Complete Genome Sequence of Actinobacillus succinogenes GXAS137, a Highly Efficient Producer of Succinic Acid

Comparative Transcriptome Analysis Reveals the Molecular Mechanisms of Acetic Acid Reduction by Adding NaHSO3 in Actinobacillus succinogenes GXAS137

Acetic acid (AC) is a major by-product from fermentation processes for producing succinic acid (SA) using Actinobacillus succinogenes. Previous experiments have demonstrated that sodium bisulfate (NaHSO3) can significantly decrease AC production by A. succinogenes GXAS137 during SA fermentation. However, the mechanism of AC reduction is poorly understood. In this study, the transcriptional profiles of the strain were compared through Illumina RNA-seq to identify differentially expressed genes (DEGs). A total of 210 DEGs were identified by expression analysis: 83 and 127 genes up-regulated and down-regulated, respectively, in response to NaHSO3 treatment. The functional annotation analysis of DEGs showed that the genes were mainly involved in carbohydrates, inorganic ions, amino acid transport, metabolism, and energy production and conversion. The mechanisms of AC reduction might be related to two aspects: (i) the lipoic acid synthesis pathway (LipA, LipB) was significantly down-regulated, which blocked the pathway catalyzed by pyruvate dehydrogenase complex to synthesize acetyl-coenzyme A (acetyl-CoA) from pyruvate; (ii) the expression level of the gene encoding bifunctional acetaldehyde-alcohol dehydrogenase was significantly up-regulated, and this effect facilitated the synthesis of ethanol from acetyl-CoA. However, the reaction of NaHSO3 with the intermediate metabolite acetaldehyde blocked the production of ethanol and consumed acetyl-CoA, thereby decreasing AC production. Thus, our study provides new insights into the molecular mechanism of AC decreased underlying the treatment of NaHSO3 and will deepen the understanding of the complex regulatory mechanisms of A. succinogenes.

Reduced acetic acid formation using NaHSO3 as a steering agent by Actinobacillus succinogenes GXAS137

The high production of acetic acid (AC) as a by-product leads to difficult separation and purification of succinic acid (SA) and increases production costs in SA fermentation by Actinobacillus succinogenes. NaHSO₃ as a steering agent was used to reduce AC production. Herein, the optimum fermentation conditions were achieved by single-factor and orthogonal tests as follows: glucose 60 g/L; MgCO₃ 60 g/L; NaHSO₃ 0.15% (w/v); and NaHSO₃ addition time, 8 h after inoculation. After optimization, the SA and AC contents were 44.42 and 5.73 g/L. The SA improved by 100.72%, the AC decreased by 21.18% compared with the unfermented. The acetate kinase activity decreased by 14.36% and acetyl-CoA content improved by 97.55% in the group of NaHSO₃ addition compared with control check (CK). The mechanism of NaHSO₃ is formation acetaldehyde-sodium bisulfite compound and reduction the activity of acetate kinase. These findings indicated a new way of using NaHSO₃ as a steering agent to reduce AC generation and may help promote the development of SA industrial production.

Effects of down-regulation of ackA expression by CRISPR-dCpf1 on succinic acid production in Actinobacillus succinogenes

Succinic acid (SA), a key intermediate in the cellular tricarboxylic acid cycle (TCA), is a 4-carbon dicarboxylic acid of great industrial value. Actinobacillus succinogenes can ferment various carbon sources and accumulate relatively high concentrations of SA, but few reliable genetic engineering tools exist for A. succinogenes and this has hindered strain improvement to increase SA production for industrial application. Two different repressors, endonuclease-deactivated Cas9 (dCas9) from Streptococcus pyogenes and Cpf1 (dCpf1) from Francisella tularensis, were applied to construct a CRISPRi system in A. succinogenes. Codon-optimized Cas9 and native Cpf1 were successfully expressed in A. succinogenes, and the corresponding sgRNA and crRNA expression elements, promoted by the fumarate reductase promoter, frd, were introduced into the CRISPRi plasmid. The highest repression of the ackA gene (encoding acetate kinase) and thereby acetic acid production (~ eightfold) was achieved by the dCpf1-based CRISPRi system, in which the mutation site, E1006A acted at the start of the coding region of ackA, the gene which regulates acetic acid biosynthesis. Compared with the ackA gene knockout mutant, cell growth was moderately improved and SA production increased by 6.3%. Further, the SA titer and productivity in a 3 L fermenter reached 57.06 g/L and 1.87 g/L/h, and there was less acetic acid production. A dCpf1-based CRISPRi-mediated gene repression system was successfully established for the first time, providing a simple and effective tool for studying functional genomics in A. succinogenes and optimizing SA production.

Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.

Metabolic Regulation of Organic Acid Biosynthesis in Actinobacillus succinogenes

Actinobacillus succinogenes is one of the most promising strains for succinic acid production; however, the lack of efficient genetic tools for strain modification development hinders its further application. In this study, a markerless knockout method for A. succinogenes using in-frame deletion was first developed. The resulting ΔpflA (encode pyruvate formate lyase 1-activating protein) strain displayed distinctive organic acid synthesis capacity under different cultivation modes. Additional acetate accumulation was observed in the ΔpflA strain relative to that of the wild type under aerobic conditions, indicating that acetate biosynthetic pathway was activated. Importantly, pyruvate was completely converted to lactate under anaerobic fermentation. The transcription analysis and enzyme assay revealed that the expression level and specific activity of lactate dehydrogenase (LDH) were significantly increased. In addition, the mRNA expression level of ldh was nearly increased 85-fold compared to that of the wild-type strain during aerobic-anaerobic dual-phase fermentation, resulting in 43.05 g/L lactate. These results demonstrate that pflA plays an important role in the regulation of C3 flux distribution. The deletion of pflA leads to the improvement of acetic acid production under aerobic conditions and activates lactic acid biosynthesis under anaerobic conditions. This study will help elaborate the mechanism governing organic acid biosynthesis 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.