Engineering of the Small Noncoding RNA (sRNA) DsrA Together with the sRNA Chaperone Hfq Enhances the Acid Tolerance of Escherichia coli

Regulation of the sRNA ncBCG427 on mycobacterial stress adaptation

BACKGROUND

Mycobacterium tuberculosis complex (MTBC) comprises the primary pathogens responsible for tuberculosis in humans and animals, including the virulent Mycobacterium tuberculosis (M. tb) and Mycobacterium bovis (M. bovis). As a group of intracellular bacteria, MTBC has developed intricate mechanisms for infection and survival within host cells. Among these mechanisms, small non-coding RNAs (sRNAs) play essential roles in regulating post-transcriptional pathways that may aid in stress adaptation in mycobacteria. In our previous research, we identified a novel sRNA, ncBCG427, in BCG, the attenuated strain of M. bovis. This sRNA is differentially expressed under various stress conditions, and homologs exist in both M. tb and M. bovis.

METHOD AND RESULTS

To explore the regulatory capabilities of ncBCG427 on bacterial stress adaptation in the original BCG strain, we constructed overexpression (BCG_ncBCG427) and control (BCG_Vector) strains. Our findings demonstrated that ncBCG427 significantly enhanced BCG survival under carbon starvation and acid stress conditions, while it resulted in decreased survival under iron starvation conditions. Transcriptomic analyses revealed that overexpression of ncBCG427 substantially altered gene expression profiles in these three stress environments, with differentially expressed genes (DEGs) in the same pathways enriched for different stressors. Notably, we identified 22 DEGs that responded to two or three stress conditions, implicating their involvement in pathways related to the sulfur relay system, ribosome function, folate biosynthesis, and the biosynthesis of cofactors. This suggested that these genes may served as key regulators in ncBCG427-mediated stress adaptation. Furthermore, quantitative PCR (qPCR) was employed to verify the expression levels of 16 DEGs in BCG, with 14 of them matching homologous genes in M. tb. We then created a ncBCG427 overexpression strain in M. tb (MTB_ncBCG427) alongside a control strain (MTB_Vector). Interestingly, 4 of the 14 genes displayed consistent expression trends in both M. tb and BCG under different stress conditions.

CONCLUSION

In conclusion, our study underscored the significant role of the sRNA ncBCG427 in enhancing mycobacterial survival under stress conditions and proposed potential target genes for further exploration into the mechanisms of stress adaptation in mycobacteria.

Advances in stress-tolerance elements for microbial cell factories

Microorganisms, particularly extremophiles, have evolved multiple adaptation mechanisms to address diverse stress conditions during survival in unique environments. Their responses to environmental coercion decide not only survival in severe conditions but are also an essential factor determining bioproduction performance. The design of robust cell factories should take the balance of their growing and bioproduction into account. Thus, mining and redesigning stress-tolerance elements to optimize the performance of cell factories under various extreme conditions is necessary. Here, we reviewed several stress-tolerance elements, including acid-tolerant elements, saline-alkali-resistant elements, thermotolerant elements, antioxidant elements, and so on, providing potential materials for the construction of cell factories and the development of synthetic biology. Strategies for mining and redesigning stress-tolerance elements were also discussed. Moreover, several applications of stress-tolerance elements were provided, and perspectives and discussions for potential strategies for screening stress-tolerance elements were made.

Engineering quorum sensing-based genetic circuits enhances growth and productivity robustness of industrial E. coli at low pH

BACKGROUND

Microbial organisms hold significant potential for converting renewable substrates into valuable chemicals. Low pH fermentation in industrial settings offers key advantages, including reduced neutralizer usage and decreased wastewater generation, particularly in the production of amino acids and organic acids. Engineering acid-tolerant strains represents a viable strategy to enhance productivity in acidic environments. Synthetic biology provides dynamic regulatory tools, such as gene circuits, facilitating precise expression of acid resistance (AR) modules in a just-in-time and just-enough manner.

RESULTS

In this study, we aimed to enhance the robustness and productivity of Escherichia coli, a workhorse for amino acid and organic acid production, in industrial fermentation under mild acidic conditions. We employed an Esa-type quorum sensing circuit to dynamically regulate the expression of an AR module (DsrA-Hfq) in a just-in-time and just-enough manner. Through careful engineering of the critical promoter PesaS and stepwise evaluation, we developed an optimal Esa-PBD(L) circuit that conferred upon an industrial E. coli strain SCEcL3 comparable lysine productivity and enhanced yield at pH 5.5 compared to the parent strain at pH 6.8.

CONCLUSIONS

This study exemplifies the practical application of gene circuits in industrial environments, which present challenges far beyond those of well-controlled laboratory conditions.

Achieving robust synthetic tolerance in industrial E. coli through negative auto-regulation of a DsrA-Hfq module

In industrial fermentation processes, microorganisms often encounter acid stress, which significantly impact their productivity. This study focused on the acid-resistant module composed of small RNA (sRNA) DsrA and the sRNA chaperone Hfq. Our previous study had shown that this module improved the cell growth of Escherichia coli MG1655 at low pH, but failed to obtain this desired phenotype in industrial strains. Here, we performed a quantitative analysis of DsrA-Hfq module to determine the optimal expression mode. We then assessed the potential of the CymR-based negative auto-regulation (NAR) circuit for industrial application, under different media, strains and pH levels. Growth assay at pH 4.5 revealed that NAR-05D04H circuit was the best acid-resistant circuit to improve the cell growth of E. coli MG1655. This circuit was robust and worked well in the industrial lysine-producing strain E. coli SCEcL3 at a starting pH of 6.8 and without pH control, resulting in a 250 % increase in lysine titer and comparable biomass in shaking flask fermentation compared to the parent strain. This study showed the practical application of NAR circuit in regulating DsrA-Hfq module, effectively and robustly improving the acid tolerance of industrial strains, which provides a new approach for breeding industrial strains with tolerance phenotype.

Characterization of Mild Acid Stress Response in an Engineered Acid-Tolerant Escherichia coli Strain

Engineering acid-tolerant microbial strains is a cost-effective approach to overcoming acid stress during industrial fermentation. We previously constructed an acid-tolerant strain (Escherichia coli SC3124) with enhanced growth robustness and productivity under mildly acidic conditions by fine-tuning the expression of synthetic acid-tolerance module genes consisting of a proton-consuming acid resistance system (gadE), a periplasmic chaperone (hdeB), and ROS scavengers (sodB, katE). However, the precise acid-tolerance mechanism of E. coli SC3124 remained unclear. In this study, the growth of E. coli SC3124 under mild acid stress (pH 6.0) was determined. The final OD600 of E. coli SC3124 at pH 6.0 was 131% and 124% of that of the parent E. coli MG1655 at pH 6.8 and pH 6.0, respectively. Transcriptome analysis revealed the significant upregulation of the genes involved in oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, and lysine-dependent acid-resistance system in E. coli SC3124 at pH 6.0. Subsequently, a weighted gene coexpression network analysis was performed to systematically determine the metabolic perturbations of E. coli SC3124 with mild acid treatment, and we extracted the gene modules highly associated with different acid traits. The results showed two biologically significant coexpression modules, and 263 hub genes were identified. Specifically, the genes involved in ATP-binding cassette (ABC) transporters, oxidative phosphorylation, the TCA cycle, amino acid metabolism, and purine metabolism were highly positively associated with mild acid stress responses. We propose that the overexpression of synthetic acid-tolerance genes leads to metabolic changes that confer mild acid stress resistance in E. coli. Integrated omics platforms provide valuable information for understanding the regulatory mechanisms of mild acid tolerance in E. coli and highlight the important roles of oxidative phosphorylation and ABC transporters in mild acid stress regulation. These findings offer novel insights to better the design of acid-tolerant chasses to synthesize value-added chemicals in a green and sustainable manner.

Strategies to increase the robustness of microbial cell factories

Engineering microbial cell factories have achieved much progress in producing fuels, natural products and bulk chemicals. However, in industrial fermentation, microbial cells often face various predictable and stochastic disturbances resulting from intermediate metabolites or end product toxicity, metabolic burden and harsh environment. These perturbances can potentially decrease productivity and titer. Therefore, strain robustness is essential to ensure reliable and sustainable production efficiency. In this review, the current strategies to improve host robustness were summarized, including knowledge-based engineering approaches, such as transcription factors, membrane/transporters and stress proteins, and the traditional adaptive laboratory evolution based on natural selection. Computation-assisted (e.g. GEMs, deep learning and machine learning) design of robust industrial hosts was also introduced. Furthermore, the challenges and future perspectives on engineering microbial host robustness are proposed to promote the development of green, efficient and sustainable biomanufacturers.

Insights into the complementation potential of the extreme acidophile's orthologue in replacing Escherichia coli hfq gene-particularly in bacterial resistance to environmental stress

Acidithiobacillus caldus is a typical extreme acidophile widely used in the biohydrometallurgical industry, which often experiences extreme environmental stress in its natural habitat. Hfq, an RNA-binding protein, typically functions as a global regulator involved in various cellular physiological processes. Yet, the biological functions of Hfq derived from such extreme acidophile have not been extensively investigated. In this study, the recombinant strain Δhfq/Achfq, constructed by CRISPR/Cas9-mediated chromosome integration, fully or partially restored the phenotypic defects caused by hfq deletion in Escherichia coli, including impaired growth performance, abnormal cell morphology, impaired swarming motility, decreased stress resistance, decreased intracellular ATP and free amino acid levels, and attenuated biofilm formation. Particularly noteworthy, the intracellular ATP level and biofilm production of the recombinant strain were increased by 12.2% and 7.0%, respectively, compared to the Δhfq mutant. Transcriptomic analysis revealed that even under heterologous expression, AcHfq exerted global regulatory effects on multiple cellular processes, including metabolism, environmental signal processing, and motility. Finally, we established a potential working model to illustrate the regulatory mechanism of AcHfq in bacterial resistance to environmental stress.

Gram-negative bacterial sRNAs encapsulated in OMVs: an emerging class of therapeutic targets in diseases

Small regulatory RNAs (sRNAs) encapsulated in outer membrane vesicles (OMVs) are critical post-transcriptional regulators of gene expression in prokaryotic and eukaryotic organisms. OMVs are small spherical structures released by Gram-negative bacteria that serve as important vehicles for intercellular communication and can also play an important role in bacterial virulence and host-pathogen interactions. These molecules can interact with mRNAs or proteins and affect various cellular functions and physiological processes in the producing bacteria. This review aims to provide insight into the current understanding of sRNA localization to OMVs in Gram-negative bacteria and highlights the identification, characterization and functional implications of these encapsulated sRNAs. By examining the research gaps in this field, we aim to inspire further exploration and progress in investigating the potential therapeutic applications of OMV-encapsulated sRNAs in various diseases.

Involvement of OxyR and Dps in the repression of replication initiation by DsrA small RNA in Escherichia coli

Regulation of the cell cycle process is an effective measure to ensure the stability and fidelity of genetic material during the reproduction of bacteria under different stresses. The small RNA DsrA helps bacteria adapt to environments by binding to multiple targets, but its association with the cell cycle remains unclear. Detection by flow cytometry, we first found that the knockout of dsrA promoted replication initiation, and corresponding overexpression of DsrA inhibited replication initiation in Escherichia coli. The absence of the chaperone protein Hfq, the DNA replication negative regulator protein Dps, or the transcription factor OxyR, was found to cause DsrA to no longer inhibit replication initiation. Excess DsrA promotes expression of the oxyR and dps gene, whereas β-galactosidase activity assay showed that deleting oxyR limited the enhancement of dps promoter transcriptional activity by DsrA. OxyR is a known positive regulator of Dps. Our data suggests that the effect of DsrA on replication initiation requires Hfq and that the upregulation of Dps expression by OxyR in response to DsrA levels may be a potential regulatory pathway for the negative regulation of DNA replication initiation.

Acid-tolerant bacteria and prospects in industrial and environmental applications

Acid-tolerant bacteria such as Streptococcus mutans, Acidobacterium capsulatum, Escherichia coli, and Propionibacterium acidipropionici have developed several survival mechanisms to sustain themselves in various acid stress conditions. Some bacteria survive by minor changes in the environmental pH. In contrast, few others adapt different acid tolerance mechanisms, including amino acid decarboxylase acid resistance systems, mainly glutamate-dependent acid resistance (GDAR) and arginine-dependent acid resistance (ADAR) systems. The cellular mechanisms of acid tolerance include cell membrane alteration in Acidithiobacillus thioxidans, proton elimination by F₁-F₀-ATPase in Streptococcus pyogenes, biofilm formation in Pseudomonas aeruginosa, cytoplasmic urease activity in Streptococcus mutans, synthesis of the protective cloud of ammonia, and protection or repair of macromolecules in Bacillus caldontenax. Apart from cellular mechanisms, there are several acid-tolerant genes such as gadA, gadB, adiA, adiC, cadA, cadB, cadC, speF, and potE that help the bacteria to tolerate the acidic environment. This acid tolerance behavior provides new and broad prospects for different industrial applications and the bioremediation of environmental pollutants. The development of engineered strains with acid-tolerant genes may improve the efficiency of the transgenic bacteria in the treatment of acidic industrial effluents. KEY POINTS: • Bacteria tolerate the acidic stress by methylating unsaturated phospholipid tail • The activity of decarboxylase systems for acid tolerance depends on pH • Genetic manipulation of acid-tolerant genes improves acid tolerance by the bacteria.

Enhancement of acid tolerance of Escherichia coli by introduction of molecule chaperone CbpA from extremophile

Molecular chaperone CbpA from extreme acidophile Acidithiobacillus caldus was applied to improve acid tolerance of Escherichia coli via CRISPR/Cas9. Cell growth and viability of plasmid complementary strain indicated the importance of cbpA^Ac for bacteria acid tolerance. With in situ gene replacement by CRISPR/Cas9 system, colony formation unit (CFU) of genome recombinant strain BL21-ΔcbpA/AccbpA showed 7.7 times higher cell viability than deficient strain BL21-ΔcbpA and 2.3 times higher than wild type. Cell morphology observation using Field Emission Scanning Electron Microscopy (FESEM) revealed cell breakage of BL21-ΔcbpA and significant recovery of BL21-ΔcbpA/AccbpA. The intracellular ATP level of all strains gradually decreased along with the increased stress time. Particularly, the value of recombinant strain was 56.0% lower than that of deficient strain after 5 h, indicating that the recombinant strain consumed a lot of energy to resist acid stress. The arginine concentration in BL21-ΔcbpA/AccbpA was double that of BL21-ΔcbpA, while the aspartate and glutamate contents were 14.8% and 6.2% higher, respectively, compared to that of wild type. Moreover, RNA-Seq analysis examined 93 genes down-regulated in BL21-ΔcbpA compared to wild type strain, while 123 genes were up-regulated in BL21-ΔcbpA/AccbpA compared to BL21-ΔcbpA, with an emphasis on energy metabolism, transport, and cell components. Finally, the working model in response to acid stress of cbpA from A. caldus was developed. This study constructed a recombinant strain resistant to acid stress and also provided a reference for enhancing microorganisms' robustness to various conditions.

Improving acid resistance of Escherichia coli base on the CfaS-mediated membrane engineering strategy derived from extreme acidophile

Industrial microorganisms used for the production of organic acids often face challenges such as inhibited cell growth and reduced production efficiency due to the accumulation of acidic metabolites. One promising way for improving the acid resistance of microbial cells is to reconstruct their membranes. Herein, the overexpression of cfa2 from extreme acidophile endowed E. coli with high-performance on resistance to the acid stress. The engineered strain M1-93-Accfa2, constructed by CRISPR/Cas9-mediated chromosome integration, also exhibited a significantly higher resistance to severe acid stress. The analysis of fatty acid profiles indicated that the proportion of Cy-19:0 in the cell membrane of M1-93-Accfa2 increased by 5.26 times compared with the control, while the proportion of C18:1w9c decreased by 5.81 times. Correspondingly, the permeability and fluidity of the membrane decreased significantly. HPLC analysis demonstrated that the contents of intracellular glutamic acid, arginine, methionine and aspartic acid of M1-93-Accfa2 were 2.59, 2.04, 22.07 and 2.65 times that of the control after environmental acidification, respectively. Meanwhile, transmission electron microscopy observation indicated that M1-93-Accfa2 could maintain a plumper cell morphology after acid stimulation. M1-93-Accfa2 also exhibited higher-performance on the resistance to organic acids, especially succinic acid stress. These results together demonstrated the great potential of M1-93-Accfa2 constructed here in the production of organic acids.

Improving the productivity of malic acid by alleviating oxidative stress during Aspergillus niger fermentation

BACKGROUND

As an attractive platform chemical, malic acid has been commonly used in the food, feed and pharmaceutical field. Microbial fermentation of biobased sources to produce malic acid has attracted great attention because it is sustainable and environment-friendly. However, most studies mainly focus on improving yield and ignore shortening fermentation time. A long fermentation period means high cost, and hinders the industrial applications of microbial fermentation. Stresses, especially oxidative stress generated during fermentation, inhibit microbial growth and production, and prolong fermentation period. Previous studies have shown that polypeptides could effectively relieve stresses, but the underlying mechanisms were poorly understood.

RESULTS

In this study, polypeptides (especially elastin peptide) addition improves the productivity of malic acid in A. niger, resulting in shortening of fermentation time from 120 to 108 h. Transcriptome and biochemical analyses demonstrated that both antioxidant enzyme-mediated oxidative stress defense system, such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), and nonenzymatic antioxidant system, such as glutathione, were enhanced in the presence of elastin peptide, suggesting elastin peptide relieving oxidative stresses is involved in many pathways. In order to further investigate the relationship between oxidative stress defense and malic acid productivity, we overexpressed three enzymes (Sod1, CAT, Tps1) related to oxidation resistance in A. niger, respectively, and these resulting strains display varying degree of improvement in malic acid productivity. Especially, the strain overexpressing the Sod1 gene achieved a malate titer of 91.85 ± 2.58 g/L in 96 h, corresponding to a productivity of 0.96 g/L/h, which performs better than elastin peptide addition.

CONCLUSIONS

Our investigation provides an excellent reference for alleviating the stress of the fungal fermentation process and improving fermentation efficiency.

Production of (2S)-sakuranetin from (2S)-naringenin in Escherichia coli by strengthening methylation process and cell resistance

(2S)-Sakuranetin is a 7-O-methylflavonoid that has anticancer, antiviral, and antimicrobial activities. Methylation process is involved in biosynthesizing (2S)-sakuranetin from (2S)-naringenin, in which S-adenosylmethionine (SAM) serves as the methyl donor. In this study, after methyl donor and substrate inhibition were identified as limiting factors for (2S)-sakuranetin biosynthesis, an efficient (2S)-sakuranetin-producing strain was constructed by enhancing methyl donor supply and cell tolerance to (2S)-naringenin. Firstly, PfOMT3 from Perilla frutescens was selected as the optimal flavonoid 7-O-methyltransferase (F7-OMT) for the conversion of (2S)-naringenin to (2S)-sakuranetin. Then, the methylation process was upregulated by regulating pyridoxal 5′-phosphate (PLP) content, key enzymes in methionine synthesis pathway, and the availability of ATP. Furthermore, genes that can enhance cell resistance to (2S)-naringenin were identified from molecular chaperones and sRNAs. Finally, by optimizing the fermentation process, 681.44 mg/L of (2S)-sakuranetin was obtained in 250-mL shake flasks. The titer of (2S)-sakuranetin reached 2642.38 mg/L in a 5-L bioreactor, which is the highest titer ever reported. This work demonstrates the importance of cofactor PLP in methylation process, and provides insights to biosynthesize other O-methylated flavonoids efficiently in E. coli.

Profiles of Small Regulatory RNAs at Different Growth Phases of Streptococcus thermophilus During pH-Controlled Batch Fermentation

Small regulatory RNA (sRNA) has been shown to play an important role under various stress conditions in bacteria, and it plays a vital role in regulating growth, adaptation and survival through posttranscriptional control of gene expression in bacterial cells. Streptococcus thermophilus is widely used as a starter culture in the manufacture of fermented dairy products. However, the lack of reliable information on the expression profiles and potential physiological functions of sRNAs in this species hinders our understanding of the importance of sRNAs in S. thermophilus. The present study was conducted to assess the expression profiles of sRNAs in S. thermophilus and to identify sRNAs that exhibited significant changes. A total of 530 potential sRNAs were identified, including 198 asRNAs, 135 sRNAs from intergenic regions, and 197 sRNAs from untranslated regions (UTRs). Significant changes occurred in the expression of 238, 83, 194, and 139 sRNA genes during the lag, early exponential growth, late exponential growth, and stationary phases, respectively. The expression of 14 of the identified sRNAs was verified by qRT-PCR. Predictions of the target genes of these candidate sRNAs showed that the primary metabolic pathways targeted were involved in carbon metabolism, biosynthesis of amino acids, ABC transporters, the metabolism of amino and nucleotide sugars, purine metabolism, and the phosphotransferase system. The expression of the predicted target genes was further analyzed to better understand the roles of sRNAs during different growth stages. The results suggested that these sRNAs play crucial roles by regulating biological pathways during different growth phases of S. thermophilus. According to the results, sRNAs sts141, sts392, sts318, and sts014 are involved in the regulation of osmotic stress. sRNAs sts508, sts087, sts372, sts141, sts375, and sts119 are involved in the regulation of starvation stress. sRNAs sts129, sts226, sts166, sts231, sts204, sts145, and sts236 are involved in arginine synthesis. sRNAs sts033, sts341, sts492, sts140, sts230, sts172, and sts377 are involved in the ADI pathway. The present study provided valuable information for the functional study of sRNAs in S. thermophilus and indicated a future research direction for sRNA in S. thermophilus. Overall, our results provided new insights for understanding the complex regulatory network of sRNAs in S. thermophilus.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.