Metabolic networks to generate pyruvate, PEP and ATP from glycerol in Pseudomonas fluorescens

The tricarboxylic acid (TCA) cycle: a malleable metabolic network to counter cellular stress

The tricarboxylic acid (TCA) cycle is a primordial metabolic pathway that is conserved from bacteria to humans. Although this network is often viewed primarily as an energy producing engine fueling ATP synthesis via oxidative phosphorylation, mounting evidence reveals that this metabolic hub orchestrates a wide variety of pivotal biological processes. It plays an important part in combatting cellular stress by modulating NADH/NADPH homeostasis, scavenging ROS (reactive oxygen species), producing ATP by substrate-level phosphorylation, signaling and supplying metabolites to quell a range of cellular disruptions. This review elaborates on how the reprogramming of this network prompted by such abiotic stress as metal toxicity, oxidative tension, nutrient challenge and antibiotic insult is critical for countering these conditions in mostly microbial systems. The cross-talk between the stressors and the participants of TCA cycle that results in changes in metabolite and nucleotide concentrations aimed at combatting the abiotic challenge is presented. The fine-tuning of metabolites mediated by disparate enzymes associated with this metabolic hub is discussed. The modulation of enzymatic activities aimed at generating metabolic moieties dedicated to respond to the cellular perturbation is explained. This ancient metabolic network has to be recognized for its ability to execute a plethora of physiological functions beyond its well-established traditional roles.

Toxic reactive oxygen species stresses for reconfiguring central carbon metabolic fluxes in foodborne bacteria: Sources, mechanisms and pathways

The toxic reactive oxygen species (toxROS) is the reactive oxygen species (ROS) beyond the normal concentration of cells, which has inactivation and disinfection effects on foodborne bacteria. However, foodborne bacteria can adapt and survive by physicochemical regulation of antioxidant systems, especially through central carbon metabolism (CCM), which is a significant concern for food safety. It is thus necessary to study the antioxidant regulation mechanisms of CCM in foodborne bacteria under toxROS stresses. Therefore, the purpose of this review is to provide an update and comprehensive overview of the reconfiguration of CCM fluxes in foodborne bacteria that respond to different toxROS stresses. In this review, two key types of toxROS including exogenous toxROS (exo-toxROS) and endogenous toxROS (endo-toxROS) are introduced. Exo-toxROS are produced by disinfectants, such as H₂O₂ and HOCl, or during food non-thermal processing such as ultraviolet (UV/UVA), cold plasma (CP), ozone (O₃), electrolyzed water (EW), pulsed electric field (PEF), pulsed light (PL), and electron beam (EB) processing. Endo-toxROS are generated by bioreagents such as antibiotics (aminoglycosides, quinolones, and β-lactams). Three main pathways for CCM in foodborne bacteria under the toxROS stress are also highlighted, which are glycolysis (EMP), pentose phosphate pathway (PPP), and tricarboxylic acid cycle (TCA). In addition, energy metabolisms throughout these pathways are discussed. Finally, challenges and future work in this area are suggested. It is hoped that this review should be beneficial in providing insights for future research on bacterial antioxidant CCM defence under both exo-toxROS stresses and endo-toxROS stresses.

DsrA Modulates Central Carbon Metabolism and Redox Balance by Directly Repressing pflB Expression in Salmonella Typhimurium

Bacterial small RNAs (sRNAs) function as vital regulators in response to various environmental stresses by base pairing with target mRNAs. The sRNA DsrA, an important posttranscriptional regulator, has been reported to play a crucial role in defense against oxidative stress in Salmonella enterica serovar Typhimurium, but its regulatory mechanism remains unclear. The transcriptome sequencing (RNA-seq) results in this study showed that the genes involved in glycolysis, pyruvate metabolism, the tricarboxylic acid (TCA) cycle, and NADH-dependent respiration exhibited significantly different expression patterns between S. Typhimurium wild type (WT) and the dsrA deletion mutant (ΔdsrA strain) before and after H₂O₂ treatment. This indicated the importance of DsrA in regulating central carbon metabolism (CCM) and NAD(H) homeostasis of S. Typhimurium. To reveal the direct target of DsrA action, fusion proteins of six candidate genes (acnA, srlE, tdcB, nuoH, katG, and pflB) with green fluorescent protein (GFP) were constructed, and the fluorescence analysis showed that the expression of pflB encoding pyruvate-formate lyase was repressed by DsrA. Furthermore, site-directed mutagenesis and RNase E-dependent experiments showed that the direct base pairing of DsrA with pflB mRNA could recruit RNase E to degrade pflB mRNA and reduce the stability of pflB mRNA. In addition, the NAD⁺/NADH ratio in WT-ppflB-pdsrA was significantly lower than that in WT-ppflB, suggesting that the repression of pflB by DsrA could contribute greatly to the redox balance in S. Typhimurium. Taken together, a novel target of DsrA was identified, and its regulatory role was clarified, which demonstrated that DsrA could modulate CCM and redox balance by directly repressing pflB expression in S. Typhimurium.

IMPORTANCE Small RNA DsrA plays an important role in defending against oxidative stress in bacteria. In this study, we identified a novel target (pflB, encoding pyruvate-formate lyase) of DsrA and demonstrated its potential regulatory mechanism in S. Typhimurium by transcriptome analysis. In silico prediction revealed a direct base pairing between DsrA and pflB mRNA, which was confirmed in site-directed mutagenesis experiments. The interaction of DsrA-pflB mRNA could greatly contribute to the regulation of central carbon metabolism and intracellular redox balance in S. Typhimurium. These findings provided a better understanding of the critical roles of small RNA in central metabolism and stress responses in foodborne pathogens.

Screening and functional identification of antioxidant microRNA-size sRNAs from Spirulina platensis using high-throughput sequencing

MiRNA-size small RNAs, abbreviated as sRNAs, are increasingly being discovered as research progresses and omics technologies development in prokaryotes. However, there is a paucity of data concerning whether or not sRNAs exist in cyanobacteria and regulate the resistance to oxidative stress. In this investigation, small RNA libraries were constructed from the control, 50-nM and 100-nM H2O2 treatments of Spirulina platensis. By high-throughput sequencing, 23 candidate sRNAs showed significantly differential expression under oxidative stress, among which eight sRNAs were identified with the similar expression patterns as the sequencing results by real-time qPCR. By nucleic acid hybridisation, the corresponding expression changes also demonstrated that sequencing results of sRNAs were feasible and credible. By bioinformatics prediction and structure identification, 43 target genes were predicted for 8 sRNAs in plant miRNA database, among which 29 were annotated into the genome and related metabolic pathways of S. platensis. By COG functional classification and KEGG pathway analysis, 31 target genes were predicted to be directly or indirectly involved in the defence mechanism of H2O2 stress. Thirteen target genes displayed reversely changing patterns compared with those of their sRNAs under H2O2 treatment. These findings provide compelling evidence that these sRNAs in S. platensis play a crucial role in oxidative stress responses, and thus provide a theoretical reference for improving the stress-triggering physiological regulation.

Reactive Oxygen Species in Pathogen Clearance: The Killing Mechanisms, the Adaption Response, and the Side Effects

Reactive oxygen species (ROS) are attractive weapons in both antibiotic-mediated killing and host-mediated killing. However, the involvement of ROS in antibiotic-mediated killing and complexities in host environments challenge the paradigm. In the case of bacterial pathogens, the examples of some certain pathogens thriving under ROS conditions prompt us to focus on the adaption mechanism that pathogens evolve to cope with ROS. Based on these, we here summarized the mechanisms of ROS-mediated killing of either antibiotics or the host, the examples of bacterial adaption that successful pathogens evolved to defend or thrive under ROS conditions, and the potential side effects of ROS in pathogen clearance. A brief section for new antibacterial strategies centered around ROS was also addressed.

Metabolic manipulation by Pseudomonas fluorescens: a powerful stratagem against oxidative and metal stress

Metabolism is the foundation of all living organisms and is at the core of numerous if not all biological processes. The ability of an organism to modulate its metabolism is a central characteristic needed to proliferate, to be dormant and to survive any assault. Pseudomonas fluorescens is bestowed with a uniquely versatile metabolic framework that enables the microbe to adapt to a wide range of conditions including disparate nutrients and toxins. In this mini-review we elaborate on the various metabolic reconfigurations evoked by this microbial system to combat reactive oxygen/nitrogen species and metal stress. The fine-tuning of the NADH/NADPH homeostasis coupled with the production of α-keto-acids and ATP allows for the maintenance of a reductive intracellular milieu. The metabolic networks propelling the synthesis of metabolites like oxalate and aspartate are critical to keep toxic metals at bay. The biochemical processes resulting from these defensive mechanisms provide molecular clues to thwart infectious microbes and reveal elegant pathways to generate value-added products.

Metabolic adaptation and NADPH homeostasis evoked by a sulfur-deficient environment in Pseudomonas fluorescens

Sulfur is essential for all living organisms due to its ability to mediate a variety of enzymatic reactions, signalling networks, and redox processes. The interplay between sulfhydryl group (SH) and disulfide bond (S-S) is central to the maintenance of intracellular oxidative balance. Although most aerobic organisms succumb to sulfur starvation, the nutritionally versatile soil microbe Pseudomonas fluorescens elaborates an intricate metabolic reprogramming in order to adapt to this challenge. When cultured in a sulfur-deficient medium with glutamine as the sole carbon and nitrogen source, the microbe reconfigures its metabolism aimed at the enhanced synthesis of NADPH, an antioxidant and the limited production of NADH, a pro-oxidant. While oxidative phosphorylation (OXPHOS) and tricarboxylic acid (TCA) cycle, metabolic modules known to generate reactive oxygen species are impeded, the activities NADPH-producing enzymes such as malic enzyme, and glutamate dehydrogenase (GDH) NADP-dependent are increased. The α-ketoglutarate (KG) generated from glutamine rapidly enters the TCA cycle via α-ketoglutarate dehydrogenase (KGDH), an enzyme that was prominent in the control cultures. In the S-deficient media, the severely impeded KGDH coupled with the increased activity of the reversible isocitrate dehydrogenase (ICDH) that fixes KG into isocitrate in the presence of NADH and HCO₃^- ensures a constant supply of this critical tricarboxylic acid. The up-regulation of ICDH-NADP dependent in the soluble fraction of the cells obtained from the S-deficient media results in enhanced NADPH synthesis, a reaction aided by the concomitant increase in NAD kinase activity. The latter converts NAD into NADP in the presence of ATP. Taken together, the data point to a metabolic network involving isocitrate, α-KG, and ICDH that converts NADH into NADPH in P. fluorescens subjected to a S-deprived environment.

Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation

The micro-aerophilic organisms and aerobes as well as yeast and higher organisms have evolved to gain energy through respiration (via oxidative phosphorylation), thereby enabling them to grow much faster than anaerobes. However, during respiration, reactive oxygen species (ROSs) are inherently (inevitably) generated, and threaten the cell's survival. Therefore, living organisms (or cells) must furnish the potent defense systems to keep such ROSs at harmless level, where the cofactor balance plays crucial roles. Namely, NADH is the source of energy generation (catabolism) in the respiratory chain reactions, through which ROSs are generated, while NADPH plays important roles not only for the cell synthesis (anabolism) but also for detoxifying ROSs. Therefore, the cell must rebalance the redox ratio by modulating the fluxes of the central carbon metabolism (CCM) by regulating the multi-level regulation machinery upon genetic perturbations and the change in the growth conditions. Here, we discuss about how aerobes accomplish such cofactor homeostasis against redox perturbations. In particular, we consider how single-gene mutants (including pgi, pfk, zwf, gnd and pyk mutants) modulate their metabolisms in relation to cofactor rebalance (and also by adaptive laboratory evolution). We also discuss about how the overproduction of NADPH (by the pathway gene mutation) can be utilized for the efficient production of useful value-added chemicals such as medicinal compounds, polyhydroxyalkanoates, and amino acids, all of which require NADPH in their synthetic pathways. We then discuss about the metabolic responses against oxidative stress, where αketoacids play important roles not only for the coordination between catabolism and anabolism, but also for detoxifying ROSs by non-enzymatic reactions, as well as for reducing the production of ROSs by repressing the activities of the TCA cycle and respiration (via carbon catabolite repression). Thus, we discuss about the mechanisms (basic strategies) that modulate the metabolism from respiration to respiro-fermentative metabolism causing overflow, based on the role of Pyk activity, affecting the NADPH production at the oxidative pentose phosphate (PP) pathway, and the roles of αketoacids for the change in the source of energy generation from the oxidative phosphorylation to the substrate level phosphorylation.

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.

Enhanced N-acetyl-D-neuraminic production from glycerol and N-acetyl-D-glucosamine by metabolically engineered Escherichia coli with a two-stage pH-shift control strategy

Typical N-acetyl-D-neuraminic acid (Neu5Ac) production uses N-acetyl-D-glucosamine (GlcNAc) and excess pyruvate as substrates in the enzymatic or whole-cell biocatalysis process. In a previous study, a Neu5Ac-producing biocatalytic process via engineered Escherichia coli SA-05/pDTrc-AB/pCDF-pck-ppsA was constructed without exogenous pyruvate. In this study, glycerol was found to be a good energy source compared with glucose for the catalytic system with resting cells, and Neu5Ac production increased to 13.97 ± 0.27 g L^-1. In addition, a two-stage pH shift strategy was carried out, and the Neu5Ac yield was improved to 14.61 ± 0.31 g L^-1. The GlcNAc concentration for Neu5Ac production was optimized. Finally, an integrated strategy was developed for Neu5Ac production, and the Neu5Ac yield reached as high as 18.17 ± 0.27 g L^-1. These results provide a new biocatalysis technology for Neu5Ac production without exogenous pyruvate.

Metabolic defence against oxidative stress: the road less travelled so far

Bacteria have survived, and many have thrived, since antiquity in the presence of the highly-reactive chalcogen-oxygen (O₂ ). They are known to evoke intricate strategies to defend themselves from the reactive by-products of oxygen-reactive oxygen species (ROS). Many of these detoxifying mechanisms have been extensively characterized; superoxide dismutase, catalases, alkyl hydroperoxide reductase and the glutathione (GSH)-cycling system are responsible for neutralizing specific ROS. Meanwhile, a pool of NADPH-the reductive engine of many ROS-combating enzymes-is maintained by metabolic enzymes including, but not exclusively, glucose-6 phosphate dehydrogenase (G6PDH) and NADP-dependent isocitrate dehydrogenase (ICDH-NADP). So, it is not surprising that evidence continues to emerge demonstrating the pivotal role metabolism plays in mitigating ROS toxicity. Stemming from its ability to concurrently decrease the production of the pro-oxidative metabolite, NADH, while augmenting the antioxidative metabolite, NADPH, metabolism is the fulcrum of cellular redox potential. In this review, we will discuss the mounting evidence positioning metabolism and metabolic shifts observed during oxidative stress, as critical strategies microbes utilize to thrive in environments that are rife with ROS. The contribution of ketoacids-moieties capable of non-enzymatic decarboxylation in the presence of oxidants-as ROS scavengers will be elaborated alongside the metabolic pathways responsible for their homeostases. Further, the signalling role of the carboxylic acids generated following the ketoacid-mediated detoxification of the ROS will be commented on within the context of oxidative stress.