scholarly journals 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

2020 ◽  
Vol 21 (16) ◽  
pp. 5843
Author(s):  
Pawel Wojtkiewicz ◽  
Daria Biernacka ◽  
Patrycja Gorzelak ◽  
Anna Stupak ◽  
Gracjana Klein ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Folding ◽  
Acid Resistance ◽  
Transcriptional Factors ◽  
Rnase H ◽  
Amino Acid Residues ◽  
Ppiase Activity ◽  
Multicopy Suppressor ◽  
Rate Limiting Step ◽  
Genes Encoding

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.

Selective cloning of genes encoding RNase H from Salmonella typhimurium, Saccharomyces cerevisiae and Escherichia coli rnh mutant

1991 ◽  
Vol 227 (3) ◽  
pp. 438-445 ◽  
Author(s):  
Mitsuhiro Itaya ◽  
Dorothy McKelvin ◽  
Sunil K. Chatterjie ◽  
Robert J. Crouch
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Salmonella Typhimurium ◽  
Rnase H ◽  
Genes Encoding

scholarly journals Involvement of PatE, a Prophage-Encoded AraC-Like Regulator, in the Transcriptional Activation of Acid Resistance Pathways of Enterohemorrhagic Escherichia coli Strain EDL933

2012 ◽  
Vol 78 (15) ◽  
pp. 5083-5092 ◽  
Author(s):  
Jennifer K. Bender ◽  
Judyta Praszkier ◽  
Matthew J. Wakefield ◽  
Kathryn Holt ◽  
Marija Tauschek ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Transcriptional Activation ◽  
Regulatory Protein ◽  
Acid Resistance ◽  
Enterohemorrhagic Escherichia Coli ◽  
Transcriptional Analysis ◽  
Mobility Shift ◽  
Content Type ◽  
Infectious Dose ◽  
Genes Encoding

ABSTRACTEnterohemorrhagicEscherichia coli(EHEC) O157:H7 is a lethal human intestinal pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome. EHEC is transmitted by the fecal-oral route and has a lower infectious dose than most other enteric bacterial pathogens in that fewer than 100 CFU are able to cause disease. This low infectious dose has been attributed to the ability of EHEC to survive in the acidic environment of the human stomach.In silicoanalysis of the genome of EHEC O157:H7 strain EDL933 revealed a gene,patE, for a putative AraC-like regulatory protein within the prophage island, CP-933H. Transcriptional analysis inE. colishowed that the expression ofpatEis induced during stationary phase. Data from microarray assays demonstrated that PatE activates the transcription of genes encoding proteins of acid resistance pathways. In addition, PatE downregulated the expression of a number of genes encoding heat shock proteins and the type III secretion pathway of EDL933. Transcriptional analysis and electrophoretic mobility shift assays suggested that PatE also activates the transcription of the gene for the acid stress chaperonehdeAby binding to its promoter region. Finally, assays of acid tolerance showed that increasing the expression of PatE in EHEC greatly enhanced the ability of the bacteria to survive in different acidic environments. Together, these findings indicate that EHEC strain EDL933 carries a prophage-encoded regulatory system that contributes to acid resistance.

scholarly journals GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli

2004 ◽  
Vol 186 (20) ◽  
pp. 6698-6705 ◽  
Author(s):  
Jason A. Opdyke ◽  
Ju-Gyeong Kang ◽  
Gisela Storz
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Small Rna ◽  
Acid Resistance ◽  
Base Pairs ◽  
Gene Encoding ◽  
Mrna Accumulation ◽  
Long Form ◽  
Genes Encoding ◽  
Opposite Strand

ABSTRACT A previous bioinformatics-based search for small RNAs in Escherichia coli identified a novel RNA named IS183. The gene encoding this small RNA is located between and on the opposite strand of genes encoding two transcriptional regulators of the acid response, gadX (yhiX) and gadW (yhiW). Given that IS183 is encoded in the gad gene cluster and because of its role in regulating acid response genes reported here, this RNA has been renamed GadY. We show that GadY exists in three forms, a long form consisting of 105 nucleotides and two processed forms, consisting of 90 and 59 nucleotides. The expression of this small RNA is highly induced during stationary phase in a manner that is dependent on the alternative sigma factor σS. Overexpression of the three GadY RNA forms resulted in increased levels of the mRNA encoding the GadX transcriptional activator, which in turn caused increased levels of the GadA and GadB glutamate decarboxylases. A promoter mutation which abolished gadY expression resulted in a reduction in the amount of gadX mRNA during stationary phase. The gadY gene was shown to overlap the 3′ end of the gadX gene, and this overlap region was found to be necessary for the GadY-dependent accumulation of gadX mRNA. We suggest that during stationary phase, GadY forms base pairs with the 3′-untranslated region of the gadX mRNA and confers increased stability, allowing for gadX mRNA accumulation and the increased expression of downstream acid resistance genes.

scholarly journals FK506 Binding Protein from the Hyperthermophilic Archaeon Pyrococcus horikoshii Suppresses the Aggregation of Proteins in Escherichia coli

2002 ◽  
Vol 68 (2) ◽  
pp. 464-469 ◽  
Author(s):  
Akira Ideno ◽  
Masahiro Furutani ◽  
Yoshitaka Iba ◽  
Yoshikazu Kurosawa ◽  
Tadashi Maruyama
Keyword(s):  
Escherichia Coli ◽  
Protein Folding ◽  
Binding Protein ◽  
Fab Fragment ◽  
Ppiase Activity ◽  
Pyrococcus Horikoshii ◽  
E Coli ◽  
Fk506 Binding Protein ◽  
Soluble Recombinant Protein

ABSTRACT The 29-kDa FK506 binding protein (FKBP) gene is the only peptidyl-prolyl cis-trans isomerase (PPIase) gene in the genome of Pyrococcus horikoshii. We characterized the function of this FKBP (PhFKBP29) and used it to increase the production yield of soluble recombinant protein in Escherichia coli. The PPIase activity (k cat/Km ) of PhFKBP29 was found to be much lower than that of other archaeal 16- to 18-kDa FKBPs by a chymotrypsin-coupled assay of the oligo-peptidyl substrate at 15�C. Besides this low PPIase activity, PhFKBP29 showed chaperone-like protein folding activity which enhanced the refolding yield of chemically unfolded rhodanese in vitro. In addition, it suppressed thermal protein aggregation in a temperature range of 45 to 100�C. When the PhFKBP29 gene was coexpressed with the recombinant Fab fragment gene of the anti-hen egg lysozyme antibody in the cytoplasm of E. coli, whose expressed product tended to form an inactive aggregate in E. coli, it improved the yield of the soluble Fab fragments with antibody specificity. PhFKBP29 exerted protein folding and aggregation suppression in E. coli cells.

scholarly journals Discriminatory Detection of Inhibitor-Resistant β-Lactamases in Escherichia coli by Single-Strand Conformation Polymorphism-PCR

1998 ◽  
Vol 42 (4) ◽  
pp. 879-884 ◽  
Author(s):  
Valérie Speldooren ◽  
Beate Heym ◽  
Roger Labia ◽  
Marie-Hélène Nicolas-Chanoine
Keyword(s):  
Escherichia Coli ◽  
Clavulanic Acid ◽  
Consensus Sequence ◽  
Acid Resistance ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Genes Encoding ◽  
Amoxicillin Clavulanic Acid ◽  
Pcr Method ◽  
Conformation Polymorphism

ABSTRACT Plasmid-mediated mechanisms, comprising TEM hyperproduction, TEM derivative production, and OXA production, lead to amoxicillin-clavulanic acid resistance in enterobacteria. The ability of the single-strand conformation polymorphism (SSCP)-PCR method to differentiate the genes encoding inhibitor-resistant β-lactamases was evaluated with three bla TEM primer pairs. Thebla TEM genes, which were known to be different on the basis of their nucleotide sequences (bla TEM-1A, bla TEM-1B,bla TEM-2, bla TEM-30,bla TEM-32, andbla TEM-35), were identified as different by their electrophoretic mobilities. Thebla TEM-33, bla TEM-34,bla TEM-36, bla TEM-37,bla TEM-38, andbla TEM-39 genes, whose sequence differences have been established by oligotyping, displayed different SSCP profiles for different fragments, suggesting genetic differences in addition to those defined by oligotyping. Confirmed by sequencing, these additional genetic events concerned silent mutations at certain positions and, notably, a G→T transversion at position 1 of the −10 consensus sequence in bla TEM-34,bla TEM-36, bla TEM-37, and bla TEM-39. Applied to eight clinical isolates of Escherichia coli resistant to amoxicillin-clavulanic acid, the SSCP method detected TEM-1 in three strains and TEM-30, TEM-32, and TEM-35 in three other strains, respectively. A novel TEM derivative (TEM-58) was detected in another strain, and the deduced amino acid sequence showed two substitutions: Arg244Ser, which is known to confer amoxicillin-clavulanic acid resistance in TEM-30, and Val261Ile, which has not been described previously. The eighth strain produced an OXA β-lactamase. Given the discriminatory power and the applicability of SSCP-PCR, this method can be proposed as a means of following the evolution of the frequencies of the different inhibitor-resistant β-lactamases.

scholarly journals Gain-of-function mutations in acid stress response (evgS) protect Escherichia coli from killing by gallium nitrate, an antimicrobial candidate

2020 ◽  
Author(s):  
Jie Zeng ◽  
Liwen Wu ◽  
Zhou Liu ◽  
Yihua Lv ◽  
Jinzhi Feng ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acid Stress ◽  
Acid Resistance ◽  
Tca Cycle ◽  
Resistant Mutant ◽  
Gallium Nitrate ◽  
Gain Of Function ◽  
Antimicrobial Drugs ◽  
Ros Accumulation ◽  
Genes Encoding

Widespread antimicrobial resistance encourages repurposing/refining of non-antimicrobial drugs for antimicrobial indications. Gallium nitrate (GaNt), an FDA-approved medication for cancer-related hypercalcemia, recently showed good activity against several clinically significant bacteria. However, the mechanism of GaNt antibacterial action is still poorly understood. In the present work, resistant and tolerant mutants of Escherichia coli were sought via multiple rounds of killing by GaNt. Multi-round-enrichment yielded no resistant mutant; whole-genome sequencing of one representative GaNt-tolerant mutant uncovered mutations in three genes (evgS, arpA, kdpD) potentially linked to protection from GaNt-mediated killing. Subsequent genetic analysis ruled out a role for arpA and kdpD, but two gain-of-function mutations in evgS conferred tolerance. The evgS mutation-mediated GaNt tolerance depended on EvgS to EvgA phosphor-transfer; EvgA-mediated up-regulation of GadE. YdeO, and SarfA also contributed to tolerance, the latter two likely through their regulation of GadE. GaNt-mediated killing of wild-type cells correlated with increased intracellular ROS accumulation that was abolished by the evgS-tolerant mutation. Moreover, GaNt-mediated killing was mitigated by dimethyl sulfoxide, and the evgS-tolerant mutation upregulated genes encoding enzymes involved in ROS detoxification and in the glyoxylate shunt of the TCA cycle. Collectively, these findings indicate that GaNt kills bacteria through elevation of ROS; gain-of-function mutations in evgS confer tolerance by constitutively activating the EvgA-YdeO/GadE cascade of acid-resistance pathways and by preventing GaNt-stimulated ROS accumulation by upregulating ROS detoxification and shifting TCA cycle carbon flux. The striking lethal activity of GaNt suggests that clinical use of the agent may not quickly lead to resistance.

scholarly journals Loss of topoisomerase I function affects the RpoS-dependent and GAD systems of acid resistance in Escherichia coli

Microbiology ◽  
2005 ◽  
Vol 151 (8) ◽  
pp. 2783-2791 ◽  
Author(s):  
Natalee Stewart ◽  
Jingyang Feng ◽  
Xiaoping Liu ◽  
Devyani Chaudhuri ◽  
John W. Foster ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Blot Analysis ◽  
Topoisomerase I ◽  
Northern Blot Analysis ◽  
Acid Resistance ◽  
Arginine Decarboxylase ◽  
Rnase H ◽  
Loop Formation ◽  
Human Gastrointestinal Tract ◽  
Insertion Mutations

Acid resistance (AR) in Escherichia coli is important for its survival in the human gastrointestinal tract and involves three systems. The first AR system is dependent on the sigma factor RpoS. The second system (the GAD system) requires the glutamate decarboxylase isoforms encoded by the gadA and gadB genes. The third system (the ARG system) requires the arginine decarboxylase encoded by adiA. Loss of topoisomerase I function from topA deletion or Tn10 insertion mutations lowered the resistance to killing by pH 2 or 2·5 treatment by 10-fold to >100-fold. The RpoS and GAD systems were both affected by the topA mutation, but the ARG system of AR was not affected. Northern blot analysis showed that induction of gadA and gadB transcription in stationary phase and at pH 5·5 was decreased in the topA mutant. Western blot analysis showed that the topA mutation did not affect accumulation of RpoS, GadX or GadW proteins. Topoisomerase I might have a direct influence on the transcription of AR genes. This influence does not involve R-loop formation as the overexpression of RNase H did not alleviate the decrease of AR caused by the topA mutation. The effect of the topA mutation could be suppressed by an hns mutation, so topoisomerase I might be required to counteract the effect of H-NS protein on gene expression, in addition to its influence on RpoS-dependent transcription.

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