay information. Here, we report conformation switching models of the recently discovered tetrahydrofolic acid-responsive second class of tetrahydrofolate (THF-II) riboswitches in response to ligand binding. Using a combination of selective 2′-hydroxyl acylation, analyzed by primer extension (SHAPE) assay, 3D modeling and small-angle X-ray scattering (SAXS), we found that the ligand specifically recognizes and reshapes the THF-II riboswitch loop regions, but does not affect the stability of the P3 helix. Our results show that the THF-II riboswitch undergoes only local conformation changes in response to ligand binding, rearranging the Loop1-P3-Loop2 region and rotating Loop1 from a ~120° angle to a ~75° angle. This distinct conformation changes suggest a unique regulatory mechanism of the THF-II riboswitch, previously unseen in other riboswitches. Our findings may contribute to the fields of RNA sensors and drug design.

Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology

Aerobic carboxydotrophic bacteria are a group of microorganisms which possess the unique trait to oxidize carbon monoxide (CO) as sole energy source with molecular oxygen (O₂) to produce carbon dioxide (CO₂) which subsequently is used for biomass formation via the Calvin-Benson-Bassham cycle. Moreover, most carboxydotrophs are also able to oxidize hydrogen (H₂) with hydrogenases to drive the reduction of carbon dioxide in the absence of CO. As several abundant industrial off-gases contain significant amounts of CO, CO₂, H₂ as well as O₂, these bacteria come into focus for industrial application to produce chemicals and fuels from such gases in gas fermentation approaches. Since the group of carboxydotrophic bacteria is rather unknown and not very well investigated, we will provide an overview about their lifestyle and the underlying metabolic characteristics, introduce promising members for industrial application, and give an overview of available genetic engineering tools. We will point to limitations and discuss challenges, which have to be overcome to apply metabolic engineering approaches and to utilize aerobic carboxydotrophs in the industrial environment.