Genetic Mechanisms Involved in Microbial Stress Responses

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (10 June 2023) | Viewed by 16325

Special Issue Editor


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Guest Editor
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid, 28049 Madrid, Spain
Interests: Leishmania; Trypanosoma; heat shock proteins; RNA binding proteins; regulation of gene expression; genomics; transcriptomics
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Special Issue Information

Dear Colleagues, 

Organisms cope with environmental changes that often represent stress situations, including elevated temperatures, chemical stress or oxidative injury. Cells need to counteract those stressful stimuli through coordinated changes in gene expression leading to the synthesis of specialized molecules. This response, known as the stress response, is universal, being found in every living form, from bacteria to mammalian cells. Given their relative cellular simplicity, bacteria and eukaryotic microorganisms are very useful for studying the stress response and its regulation. Moreover, among them, pathogenic microorganisms are subjected to sudden environmental challenges throughout their life cycle, including large changes in temperature, availability of nutrients and exposure to host immune defenses. Thus, pathogenic microorganisms have integrated the stress response into their life cycles, in which stress signaling pathways and the stress proteins also play specific functions in their differentiation program.

The aim of this Special Issue is to provide the state of the art on the proteins and molecular mechanisms involved in the stress response in unicellular organisms: bacteria, yeast and protists. More precisely, articles focusing on stress proteins, changes in gene expression associated with stressful conditions (including antibiotic and drug resistance), damage–repair proteins, and metabolic changes in response to stress, among others, are welcome.

Dr. Jose M. Requena
Guest Editor

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Keywords

  • heat shock proteins and genes
  • stress response molecular mechanisms
  • bacteria
  • yeast
  • protists
  • unicellular pathogens

Published Papers (7 papers)

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Research

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23 pages, 3658 KiB  
Article
Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts
by Steven Minden, Maria Aniolek, Henk Noorman and Ralf Takors
Genes 2023, 14(5), 997; https://doi.org/10.3390/genes14050997 - 27 Apr 2023
Cited by 1 | Viewed by 1729
Abstract
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch [...] Read more.
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus–response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts. Full article
(This article belongs to the Special Issue Genetic Mechanisms Involved in Microbial Stress Responses)
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10 pages, 288 KiB  
Article
Phenotypic and Genomic Insights into Biofilm Formation in Antibiotic-Resistant Clinical Coagulase-Negative Staphylococcus Species from South Africa
by Jonathan Asante, Akebe L. K. Abia, Daniel Anokwah, Bakoena A. Hetsa, Dorcas O. Fatoba, Linda A. Bester and Daniel G. Amoako
Genes 2023, 14(1), 104; https://doi.org/10.3390/genes14010104 - 29 Dec 2022
Cited by 2 | Viewed by 1526
Abstract
The work aims to investigate biofilm formation and biofilm/adhesion-encoding genes in coagulase-negative staphylococci (CoNS) species recovered from blood culture isolates. Eighty-nine clinical CoNS were confirmed using the VITEK 2 system, and antibiotic susceptibility testing of isolates was conducted using the Kirby-Bauer disk diffusion [...] Read more.
The work aims to investigate biofilm formation and biofilm/adhesion-encoding genes in coagulase-negative staphylococci (CoNS) species recovered from blood culture isolates. Eighty-nine clinical CoNS were confirmed using the VITEK 2 system, and antibiotic susceptibility testing of isolates was conducted using the Kirby-Bauer disk diffusion method against a panel of 20 antibiotics. Isolates were qualitatively screened using the Congo red agar medium. Quantitative assays were performed on microtiter plates, where the absorbances of the solubilised biofilms were recorded as optical densities and quantified. In all, 12.4% of the isolates were strong biofilm formers, 68.5% had moderate biofilm capacity, and 17.9% showed weak capacity. A subset of 18 isolates, mainly methicillin-resistant S. epidermidis, were investigated for adherence-related genes using whole-genome sequencing and bioinformatics analysis. The highest antibiotic resistance rates for strongly adherent isolates were observed against penicillin (100%) and cefoxitin (81.8%), but the isolates showed no resistance to linezolid (0.0%) and tigecycline (0.0%). The icaABC genes involved in biofilm formation were detected in 50% of the screened isolates. Other adherence-related genes, including autolysin gene atl (88.8%), elastin binding protein gene ebp (94.4%), cell wall-associated fibronectin-binding protein gene ebh (66.7%), clumping factor A gene clfA (5.5%), and pili gene ebpC (22.2%) were also found. The insertion sequence IS256, involved in biofilm formation, was found in 10/18 (55.5%) screened isolates. We demonstrate a high prevalence of biofilm-forming coagulase-negative staphylococci associated with various resistance phenotypes and a substantial agreement between the possession of biofilm-associated genes and the biofilm phenotype. Full article
(This article belongs to the Special Issue Genetic Mechanisms Involved in Microbial Stress Responses)
11 pages, 1380 KiB  
Article
A High-Copy Suppressor Screen Reveals a Broad Role of Prefoldin-like Bud27 in the TOR Signaling Pathway in Saccharomyces cerevisiae
by Francisco Gutiérrez-Santiago, María Cintas-Galán, Manuel Martín-Expósito, Maria del Carmen Mota-Trujillo, Cristina Cobo-Huesa, Jorge Perez-Fernandez and Francisco Navarro Gómez
Genes 2022, 13(5), 748; https://doi.org/10.3390/genes13050748 - 24 Apr 2022
Cited by 2 | Viewed by 1965
Abstract
Bud27 is a prefoldin-like, a member of the family of ATP-independent molecular chaperones that associates with RNA polymerases I, II, and III in Saccharomyces cerevisiae. Bud27 and its human ortholog URI perform several functions in the cytoplasm and the nucleus. Both proteins [...] Read more.
Bud27 is a prefoldin-like, a member of the family of ATP-independent molecular chaperones that associates with RNA polymerases I, II, and III in Saccharomyces cerevisiae. Bud27 and its human ortholog URI perform several functions in the cytoplasm and the nucleus. Both proteins participate in the TOR signaling cascade by coordinating nutrient availability with gene expression, and lack of Bud27 partially mimics TOR pathway inactivation. Bud27 regulates the transcription of the three RNA polymerases to mediate the synthesis of ribosomal components for ribosome biogenesis through the TOR cascade. This work presents a high-copy suppression screening of the temperature sensitivity of the bud27Δ mutant. It shows that Bud27 influences different TOR-dependent processes. Our data also suggest that Bud27 can impact some of these TOR-dependent processes: cell wall integrity and autophagy induction. Full article
(This article belongs to the Special Issue Genetic Mechanisms Involved in Microbial Stress Responses)
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10 pages, 1774 KiB  
Article
Increase in Ribosomal Fidelity Benefits Salmonella upon Bile Salt Exposure
by Zhihui Lyu and Jiqiang Ling
Genes 2022, 13(2), 184; https://doi.org/10.3390/genes13020184 - 21 Jan 2022
Cited by 2 | Viewed by 1476
Abstract
Translational fidelity is maintained by multiple quality control steps in all three domains of life. Increased translational errors (mistranslation) occur due to genetic mutations and external stresses. Severe mistranslation is generally harmful, but moderate levels of mistranslation may be favored under certain conditions. [...] Read more.
Translational fidelity is maintained by multiple quality control steps in all three domains of life. Increased translational errors (mistranslation) occur due to genetic mutations and external stresses. Severe mistranslation is generally harmful, but moderate levels of mistranslation may be favored under certain conditions. To date, little is known about the link between translational fidelity and host–pathogen interactions. Salmonella enterica can survive in the gall bladder during systemic or chronic infections due to bile resistance. Here we show that increased translational fidelity contributes to the fitness of Salmonella upon bile salt exposure, and the improved fitness depends on an increased level of intracellular adenosine triphosphate (ATP). Our work thus reveals a previously unknown linkage between translational fidelity and bacterial fitness under bile stress. Full article
(This article belongs to the Special Issue Genetic Mechanisms Involved in Microbial Stress Responses)
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19 pages, 4112 KiB  
Article
A Detailed Gene Expression Map of Giardia Encystation
by Laura Rojas-López, Sascha Krakovka, Elin Einarsson, Ulf Ribacke, Feifei Xu, Jon Jerlström-Hultqvist and Staffan G. Svärd
Genes 2021, 12(12), 1932; https://doi.org/10.3390/genes12121932 - 30 Nov 2021
Cited by 7 | Viewed by 2921
Abstract
Giardia intestinalis is an intestinal protozoan parasite that causes diarrheal infections worldwide. A key process to sustain its chain of transmission is the formation of infectious cysts in the encystation process. We combined deep RNAseq of a broad range of encystation timepoints to [...] Read more.
Giardia intestinalis is an intestinal protozoan parasite that causes diarrheal infections worldwide. A key process to sustain its chain of transmission is the formation of infectious cysts in the encystation process. We combined deep RNAseq of a broad range of encystation timepoints to produce a high-resolution gene expression map of Giardia encystation. This detailed transcriptomic map of encystation confirmed a gradual change of gene expression along the time course of encystation, showing the most significant gene expression changes during late encystation. Few genes are differentially expressed early in encystation, but the major cyst wall proteins CWP-1 and -2 are highly up-regulated already after 3.5 h encystation. Several transcription factors are sequentially up-regulated throughout the process, but many up-regulated genes at 7, 10, and 14 h post-induction of encystation have binding sites in the upstream regions for the Myb2 transcription factor, suggesting that Myb2 is a master regulator of encystation. We observed major changes in gene expression of several meiotic-related genes from 10.5 h of encystation to the cyst stage, and at 17.5 h encystation, there are changes in many different metabolic pathways and protein synthesis. Late encystation, 21 h to cysts, show extensive gene expression changes, most of all in VSP and HCMP genes, which are involved in antigenic variation, and genes involved in chromatin modifications. This high-resolution gene expression map of Giardia encystation will be an important tool in further studies of this important differentiation process. Full article
(This article belongs to the Special Issue Genetic Mechanisms Involved in Microbial Stress Responses)
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12 pages, 2317 KiB  
Article
Effect of High Hydrostatic Pressure on Stress-Related dnaK, hrcA, and ctsR Expression Patterns in Selected Lactobacilli Strains
by Joanna Bucka-Kolendo, Edyta Juszczuk-Kubiak and Barbara Sokołowska
Genes 2021, 12(11), 1720; https://doi.org/10.3390/genes12111720 - 28 Oct 2021
Cited by 6 | Viewed by 1429
Abstract
Lactic acid bacteria (LAB) in the natural environment meet multiple stressors such as pH and temperature variations, increased nutrition and metabolite concentrations, harmful chemicals, acidic/oxidative conditions, osmotic pressure, and starvation. However, LAB strains are not subjected to high hydrostatic pressure (HHP) which currently [...] Read more.
Lactic acid bacteria (LAB) in the natural environment meet multiple stressors such as pH and temperature variations, increased nutrition and metabolite concentrations, harmful chemicals, acidic/oxidative conditions, osmotic pressure, and starvation. However, LAB strains are not subjected to high hydrostatic pressure (HHP) which currently is the most common non-thermal decontamination technology in the food industry. In this context, the LAB response to HHP is more difficult to identify compared to other stress-induced responses, and dnaK, ctsR, and hrcA can serve as essential regulators in this reaction. In the present study, the expression level of dnaK, ctsR, and hrcA mRNAs in 15 LAB strains after the HHP (300 MPa/5′) exposure was evaluated. As a result, the HHP-treatment affected the up-regulation of dnaK, ctsR, and hrcA in L. backii KKP 3565, L. backii KKP 3566, L. rhamnosus KKP 3570, L. brevis KKP 3575 strains, whereas, in L. plantarum KKP 3569, L. rhamnosus KKP 3571, L. brevis KKP 3573 all genes were lower expressed. The relative expression level of the dnaK, ctsR, and hrcA either before or after the pressure treatment for L. brevis DSM 6235, L. rhamnosus KKP 3572, L. brevis KKP 3574, L. brevis KKP 3576, L. rossiae KKP 3577, L. curvatus KKP 3578 strains were undetectable. Significant differences in the expression levels were observed, between the control and the HHP treatment strains for dnaK in L. backii KKP 3565, L. backii KKP 3566, L. plantarum KKP 3569, L. rhamnosus KKP 3570, L. rhamnosus KKP 3571, ctsR in, L. backii KKP 3565, L. rhamnosus KKP 3570, L. rhamnosus KKP 3571, and hrcA in L. plantarum KKP 3569, L. rhamnosus KKP 3571. Overall, the studied genes, dnaK, ctsR, and hrcA can be useful markers to indicate the LAB cellular response to HHP. These molecular parameters can help to optimize the desirable LAB growing conditions in industrial processes and to understand the complexity of the stress-related mechanism. Full article
(This article belongs to the Special Issue Genetic Mechanisms Involved in Microbial Stress Responses)
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Review

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15 pages, 1353 KiB  
Review
The Astonishing Large Family of HSP40/DnaJ Proteins Existing in Leishmania
by Jose Carlos Solana, Lorena Bernardo, Javier Moreno, Begoña Aguado and Jose M. Requena
Genes 2022, 13(5), 742; https://doi.org/10.3390/genes13050742 - 23 Apr 2022
Cited by 5 | Viewed by 3979
Abstract
Abrupt environmental changes are faced by Leishmania parasites during transmission from a poikilothermic insect vector to a warm-blooded host. Adaptation to harsh environmental conditions, such as nutrient deprivation, hypoxia, oxidative stress and heat shock needs to be accomplished by rapid reconfiguration of gene [...] Read more.
Abrupt environmental changes are faced by Leishmania parasites during transmission from a poikilothermic insect vector to a warm-blooded host. Adaptation to harsh environmental conditions, such as nutrient deprivation, hypoxia, oxidative stress and heat shock needs to be accomplished by rapid reconfiguration of gene expression and remodeling of protein interaction networks. Chaperones play a central role in the maintenance of cellular homeostasis, and they are responsible for crucial tasks such as correct folding of nascent proteins, protein translocation across different subcellular compartments, avoiding protein aggregates and elimination of damaged proteins. Nearly one percent of the gene content in the Leishmania genome corresponds to members of the HSP40 family, a group of proteins that assist HSP70s in a variety of cellular functions. Despite their expected relevance in the parasite biology and infectivity, little is known about their functions or partnership with the different Leishmania HSP70s. Here, we summarize the structural features of the 72 HSP40 proteins encoded in the Leishmania infantum genome and their classification into four categories. A review of proteomic data, together with orthology analyses, allow us to postulate cellular locations and possible functional roles for some of them. A detailed study of the members of this family would provide valuable information and opportunities for drug discovery and improvement of current treatments against leishmaniasis. Full article
(This article belongs to the Special Issue Genetic Mechanisms Involved in Microbial Stress Responses)
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