scholarly journals In silico analysis of virulence associated genes in genomes of Escherichia coli strains causing colibacillosis in poultry

2017 ◽  
Vol 61 (4) ◽  
pp. 421-426 ◽  
Author(s):  
Joanna Kołsut ◽  
Paulina Borówka ◽  
Błażej Marciniak ◽  
Ewelina Wójcik ◽  
Arkadiusz Wojtasik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Virulence Factors ◽  
De Novo ◽  
Protein Sequences ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Common Disease ◽  
Bacterial Genomes ◽  
E Coli

AbstractIntroduction: Colibacillosis – the most common disease of poultry, is caused mainly by avian pathogenic Escherichia coli (APEC). However, thus far, no pattern to the molecular basis of the pathogenicity of these bacteria has been established beyond dispute. In this study, genomes of APEC were investigated to ascribe importance and explore the distribution of 16 genes recognised as their virulence factors.Material and Methods: A total of 14 pathogenic for poultry E. coli strains were isolated, and their DNA was sequenced, assembled de novo, and annotated. Amino acid sequences from these bacteria and an additional 16 freely available APEC amino acid sequences were analysed with the DIFFIND tool to define their virulence factors.Results: The DIFFIND tool enabled quick, reliable, and convenient assessment of the differences between compared amino acid sequences from bacterial genomes. The presence of 16 protein sequences indicated as pathogenicity factors in poultry resulted in the generation of a heatmap which categorises genomes in terms of the existence and similarity of the analysed protein sequences.Conclusion: The proposed method of detection of virulence factors using the capabilities of the DIFFIND tool may be useful in the analysis of similarities of E. coli and other sequences deriving from bacteria. Phylogenetic analysis resulted in reliable segregation of 30 APEC strains into five main clusters containing various virulence associated genes (VAGs).

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

scholarly journals Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 8 ◽  
Author(s):  
Michael S. Wang ◽  
Kenric J. Hoegler ◽  
Michael H. Hecht
Keyword(s):  
Amino Acid ◽  
Transition Metals ◽  
Metal Binding ◽  
Combinatorial Library ◽  
De Novo ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Ancestral Sequences ◽  
Wide Range ◽  
Catalytic Functions

Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads one to ask whether metal binding is an evolved trait that occurred only rarely in ancestral sequences, or alternatively, whether it is an innate property of amino acid sequences, occurring frequently in unevolved sequence space. To address this question, we studied 52 proteins from a combinatorial library of novel sequences designed to fold into 4-helix bundles. Although these sequences were neither designed nor evolved to bind metals, the majority of them have innate tendencies to bind the transition metals copper, cobalt, and zinc with high nanomolar to low-micromolar affinity.

Subunit II (b') and Not Subunit I (b) of Photosynthetic ATP Synthases is Equivalent to Subunit b of the ATP Synthases from Nonphotosynthetic Eubacteria. Evidence for a New Assignment of b-Type F0 Subunits

1997 ◽  
Vol 52 (11-12) ◽  
pp. 789-798 ◽  
Author(s):  
Hans-Jürgen Tiburzy ◽  
Richard J. Berzborn
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Structural Feature ◽  
Atp Synthase ◽  
Primary Structure ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
E Coli ◽  
Subunit B ◽  
Atp Synthases

Abstract Subunit I of chloroplast ATP synthase is reviewed until now to be equivalent to subunit b of Escherichia coli ATP synthase, whereas subunit II is suggested to be an additional subunit in photosynthetic ATP synthases lacking a counterpart in E. coli. After publication of some sequences of subunits II a revision of this assignment is necessary. Based on the analysis of 51 amino acid sequences of b-type subunits concerning similarities in primary structure, iso­electric point and a discovered discontinuous structural feature, our data provide evidence that chloroplast subunit II (subunit b' of photosynthetic eubacteria) and not chloroplast subunit I (subunit b of photosynthetic eubacteria) is the equivalent of subunit b of nonphoto­ synthetic eubacteria, and therefore does have a counterpart in e.g. E. coli. In consequence, structural features essential for function should be looked for on subunit II (b').

scholarly journals Characterization of human and mouse granulocyte-macrophage-colony-stimulating factors derived from Escherichia coli

1987 ◽  
Vol 247 (1) ◽  
pp. 195-199 ◽  
Author(s):  
J L Schrimsher ◽  
K Rose ◽  
M G Simona ◽  
P Wingfield
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Natural Material ◽  
Animal Cells ◽  
Colony Stimulating Factors ◽  
E Coli ◽  
Macrophage Colony ◽  
The One ◽  
Human And Mouse

Human and mouse granulocyte-macrophage-colony-stimulating factors (hGM-CSF and mGM-CSF, respectively), isolated from Escherichia coli cells expressing the corresponding human and mouse genes, have been characterized. The observed properties of the proteins have been compared with those properties which can be deduced from the DNA sequence alone and the published properties of natural GM-CSFs. The purified E. coli-derived proteins were found to have the expected molecular masses, amino acid compositions and N- and C-terminal amino acid sequences. The finding of 70-90% unprocessed N-terminal methionine for both proteins is discussed. The four Cys residues were found to be involved in two intramolecular disulphide bonds, linking the first and third, and second and fourth Cys residues. This disulphide bond arrangement is probably the one existing in natural material, since, although not glycosylated, both E. coli-derived proteins showed biological activity (colony stimulating assay for hGM-CSF, and cell proliferation assay for mGM-CSF) comparable with that reported for the respective proteins purified from animal cells.

Expression and Regulation of the Arsenic Resistance Operon of Acidiphilium multivorum AIU 301 Plasmid pKW301 in Escherichia coli

1998 ◽  
Vol 64 (2) ◽  
pp. 411-418 ◽  
Author(s):  
Katsuhisa Suzuki ◽  
Norio Wakao ◽  
Tetsuya Kimura ◽  
Kazuo Sakka ◽  
Kunio Ohmiya
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Constitutive Expression ◽  
Amino Acid Sequences ◽  
Gene Products ◽  
Arsenic Resistance ◽  
E Coli ◽  
Molecular Weights ◽  
Rna Polymerase Promoter ◽  
Extension Analysis

ABSTRACT The arsenic resistance (ars) operon from plasmid pKW301 of Acidiphilium multivorum AIU 301 was cloned and sequenced. This DNA sequence contains five genes in the following order: arsR, arsD, arsA,arsB, arsC. The predicted amino acid sequences of all of the gene products are homologous to the amino acid sequences of the ars gene products of Escherichia coliplasmid R773 and IncN plasmid R46. The ars operon cloned from A. multivorum conferred resistance to arsenate and arsenite on E. coli. Expression of the arsgenes with the bacteriophage T7 RNA polymerase-promoter system allowedE. coli to overexpress ArsD, ArsA, and ArsC but not ArsR or ArsB. The apparent molecular weights of ArsD, ArsA, and ArsC were 13,000, 64,000, and 16,000, respectively. A primer extension analysis showed that the ars mRNA started at a position 19 nucleotides upstream from the arsR ATG in E. coli. Although the arsR gene of A. multivorum AIU 301 encodes a polypeptide of 84 amino acids that is smaller and less homologous than any of the other ArsR proteins, inactivation of the arsR gene resulted in constitutive expression of the ars genes, suggesting that ArsR of pKW301 controls the expression of this operon.

Ribosomal RNA: the message or matrix for ribosomal proteins

1976 ◽  
Vol 54 (2) ◽  
pp. 192-193
Author(s):  
D. R. Miller ◽  
A. T. Matheson ◽  
L. P. Visentin
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
16S Ribosomal Rna ◽  
Degree Of Similarity

The known nucleotide sequence of Escherichia coli 16S ribosomal RNA has been converted to amino acid sequences in all possible ways, and compared to known ribosomal protein sequences. The degree of similarity is precisely what one would expect by chance alone, providing additional evidence that ribosomal proteins cannot be coded for by ribosomal RNA.

scholarly journals Characterization of a 12-Kilodalton Rhodanese Encoded byglpE of Escherichia coli and Its Interaction with Thioredoxin

2000 ◽  
Vol 182 (8) ◽  
pp. 2277-2284 ◽  
Author(s):  
W. Keith Ray ◽  
Gang Zeng ◽  
M. Benjamin Potters ◽  
Aqil M. Mansuri ◽  
Timothy J. Larson
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Active Site ◽  
Amino Acid Sequences ◽  
E Coli ◽  
Active Site Cysteine ◽  
Clusters Of Orthologous Groups ◽  
Thioredoxin 1 ◽  
First Time

ABSTRACT Rhodaneses catalyze the transfer of the sulfane sulfur from thiosulfate or thiosulfonates to thiophilic acceptors such as cyanide and dithiols. In this work, we define for the first time the gene, and hence the amino acid sequence, of a 12-kDa rhodanese fromEscherichia coli. Well-characterized rhodaneses are comprised of two structurally similar ca. 15-kDa domains. Hence, it is thought that duplication of an ancestral rhodanese gene gave rise to the genes that encode the two-domain rhodaneses. The glpEgene, a member of the sn-glycerol 3-phosphate (glp) regulon of E. coli, encodes the 12-kDa rhodanese. As for other characterized rhodaneses, kinetic analysis revealed that catalysis by purified GlpE occurs by way of an enzyme-sulfur intermediate utilizing a double-displacement mechanism requiring an active-site cysteine. TheKm s for SSO3 2− and CN− were 78 and 17 mM, respectively. The apparent molecular mass of GlpE under nondenaturing conditions was 22.5 kDa, indicating that GlpE functions as a dimer. GlpE exhibited ak cat of 230 s−1. Thioredoxin 1 from E. coli, a small multifunctional dithiol protein, served as a sulfur acceptor substrate for GlpE with an apparentKm of 34 μM when thiosulfate was near itsKm , suggesting that thioredoxin 1 or related dithiol proteins could be physiological substrates for sulfurtransferases. The overall degree of amino acid sequence identity between GlpE and the active-site domain of mammalian rhodaneses is limited (∼17%). This work is significant because it begins to reveal the variation in amino acid sequences present in the sulfurtransferases. GlpE is the first among the 41 proteins in COG0607 (rhodanese-related sulfurtransferases) of the database Clusters of Orthologous Groups of proteins (http://www.ncbi.nlm.nih.gov/COG/ ) for which sulfurtransferase activity has been confirmed.

scholarly journals The Remarkable Dual-Level Diversity of Prokaryotic Flagellins

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Dalong Hu ◽  
Peter R. Reeves
Keyword(s):  
Escherichia Coli ◽  
Hypervariable Region ◽  
Protein Sequences ◽  
Variable Region ◽  
Amino Acid Sequences ◽  
Variable Regions ◽  
Content Type ◽  
E Coli ◽  
Unique Amino Acid ◽  
Level Analysis

ABSTRACT Flagellin, the agent of prokaryotic flagellar motion, is very widely distributed and is the H antigen of serology. Flagellin molecules have a variable region that confers serotype specificity, encoded by the middle of the gene, and also conserved regions encoded by the two ends of the gene. We collected all available prokaryotic flagellin protein sequences and found the variable region diversity to be at two levels. In each species investigated, there are hypervariable region (HVR) forms without detectable homology in protein sequences between them. There is also considerable variation within HVR forms, indicating that some have been diverging for thousands of years and that interphylum horizontal gene transfers make a major contribution to the evolution of such atypical diversity. IMPORTANCE Bacterial and archaeal flagellins are remarkable in having a shared region with variation in housekeeping proteins and a region with extreme diversity, perhaps greater than for any other protein. Analysis of the 113,285 available full-gene sequences of flagellin genes from published bacterial and archaeal sequences revealed the nature and enormous extent of flagellin diversity. There were 35,898 unique amino acid sequences that were resolved into 187 clusters. Analysis of the Escherichia coli and Salmonella enterica flagellins revealed that the variation occurs at two levels. The first is the division of the variable regions into sequence forms that are so divergent that there is no meaningful alignment even within species, and these corresponded to the E. coli or S. enterica H-antigen groups. The second level is variation within these groups, which is extensive in both species. Shared sequence would allow PCR of the variable regions and thus strain-level analysis of microbiome DNA.

Immunogenic peptide mimotopes from an epitope of Escherichia coli O157 LPS

2016 ◽  
Vol 473 (21) ◽  
pp. 3791-3804 ◽  
Author(s):  
Armando Navarro ◽  
Ulises Hernández-Chiñas ◽  
Delia Licona-Moreno ◽  
Edgar Zenteno ◽  
Alejandro Cravioto ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Escherichia Coli O157 ◽  
Serum Samples ◽  
Haemolytic Uremic Syndrome ◽  
E Coli ◽  
Positive Reactivity ◽  
Peptide Mimotopes ◽  
Uremic Syndrome

Escherichia coli O157:H7 is a subtype of Shiga toxin-producing E. coli that is associated with haemorrhagic colitis and haemolytic uremic syndrome (HUS). Studies of populations in endemic areas have reported that the presence of specific antibodies against the O157 lipopolysaccharide (LPS) is associated with a lower incidence of diarrhoea and HUS. Phage display and IgG anti-O157 LPS antibodies were used in the present study to select peptide mimotopes of O157 LPS expressed in protein III of the M13 phage. Synthetic peptides (SP) were designed using the derived amino acid sequences obtained from DNA nucleotides of 63 selected phagotopes. The LxP/YP/SxL motif was identified in five of the phagotope amino acid sequences. Antibody responses against the phagotopes and their corresponding SPs were evaluated. SP12, one of the designed SP, induced the production of antibodies against the homologous peptide (1:800) and O157 LPS (1:200). The specificity of anti-SP12 antiserum was confirmed by analyzing its response to SP3, an SP with a different amino acid sequence than that of SP12, as well as against an E. coli LPS different from O157. Competitive studies with SP12 and O157 LPS showed a significant decrease in anti-SP12 and anti-LPS O157 antiserum responses against SP12 and O157 LPS, respectively. Eighteen (82%) of the 22 human serum samples with positive reactivity against E. coli O157 LPS reacted with SP12 SP (cut-off >0.4). These results support the idea that SP12 is an immunogenic mimotope of O157 LPS.

Cloning and Sequencing of the Histidine Decarboxylase Gene from Photobacterium phosphoreum and its Functional Expression in Escherichia coli

2006 ◽  
Vol 69 (8) ◽  
pp. 1768-1776 ◽  
Author(s):  
HIDEAKI MORII ◽  
KENTARO KASAMA ◽  
RAUL HERRERA-ESPINOZA
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Histidine Decarboxylase ◽  
Halophilic Bacteria ◽  
Trna Synthetase ◽  
Amino Acid Sequences ◽  
Photobacterium Phosphoreum ◽  
Bootstrap Support ◽  
Amino Acid Permease ◽  
E Coli

The major causative agent of scombroid poisoning is histamine formed by bacterial decarboxylation of histidine. We reported previously that histamine was exclusively formed by the psychrotrophic halophilic bacteria Photobacterium phosphoreum in scombroid fish during storage at or below 10°C. Moreover, histamine-forming ability was affected by two histidine decarboxylases (HDCs): constitutive and inducible enzymes. In this study, the gene encoding P. phosphoreum HDC was cloned into Escherichia coli and sequenced. A sequence analysis of the DNA corresponding to the hdc gene revealed an open reading frame of 1,140 bp coding for a pyridoxal-5′-phosphate-dependent HDC of 380 amino acid residues with a predicted molecular mass of 42.6 kDa. The HDC amino acid sequences formed a phylogenetic clade with strong bootstrap support and revealed high sequence similarities among the P. phosphoreum isolate and species of the family Enterobacteriaceae and a separate phylogenetic branch with the lowest sequence similarity between the isolate and the taxonomically closer Listonella anguillarum. The T7 promoter was used to overexpress the hdc gene in E. coli cells. The recombinant clone, E. coli BL21(DE3), displayed significant levels of HDC activity. The recombinant hdc gene was suggested to code the inducible HDC; therefore, the optimum reaction conditions of the recombinant HDC were similar to those of the inducible HDC in the P. phosphoreum isolate. In addition, a putative catabolite-repressor protein binding site, amino acid permease gene, and histidine-tRNA synthetase gene were found in flanking regions of the hdc gene.

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