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Yamada M. Molecular basis and functional development of membrane-based microbial metabolism. Biosci Biotechnol Biochem 2024; 88:461-474. [PMID: 38366612 DOI: 10.1093/bbb/zbae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Abstract
My research interest has so far been focused on metabolisms related to the "membrane" of microorganisms, such as the respiratory chain, membrane proteins, sugar uptake, membrane stress and cell lysis, and fermentation. These basic metabolisms are important for the growth and survival of cell, and their knowledge can be used for efficient production of useful materials. Notable achievements in research on metabolisms are elucidation of the structure and function of membrane-bound glucose dehydrogenase as a primary enzyme in the respiratory chain, elucidation of ingenious expression regulation of several operons or by divergent promoters, elucidation of stress-induced programed-cell lysis and its requirement for survival during a long-term stationary phase, elucidation of molecular mechanism of survival at a critical high temperature, elucidation of thermal adaptation and its limit, isolation of thermotolerant fermenting yeast strains, and development of high-temperature fermentation and green energy production technologies. These achievements are described together in this review.
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Affiliation(s)
- Mamoru Yamada
- Graduate School of Sciences and Technology for Innovation, and Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
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Gan Y, Zhao G, Wang Z, Zhang X, Wu MX, Lu M. Bacterial Membrane Vesicles: Physiological Roles, Infection Immunology, and Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301357. [PMID: 37357142 PMCID: PMC10477901 DOI: 10.1002/advs.202301357] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/19/2023] [Indexed: 06/27/2023]
Abstract
Bacterial or fungal membrane vesicles, traditionally considered as microbial metabolic wastes, are secreted mainly from the outer membrane or cell membrane of microorganisms. However, recent studies have shown that these vesicles play essential roles in direct or indirect communications among microorganisms and between microorganisms and hosts. This review aims to provide an updated understanding of the physiological functions and emerging applications of bacterial membrane vesicles, with a focus on their biogenesis, mechanisms of adsorption and invasion into host cells, immune stimulatory effects, and roles in the much-concerned problem of bacterial resistance. Additionally, the potential applications of these vesicles as biomarkers, vaccine candidates, and drug delivery platforms are discussed.
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Affiliation(s)
- Yixiao Gan
- Department of Transfusion MedicineHuashan HospitalFudan UniversityShanghai200040P. R. China
| | - Gang Zhao
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200240P. R. China
| | - Zhicheng Wang
- Department of Transfusion MedicineHuashan HospitalFudan UniversityShanghai200040P. R. China
| | - Xingcai Zhang
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
| | - Mei X. Wu
- Wellman Center for PhotomedicineMassachusetts General HospitalDepartment of DermatologyHarvard Medical School, 50 Blossom StreetBostonMA02114USA
| | - Min Lu
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200240P. R. China
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Deletion of Yersinia pestis ail causes temperature sensitive pleiotropic effects including cell lysis that are suppressed by carbon source, cations, or loss of phospholipase A activity. J Bacteriol 2021; 203:e0036121. [PMID: 34398663 PMCID: PMC8508112 DOI: 10.1128/jb.00361-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Maintenance of phospholipid (PL) and lipopoly- or lipooligo-saccharide (LPS or LOS) asymmetry in the outer membrane (OM) of Gram-negative bacteria is essential but poorly understood. The Yersinia pestis OM Ail protein was required to maintain lipid homeostasis and cell integrity at elevated temperature (37° C). Loss of this protein had pleiotropic effects. A Y. pestis Δail mutant and KIM6+ wild- type were systematically compared for (i) growth requirements at 37° C, (ii) cell structure, (iii) antibiotic and detergent sensitivity, (iv) proteins released into supernates, (v) induction of the heat shock response, and (vi) physiological and genetic suppressors that restored the wild- type phenotype. The Δail mutant grew normally at 28° C but lysed at 37° C when it entered stationary phase as shown by cell count, SDS-PAGE of cell supernatants, and electron microscopy. Immuno-fluorescent microscopy showed that the Δail mutant did not assemble Caf1 capsule. Expression of heat shock promoters rpoE or rpoH fused to a lux operon reporter were not induced when the Δail mutant was shifted from the 28° C to 37° C (p<0.001 and p<0.01 respectively). Mutant lysis was suppressed by addition of 11 mM glucose, 22 or 44 mM glycerol, 2.5 mM Ca2+, or 2.5 mM Mg2+ to the growth medium, or by a mutation in the phospholipase A gene (pldA::miniTn5, ΔpldA, or PldAS164A). A model, accounting for the temperature-sensitive lysis of the Δail mutant and the Ail-dependent stabilization of the OM tetraacylated LOS at 37°C is presented. IMPORTANCE The Gram-negative pathogen, Yersinia pestis, transitions between a flea vector (ambient temperature) and a mammalian host (37° C). In response to 37° C, Y. pestis modifies its outer membrane (OM) by reducing the fatty acid content in lipid A, changing the outer leaflet from being predominantly hexaacylated to being predominantly tetraacylated. It also increases the Ail concentration, so it becomes the most prominent OM protein. Both measures are needed for Y. pestis to evade the host innate immune response. Deletion of ail destabilizes the OM at 37° C causing the cells to lyse. These results show that a protein is essential for maintaining lipid asymmetry and lipid homeostasis in the bacterial OM.
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Murata M, Nakamura K, Kosaka T, Ota N, Osawa A, Muro R, Fujiyama K, Oshima T, Mori H, Wanner BL, Yamada M. Cell Lysis Directed by SulA in Response to DNA Damage in Escherichia coli. Int J Mol Sci 2021; 22:ijms22094535. [PMID: 33926096 PMCID: PMC8123628 DOI: 10.3390/ijms22094535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/24/2022] Open
Abstract
The SOS response is induced upon DNA damage and the inhibition of Z ring formation by the product of the sulA gene, which is one of the LexA-regulated genes, allows time for repair of damaged DNA. On the other hand, severely DNA-damaged cells are eliminated from cell populations. Overexpression of sulA leads to cell lysis, suggesting SulA eliminates cells with unrepaired damaged DNA. Transcriptome analysis revealed that overexpression of sulA leads to up-regulation of numerous genes, including soxS. Deletion of soxS markedly reduced the extent of cell lysis by sulA overexpression and soxS overexpression alone led to cell lysis. Further experiments on the SoxS regulon suggested that LpxC is a main player downstream from SoxS. These findings suggested the SulA-dependent cell lysis (SDCL) cascade as follows: SulA→SoxS→LpxC. Other tests showed that the SDCL cascade pathway does not overlap with the apoptosis-like and mazEF cell death pathways.
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Affiliation(s)
- Masayuki Murata
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
| | - Keiko Nakamura
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
| | - Tomoyuki Kosaka
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Natsuko Ota
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
| | - Ayumi Osawa
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
| | - Ryunosuke Muro
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
| | - Kazuya Fujiyama
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan;
| | - Hirotada Mori
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan;
| | - Barry L. Wanner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA;
| | - Mamoru Yamada
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan
- Correspondence: ; Tel.: +81-83-933-5869
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Wong S, Alattas H, Slavcev RA. A snapshot of the λ T4rII exclusion (Rex) phenotype in Escherichia coli. Curr Genet 2021; 67:739-745. [PMID: 33877398 DOI: 10.1007/s00294-021-01183-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/20/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
The lambda (λ) T4rII exclusion (Rex) phenotype is defined as the inability of T4rII to propagate in Escherichia coli lysogenized by bacteriophage λ. The Rex system requires the presence of two lambda immunity genes, rexA and rexB, to exclude T4 (rIIA-rIIB) from plating on a lawn of E. coli λ lysogens. The onset of the Rex phenotype by T4rII infection imparts a harsh cellular environment that prevents T4rII superinfection while killing the majority of the cell population. Since the discovery of this powerful exclusion system in 1955 by Seymour Benzer, few mechanistic models have been proposed to explain the process of Rex activation and the physiological manifestations associated with Rex onset. For the first time, key host proteins have recently been linked to Rex, including σE, σS, TolA, and other membrane proteins. Together with the known Rex system components, the RII proteins of bacteriophage T4 and the Rex proteins from bacteriophage λ, we are closer than ever to solving the mystery that has eluded investigators for over six decades. Here, we review the fundamental Rex components in light of this new knowledge.
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Affiliation(s)
- Shirley Wong
- School of Pharmacy, University of Waterloo, ON, N2L 3G1, Canada
| | - Hibah Alattas
- School of Pharmacy, University of Waterloo, ON, N2L 3G1, Canada.
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Alattas H, Wong S, Slavcev RA. Identification of Escherichia coli Host Genes That Influence the Bacteriophage Lambda (λ) T4 rII Exclusion (Rex) Phenotype. Genetics 2020; 216:1087-1102. [PMID: 33033112 PMCID: PMC7768251 DOI: 10.1534/genetics.120.303643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
The T4rII exclusion (Rex) phenotype is the inability of T4rII mutant bacteriophage to propagate in hosts (Escherichia coli) lysogenized by bacteriophage lambda (λ). The Rex phenotype, triggered by T4rII infection of a rex+ λ lysogen, results in rapid membrane depolarization imposing a harsh cellular environment that resembles stationary phase. Rex "activation" has been proposed as an altruistic cell death system to protect the λ prophage and its host from T4rII superinfection. Although well studied for over 60 years, the mechanism behind Rex still remains unclear. We have identified key nonessential genes involved in this enigmatic exclusion system by examining T4rII infection across a collection of rex+ single-gene knockouts. We further developed a system for rapid, one-step isolation of host mutations that could attenuate/abrogate the Rex phenotype. For the first time, we identified host mutations that influence Rex activity and rex+ host sensitivity to T4rII infection. Among others, notable genes include tolA, ompA, ompF, ompW, ompX, ompT, lpp, mglC, and rpoS They are critical players in cellular osmotic balance and are part of the stationary phase and/or membrane distress regulons. Based on these findings, we propose a new model that connects Rex to the σS, σE regulons and key membrane proteins.
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Affiliation(s)
- Hibah Alattas
- School of Pharmacy, University of Waterloo, Ontario N2L 3G1, Canada
| | - Shirley Wong
- School of Pharmacy, University of Waterloo, Ontario N2L 3G1, Canada
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Toyofuku M, Nomura N, Eberl L. Types and origins of bacterial membrane vesicles. Nat Rev Microbiol 2018; 17:13-24. [DOI: 10.1038/s41579-018-0112-2] [Citation(s) in RCA: 396] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Construction of Halomonas bluephagenesis capable of high cell density growth for efficient PHA production. Appl Microbiol Biotechnol 2018; 102:4499-4510. [DOI: 10.1007/s00253-018-8931-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 12/13/2022]
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Coquet L, Obry A, Borghol N, Hardouin J, Mora L, Othmane A, Jouenne T. Impact of chlorhexidine digluconate and temperature on curli production in Escherichia coli-consequence on its adhesion ability. AIMS Microbiol 2017; 3:915-937. [PMID: 31294198 PMCID: PMC6604964 DOI: 10.3934/microbiol.2017.4.915] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/27/2017] [Indexed: 11/18/2022] Open
Abstract
Chlorhexidine-Digluconate (CHX-Dg) is a biocide widely used as disinfectant or antiseptic in clinical and domestic fields. It is often found in the formulation of solutions to treat superficial wounds. Nevertheless, few studies have focused on its effects on Escherichia coli while this bacterium is commonly involved in mixed infections. Therefore, the impact of CHX-Dg and temperature on E. coli was investigated; particularly the curli production. In accordance with bibliographic data, the curli production decreased when the temperature of the culture was shift from 30 °C to 37 °C. The bacterial adhesion to abiotic surfaces was also reduced. Surprisingly, the curli production at 37 °C was maintained in presence of antiseptic and the bacterial adhesion was improved at a very low concentration (1 µg ml-1) of CHX-Dg. Complementary investigations with a cpxR mutant demonstrated that the CpxA/R-TCS (Two-Component System) is involved in the temperature-dependent control of the curli expression. Indeed, the curli production was not altered by the growth temperature in the mutant. Otherwise, no relationship between CHX-Dg and the Cpx-TCS was shown. A subsequent proteomic investigation revealed the alteration of the production of 44 periplasmic and outer membrane proteins in presence of CHX-Dg. These proteins are involved in the transport of small molecules, the envelope integrity, the stress response as well as the protein folding.
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Affiliation(s)
- Laurent Coquet
- CNRS UMR6270, Normandie University, UNIROUEN, Plate-forme PISSARO, Mont-Saint-Aignan, France
| | - Antoine Obry
- INSERM U905, Normandie University, UNIROUEN, Plate-forme PISSARO, France
| | - Nabil Borghol
- Biophysical Laboratory, Faculty of Medicine of Monastir, Monastir, Tunisia.,INSERM U1148, Laboratory for Vascular Transitional Sciences, Galileo Institute, Paris 13 University, Sorbonne Paris Cité, Villetaneuse, France
| | - Julie Hardouin
- CNRS UMR6270, Normandie University, UNIROUEN, Plate-forme PISSARO, Mont-Saint-Aignan, France
| | - Laurence Mora
- INSERM U1148, Laboratory for Vascular Transitional Sciences, Galileo Institute, Paris 13 University, Sorbonne Paris Cité, Villetaneuse, France
| | - Ali Othmane
- Biophysical Laboratory, Faculty of Medicine of Monastir, Monastir, Tunisia
| | - Thierry Jouenne
- CNRS UMR6270, Normandie University, UNIROUEN, Plate-forme PISSARO, Mont-Saint-Aignan, France
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A Suppressor Mutation That Creates a Faster and More Robust σE Envelope Stress Response. J Bacteriol 2016; 198:2345-51. [PMID: 27325680 DOI: 10.1128/jb.00340-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED The σE envelope stress response is an essential signal transduction pathway which detects and removes mistargeted outer membrane (OM) β-barrel proteins (OMPs) in the periplasm of Escherichia coli It relies on σE, an alternative sigma factor encoded by the rpoE gene. Here we report a novel mutation, a nucleotide change of C to A in the third base of the second codon, which increases levels of σE (rpoE_S2R). The rpoE_S2R mutation does not lead to the induction of the stress response during normal growth but instead changes the dynamics of induction upon periplasmic stress, resulting in a faster and more robust response. This allows cells to adapt faster to the periplasmic stress, avoiding lethal accumulation of unfolded OMPs in the periplasm caused by severe defects in the OMP assembly pathway. IMPORTANCE Survival of bacteria under conditions of external or internal stresses depends on timely induction of stress response signaling pathways to regulate expression of appropriate genes that function to maintain cellular homeostasis. Previous studies have shown that strong preinduction of envelope stress responses can allow bacteria to survive a number of lethal genetic perturbations. In our paper, we describe a unique mutation that enhances kinetics of the σE envelope stress response pathway rather than preinducing the response. This allows bacteria to quickly adapt to sudden and severe periplasmic stress.
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Liu X, Hu W, An Z, Bai Z, Dai X, Yang Y. Exploration of cell lysis in a bioreactor using Escherichia coli expressing single-chain variable-domain antibody fragments. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1202-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Sakil Munna M, Tahera J, Mohibul Hassan Afrad M, Nur IT, Noor R. Survival of Bacillus spp. SUBB01 at high temperatures and a preliminary assessment of its ability to protect heat-stressed Escherichia coli cells. BMC Res Notes 2015; 8:637. [PMID: 26526722 PMCID: PMC4630936 DOI: 10.1186/s13104-015-1631-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 10/26/2015] [Indexed: 12/18/2022] Open
Abstract
Background The bacterial stressed state upon temperature raise has widely been observed especially in Escherichia coli cells. The current study extended such physiological investigation on Bacillus spp. SUBB01 under aeration at 100 rpm on different culture media along with the high temperature exposure at 48, 50, 52, 53 and 54 °C. Bacterial growth was determined through the enumeration of the viable and culturable cells; i.e., cells capable of producing the colony forming units on Luria–Bertani and nutrient agar plates up to 24 h. Microscopic experiments were conducted to scrutinize the successive physiological changes. Suppression of bacterial growth due to the elevated heat was further confirmed by the observation of non-viability through spot tests. Results As expected, a quick drop in both cell turbidity and colony forming units (~104) along with spores were observed after 12–24 h of incubation period, when cells were grown at 54 °C in both Luria–Bertani and nutrient broth and agar. The critical temperature (the temperature above which it is no longer possible to survive) of Bacillus spp. SUBB01 was estimated to be 53 °C. Furthermore, a positive impact was observed on the inhibited E. coli SUBE01 growth at 45 and 47 °C, upon the supplementation of the extracellular fractions of Bacillus species into the growing culture. Conclusions Overall the present analysis revealed the conversion of the culturable cells into the viable and nonculturable (VBNC) state as a result of heat shock response in Bacillus spp. SUBB01 and the cellular adaptation at extremely high temperature.
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Affiliation(s)
- Md Sakil Munna
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Jannatun Tahera
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Md Mohibul Hassan Afrad
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Ifra Tun Nur
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Rashed Noor
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
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Mechanism to control the cell lysis and the cell survival strategy in stationary phase under heat stress. SPRINGERPLUS 2015; 4:599. [PMID: 26543734 PMCID: PMC4627973 DOI: 10.1186/s40064-015-1415-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 10/07/2015] [Indexed: 11/10/2022]
Abstract
An array of stress signals triggering the bacterial cellular stress response is well known in Escherichia coli and other bacteria. Heat stress is usually sensed through the misfolded outer membrane porin (OMP) precursors in the periplasm, resulting in the activation of σ(E) (encoded by rpoE), which binds to RNA polymerase to start the transcription of genes required for responding against the heat stress signal. At the elevated temperatures, σ(E) also serves as the transcription factor for σ(H) (the main heat shock sigma factor, encoded by rpoH), which is involved in the expression of several genes whose products deal with the cytoplasmic unfolded proteins. Besides, oxidative stress in form of the reactive oxygen species (ROS) that accumulate due to heat stress, has been found to give rise to viable but non-culturable (VBNC) cells at the early stationary phase, which is in turn lysed by the σ(E)-dependent process. Such lysis of the defective cells may generate nutrients for the remaining population to survive with the capacity of formation of colony forming units (CFUs). σ(H) is also known to regulate the transcription of the major heat shock proteins (HSPs) required for heat shock response (HSR) resulting in cellular survival. Present review concentrated on the cellular survival against heat stress employing the harmonized impact of σ(E) and σ(H) regulons and the HSPs as well as their inter connectivity towards the maintenance of cellular survival.
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Munna MS, Humayun S, Noor R. Influence of heat shock and osmotic stresses on the growth and viability of Saccharomyces cerevisiae SUBSC01. BMC Res Notes 2015; 8:369. [PMID: 26298101 PMCID: PMC4546815 DOI: 10.1186/s13104-015-1355-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 08/17/2015] [Indexed: 01/11/2023] Open
Abstract
Background With a preceding scrutiny of bacterial cellular responses against heat shock and oxidative stresses, current research further investigated such impact on yeast cell. Present study attempted to observe the influence of high temperature (44–46 °C) on the growth and budding pattern of Saccharomyces cerevisiae SUBSC01. Effect of elevated sugar concentrations as another stress stimulant was also observed. Cell growth was measured through the estimation of the optical density at 600 nm (OD600) and by the enumeration of colony forming units on the agar plates up to 450 min. Results Subsequent transformation in the yeast morphology and the cellular arrangement were noticed. A delayed and lengthy lag phase was observed when yeast strain was grown at 30, 37, and 40 °C, while at 32.5 °C, optimal growth pattern was noticed. Cells were found to lose culturability completely at 46 °C whereby cells without the cytoplasmic contents were also observed under the light microscope. Thus the critical growth temperature was recorded as 45 °C which was the highest temperature at which S. cerevisiae SUBSC01 could grow. However, a complete growth retardation was observed at 45 °C with the high concentrations of dextrose (0.36 g/l) and sucrose (0.18 g/l). Notably, yeast budding was found at 44 and 45 °C up to 270 min of incubation, which was further noticed to be suppressed at 46 °C. Conclusions Present study revealed that the optimal and the critical growth temperatures of S. cerevisiae SUBSC01 were 32.5 and 45 °C, respectively; and also projected on the inhibitory concentrations of sugars on yeast growth at that temperature.
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Affiliation(s)
- Md Sakil Munna
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Sanjida Humayun
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Rashed Noor
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
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Dai J, Wei H, Tian C, Damron FH, Zhou J, Qiu D. An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis. BMC Microbiol 2015; 15:34. [PMID: 25887418 PMCID: PMC4336711 DOI: 10.1186/s12866-015-0357-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022] Open
Abstract
Background Bacteria use alternative sigma factors (σs) to regulate condition-specific gene expression for survival and Shewanella harbors multiple ECF (extracytoplasmic function) σ genes and cognate anti-sigma factor genes. Here we comparatively analyzed two of the rpoE-like operons in the strain MR-1: rpoE-rseA-rseB-rseC and rpoE2-chrR. Results RpoE was important for bacterial growth at low and high temperatures, in the minimal medium, and high salinity. The degP/htrA orthologue, required for growth of Escherichia coli and Pseudomonas aeruginosa at high temperature, is absent in Shewanella, while the degQ gene is RpoE-regulated and is required for bacterial growth at high temperature. RpoE2 was essential for the optimal growth in oxidative stress conditions because the rpoE2 mutant was sensitive to hydrogen peroxide and paraquat. The operon encoding a ferrochelatase paralogue (HemH2) and a periplasmic glutathione peroxidase (PgpD) was identified as RpoE2-dependent. PgpD exhibited higher activities and played a more important role in the oxidative stress responses than the cytoplasmic glutathione peroxidase CgpD under tested conditions. The rpoE2-chrR operon and the identified regulon genes, including pgpD and hemH2, are coincidently absent in several psychrophilic and/or deep-sea Shewanella strains. Conclusion In S. oneidensis MR-1, the RpoE-dependent degQ gene is required for optimal growth under high temperature. The rpoE2 and RpoE2-dependent pgpD gene encoding a periplasmic glutathione peroxidase are involved in oxidative stress responses. But rpoE2 is not required for bacterial growth at low temperature and it even affected bacterial growth under salt stress, indicating that there is a tradeoff between the salt resistance and RpoE2-mediated oxidative stress responses. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0357-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hehong Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chunyuan Tian
- School of Life Sciences and Technology, Hubei University of Engineering, 272 Jiaotong Avenue, Xiaogan, 432000, China.
| | - Fredrick Heath Damron
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, The University of Oklahoma, Stephenson Research and Technology Center, 101 David L. Boren Blvd, Norman, OK 73019, USA.
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Shimizu K. Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 155:1-54. [PMID: 25712586 DOI: 10.1007/10_2015_320] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Living organisms have sophisticated but well-organized regulation system. It is important to understand the metabolic regulation mechanisms in relation to growth environment for the efficient design of cell factories for biofuels and biochemicals production. Here, an overview is given for carbon catabolite regulation, nitrogen regulation, ion, sulfur, and phosphate regulations, stringent response under nutrient starvation as well as oxidative stress regulation, redox state regulation, acid-shock, heat- and cold-shock regulations, solvent stress regulation, osmoregulation, and biofilm formation, and quorum sensing focusing on Escherichia coli metabolism and others. The coordinated regulation mechanisms are of particular interest in getting insight into the principle which governs the cell metabolism. The metabolism is controlled by both enzyme-level regulation and transcriptional regulation via transcription factors such as cAMP-Crp, Cra, Csr, Fis, P(II)(GlnB), NtrBC, CysB, PhoR/B, SoxR/S, Fur, MarR, ArcA/B, Fnr, NarX/L, RpoS, and (p)ppGpp for stringent response, where the timescales for enzyme-level and gene-level regulations are different. Moreover, multiple regulations are coordinated by the intracellular metabolites, where fructose 1,6-bisphosphate (FBP), phosphoenolpyruvate (PEP), and acetyl-CoA (AcCoA) play important roles for enzyme-level regulation as well as transcriptional control, while α-ketoacids such as α-ketoglutaric acid (αKG), pyruvate (PYR), and oxaloacetate (OAA) play important roles for the coordinated regulation between carbon source uptake rate and other nutrient uptake rate such as nitrogen or sulfur uptake rate by modulation of cAMP via Cya.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan. .,Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
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Regulation Systems of Bacteria such as Escherichia coli in Response to Nutrient Limitation and Environmental Stresses. Metabolites 2013; 4:1-35. [PMID: 24958385 PMCID: PMC4018673 DOI: 10.3390/metabo4010001] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/18/2013] [Accepted: 12/06/2013] [Indexed: 11/16/2022] Open
Abstract
An overview was made to understand the regulation system of a bacterial cell such as Escherichia coli in response to nutrient limitation such as carbon, nitrogen, phosphate, sulfur, ion sources, and environmental stresses such as oxidative stress, acid shock, heat shock, and solvent stresses. It is quite important to understand how the cell detects environmental signals, integrate such information, and how the cell system is regulated. As for catabolite regulation, F1,6B P (FDP), PEP, and PYR play important roles in enzyme level regulation together with transcriptional regulation by such transcription factors as Cra, Fis, CsrA, and cAMP-Crp. αKG plays an important role in the coordinated control between carbon (C)- and nitrogen (N)-limitations, where αKG inhibits enzyme I (EI) of phosphotransferase system (PTS), thus regulating the glucose uptake rate in accordance with N level. As such, multiple regulation systems are co-ordinated for the cell synthesis and energy generation against nutrient limitations and environmental stresses. As for oxidative stress, the TCA cycle both generates and scavenges the reactive oxygen species (ROSs), where NADPH produced at ICDH and the oxidative pentose phosphate pathways play an important role in coping with oxidative stress. Solvent resistant mechanism was also considered for the stresses caused by biofuels and biochemicals production in the cell.
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Nagamitsu H, Murata M, Kosaka T, Kawaguchi J, Mori H, Yamada M. Crucial roles of MicA and RybB as vital factors for σ-dependent cell lysis in Escherichia coli long-term stationary phase. J Mol Microbiol Biotechnol 2013; 23:227-32. [PMID: 23594456 DOI: 10.1159/000350370] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
σ(E)-dependent cell lysis has been proposed to eliminate damaged cells in the stationary phase in Escherichia coli. In order to explore the relationship of this process to long-term stationary phase existence, we considered that micA and rybB could be important small regulatory RNA (sRNA) genes for σ(E)-dependent cell lysis. A long-term stationary phase was observed at temperatures of <37°C, but not >38°C, and was found even in an rpoS knock-out background. Strains with disrupted micA or rybB were incapable of long-term stationary phase existence. Both strains drastically lost survivability accompanied by a dramatic accumulation of mutations. These findings allow us to speculate that σ(E)-dependent cell lysis plays a key role in the establishment of the long-term stationary phase, presumably by eliminating damaged cells and thus preventing the over-accumulation of mutations.
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Affiliation(s)
- Hiroshi Nagamitsu
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, Japan
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