Bacterial Acid Resistance Toward Organic Weak Acid Revealed by RNA-Seq Transcriptomic Analysis in Acetobacter pasteurianus

Abstract

Under extreme acidic environments, bacteria exploit several acid resistance (AR) mechanisms for enhancing their survival, which is concerned with several aspects, such as issues in human health and fermentation for acidic products. Currently, knowledge of bacterial AR mainly comes from the strong acid (such as hydrochloric acid) stresses, whereas AR mechanisms against organic weak acids (such as acetic acid), which are indeed encountered by bacteria, are less understood. Acetic acid bacteria (AAB), with the ability to produce acetic acid up to 20 g/100 mL, possess outstanding acetic acid tolerance, which is conferred by their unique AR mechanisms, including pyrroloquinoline quinine-dependent alcohol dehydrogenase, acetic acid assimilation and molecular chaperons. The distinguished AR of AAB toward acetic acid may provide a paradigm for research in bacterial AR against weak organic acids. In order to understand AAB’s AR mechanism more holistically, omics approaches have been employed in the corresponding field. However, the currently reported transcriptomic study was processed under a low-acidity (1 g/100 mL) environment, which could not reflect the general conditions that AAB are usually faced with. This study performed RNA-Seq transcriptomic analysis investigating AR mechanisms in Acetobacter pasteurianus CGMCC 1.41, a widely used vinegar-brewing AAB strain, at different stages of fermentation, namely, under different acetic acid concentrations (from 0.6 to 6.03 g/100 mL). The results demonstrated the even and clustered genomic distribution of up- and down-regulated genes, respectively. Difference in AR between AAB and other microorganisms was supported by the down-regulation of urea degradation and trehalose synthesis-related genes in response to acetic acid. Detailed analysis reflected the role of ethanol respiration as the main energy source and the limited effect of acetic acid assimilation on AR during fermentation as well as the competition between ethanol respiratory chain and NADH, succinate dehydrogenase-based common respiratory chain. Molecular chaperons contribute to AR, too, but their regulatory mechanisms require further investigation. Moreover, pathways of glucose catabolism and fatty acid biosynthesis are also related to AR. Finally, 2-methylcitrate cycle was proposed as an AR mechanism in AAB for the first time. This study provides new insight into AR mechanisms of AAB, and it also indicates the existence of numerous undiscovered AR mechanisms.

Transcriptome Analysis of Komagataeibacter europaeus CGMCC 20445 Responses to Different Acidity Levels During Acetic Acid Fermentation

“…Oxidative phosphorylation. A. pasteurianus was separately cultured in an ethanol-containing and ethanol-free medium ( Yang et al 2019 ). Compared with the culture without ethanol, ethanol dehydrogenase and acetaldehyde dehydrogenase were continuously upregulated in the ethanol-containing culture during fermentation, while NADH dehydrogenase complex (complex I) and succinate dehydrogenase complex (complex II) were continuously downregulated in the ethanol-containing culture during fermentation ( Yang et al 2019 ).…”

“…A. pasteurianus was separately cultured in an ethanol-containing and ethanol-free medium ( Yang et al 2019 ). Compared with the culture without ethanol, ethanol dehydrogenase and acetaldehyde dehydrogenase were continuously upregulated in the ethanol-containing culture during fermentation, while NADH dehydrogenase complex (complex I) and succinate dehydrogenase complex (complex II) were continuously downregulated in the ethanol-containing culture during fermentation ( Yang et al 2019 ). At the middle stage and late stage of fermentation, ethanol dehydrogenase and acetaldehyde dehydrogenase were upregulated, while the downregulation of NADH dehydrogenase complex (complex I) and succinate dehydrogenase complex (complex II) showed a decreasing trend ( Yang et al 2019 ).…”

“…Table SIII.6 shows the expression levels of genes associated with pentose phosphate pathway. Glucose was continuously consumed during fermentation, and pentose phosphate pathway genes were continuously upregulated during fermentation in A. pasteurianus ( Yang et al 2019 ). The structure and chemical composition of the cell membrane affects acid resistance in acetic acid bacteria.…”

“… Sakurai et al (2011) studied the transcriptomes of Acetobacter aceti NBRC 14818 using ethanol, acetate, and glucose as the carbon source and found differences in transcript levels of genes in the central carbon metabolic pathway and respiratory chain under different carbon source conditions. Yang et al (2019) used A. pasteurianus CGMCC 1.41, which is commonly used for vinegar fermentation, to test fermentation under different initial ethanol concentrations, using transcriptome sequencing to examine the acid-resistance mechanisms. Ryngajłło et al (2019) used the RNA-seq technology to study the effect of adding ethanol to the culture medium on the gene expression profile of Komagataeibacter xylinus E25.…”

Microbial response to acid stress: mechanisms and applications

“…Adaptive evolution and genome shuffling (Jakob et al 2007) P. acidipropionici (Zhang and Yang 2009;Guan et al 2013) Bacillus (Shobharani and Halami 2014) S. cerevisiae (Casal et al 2016) C. glabrata (Zhou et al 2011) Zygosaccharomyces bailii (Palma et al 2015) Decarboxylation and deamination E. coli (Iyer et al 2003;Sun et al 2012a;Lu et al 2013 Kumar et al 2015;Cheng et al 2016) were also used to improve the acid tolerance of Lactobacillus (Patnaik et al 2002;Zhang et al 2012), whereby the production of lactic acid increased significantly. RNA-Seq transcriptomic analysis was performed to investigate the acid-resistant mechanisms of Acetobacter pasteurianus, providing more basics and opportunities for higher acid tolerance and acetic acid production (Yang et al 2019). Similarly, omics were also introduced to analyze acetic acid tolerance in Saccharomyces cerevisiae (Geng et al 2017).…”