scholarly journals Novel modification by L/F-tRNA-protein transferase (LFTR) generates a Leu/N-degron ligand in Escherichia coli.

2021 ◽  
Author(s):  
Ralf D. Ottofuelling ◽  
Robert L. Ninnis ◽  
Kaye N. Truscott ◽  
David A. Dougan
Keyword(s):  
Physiological Role ◽  
The Novel ◽  
Peptide Arrays ◽  
Systematic Analysis ◽  
E Coli ◽  
Endoproteolytic Cleavage ◽  
Escherchia Coli ◽  
Clpap Protease ◽  
Dependent Modification

The N-degron pathways are a set of proteolytic systems that relate the half-life of a protein to its N-terminal (Nt) residue. In Escherchia coli the principal N-degron pathway is known as the Leu/N-degron pathway of which an Nt Leu is a key feature of the degron. Although the physiological role of the Leu/N-degron pathway is currently unclear, many of the components of the pathway are well defined. Proteins degraded by this pathway contain an Nt degradation signal (N-degron) composed of an Nt primary destabilizing (Nd1) residue (Leu, Phe, Trp or Tyr) and an unstructured region which generally contains a hydrophobic element. Most N-degrons are generated from a pro-N-degron, either by endoproteolytic cleavage, or by enzymatic attachment of a Nd1 residue (Leu or Phe) to the N-terminus of a protein (or protein fragment) by the enzyme Leu/Phe tRNA protein transferase (LFTR) in a non-ribosomal manner. Regardless of the mode of generation, all Leu/N-degrons are recognized by ClpS and delivered to the ClpAP protease for degradation. To date, only two physiological Leu/N-degron bearing substrates have been verified, one of which (PATase) is modified by LFTR. In this study, we have examined the substrate proteome of LFTR during stationary phase. From this analysis, we have identified several additional physiological Leu/N-degron ligands, including AldB, which is modified by a previously undescribed activity of LFTR. Importantly, the novel specificity of LFTR was confirmed in vitro, using a range of model proteins. Our data shows that processing of the Nt-Met of AldB generates a novel substrate for LFTR. Importantly, the LFTR-dependent modification of T2-AldB is essential for its turnover by ClpAPS, in vitro. To further examine the acceptor specificity of LFTR, we performed a systematic analysis using a series of peptide arrays. These data reveal that the identity of the second residue modulates substrate conjugation with positively charged residues being favored and negatively charged and aromatic residues being disfavored. Collectively, these findings extend our understanding of LFTR specificity and the Leu/N-degron pathway in E. coli.

Formation, translocation and resolution of Holliday junctions during homologous genetic recombination

1995 ◽  
Vol 347 (1319) ◽  
pp. 21-25 ◽  
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Recombination ◽  
Holliday Junctions ◽  
The Novel ◽  
E Coli ◽  
The Past ◽  
Endonucleolytic Cleavage ◽  
Insight Into ◽  
Made In

Over the past three or four years, great strides have been made in our understanding of the proteins involved in recombination and the mechanisms by which recombinant molecules are formed. This review summarizes our current understanding of the process by focusing on recent studies of proteins involved in the later steps of recombination in bacteria. In particular, biochemical investigation of the in vitro properties of the E. coli RuvA, RuvB and RuvC proteins have provided our first insight into the novel molecular mechanisms by which Holliday junctions are moved along DNA and then resolved by endonucleolytic cleavage.

Design and Synthesis of Novel Sulfonamide-Derived Triazoles and Bioactivity Exploration

2020 ◽  
Vol 16 (1) ◽  
pp. 104-118 ◽  
Author(s):  
Shi-Chao He ◽  
Hui-Zhen Zhang ◽  
Hai-Juan Zhang ◽  
Qing Sun ◽  
Cheng-He Zhou
Keyword(s):  
Chlorosulfonic Acid ◽  
Antibacterial Activities ◽  
Structural Features ◽  
The Novel ◽  
E Coli ◽  
Design And Synthesis ◽  
Chemical Studies ◽  
Antimicrobial Evaluation ◽  
Better Than

Objective: Due to the incidence of resistance, a series of sulfonamide-derived 1,2,4- triazoles were synthesized and evaluated. Method: The novel sulfonamide-derived 1,2,4-triazoles were prepared starting from commercial acetaniline and chlorosulfonic acid by sulfonylation, aminolysis, N-alkylation and so on. The antimicrobial activity of the synthesized compounds were evaluated in vitro by two-fold serial dilution technique. Results: In vitro antimicrobial evaluation found that 2-chlorobenzyl sulfonamide 1,2,4-triazole 7c exhibited excellent antibacterial activities against MRSA, B. subtilis, B. typhi and E. coli with MIC values of 0.02−0.16 μmol/mL, which were comparable or even better than Chloromycin. The preliminary mechanism suggested that compound 7c could effectively bind with DNA, and also it could bind with human microsomal heme through hydrogen bonds in molecular docking. Computational chemical studies were performed on compound 7c to understand the structural features that are essential for activity. Additionally, compound 7c could generate a small amount of reactive oxygen species (ROS). Conclusion: Compound 7c could serve as a potential clinical antimicrobial candidate.

scholarly journals Escherichia coli DegP Protease Cleaves between Paired Hydrophobic Residues in a Natural Substrate: the PapA Pilin

2002 ◽  
Vol 184 (20) ◽  
pp. 5762-5771 ◽  
Author(s):  
C. Hal Jones ◽  
Paul Dexter ◽  
Amy K. Evans ◽  
Christopher Liu ◽  
Scott J. Hultgren ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein A ◽  
Pdz Domains ◽  
Peptide Arrays ◽  
Peptide Substrates ◽  
Hydrophobic Residues ◽  
E Coli ◽  
Hydrophobic Amino Acids ◽  
Carboxyl Terminal

ABSTRACT The DegP protein, a multifunctional chaperone and protease, is essential for clearance of denatured or aggregated proteins from the inner-membrane and periplasmic space in Escherichia coli. To date, four natural targets for DegP have been described: colicin A lysis protein, pilin subunits and MalS from E. coli, and high-molecular-weight adherence proteins from Haemophilus influenzae. In vitro, DegP has shown weak protease activity with casein and several other nonnative substrates. We report here the identification of the major pilin subunit of the Pap pilus, PapA, as a natural DegP substrate and demonstrate binding and proteolysis of this substrate in vitro. Using overlapping peptide arrays, we identified three regions in PapA that are preferentially cleaved by DegP. A 7-mer peptide was found to be a suitable substrate for cleavage by DegP in vitro. In vitro proteolysis of model peptide substrates revealed that cleavage is dependent upon the presence of paired hydrophobic amino acids; moreover, cleavage was found to occur between the hydrophobic residues. Finally, we demonstrate that the conserved carboxyl-terminal sequence in pilin subunits, although not a cleavage substrate for DegP, activates the protease and we propose that the activating peptide is recognized by DegP's PDZ domains.

scholarly journals Contributions of chaperone/usher systems to cell binding, biofilm formation and Yersinia pestis virulence

Microbiology ◽  
2011 ◽  
Vol 157 (3) ◽  
pp. 805-818 ◽  
Author(s):  
Suleyman Felek ◽  
Jenny J. Jeong ◽  
Lisa M. Runco ◽  
Susan Murray ◽  
David G. Thanassi ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Biofilm Formation ◽  
Intravenous Route ◽  
The Novel ◽  
E Coli ◽  
Qrt Pcr ◽  
Mouse Tissues ◽  
Mouse Macrophages ◽  
Capsule Locus

Yersinia pestis genome sequencing projects have revealed six intact uncharacterized chaperone/usher systems with the potential to play roles in plague pathogenesis. We cloned each locus and expressed them in the Δfim Escherichia coli strain AAEC185 to test the assembled Y. pestis surface structures for various activities. Expression of each chaperone/usher locus gave rise to specific novel fibrillar structures on the surface of E. coli. One locus, y0561-0563, was able to mediate attachment to human epithelial cells (HEp-2) and human macrophages (THP-1) but not mouse macrophages (RAW264.7), while several loci were able to facilitate E. coli biofilm formation. When each chaperone/usher locus was deleted in Y. pestis, only deletion of the previously described pH 6 antigen (Psa) chaperone/usher system resulted in decreased adhesion and biofilm formation. Quantitative RT-PCR (qRT-PCR) revealed low expression levels for each novel chaperone/usher system in vitro as well as in mouse tissues following intravenous infection. However, a Y. pestis mutant in the chaperone/usher locus y1858-1862 was attenuated for virulence in mice via the intravenous route of infection, suggesting that expression of this locus is, at some stage, sufficient to affect the outcome of a plague infection. qRT-PCR experiments also indicated that expression of the chaperone/usher-dependent capsule locus, caf1, was influenced by oxygen availability and that the well-described chaperone/usher-dependent pilus, Psa, was strongly induced in minimal medium even at 28 °C rather than 37 °C, a temperature previously believed to be required for Psa expression. These data indicate several potential roles for the novel chaperone/usher systems of Y. pestis in pathogenesis and infection-related functions such as cell adhesion and biofilm formation.

scholarly journals Bactericidal efficacy of meropenem in combination with cefmetazole against IMP-producing carbapenem-resistant Enterobacteriaceae

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Ryuichiro Abe ◽  
Hideharu Hagiya ◽  
Yukihiro Akeda ◽  
Norihisa Yamamoto ◽  
Yoshikazu Ishii ◽  
...  
Keyword(s):  
Combination Therapy ◽  
Animal Studies ◽  
Bactericidal Effect ◽  
The Novel ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Enterobacter Hormaechei ◽  
Time Kill

Abstract Objective Carbapenem-resistant Enterobacteriaceae (CRE) are among the most severe threats to public and clinical health because of their high levels of resistance to various antibiotics. We assessed the efficacy of combination therapy with meropenem (MEM) and cefmetazole (CMZ) against Imipenemase (IMP)-producing CRE, using the checkerboard method and time-killing assay on 13 Enterobacteriaceae isolates harboring blaIMP-1 (4 Enterobacter hormaechei, 5 Escherichia coli, and 4 Klebsiella pneumoniae isolates) and 13 isolates harboring blaIMP-6 (8 E. coli and 5 K. pneumoniae isolates). Results Minimum inhibitory concentrations (MICs) of MEM and CMZ ranged from 2 to 64 and 64 to 2048 μg/mL, respectively. Checkerboard method demonstrated the synergy of the MEM/CMZ combination in all the tested IMP-producing CRE isolates, and the time-kill assay indicated a bactericidal effect for both blaIMP-1 and blaIMP-6 positive CRE when MEM/CMZ combination was used. In vitro, the MEM/CMZ combination was potentially effective against IMP-1- or IMP-6-producing CRE. Further investigations including in vivo animal studies and clinical studies are warranted to corroborate the clinical utility of the novel combination therapy.

scholarly journals The Crystal Structure of the Zinc Phosphodiesterase from Escherichia coli Provides Insight into Function and Cooperativity of tRNase Z-Family Proteins

2006 ◽  
Vol 188 (4) ◽  
pp. 1607-1614 ◽  
Author(s):  
Brenda Kostelecky ◽  
Ehmke Pohl ◽  
Andreas Vogel ◽  
Oliver Schilling ◽  
Wolfram Meyer-Klaucke
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Metal Binding ◽  
Thermotoga Maritima ◽  
Physiological Role ◽  
E Coli ◽  
Ability To Act ◽  
Trnase Z ◽  
Insight Into

ABSTRACT The elaC gene product from Escherichia coli, ZiPD, is a 3′ tRNA-processing endonuclease belonging to the tRNase Z family of enzymes that have been identified in a wide variety of organisms. In contrast to the elaC homologue from Bacillus subtilis, E. coli elaC is not essential for viability, and although both enzymes process only precursor tRNA (pre-tRNA) lacking a CCA triplet at the 3′ end in vitro, the physiological role of ZiPD remains enigmatic because all pre-tRNA species in E. coli are transcribed with the CCA triplet. We present the first crystal structure of ZiPD determined by multiple anomalous diffraction at a resolution of 2.9 Å. This structure shares many features with the tRNase Z enzymes from B. subtilis and Thermotoga maritima, but there are distinct differences in metal binding and overall domain organization. Unlike the previously described homologous structures, ZiPD dimers display crystallographic symmetry and fully loaded metal sites. The ZiPD exosite is similar to that of the B. subtilis enzyme structurally, but its position with respect to the protein core differs substantially, illustrating its ability to act as a clamp in binding tRNA. Furthermore, the ZiPD crystal structure presented here provides insight into the enzyme's cooperativity and assists the ongoing attempt to elucidate the physiological function of this protein.

scholarly journals The Ubiquitous Protein Domain EAL Is a Cyclic Diguanylate-Specific Phosphodiesterase: Enzymatically Active and Inactive EAL Domains

2005 ◽  
Vol 187 (14) ◽  
pp. 4774-4781 ◽  
Author(s):  
Andrew J. Schmidt ◽  
Dmitri A. Ryjenkov ◽  
Mark Gomelsky
Keyword(s):  
Protein Domain ◽  
Protein Oligomerization ◽  
The Novel ◽  
Multiple Sequence ◽  
E Coli ◽  
Signal Transduction Protein ◽  
Domain Of Unknown Function ◽  
Hydrolysis Of

ABSTRACT The EAL domain (also known as domain of unknown function 2 or DUF2) is a ubiquitous signal transduction protein domain in the Bacteria. Its involvement in hydrolysis of the novel second messenger cyclic dimeric GMP (c-di-GMP) was demonstrated in vivo but not in vitro. The EAL domain-containing protein Dos from Escherichia coli was reported to hydrolyze cyclic AMP (cAMP), implying that EAL domains have different substrate specificities. To investigate the biochemical activity of EAL, the E. coli EAL domain-containing protein YahA and its individual EAL domain were overexpressed, purified, and characterized in vitro. Both full-length YahA and the EAL domain hydrolyzed c-di-GMP into linear dimeric GMP, providing the first biochemical evidence that the EAL domain is sufficient for phosphodiesterase activity. This activity was c-di-GMP specific, optimal at alkaline pH, dependent on Mg2+ or Mn2+, strongly inhibited by Ca2+, and independent of protein oligomerization. Linear dimeric GMP was shown to be 5′pGpG. The EAL domain from Dos was overexpressed, purified, and found to function as a c-di-GMP-specific phosphodiesterase, not as a cAMP-specific phosphodiesterase, in contrast to previous reports. The EAL domains can hydrolyze 5′pGpG into GMP, however, very slowly, thus implying that this activity is irrelevant in vivo. Therefore, c-di-GMP is the exclusive substrate of EAL. Multiple-sequence alignment revealed two groups of EAL domains hypothesized to correspond to enzymatically active and inactive domains. The domains in the latter group have mutations in residues conserved in the active domains. The enzymatic inactivity of EAL domains may explain their coexistence with GGDEF domains in proteins possessing c-di-GMP synthase (diguanulate cyclase) activity.

Synthesis and antimicrobial activity of novel thienopyrimidine linked rhodanine derivatives

2019 ◽  
Vol 97 (2) ◽  
pp. 94-99 ◽  
Author(s):  
Nagaraju Kerru ◽  
Surya Narayana Maddila ◽  
Suresh Maddila ◽  
Sreedhar Sobhanapuram ◽  
Sreekantha B. Jonnalagadda
Keyword(s):  
Antimicrobial Activity ◽  
Condensation Reaction ◽  
Dilution Method ◽  
The Novel ◽  
E Coli ◽  
H Nmr ◽  
Target Molecules ◽  
Novel Target ◽  
C Nmr

This work presents the preparation of a new series of N-(substituted phenyl)-2-(4-oxo-5-(4-(thieno[2,3-d]-pyrimidin-4-yloxy)benzylidene)-2-thioxothiazolidin-3-yl)acetamide derivatives (8a–8l). A condensation reaction of thienopyrimidin-2-thioxothiazolidin-4-one derivative (5) with various 2-chloro-N-phenylacetamides (7a–7l) was employed to afford the new thienopyrimidine tagged rhodanine derivatives under acetone solvent in the presence of potassium carbonate (K2CO3). All of the novel target molecules were characterized by IR, 1H NMR, 13C NMR, and LC–MS spectral analyses and were screened for their in vitro antimicrobial activity by using the broth dilution method. Compounds 8c, 8g, and 8h found to have antibacterial potency against E. coli, B. subtilis, B. cereus, and K. pneumonia with minimum inhibitory concentrations (MICs) of 3.25–6.25 μg/mL compared with the standard Gentamicin. Compounds 8c and 8f demonstrated better antifungal potency (MIC = 3.25–6.25 μg/mL) against A. flavus, A. niger, P. marneffei, and C. albicans when compared with Fluconazole.

scholarly journals PepN is the major aminopeptidase in Escherichia coli: insights on substrate specificity and role during sodium-salicylate-induced stress

Microbiology ◽  
2003 ◽  
Vol 149 (12) ◽  
pp. 3437-3447 ◽  
Author(s):  
Dilip Chandu ◽  
Dipankar Nandi
Keyword(s):  
Escherichia Coli ◽  
Sodium Salicylate ◽  
Physiological Role ◽  
Negative Regulator ◽  
Aminopeptidase Activity ◽  
Peptidase Activity ◽  
E Coli ◽  
Induced Stress ◽  
Hydrolysis Of

PepN and its homologues are involved in the ATP-independent steps (downstream processing) during cytosolic protein degradation. To obtain insights into the contribution of PepN to the peptidase activity in Escherichia coli, the hydrolysis of a selection of endopeptidase and exopeptidase substrates was studied in extracts of wild-type strains and two pepN mutants, 9218 and DH5αΔpepN. Hydrolysis of three of the seven endopeptidase substrates tested was reduced in both pepN mutants. Similar studies revealed that hydrolysis of 10 of 14 exopeptidase substrates studied was greatly reduced in both pepN mutants. This decreased ability to cleave these substrates is pepN-specific as there is no reduction in the ability to hydrolyse exopeptidase substrates in E. coli mutants lacking other peptidases, pepA, pepB or pepE. PepN overexpression complemented the hydrolysis of the affected exopeptidase substrates. These results suggest that PepN is responsible for the majority of aminopeptidase activity in E. coli. Further in vitro studies with purified PepN revealed a preference to cleave basic and small amino acids as aminopeptidase substrates. Kinetic characterization revealed the aminopeptidase cleavage preference of E. coli PepN to be Arg>Ala>Lys>Gly. Finally, it was shown that PepN is a negative regulator of the sodium-salicylate-induced stress in E. coli, demonstrating a physiological role for this aminoendopeptidase under some stress conditions.

ATP-Dependent Conformational Changes and Translocation of Substrates in Clpap Protease as Revealed by Cryo-Electron Microscopy

2000 ◽  
Vol 6 (S2) ◽  
pp. 260-261
Author(s):  
Takashi Ishikawa ◽  
Fabienne Beuron ◽  
Martin Kessel ◽  
Sue Wickner ◽  
Michael R. Maurizi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Conformational Changes ◽  
Layered Structure ◽  
Bacteriophage P1 ◽  
E Coli ◽  
Protein Substrates ◽  
Cryo Electron Microscopy ◽  
Clpap Protease ◽  
Image Averaging

ClpAP, an ATP-dependent protease of E. coli, recognizes and unfolds protein substrates via ClpA, its chaperonelike ATPase component, and digests them in ClpP, its protease component . ClpA forms hexameric rings with a two-layered structure, and stacks axially on either face of the double heptameric rings of ClpP. Protein substrates can bind to ClpAP in the presence of ATPγS, which is not hydrolyzed by ClpA, but are not degraded unless ATP is added. This property makes it possible to synchronize degradation in vitro by forming enzymesubstrate complexes in the presence of ATPγS and then adding ATP to trigger subsequent steps. We have used image averaging of electron micrographs of frozen hydrated and negatively stained specimens to characterize interactions of ClpA and ClpAP complexes with the model substrate, bacteriophage P1 protein, RepA.

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