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Bacterial Proteins in Stress Management
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Bacterial Proteins in Stress Management

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 19845

Special Issue Editor

Prof. Dr. Satish Raina

E-Mail Website
Guest Editor
Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
Interests: protein folding; heat shock response; peptidyl prolyl cis/trans isomerases; disulfide bond formation; RpoE sigma factor; two-component systems; envelope stress; transcription factors; lipopolysaccharide
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacteria, like all other organisms, respond to biotic and abiotic stresses by reprogramming the transcriptional landscape that leads to induction or repression of a subset of genes, whose products are required to maintain cellular homeostasis under adverse growth conditions. Bacteria do so by recruiting specific alternative sigma factors like RpoH, RpoE, RpoS and RpoN and a specific set of transcriptional factors that leads to synthesis of proteins that can combat stress. Some of these inducible genes encode proteins that aid in protein folding by acting as molecular chaperones or protein folding catalysts that accelerate rate-limiting steps in protein folding. Some protein folding factors, although synthesized constitutively, participate in stress management by assisting or accelerating proteins that can combat oxidative stress or modulate even the activity of specific transcriptional factors. Bacteria also recruit a variety of two-component systems and transcriptional factors like DksA that respond to variety of environmental stresses.

Commonly encountered stresses are: shift to either high or low temperatures, challenges by osmolarity shift, nutritional limitations, changes in pH, exposure to noxious compounds, accumulation of reactive oxygen, exposure to antibiotics, phosphate-limiting growth conditions and imbalance in divalent cations concentration. Gram-negative bacteria are faced by additional challenges due to the presence of porous outer membrane that can change protein folding milieu of cell envelope affecting its redox status that can impact folding status of abundant outer membrane proteins and even lead to modifications in lipopolysaccharide.

Some components of stress response amelioration involve universally conserved protein folding factors, protein folding catalysts and proteases. Specific transcriptional factors that change RNA polymerase properties to alter transcriptional process at different stages and maintain genome integrity are highly conserved in bacteria. Some other stress-related proteins are important for ribosome assembly, RNA processing and modification and ensuring translational fidelity. Together such stress combating proteins are essential for adaptation to diverse environmental niches and balanced synthesis of essential cellular components.

Prof. Dr. Satish Raina
Guest Editor

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Keywords

  • RNA polymerase
  • Heat shock sigma factor (RpoH)
  • Extracytoplasmic sigma factor (RpoE and its counterparts)
  • Stationary phase sigma factor RpoS
  • Anti-sigma factors
  • DksA in stringent response and sigma factor competition
  • Chaperones
  • Peptidyl prolyl cis/trans isomerase (PPIases)
  • Disulfide bond formation proteins (Dsb’s)
  • Oxidative stress regulators like OxyR
  • Two-component systems (PhoB/R, PhoP/Q)
  • DNA repair systems
  • Redox sensing proteins
  • Osmolarity stress
  • Envelope stress
  • Ribosome assembly
  • Proteases
  • Phosphatases and kinases
  • Periplasmic protein folding
  • Bacterial virulence
  • Toxin-antitoxin systems
  • Lipopolysaccharide and its structural modifications in response to stress

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Published Papers (5 papers)

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Research

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14 pages, 10080 KiB  
Article
Cell Lysis Directed by SulA in Response to DNA Damage in Escherichia coli
by Masayuki Murata, Keiko Nakamura, Tomoyuki Kosaka, Natsuko Ota, Ayumi Osawa, Ryunosuke Muro, Kazuya Fujiyama, Taku Oshima, Hirotada Mori, Barry L. Wanner and Mamoru Yamada
Int. J. Mol. Sci. 2021, 22(9), 4535; https://doi.org/10.3390/ijms22094535 - 26 Apr 2021
Cited by 5 | Viewed by 2926
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Bacterial Proteins in Stress Management)
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20 pages, 3987 KiB  
Article
Role of Hibernation Promoting Factor in Ribosomal Protein Stability during Pseudomonas aeruginosa Dormancy
by Sokuntheary Theng, Kerry S. Williamson and Michael J. Franklin
Int. J. Mol. Sci. 2020, 21(24), 9494; https://doi.org/10.3390/ijms21249494 - 14 Dec 2020
Cited by 9 | Viewed by 3509
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes biofilm-associated infections. P. aeruginosa can survive in a dormant state with reduced metabolic activity in nutrient-limited environments, including the interiors of biofilms. When entering dormancy, the bacteria undergo metabolic remodeling, which includes reduced translation and [...] Read more.
Pseudomonas aeruginosa is an opportunistic pathogen that causes biofilm-associated infections. P. aeruginosa can survive in a dormant state with reduced metabolic activity in nutrient-limited environments, including the interiors of biofilms. When entering dormancy, the bacteria undergo metabolic remodeling, which includes reduced translation and degradation of cellular proteins. However, a supply of essential macromolecules, such as ribosomes, are protected from degradation during dormancy. The small ribosome-binding proteins, hibernation promoting factor (HPF) and ribosome modulation factor (RMF), inhibit translation by inducing formation of inactive 70S and 100S ribosome monomers and dimers. The inactivated ribosomes are protected from the initial steps in ribosome degradation, including endonuclease cleavage of the ribosomal RNA (rRNA). Here, we characterized the role of HPF in ribosomal protein (rProtein) stability and degradation during P. aeruginosa nutrient limitation. We determined the effect of the physiological status of P. aeruginosa prior to starvation on its ability to recover from starvation, and on its rRNA and rProtein stability during cell starvation. The results show that the wild-type strain and a stringent response mutant (∆relA∆spoT strain) maintain high cellular abundances of the rProteins L5 and S13 over the course of eight days of starvation. In contrast, the abundances of L5 and S13 reduce in the ∆hpf mutant cells. The loss of rProteins in the ∆hpf strain is dependent on the physiology of the cells prior to starvation. The greatest rProtein loss occurs when cells are first cultured to stationary phase prior to starvation, with less rProtein loss in the ∆hpf cells that are first cultured to exponential phase or in balanced minimal medium. Regardless of the pre-growth conditions, P. aeruginosa recovery from starvation and the integrity of its rRNA are impaired in the absence of HPF. The results indicate that protein remodeling during P. aeruginosa starvation includes the degradation of rProteins, and that HPF is essential to prevent rProtein loss in starved P. aeruginosa. The results also indicate that HPF is produced throughout cell growth, and that regardless of the cellular physiological status, HPF is required to protect against ribosome loss when the cells subsequently enter starvation phase. Full article
(This article belongs to the Special Issue Bacterial Proteins in Stress Management)
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32 pages, 9252 KiB  
Article
Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease
by Daria Biernacka, Patrycja Gorzelak, Gracjana Klein and Satish Raina
Int. J. Mol. Sci. 2020, 21(23), 9088; https://doi.org/10.3390/ijms21239088 - 29 Nov 2020
Cited by 22 | Viewed by 5246
Abstract
We previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, [...] Read more.
We previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation of LpxC, providing the first alternative pathway of LpxC degradation. Isolation and characterization of an extragenic suppressor mutation that prevents lethality of ΔlapB by restoration of normal LPS synthesis identified a frame-shift mutation after 377 aa in the essential gene designated lapC, suggesting LapB and LapC act antagonistically. The same lapC gene was identified during selection for mutations that induce transcription from LPS defects-responsive rpoEP3 promoter, confer sensitivity to LpxC inhibitor CHIR090 and a temperature-sensitive phenotype. Suppressors of lapC mutants that restored growth at elevated temperatures mapped to lapA/lapB, lpxC and ftsH genes. Such suppressor mutations restored normal levels of LPS and prevented proteolysis of LpxC in lapC mutants. Interestingly, a lapC deletion could be constructed in strains either overproducing LpxC or in the absence of LapB, revealing that FtsH, LapB and LapC together regulate LPS synthesis by controlling LpxC amounts. Full article
(This article belongs to the Special Issue Bacterial Proteins in Stress Management)
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33 pages, 5965 KiB  
Article
Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl cis/trans Isomerases Identifies Three New PPIase Activities in Escherichia coli That Includes the DksA Transcription Factor
by Pawel Wojtkiewicz, Daria Biernacka, Patrycja Gorzelak, Anna Stupak, Gracjana Klein and Satish Raina
Int. J. Mol. Sci. 2020, 21(16), 5843; https://doi.org/10.3390/ijms21165843 - 14 Aug 2020
Cited by 9 | Viewed by 3726
Abstract
Consistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of [...] Read more.
Consistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S), transcriptional factors (DksA and SrrA), replication proteins Hda/DiaA, asparatokinase MetL, Cmk and acid resistance regulator (AriR) overcome some defects of Δ6ppi strains. Interestingly, viability of Δ6ppi bacteria requires the presence of transcriptional factors DksA, SrrA, Cmk or Hda. DksA, MetL and Cmk are for the first time shown to exhibit PPIase activity in chymotrypsin-coupled and RNase T1 refolding assays and their overexpression also restores growth of a Δ(dnaK/J/tig) strain, revealing their mechanism of suppression. Mutagenesis of DksA identified that D74, F82 and L84 amino acid residues are critical for its PPIase activity and their replacement abrogated multicopy suppression ability. Mutational studies revealed that DksA-mediated suppression of either Δ6ppi or ΔdnaK/J is abolished if GroL/S and RpoE are limiting, or in the absence of either major porin regulatory sensory kinase EnvZ or RNase H, transporter TatC or LepA GTPase or Pi-signaling regulator PhoU. Full article
(This article belongs to the Special Issue Bacterial Proteins in Stress Management)
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Review

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27 pages, 19185 KiB  
Review
Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses
by Rubén de Dios, Eduardo Santero and Francisca Reyes-Ramírez
Int. J. Mol. Sci. 2021, 22(8), 3900; https://doi.org/10.3390/ijms22083900 - 9 Apr 2021
Cited by 13 | Viewed by 3601
Abstract
The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most [...] Read more.
The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria. Full article
(This article belongs to the Special Issue Bacterial Proteins in Stress Management)
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