Transcriptome analysis and anaerobic C4 -dicarboxylate transport in Actinobacillus succinogenes

Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics

The antibiotic resistance crisis, fueled by misuse and bacterial evolution, is a major global health threat. Traditional perspectives tie resistance to drug target mechanisms, viewing antibiotics as mere growth inhibitors. New insights revealed that low-dose antibiotics may also serve as signals, unexpectedly promoting bacterial growth. Yet, the development of resistance under these conditions remains unknown. Our study investigated resistance evolution under stimulatory antibiotics and uncovered new genetic mechanisms of resistance linked to metabolic remodeling. We documented a shift from a fast, reversible mechanism driven by methylation in central metabolic pathways to a slower, stable mechanism involving mutations in key metabolic genes. Both mechanisms contribute to a metabolic profile transition from glycolysis to rapid gluconeogenesis. In addition, our findings demonstrated that rising environmental temperatures associated with metabolic evolution accelerated this process, increasing the prevalence of metabolic gene mutations, albeit with a trade-off in interspecific fitness. These findings expand beyond the conventional understanding of resistance mechanisms, proposing a broader metabolic mechanism within the selective window of stimulatory sub-MIC antibiotics, particularly in the context of climate change.

Asuc_0142 of Actinobacillus succinogenes 130Z is the l-aspartate/C4-dicarboxylate exchanger DcuA

Anaerobic bacteria often use antiporters DcuB (malate/succinate antiport) or DcuA (l-aspartate/succinate antiport) for the excretion of succinate during fumarate respiration. The rumen bacterium Actinobacillus succinogenes is able to produce large amounts of succinate by fumarate respiration, using the DcuB-type transporter DcuE for l-malate/succinate antiport. Asuc_0142 was annotated as a second DcuB-type transporter. Deletion of Asuc_0142 decreased the uptake rate for l-[14C]aspartate into A. succinogenes cells. Properties of transport by heterologously expressed Asuc_0142 were investigated in an Escherichia coli mutant deficient of anaerobic C4DC transporters. Expression of Asuc_0142 resulted in high uptake activity for l-[14C]fumarate or l-[14C]aspartate, but the former showed a strong competitive inhibition by l-aspartate. In E. coli loaded with l-[14C]aspartate, [14C]succinate or [14C]fumarate, extracellular C4DCs initiated excretion of the intracellular substrates, with a preference for l-aspartateex/succinatein or l-aspartateex/fumaratein antiport. These findings indicate that Asuc_0142 represents a DcuA-type transporter for l-aspartate uptake and l-aspartateex/C4DCin antiport, differentiating it from the DcuB-type transporter DcuE for l-malateex/succinatein antiport. Sequence analysis and predicted structural characteristics confirm structural similarity of Asuc_0142 to DcuA, and Asuc_0142 was thus re-named as DcuAAs. The bovine rumen fluid contains l-aspartate (99.6 µM), whereas fumarate and l-malate are absent. Therefore, bovine rumen colonisers depend on l-aspartate as an exogenous substrate for fumarate respiration. A. succinogenes encodes HemG (protoporphyrinogen oxidase) and PyrD (dihydroorotate dehydrogenase) for haem and pyrimidine biosynthesis. The enzymes require fumarate as an electron acceptor, suggesting an essential role for l-aspartate, DcuAAs, and fumarate respiration for A. succinogenes growing in the bovine rumen.

The role of dctP gene in regulating colonization, adhesion and pathogenicity of Vibrio alginolyticus strain HY9901

Vibriosis caused by Vibrio alginolyticus has severely affected the development of mariculture industry in recent decades. DctP, a tripartite ATP-independent periplasmic transporter solute-binding subunit, is thought to be one of the virulence factors in Vibrio. In this study, the results displayed no difference in morphological characteristics and growth between ΔdctP (dctP mutant strain) and WT (wild-type strain). Nevertheless, the ability of swarming motility, biofilm formation, ECPase formation, cell adhesion and colonized ability of ΔdctP significantly decreased compared to those of WT. The LD₅₀ of ΔdctP significantly increased by 40-fold compared to that of WT. The transcriptome analysis demonstrated the deletion mutation of dctP could regulate the expression levels of 22 genes related to colonization, adhesion and pathogenicity in V. alginolyticus. The analysis of qRT-PCR showed the transcriptome data were reliable. These results reveal the effect of attenuated function of DctP on colonization, adherence and pathogenicity by controlling the expression of related gene.

Well Knowledge of the Physiology of Actinobacillus succinogenes to Improve Succinic Acid Production

The anaerobic fermentation of glucose and fructose was performed by Actinobacillus succinogenes 130Z in batch mode using three different volume of bioreactors (0.25, 1 and 3 L). The strategy used was the addition of MgCO3 and fumaric acid (FA) as mineral carbon and the precursor of succinic acid, respectively, in the culture media. Kinetics and yields of succinic acid (SA) production in the presence of sugars in a relevant synthetic medium were investigated. Work on the bench scale (3 L) showed the best results when compared to the small anaerobic reactor’s succinic acid yield and productivity after 96 h of fermentation. For an equal mixture of glucose and fructose used as substrate at 0.4 mol L−1 with the addition of FA as enhancer and under proven optimal conditions (pH 6.8, T = 37 °C, anaerobic condition and 1% v/v of biomass), about 0.5 mol L−1 of SA was obtained, while the theoretical production of succinic acid was 0.74 mol L−1. This concentration corresponded to an experimental yield of 0.88 (mol-C SA/mol-C sugars consumed anaerobically) and a volumetric productivity of 0.48 g-SA L−1 h−1. The succinic acid yield and concentration obtained were significant and in the order of those reported in the literature.

High-affinity l-malate transporter DcuE of Actinobacillus succinogenes catalyses reversible exchange of C4-dicarboxylates

Actinobacillus succinogenes is a natural succinate producer, which is the result of fumarate respiration. Succinate production from anaerobic growth with C₄ -dicarboxylates requires transporters catalysing uptake and efflux of C₄ -dicarboxylates. Transporter Asuc_1999 (DcuE) found in A. succinogenes belongs to the Dcu family and was considered the main transporter for fumarate respiration. However, deletion of dcuE affected l-malate uptake of A. succinogenes rather than fumarate uptake. DcuE complemented anaerobic growth of Escherichia coli on l-malate or fumarate; thus, the transporter was characterized in E. coli heterologously. Time-dependent uptake and competitive inhibition assays demonstrated that l-malate is the most preferred substrate for uptake by DcuE. The V_max of DcuE for l-malate was 20.04 μmol/gDW·min with K_m of 57 μM. The V_max for l-malate was comparable to that for fumarate, whereas the K_m for l-malate was 8 times lower than that for fumarate. The catalytic efficiency of DcuE for l-malate was 7.3-fold higher than that for fumarate, showing high efficiency and high affinity for l-malate. Furthermore, DcuE catalysed the reversible exchange of three C₄ -dicarboxylates - l-malate, fumarate and succinate - but the preferred substrate for uptake was l-malate. Under physiological conditions, the C₄ -dicarboxylates were reduced to succinate. Therefore, DcuE is proposed as the l-malate/succinate antiporter in A. succinogenes.

Opportunities, challenges, and future perspectives of succinic acid production by Actinobacillus succinogenes

Due to environmental issues and the depletion of fossil-based resources, ecofriendly sustainable biomass-based chemical production has been given more attention recently. Succinic acid (SA) is one of the top value added bio-based chemicals. It can be synthesized through microbial fermentation using various waste steam bioresources. Production of chemicals from waste streams has dual function as it alleviates environmental concerns; they could have caused because of their improper disposal and transform them into valuable products. To date, Actinobacillus succinogenes is termed as the best natural SA producer. However, few reviews regarding SA production by A. succinogenes were reported. Herewith, pathways and metabolic engineering strategies, biomass pretreatment and utilization, and process optimization related with SA fermentation by A. succinogenes were discussed in detail. In general, this review covered vital information including merits, achievements, progresses, challenges, and future perspectives in SA production using A. succinogenes. Therefore, it is believed that this review will provide platform to understand the potential of the strain and tackle existing hurdles so as to develop superior strain for industrial applications. It will also be used as a baseline for identification, isolation, and improvement of other SA-producing microbes.

Transcriptome analysis and anaerobic C4 -dicarboxylate transport in Actinobacillus succinogenes

A global transcriptome analysis of the natural succinate producer Actinobacillus succinogenes revealed that 353 genes were differentially expressed when grown on various carbon and energy sources, which were categorized into six functional groups. We then analyzed the expression pattern of 37 potential C₄‐dicarboxylate transporters in detail. A total of six transporters were considered potential fumarate transporters: three transporters, Asuc_1999 (Dcu), Asuc_0304 (DASS), and Asuc_0270‐0273 (TRAP), were constitutively expressed, whereas three others, Asuc_1568 (DASS), Asuc_1482 (DASS), and Asuc_0142 (Dcu), were differentially expressed during growth on fumarate. Transport assays under anaerobic conditions with [¹⁴C]fumarate and [¹⁴C]succinate were performed to experimentally verify that A. succinogenes possesses multiple C₄‐dicarboxlayte transport systems with different substrate affinities. Upon uptake of 5 mmol/L fumarate, the systems had substrate specificity for fumarate, oxaloacetate, and malate, but not for succinate. Uptake was optimal at pH 7, and was dependent on both proton and sodium gradients. Asuc_1999 was suspected to be a major C₄‐dicarboxylate transporter because of its noticeably high and constitutive expression. An Asuc_1999 deletion (∆1999) decreased fumarate uptake significantly at approximately 5 mmol/L fumarate, which was complemented by the introduction of Asuc_1999. Asuc_1999 expressed in Escherichia coli catalyzed fumarate uptake at a level of 21.6 μmol·gDW⁻¹·min⁻¹. These results suggest that C₄‐dicarboxylate transport in A. succinogenes is mediated by multiple transporters, which transport various types and concentrations of C₄‐dicarboxylates.