scholarly journals Microbial mechanisms of tolerance to weak acid stress

2013 ◽  
Vol 4 ◽  
Author(s):  
Nuno P. Mira ◽  
Miguel C. Teixeira
Keyword(s):  
Acid Stress ◽  
Weak Acid ◽  
Weak Acid Stress

scholarly journals Stress-induced cross-feeding of internal metabolites provides a dynamic mechanism of microbial cooperation

2021 ◽  
Author(s):  
Kapil Amarnath ◽  
Avaneesh V. Narla ◽  
Sammy Pontrelli ◽  
Jiajia Dong ◽  
Tolga Caglar ◽  
...  
Keyword(s):  
Species Coexistence ◽  
Bacterial Species ◽  
Stress Gradient ◽  
Acid Stress ◽  
Weak Acid ◽  
Physiological Basis ◽  
Fermentation Products ◽  
Physiological Characterization ◽  
Weak Acid Stress ◽  
The Individual

AbstractDespite the ubiquity of microbial diversity observed across environments, mechanisms of cooperativity that enable species coexistence beyond the classical limit of one-species-per-niche have been elusive. Here we report the observation of a transient but substantial cross-feeding of internal metabolites between two marine bacterial species under acid stress, and further establish through quantitative physiological characterization of the individual strains that this cross-feeding is central to the survival and coexistence of these species in growth-dilution cycles. The coculture self-organizes into a limit cycle in which acid-stressed producers excrete various internal metabolites upon entering growth arrest, enabling the cross-feeders to grow, restore medium pH, and protect the producers from death. These results establish a rare, mechanistic example of inter-species cooperation under stress, as anticipated long ago by the stress gradient hypothesis. As the accumulation of acetate and other fermentation products occurs ubiquitously in habitats ranging from the gut to wastewater, and the excretion of internal metabolites is an obligatory physiological response by bacteria under weak acid stress, stress-induced cross-feeding provides a general physiological basis for the extensive sharing of metabolic resources to promote the coexistence of diverse species in microbial communities.

scholarly journals Intracellular pH Response to Weak Acid Stress in Individual Vegetative Bacillus subtilis Cells

2016 ◽  
Vol 82 (21) ◽  
pp. 6463-6471 ◽  
Author(s):  
Rachna Pandey ◽  
Norbert O. E. Vischer ◽  
Jan P. P. M. Smelt ◽  
Johan W. A. van Beilen ◽  
Alexander Ter Beek ◽  
...  
Keyword(s):  
Organic Acid ◽  
Single Cell ◽  
Acid Stress ◽  
Weak Acid ◽  
Food Preservation ◽  
Cell Level ◽  
Food Preservatives ◽  
Content Type ◽  
Weak Organic Acid ◽  
Weak Acid Stress

ABSTRACTIntracellular pH (pHi) critically affects bacterial cell physiology. Hence, a variety of food preservation strategies are aimed at perturbing pHihomeostasis. Unfortunately, accurate pHiquantification with existing methods is suboptimal, since measurements are averages across populations of cells, not taking into account interindividual heterogeneity. Yet, physiological heterogeneity in isogenic populations is well known to be responsible for differences in growth and division kinetics of cells in response to external stressors. To assess in this context the behavior of intracellular acidity, we have developed a robust method to quantify pHiat single-cell levels inBacillus subtilis. Bacilli spoil food, cause disease, and are well known for their ability to form highly stress-resistant spores. Using an improved version of the genetically encoded ratiometric pHluorin (IpHluorin), we have quantified pHiin individualB. subtiliscells, cultured at an external pH of 6.4, in the absence or presence of weak acid stresses. In the presence of 3 mM potassium sorbate, a decrease in pHiand an increase in the generation time of growing cells were observed. Similar effects were observed when cells were stressed with 25 mM potassium acetate. Time-resolved analysis of individual bacteria in growing colonies shows that after a transient pH decrease, long-term pH evolution is highly cell dependent. The heterogeneity at the single-cell level shows the existence of subpopulations that might be more resistant and contribute to population survival. Our approach contributes to an understanding of pHiregulation in individual bacteria and may help scrutinizing effects of existing and novel food preservation strategies.IMPORTANCEThis study shows how the physiological response to commonly used weak organic acid food preservatives, such as sorbic and acetic acids, can be measured at the single-cell level. These data are key to coupling often-observed single-cell heterogeneous growth behavior upon the addition of weak organic acid food preservatives. Generally, these data are gathered in the form of plate counting of samples incubated with the acids. Here, we visualize the underlying heterogeneity in cellular pH homeostasis, opening up avenues for mechanistic analyses of the heterogeneity in the weak acid stress response. Thus, microbial risk assessment can become more robust, widening the scope of use of these well-known weak organic acid food preservatives.

scholarly journals Metabolic engineering with ATP-citrate lyase and nitrogen source supplementation improves itaconic acid production in Aspergillus niger

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Abeer H. Hossain ◽  
Roy van Gerven ◽  
Karin M. Overkamp ◽  
Peter S. Lübeck ◽  
Hatice Taşpınar ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Aspergillus Niger ◽  
Acid Stress ◽  
Weak Acid ◽  
Glycolytic Flux ◽  
Atp Citrate Lyase ◽  
Nitrogen Supplementation ◽  
Fermentation Conditions ◽  
Citrate Lyase ◽  
Weak Acid Stress

Abstract Background Bio-based production of organic acids promises to be an attractive alternative for the chemicals industry to substitute petrochemicals as building-block chemicals. In recent years, itaconic acid (IA, methylenesuccinic acid) has been established as a sustainable building-block chemical for the manufacture of various products such as synthetic resins, coatings, and biofuels. The natural IA producer Aspergillus terreus is currently used for industrial IA production; however, the filamentous fungus Aspergillus niger has been suggested to be a more suitable host for this purpose. In our previous report, we communicated the overexpression of a putative cytosolic citrate synthase citB in an A. niger strain carrying the full IA biosynthesis gene cluster from A. terreus, which resulted in the highest final titer reported for A. niger (26.2 g/L IA). In this research, we have attempted to improve this pathway by increasing the cytosolic acetyl-CoA pool. Additionally, we have also performed fermentation optimization by varying the nitrogen source and concentration. Results To increase the cytosolic acetyl-CoA pool, we have overexpressed genes acl1 and acl2 that together encode for ATP-citrate lyase (ACL). Metabolic engineering of ACL resulted in improved IA production through an apparent increase in glycolytic flux. Strains that overexpress acl12 show an increased yield, titer and productivity in comparison with parental strain CitB#99. Furthermore, IA fermentation conditions were improved by nitrogen supplementation, which resulted in alkalization of the medium and thereby reducing IA-induced weak-acid stress. In turn, the alkalizing effect of nitrogen supplementation enabled an elongated idiophase and allowed final titers up to 42.7 g/L to be reached at a productivity of 0.18 g/L/h and yield of 0.26 g/g in 10-L bioreactors. Conclusion Ultimately, this study shows that metabolic engineering of ACL in our rewired IA biosynthesis pathway leads to improved IA production in A. niger due to an increase in glycolytic flux. Furthermore, IA fermentation conditions were improved by nitrogen supplementation that alleviates IA induced weak-acid stress and extends the idiophase.

scholarly journals Global Phenotypic Analysis and Transcriptional Profiling Defines the Weak Acid Stress Response Regulon inSaccharomyces cerevisiae

2004 ◽  
Vol 15 (2) ◽  
pp. 706-720 ◽  
Author(s):  
Christoph Schüller ◽  
Yasmine M. Mamnun ◽  
Mehdi Mollapour ◽  
Gerd Krapf ◽  
Michael Schuster ◽  
...  
Keyword(s):  
Target Genes ◽  
Ectopic Expression ◽  
Acid Stress ◽  
Weak Acid ◽  
Food Preservation ◽  
Yeast Genome ◽  
Phenotypic Screening ◽  
Functional Assays ◽  
Genome Wide ◽  
Weak Acid Stress

Weak organic acids such as sorbate are potent fungistatic agents used in food preservation, but their intracellular targets are poorly understood. We thus searched for potential target genes and signaling components in the yeast genome using contemporary genome-wide functional assays as well as DNA microarray profiling. Phenotypic screening of the EUROSCARF collection revealed the existence of numerous sorbate-sensitive strains. Sorbate hypersensitivity was detected in mutants of the shikimate biosynthesis pathway, strains lacking the PDR12 efflux pump or WAR1, a transcription factor mediating stress induction of PDR12. Using DNA microarrays, we also analyzed the genome-wide response to acute sorbate stress, allowing for the identification of more than 100 genes rapidly induced by weak acid stress. Moreover, a novel War1p- and Msn2p/4p-independent regulon that includes HSP30 was identified. Although induction of the majority of sorbate-induced genes required Msn2p/4p, weak acid tolerance was unaffected by a lack of Msn2p/4p. Ectopic expression of PDR12 from the GAL1-10 promoter fully restored sorbate resistance in a strain lacking War1p, demonstrating that PDR12 is the major target of War1p under sorbic acid stress. Interestingly, comparison of microarray data with results from the phenotypic screening revealed that PDR12 remained as the only gene, which is both stress inducible and required for weak acid resistance. Our results suggest that combining functional assays with transcriptome profiling allows for the identification of key components in large datasets such as those generated by global microarray analysis.

scholarly journals Casein Kinase I Isoform Hrr25 Is a Negative Regulator of Haa1 in the Weak Acid Stress Response Pathway in Saccharomyces cerevisiae

2017 ◽  
Vol 83 (13) ◽  
Author(s):  
Morgan E. Collins ◽  
Joshua J. Black ◽  
Zhengchang Liu
Keyword(s):  
Acetic Acid ◽  
Target Genes ◽  
Acid Stress ◽  
Weak Acid ◽  
Casein Kinase ◽  
Negative Regulator ◽  
Weak Acids ◽  
Casein Kinase I ◽  
Content Type ◽  
Weak Acid Stress

ABSTRACT Haa1 is a transcription factor that adapts Saccharomyces cerevisiae cells to weak organic acid stresses by activating the expression of various genes. Many of these genes encode membrane proteins, such as TPO2 and YRO2. How Haa1 is activated by weak acids is not clear. Here, we show that casein kinase I isoform Hrr25 is an important negative regulator of Haa1. Haa1 is known to be multiply phosphorylated. We found that mutations in HRR25 lead to reduced Haa1 phosphorylation and increased expression of Haa1 target genes and that Hrr25 interacts with Haa1. The other three casein kinase I isoforms, Yck1, Yck2, and Yck3, do not seem to play critical roles in Haa1 regulation. Hrr25 has a 200-residue C-terminal region, including a proline- and glutamine-rich domain. Our data suggest that the C-terminal region of Hrr25 is required for normal inhibition of expression of Haa1 target genes TPO2 and YRO2 and is important for cell growth but is not required for cell morphogenesis. We propose that Hrr25 is an important regulator of cellular adaptation to weak acid stress by inhibiting Haa1 through phosphorylation. IMPORTANCE Our study has revealed the casein kinase I protein Hrr25 to be a negative regulator of Haa1, a transcription factor mediating the cellular response to stresses caused by weak acids. Many studies have focused on the target genes of Haa1 and their roles in weak acid stress responses, but little has been reported on the regulatory mechanism of Haa1. Weak acids, such as acetic acid, have long been used for food preservation by slowing down the growth of fungal species, including S. cerevisiae. In the biofuel industry, acetic acid in the lignocellulosic hydrolysates limits the production of ethanol, which is undesirable. By understanding how Haa1 is regulated, we can make advances in the field of food sciences to better preserve food and engineer acetic acid-resistant strains that will increase productivity in the biofuel industry.

scholarly journals Defining the RNA Interactome by Total RNA-Associated Protein Purification

2018 ◽  
Author(s):  
Vadim Shchepachev ◽  
Stefan Bresson ◽  
Christos Spanos ◽  
Elisabeth Petfalski ◽  
Lutz Fischer ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Acid Stress ◽  
Weak Acid ◽  
Binding Activity ◽  
Bioinformatics Pipeline ◽  
E Coli ◽  
Uva Irradiation ◽  
Weak Acid Stress

ABSTRACTUV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), was applied to yeast (S. cerevisiae) and bacteria (E. coli). In all analyses, SILAC labelling was used to quantify protein recovery in the presence and absence of irradiation. For S. cerevisiae, we also compared crosslinking using 254 nm (UVC) irradiation (TRAPP) with 4-thiouracil (4tU) labelling combined with ~350 nm (UVA) irradiation (PAR-TRAPP). Recovery of proteins not anticipated to show RNA-binding activity was substantially higher in TRAPP compared to PAR-TRAPP. As an example of preferential TRAPP-crosslinking, we tested enolase (Eno1) and demonstrated its binding to tRNA loops in vivo. We speculate that many protein-RNA interactions have biophysical effects on localization and/or accessibility, by opposing or promoting phase separation for highly abundant protein. Homologous metabolic enzymes showed RNA crosslinking in S. cerevisiae and E. coli, indicating conservation of this property. TRAPP allows alterations in RNA interactions to be followed and we initially analyzed the effects of weak acid stress. This revealed specific alterations in RNA-protein interactions; for example, during late 60S ribosome subunit maturation. Precise sites of crosslinking at the level of individual amino acids (iTRAPP) were identified in 395 peptides from 155 unique proteins, following phospho-peptide enrichment combined with a bioinformatics pipeline (Xi). TRAPP is quick, simple and scalable, allowing rapid characterization of the RNA-bound proteome in many systems.

scholarly journals MNL1Regulates Weak Acid–induced Stress Responses of the Fungal PathogenCandida albicans

2008 ◽  
Vol 19 (10) ◽  
pp. 4393-4403 ◽  
Author(s):  
Mark Ramsdale ◽  
Laura Selway ◽  
David Stead ◽  
Jan Walker ◽  
Zhikang Yin ◽  
...  
Keyword(s):  
Stress Responses ◽  
Acid Stress ◽  
Transcriptional Response ◽  
Weak Acid ◽  
Ras Pathway ◽  
Induced Stress ◽  
Pathway Activation ◽  
Weak Acid Stress ◽  
Dying Cells

MNL1, the Candida albicans homologue of an orphan Msn2-like gene (YER130c in Saccharomyces cerevisiae) has no known function. Here we report that MNL1 regulates weak acid stress responses. Deletion of MNL1 prevents the long-term adaptation of C. albicans cells to weak acid stresses and compromises their global transcriptional response under these conditions. The promoters of Mnl1-dependent genes contain a novel STRE-like element (SLE) that imposes Mnl1-dependent, weak acid stress–induced transcription upon a lacZ reporter in C. albicans. The SLE (HHYYCCCCTTYTY) is related to the Nrg1 response element (NRE) element recognized by the transcriptional repressor Nrg1. Deletion of NRG1 partially restores the ability of C. albicans mnl1 cells to adapt to weak acid stress, indicating that Mnl1 and Nrg1 act antagonistically to regulate this response. Molecular, microarray, and proteomic analyses revealed that Mnl1-dependent adaptation does not occur in cells exposed to proapoptotic or pronecrotic doses of weak acid, suggesting that Ras-pathway activation might suppress the Mnl1-dependent weak acid response in dying cells. Our work defines a role for this YER130c orthologue in stress adaptation and cell death.

scholarly journals War1p, a Novel Transcription Factor Controlling Weak Acid Stress Response in Yeast

2003 ◽  
Vol 23 (5) ◽  
pp. 1775-1785 ◽  
Author(s):  
Angelika Kren ◽  
Yasmine M. Mamnun ◽  
Bettina E. Bauer ◽  
Christoph Schüller ◽  
Hubert Wolfger ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcriptional Activation ◽  
Acid Stress ◽  
Weak Acid ◽  
Stress Adaptation ◽  
Band Shift ◽  
Promoter Deletion Analysis ◽  
Weak Acid Stress

ABSTRACT The Saccharomyces cerevisiae ATP-binding cassette (ABC) transporter Pdr12p effluxes weak acids such as sorbate and benzoate, thus mediating stress adaptation. In this study, we identify a novel transcription factor, War1p, as the regulator of this stress adaptation through transcriptional induction of PDR12. Cells lacking War1p are weak acid hypersensitive, since they fail to induce Pdr12p. The nuclear Zn2Cys6 transcriptional regulator War1p forms homodimers and is rapidly phosphorylated upon sorbate stress. The appearance of phosphorylated War1p isoforms coincides with transcriptional activation of PDR12. Promoter deletion analysis identified a novel cis-acting weak acid response element (WARE) in the PDR12 promoter required for PDR12 induction. War1p recognizes and decorates the WARE both in vitro and in vivo, as demonstrated by band shift assays and in vivo footprinting. Importantly, War1p occupies the WARE in the presence and absence of stress, demonstrating constitutive DNA binding in vivo. Our results suggest that weak acid stress triggers phosphorylation and perhaps activation of War1p. In turn, War1p activation is necessary for the induction of PDR12 through a novel signal transduction event that elicits weak organic acid stress adaptation.

scholarly journals Erratum for Pandey et al., “Intracellular pH Response to Weak Acid Stress in Individual Vegetative Bacillus subtilis Cells”

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Rachna Pandey ◽  
Norbert O. E. Vischer ◽  
Jan P. P. M. Smelt ◽  
Johan W. A. van Beilen ◽  
Alexander Ter Beek ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Intracellular Ph ◽  
Acid Stress ◽  
Weak Acid ◽  
Ph Response ◽  
Weak Acid Stress

scholarly journals A genetic screen identifies mutations in the yeast WAR1 gene, linking transcription factor phosphorylation to weak-acid stress adaptation

FEBS Journal ◽  
2007 ◽  
Vol 274 (12) ◽  
pp. 3094-3107 ◽  
Author(s):  
Christa Gregori ◽  
Bettina Bauer ◽  
Chantal Schwartz ◽  
Angelika Kren ◽  
Christoph Schüller ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Acid Stress ◽  
Weak Acid ◽  
Genetic Screen ◽  
Stress Adaptation ◽  
Weak Acid Stress
Sign in / Sign up

Export Citation Format

Share Document