Transcriptional profiling reveals molecular basis and the role of arginine in response to low-pH stress in Pichia kudriavzevii

Abstract BackgroundThe non-conventional yeast Pichia kudriavzevii possesses a unique ability to tolerate various environmental stresses particularly low-pH stress. Thus, it is considered to be a promising biotechnological host for the production of various organic acids under low-pH conditions. However, little is known about the low-pH stress response in P. kudriavzevii, which significantly restricts its future development. ResultsIn this study, P. kudriavzevii JLY1107 showed great tolerance to low-pH stress, but its cell aggregation upon acidic conditions is unfavorable for the development of low-pH fermentation. To explore the molecular basis, we conducted RNA-Seq to compare global gene expression in response to low-pH. Among the 429 differentially expressed genes, the genes associated with regulation of membrane lipid composition, filamentous growth and arginine metabolism were selected for in-depth discussions. The up-regulation of genes associated with arginine uptake and degradation suggests a potential role of arginine in response to low-pH strsss. We therefore present data supporting the hypothesis that P. kudriavzevii maintains intracellular homeostasis by using the ammonia produced by arginine catabolism. Furthermore, external addition of arginine significantly enhances growth and reduces cell aggregation of P. kudriavzevii under low-pH conditions.ConclusionsArginine was demonstrated to be a promising molecule for improving cell growth and preventing cell aggregation under extremely low-pH conditions. Our study is a step towards developing the non-conventional yeast P. kudriavzevii as a platform host for the production of organic acids under low-pH conditions.

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Transcriptional profiling reveals molecular basis and the role of arginine in response to low-pH stress in Pichia kudriavzevii

Journal of Bioscience and Bioengineering ◽

10.1016/j.jbiosc.2020.07.014 ◽

2020 ◽

Vol 130 (6) ◽

pp. 588-595

Author(s):

Hao Ji ◽

Ke Xu ◽

Xiameng Dong ◽

Da Sun ◽

Renyi Peng ◽

...

Keyword(s):

Molecular Basis ◽

Transcriptional Profiling ◽

Low Ph ◽

Pichia Kudriavzevii ◽

Ph Stress

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Sequential Production of ᴅ-xylonate and Ethanol from Non-Detoxified Corncob at Low-pH by Pichia kudriavzevii via a Two-Stage Fermentation Strategy

Journal of Fungi ◽

10.3390/jof7121038 ◽

2021 ◽

Vol 7 (12) ◽

pp. 1038

Author(s):

Hao Ji ◽

Ke Xu ◽

Xiameng Dong ◽

Da Sun ◽

Libo Jin

Keyword(s):

Ph Control ◽

Low Ph ◽

Economic Viability ◽

Excellent Performance ◽

Two Stage ◽

Pichia Kudriavzevii ◽

Comprehensive Utilization ◽

Ph Conditions ◽

Fermentation Strategy ◽

Simultaneous Saccharification

Improving the comprehensive utilization of sugars in lignocellulosic biomass is a major challenge for enhancing the economic viability of lignocellulose biorefinement. A robust yeast Pichia kudriavzevii N-X showed excellent performance in ethanol production under high temperature and low pH conditions and was engineered for ᴅ-xylonate production without xylitol generation. The recombinant strain P. kudriavzevii N-X/S1 was employed for sequential production of ᴅ-xylonate and ethanol from ᴅ-xylose, feeding on ᴅ-glucose without pH control in a two-stage strategy of aerobic and shifting micro-aerobic fermentation. Acid-pretreated corncob without detoxification and filtration was used for ᴅ-xylonate production, then simultaneous saccharification and ethanol fermentation was performed with cellulase added at pH 4.0 and at 40 °C. By this strategy, 33.5 g/L ᴅ-xylonate and 20.8 g/L ethanol were produced at yields of 1.10 g/g ᴅ-xylose and 84.3% of theoretical value, respectively. We propose a promising approach for the sequential production of ᴅ-xylonate and ethanol from non-detoxified corncob using a single microorganism.

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CgMED3 Changes Membrane Sterol Composition To Help Candida glabrata Tolerate Low-pH Stress

Applied and Environmental Microbiology ◽

10.1128/aem.00972-17 ◽

2017 ◽

Vol 83 (17) ◽

Cited By ~ 12

Author(s):

Xiaobao Lin ◽

Yanli Qi ◽

Dongni Yan ◽

Hui Liu ◽

Xiulai Chen ◽

...

Keyword(s):

Acid Production ◽

Candida Glabrata ◽

Sterol Composition ◽

Low Ph ◽

Mediator Complex ◽

Wild Type ◽

Organic Acid Production ◽

Content Type ◽

Ph Stress

ABSTRACT Candida glabrata is a promising microorganism for organic acid production. The present study aimed to investigate the role of C. glabrata Mediator complex subunit 3 (CgMed3p) in protecting C. glabrata under low-pH conditions. To this end, genes CgMED3A and CgMED3B were deleted, resulting in the double-deletion Cgmed3ABΔ strain. The final biomass and cell viability levels of Cgmed3ABΔ decreased by 64.5% and 35.8%, respectively, compared to the wild-type strain results at pH 2.0. In addition, lack of CgMed3ABp resulted in selective repression of a subset of genes in the lipid biosynthesis and metabolism pathways. Furthermore, C18:1, lanosterol, zymosterol, fecosterol, and ergosterol were 13.2%, 80.4%, 40.4%, 78.1%, and 70.4% less abundant, respectively, in the Cgmed3ABΔ strain. In contrast, the concentration of squalene increased by about 44.6-fold. As a result, membrane integrity, rigidity, and H+-ATPase activity in the Cgmed3ABΔ strain were reduced by 62.7%, 13.0%, and 50.3%, respectively. In contrast, overexpression of CgMED3AB increased the levels of C18:0, C18:1, and ergosterol by 113.2%, 5.9%, and 26.4%, respectively. Moreover, compared to the wild-type results, dry cell weight and pyruvate production increased, irrespective of pH buffering. These results suggest that CgMED3AB regulates membrane composition, which in turn enables cells to tolerate low-pH stress. We propose that regulation of CgMed3ABp may provide a novel strategy for enhancing low-pH tolerance and increasing organic acid production by C. glabrata. IMPORTANCE The objective of this study was to investigate the role of Candida glabrata Mediator complex subunit 3 (CgMed3ABp) and its regulation of gene expression at low pH in C. glabrata. We found that CgMed3ABp was critical for cellular survival and pyruvate production during low-pH stress. Measures of the levels of plasma membrane fatty acids and sterol composition indicated that CgMed3ABp could play an important role in regulating homeostasis in C. glabrata. We propose that controlling membrane lipid composition may enhance the robustness of C. glabrata for the production of organic acids.

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Microarray-based transcriptome ofListeria monocytogenesadapted to sublethal concentrations of acetic acid, lactic acid, and hydrochloric acid

Canadian Journal of Microbiology ◽

10.1139/w2012-091 ◽

2012 ◽

Vol 58 (9) ◽

pp. 1112-1123 ◽

Cited By ~ 20

Author(s):

Girum Tadesse Tessema ◽

Trond Møretrø ◽

Lars Snipen ◽

Even Heir ◽

Askild Holck ◽

...

Keyword(s):

Acetic Acid ◽

Lactic Acid ◽

Hydrochloric Acid ◽

Organic Acids ◽

Compatible Solutes ◽

Foodborne Pathogen ◽

Acid Stress ◽

Low Ph ◽

Transcriptional Responses ◽

Ph Stress

Listeria monocytogenes , an important foodborne pathogen, commonly encounters organic acids in food-related environments. The transcriptome of L. monocytogenes L502 was analyzed after adaptation to pH 5 in the presence of acetic acid, lactic acid, or hydrochloric acid (HCl) at 25 °C, representing a condition encountered in mildly acidic ready-to-eat food kept at room temperature. The acid-treated cells were compared with a reference culture with a pH of 6.7 at the time of RNA harvesting. The number of genes and magnitude of transcriptional responses were higher for the organic acids than for HCl. Protein coding genes described for low pH stress, energy transport and metabolism, virulence determinates, and acid tolerance response were commonly regulated in the 3 acid-stressed cultures. Interestingly, the transcriptional levels of histidine and cell wall biosynthetic operons were upregulated, indicating possible universal response against low pH stress in L. monocytogenes. The opuCABCD operon, coding proteins for compatible solutes transport, and the transcriptional regulator sigL were significantly induced in the organic acids, strongly suggesting key roles during organic acid stress. The present study revealed the complex transcriptional responses of L. monocytogenes towards food-related acidulants and opens the roadmap for more specific and in-depth future studies.

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Structure and functional analysis reveal an important regulated role of arginine kinase in Patinopecten yessoensis under low pH stress

Aquatic Toxicology ◽

10.1016/j.aquatox.2020.105452 ◽

2020 ◽

Vol 222 ◽

pp. 105452

Author(s):

Zujing Yang ◽

Xiaoting Huang ◽

Huan Liao ◽

Zhengrui Zhang ◽

Fanhua Sun ◽

...

Keyword(s):

Functional Analysis ◽

Arginine Kinase ◽

Low Ph ◽

Patinopecten Yessoensis ◽

Ph Stress

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Evolution under pH stress and high population densities leads to increased density-dependent fitness in the protist Tetrahymena thermophila

10.1101/758300 ◽

2019 ◽

Author(s):

Felix Moerman ◽

Angelina Arquint ◽

Stefanie Merkli ◽

Andreas Wagner ◽

Florian Altermatt ◽

...

Keyword(s):

Abiotic Stress ◽

Tetrahymena Thermophila ◽

Low Ph ◽

High Population ◽

Population Densities ◽

Density Dependent ◽

Ph Stress ◽

Evolutionary Changes ◽

Ph Conditions ◽

Protist Species

AbstractAbiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco-evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH-stress under high population densities. Using the protist species Tetrahymena thermophila, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (r0). Overall, evolution at low pH led to the convergence of r0 and intraspecific competitive ability (α) across the four genotypes. Given the strong correlation between r0 and α, we argue that this convergence was a consequence of selection for increased density-dependent fitness at low pH under the experienced high density conditions. Increased density-dependent fitness was either attained through increase in r0, or decrease of α, depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.

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The Lipid Lysyl-Phosphatidylglycerol Is Present in Membranes of Rhizobium tropici CIAT899 and Confers Increased Resistance to Polymyxin B Under Acidic Growth Conditions

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-20-11-1421 ◽

2007 ◽

Vol 20 (11) ◽

pp. 1421-1430 ◽

Cited By ~ 65

Author(s):

Christian Sohlenkamp ◽

Kanaan A. Galindo-Lagunas ◽

Ziqiang Guan ◽

Pablo Vinuesa ◽

Sally Robinson ◽

...

Keyword(s):

Sinorhizobium Meliloti ◽

Minimal Medium ◽

Polymyxin B ◽

Growth Conditions ◽

Membrane Lipid ◽

Low Ph ◽

Wild Type ◽

Rhizobium Tropici ◽

Gram Negative ◽

Inducible Genes

Lysyl-phosphatidylglycerol (LPG) is a well-known membrane lipid in several gram-positive bacteria but is almost unheard of in gram-negative bacteria. In Staphylococcus aureus, the gene product of mprF is responsible for LPG formation. Low pH-inducible genes, termed lpiA, have been identified in the gram-negative α-proteobacteria Rhizobium tropici and Sinorhizobium medicae in screens for acid-sensitive mutants and they encode homologs of MprF. An analysis of the sequenced bacterial genomes reveals that genes coding for homologs of MprF from S. aureus are present in several classes of organisms throughout the bacterial kingdom. In this study, we show that the expression of lpiA from R. tropici in the heterologous hosts Escherichia coli and Sinorhizobium meliloti causes formation of LPG. A wild-type strain of R. tropici forms LPG (about 1% of the total lipids) when the cells are grown in minimal medium at pH 4.5 but not when grown in minimal medium at neutral pH or in complex tryptone yeast (TY) medium at either pH. LPG biosynthesis does not occur when lpiA is deleted and is restored upon complementation of lpiA-deficient mutants with a functional copy of the lpiA gene. When grown in the low-pH medium, lpiA-deficient rhizobial mutants are over four times more susceptible to the cationic peptide polymyxin B than the wild type.

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The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa

International Journal of Molecular Sciences ◽

10.3390/ijms22083982 ◽

2021 ◽

Vol 22 (8) ◽

pp. 3982

Author(s):

Karolina Kotecka ◽

Adam Kawalek ◽

Kamil Kobylecki ◽

Aneta Agnieszka Bartosik

Keyword(s):

Pseudomonas Aeruginosa ◽

Binding Sites ◽

Transcriptional Profiling ◽

Mrna Level ◽

Transcriptional Regulators ◽

Resistance Mechanisms ◽

Chronic Infections ◽

Environmental Signals ◽

Regulatory Systems

Pseudomonas aeruginosa is a facultative human pathogen, causing acute and chronic infections that are especially dangerous for immunocompromised patients. The eradication of P. aeruginosa is difficult due to its intrinsic antibiotic resistance mechanisms, high adaptability, and genetic plasticity. The bacterium possesses multilevel regulatory systems engaging a huge repertoire of transcriptional regulators (TRs). Among these, the MarR family encompasses a number of proteins, mainly acting as repressors, which are involved in response to various environmental signals. In this work, we aimed to decipher the role of PA3458, a putative MarR-type TR from P. aeruginosa. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3458 showed changes in the mRNA level of 133 genes; among them, 100 were down-regulated, suggesting the repressor function of PA3458. Concomitantly, ChIP-seq analysis identified more than 300 PA3458 binding sites in P. aeruginosa. The PA3458 regulon encompasses genes involved in stress response, including the PA3459–PA3461 operon, which is divergent to PA3458. This operon encodes an asparagine synthase, a GNAT-family acetyltransferase, and a glutamyl aminopeptidase engaged in the production of N-acetylglutaminylglutamine amide (NAGGN), which is a potent bacterial osmoprotectant. We showed that PA3458-mediated control of PA3459–PA3461 expression is required for the adaptation of P. aeruginosa growth in high osmolarity. Overall, our data indicate that PA3458 plays a role in osmoadaptation control in P. aeruginosa.

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