Outer Membrane Protein Sequences Research Articles

Computer aided novel antigenic epitopes selection from the outer membrane protein sequences of Aeromonas hydrophila and its analyses

Gram-negative bacteria are among the causative microorganisms for zoonotic diseases in humans and teleosts. Outer membrane proteins (Omps) of Aeromonas hydrophila, a gram-negative bacterium, are critical for the subcellular integration to eukaryotic cell that can modulate the functions of macrophages. Hence Omps are recognized as immune markers for the vaccine development. In the present study, a 3-D model of Omps was identified using in silico technique and recognized through the Swiss model web-server and confirmed with Procheck and ProSA server.. The B-cell binding sites of the protein were selected from sequence alignment.. Further, the identification of B-cell epitope was carried out using modules of BCpred server (i.e., BCPred and Amino Acid Pairs). The identified antigenic amino acid sequences for B-cells were used to determine the T-cell epitope (both MHC I & II allelic binding sequences) using ProPred 1 and ProPred servers. The epitopic regions (9 mer: LAGKTTNES and GFDGSQYGK) in the Omps that are bound together with the MHC molecules (MHC-I & II), and have maximum possible numbers of MHC alleles are recognized. It was observed that Omps of A. hydrophila are conserved across the serotypes and are immunogenic. These epitopes can stimulate significant immune responses and can be advantageous while preparing peptide-based vaccines against A. hydrophila infections. Thus, suggesting the use of Omps in the development of vaccines and immunotherapeutics against the bacterial diseases in humans and teleosts.

Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.

Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired bla KPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258.

Proteomic and genomic analysis reveals novel Campylobacter jejuni outer membrane proteins and potential heterogeneity

Gram-negative bacterial outer membrane proteins play important roles in the interaction of bacteria with their environment including nutrient acquisition, adhesion and invasion, and antibiotic resistance. In this study we identified 47 proteins within the Sarkosyl-insoluble fraction of Campylobacter jejuni 81-176, using LC-ESI-MS/MS. Comparative analysis of outer membrane protein sequences was visualised to reveal protein distribution within a panel of Campylobacter spp., identifying several C. jejuni-specific proteins. Smith-Waterman analyses of C. jejuni homologues revealed high sequence conservation amongst a number of hypothetical proteins, sequence heterogeneity of other proteins and several proteins which are absent in a proportion of strains.

BiotecVisions 2013, February

BiotecVisions 2013, February

Toward an improved discrimination of outer membrane proteins using a sequence-based approach

This article offers a novel sequence-based approach to discriminate outer membrane proteins (OMPs). The first step is to use a new representation approach, factor analysis scales of generalized amino acid information (FASGAI) representing hydrophobicity, alpha and turn propensities, bulky properties, compositional characteristics, local flexibility and electronic properties, etc., to characterize sequences of OMPs and non-OMPs. The subsequent data is then transformed into a uniform matrix by the auto cross covariance (ACC). The second step is to develop discrimination predictors of OMPs from non-OMPs using a support vector machine (SVM). The SVM predictors thus successfully produce a high Matthews correlation coefficient (MCC) of 0.916 on 208 OMPs from non-OMPs including 206 α-helical membrane proteins and 673 globular proteins by a fivefold cross validation test. Meanwhile, overall MCC values of 0.923 and 0.930 are obtained for the discrimination OMPs from the α-helical membrane proteins and the globular proteins, respectively. The results demonstrate that the FASGAI-ACC-SVM combination approach shows great prospect of application in the field of bioinformatics or proteomics studies.

Enhancement of protective immunity in European eel (<italic>Anguilla anguilla</italic>) against <italic>Aeromonas hydrophila</italic> and <italic>Aeromonas sobria</italic> by a recombinant <italic>Aeromonas</italic> outer membrane protein

To develop a vaccine, which can simultaneously prevent the diseases caused by various pathogenic bacteria in fish, we try to find a conserved outer membrane protein (OMP) antigen from different bacterial pathogens. In this study, an OMP fragment of 747 bp (named as Omp-G), which was highly conserved in seven Aeromonas OMP sequences from the NCBI database, was amplified by PCR from one Aeromonas sobria strain (B10) and two Aeromonas hydrophila strains (B27 and B33) with the designed specific primers. The sequence was cloned into pGEX-2T (6 × His-tag) vector, expressed in Escherichia coli system, and then the recombinant protein (named as rOmp-G) was purified with nickel chelating affinity chromatography. The purified rOmp-G showed a good immunogenicity in rabbits and well-conserved characteristics in these three pathogens by enzyme-linked immunosorbed assay. Furthermore, the rOmp-G also showed good immunogenicity in eels (Anguilla anguilla) for eliciting significantly increased specific antibodies (P < 0.01), and providing higher protection efficiencies (P < 0.05) after the pathogens challenge. The values of the relative percent survival in eels were 70% and 50% for two A. hydrophila strain challenge, and 75% for A. sobria strain challenge. This is the first report of a potential vaccination in eels that simultaneously provide protectiveness against different Aeromonas pathogens with a conserved partial OMP.

Marine MammalBrucellaGenotype Associated with Zoonotic Infection

Marine Mammal<i>Brucella</i>Genotype Associated with Zoonotic Infection

Molecular Characterization of ompA Gene of Pasteurella multocida Serotype B: 2

Singh, S., Singh, V.P., Kumar, A.A., Joseph, S., Cheema, P.S., Srivastava, S.K. and Singh, N. 2007. Molecular characterization of ompA gene of Pasteurella multocida serotype B: 2. J. Appl. Anim. Res., 31: 97–100. The ompA gene of Pasteurella multocida serotype B: 2 (strain P52) was cloned in InsT/A vector for sequencing and gene sequence was compared with that of other strains (232, 95010872, T94289 and 95120769) of serogroup A. It revealed a 1077 nucleotide and it had additional 30 bp than that of serotype A: 3. About 11.5 to 14% divergence in ompA gene sequence was observed between serotype B: 2 and various strains of serogroup A of P. multocida. A variation of about 20% in the amino acid sequence of outer membrane protein A (OmpA) was also recorded between serogroups A and B.

Motifs in outer membrane protein sequences: Applications for discrimination

Discriminating outer membrane proteins (OMPs) from other folding types of globular and membrane proteins is an important problem for predicting their secondary and tertiary structures and detecting outer membrane proteins from genomic sequences as well. In this work, we have systematically analyzed the distribution of amino acid residues in the sequences of globular and outer membrane proteins with several motifs, such as A*B, A**B, etc. We observed that the motifs E*L, A*K and L*E occur frequently in globular proteins while S*S, N*S and R*D predominantly occur in OMPs. We have devised a statistical method based on frequently occurring motifs in globular and OMPs and obtained an accuracy of 96% and 82% for correctly identifying OMPs and excluding globular proteins, respectively. Further, we noticed that the motifs of transmembrane helical (TMH) proteins are different from that of OMPs. While I*A, I*L and L*I prefer in TMH proteins S*S, N*S and N*N predominantly occur in OMPs. The information about the occurrence of A*B motifs in TMH and OMPs could discriminate them with an accuracy of 80% for excluding OMPs and 100% for identifying OMPs. The influence of protein size and structural class for discrimination is discussed.

Sensing Stress between the Membranes

The periplasm (the space between the inner and outer membranes of bacteria) is the site of activation of the periplasmic stress response. Like the cytosolic stress response and the eukaryotic endoplasmic and cytosolic stress responses, unfolded proteins trigger a transcriptional activation profile that allows cells to produce more chaperones and protein-folding agents (see Young and Hartl). Although, the periplasmic stress response is fairly well characterized, the sensor that initiates the process has remained elusive. The response consists of activation of the protease DegS, which cleaves transmembrane protein RseA, which then releases the transcription factor σ E to allow the activation of stress response genes. Walsh et al. show that DegS is inhibited by its PDZ domain and that binding of the PDZ domain toYQF motifs of outer membrane protein porins activates the protease. Bacteria expressing DegS lacking the PDZ domain showed increased σ E activity. Using an oriented peptide library, a preferred binding sequence for the PDZ domain was identified (YXF/M-COOH), and examination of the sequences of outer membrane proteins showed that several proteins terminated in these sequences. Expression of an OmpC (an outer membrane porin) COOH-terminal fragment containing the YQF motif, stimulated σ E activity, but only in cells expressing the wild-type DegS, not in cells expressing the PDZ-lacking DegS mutant. In vitro RseA was cleaved by DegS in the presence of YXF-COOH peptides. Thus, stress such as heat would promote unfolding of the porins exposing the YXF-COOH sequences that would interact with the PDZ domain of DegS and alleviate repression of the protease activity. Thus, DegS is both the sensor and the first executor of the periplasmic stress response. J. C. Young, F. U. Hartl, A stress sensor for the bacterial periplasm. Cell 113 , 1-4 (2003) [Online Journal] N. P. Walsh, B. M. Alba, B. Bose, C. A. Gross, R. T. Sauer, OMP peptide signals initiate the envelope-stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain. Cell 113 , 61-71 (2003). [Online Journal]

Nucleotide and derived amino acid sequences of the major porin of Comamonas acidovorans and comparison of porin primary structures

The DNA sequence of the gene which codes for the major outer membrane porin (Omp32) of Comamonas acidovorans has been determined. The structural gene encodes a precursor consisting of 351 amino acid residues with a signal peptide of 19 amino acid residues. Comparisons with amino acid sequences of outer membrane proteins and porins from several other members of the class Proteobacteria and of the Chlamydia trachomatis porin and the Neurospora crassa mitochondrial porin revealed a motif of eight regions of local homology. The results of this analysis are discussed with regard to common structural features of porins.

Evolutionary relationship between the TonB-dependent outer membrane transport proteins: nucleotide and amino acid sequences of the Escherichia coli colicin I receptor gene

The nucleotide sequence of the Escherichia coli colicin I receptor gene (cir) has been determined. The predicted mature protein consists of 599 amino acids and has a molecular weight of 67,169. Several previously noted characteristics of other E. coli outer membrane protein sequences were also identified in the sequence of Cir. These include an overall acidic nature, the absence of long hydrophobic stretches of amino acids, and a lack of predicted alpha-helical secondary structure. Because two classes of outer membrane proteins (the TonB-dependent transport proteins and the porins) share some structural features, protein sequences from both of these groups were aligned pairwise and scored for sequence similarity. Statistical evidence suggested that the porins were not related to the proteins in the TonB-dependent group; however, there was a significant relationship between the proteins in the TonB-dependent group. On the basis of the multiple progressive sequence alignment and the similarity scores derived from it, a tree representing evolutionary distance between five TonB-dependent outer membrane transport proteins was generated.

Primary structure of major outer membrane protein II (ompA protein) of Escherichia coli K-12.

The amino acid sequence of major outer membrane protein II (ompA protein) from Escherichia coli K-12 has been determined. The transmembrane polypeptide consists of 325 residues, resulting in a molecular weight of 35,159. The transmembrane part of the protein is located between residues 1 and 177. In this part of the protein a predominantly lipophilic 27-residue segment exists that perhaps spans the membrane in a mostly alpha-helical conformation, or a 19-residue stretch of this segment might traverse the membrane linearly. Inside the outer membrane a sequence -Ala-Pro-Ala-Pro-Ala-Pro-Ala-Pro- exists that, analogous to the -Cys-Pro-Pro-Cys-Pro- sequence in the hinge region of immunoglobulin, could assume the conformation of a polyproline helix. Computer analysis did not reveal a clear overall pattern of internal homology in the protein; besides the -Ala-Pro- repeat, only one local area (two adjacent dodecapeptide segments) shows some repetitiveness. The same analysis did not produce evidence for internal homology in the previously determined sequence of outer membrane protein I (porin) nor was any marked resemblance detected between transmembrane proteins I and II.