Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus (original) (raw)
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Predictive characterization of hypothetical proteins in Staphylococcus aureus NCTC 8325
Bioinformation, 2016
Staphylococcus aureus is one of the most common hospital acquired infections. It colonizes immunocompromised patients and with the number of antibiotic resistant strains increasing, medicine needs new treatment options. Understanding more about the proteins this organism uses would further this goal. Hypothetical proteins are sequences thought to encode a functional protein but for which little to no evidence of that function exists. About half of the genomic proteins in reference strain S. aureus NCTC 8325 are hypothetical. Since annotation of these proteins can lead to new therapeutic targets, a high demand to characterize hypothetical proteins is present. This work examines 35 hypothetical proteins from the chromosome of S. aureus NCTC 8325. Examination includes physiochemical characterization; sequence homology; structural homology; domain recognition; structure modeling; active site depiction; predicted protein-protein interactions; protein-chemical interactions; protein localization; protein stability; and protein solubility. The examination revealed some hypothetical proteins related to virulent domains and protein-protein interactions including superoxide dismutase, O-antigen, bacterial ferric iron reductase and siderophore synthesis. Yet other hypothetical proteins appear to be metabolic or transport proteins including ABC transporters, major facilitator superfamily, S-adenosylmethionine decarboxylase, and GTPases. Progress evaluating some hypothetical proteins, particularly the smaller ones, was incomplete due to limited homology and structural information in public repositories. These data characterizing hypothetical proteins will contribute to the scientific understanding of S. aureus by identifying potential drug targets and aiding in future drug discovery.
In silico functional annotation of a hypothetical protein from Staphylococcus aureus
Journal of Infection and Public Health, 2015
Unknown proteins or hypothetical proteins exist but have not been characterized or linked to known genes. Domains of unknown function are experimentally identified proteins with no known functional or structural domain. In this paper, the investigation and characterization of the likely functional aspects of a hypothetical protein, YP 001317347.1, from Staphylococcus aureus was performed using various computational methods and tools. Based on the analysis, the protein has a YbbR domain and is expected to bind ribosomal subunits. The analysis reported here helps in understanding the importance of YbbR domains and will aid in the development of novel antibacterial agents.
Bioinformation, 2016
Antibiotic resistance Staphylococcus aureus strains cause several life threatening infections. New drug treatment options are needed, but are slow to develop because 50% of the S. aureus genome is hypothetical. The goal of this is to aid in the annotation of the S. aureus NCTC 8325 genome by identifying hypothetical proteins related to the Major Facilitator Superfamily (MFS). The MFS is a broad protein group with members involved in drug efflux mechanisms causing resistance. To do this, sequences for three MFS proteins with x-ray crystal structures in E. coli were PSI-BLASTed against the S. aureus NCTC 8325 genome to identify homologs. Eleven identified hypothetical protein homologs underwent BLASTP against the non-redundant NCBI database to fit homologs specific to each hypothetical protein. ExPASy characterized the physiochemical features, CDD-BLAST and Pfam identified domains, and the SOSUI server defined transmembrane helices of each hypothetical protein. Based on size (300-700 amino acids), number of transmembrane helices (>7), CD06174 and MFS domains in CDD-BLAST and Pfam, respectively, and close relation to well-defined homologs, SAOUHSC_00058, SAOUHSC_00078, SAOUHSC_00952, SAOUHSC_02435, SAOUHSC_02752, and ABD31642.1 are members of the MFS. Further multiple-alignment and phylogeny analyses show SAOUHSC_00058 to be a quinolone resistance protein (NorB), SAOUHSC_00058 a siderophore biosynthesis protein (SbnD), SAOUHSC_00952 a glycolipid permease (LtaA), SAOUHSC_02435 a macrolide MFS transporter, SAOUHSC_02752 a chloramphenicol resistance (DHA1), and ABD31642.1 is a Bcr/CflA family drug resistance efflux transporter. These findings provide better annotation for the existing genome, and identify proteins related to antibiotic resistance in S. aureus NCTC 8325.
Staphylococcus aureus is a gram positive bacterium, responsible for both community-acquired and hospital-acquired infection, resulting in a mortality rate of 39%. 43.2% resistance to methicilin and emerging resistance to Fluroquinolone and Oxazolidinone, have evoked the necessity of the establishment of alternative and effective therapeutic approach to treat this bacteria. In this computational study, various database and online software are used to determine some specific targets of Staphylococcus aureus N315 other than those used by Penicillin, Quinolone and Oxazolidinone. For this purpose, among 302 essential proteins, 101 nonhomologous proteins were accrued and 64 proteins which are unique in several metabolic pathways of S. aureus were isolated by using metabolic pathway analysis tools. Furthermore, 7 essentially unique enzymes involved in exclusive metabolic pathways were revealed by this research, which can be potential drug target. Along with these important enzymes, 15 non-homologous proteins located on membrane were identified, which can play a vital role as potential therapeutic targets for the future researchers.
IN SILICO IDENTIFICATION OF ANTIGENIC PROTEINS IN Staphylococcus aureus
Journal of Sustainability Science and Management, 2022
Staphylococcus aureus, a Gram-positive bacterium is recognized as an opportunistic pathogen in humans and livestock. Whole-cell proteome expression in S. aureus has previously been elucidated, however, antigenicity of S. aureus proteins has not been well investigated. The present work was performed to identify antigenic proteins expressed in S. aureus using in silico approach. The proteome information of S. aureus was retrieved from World-2DPAGE Repository. A total of 657 protein sequences of S. aureus were then downloaded from UniprotKB in FASTA format and were used as queries in VaxiJen, CELLO2GO, DEG, BLASTp, STRING and SWISS-MODEL programmes. Results demonstrated that 63% of S. aureus proteins were predicted as antigenic proteins. Majority of them were found to associate with catalytic activity and metabolic process. The antigenic S. aureus proteins, such as 50S ribosomal protein L21 and an uncharacterized protein, were identified as cytoplasmic proteins, essential for survival of S. aureus, non-host homologous and hub proteins in the protein interaction network. Homology modelling of 50S ribosomal protein L21 and uncharacterized protein yielded good models based on related structures from the Protein Data Bank. The findings of the present study suggest the potential use of the identified antigenic proteins in vaccine strategy against S. aureus infections.
STAPHYLOCOCCUS AUREUS (N315). *(sher shah, 2012 hazara university mansehra) Abstact Staphylococcus aureus is a pathogen of increasing importance because of their rise resistance to antibiotics. The complete genome sequencing of various strain has been completed which showed the presence of various gene sequences for hypothetical proteins whose function is not yet known. The whole genome of Staphylococcus aureus N315 has been sequenced and provides an opportunity to reveal the mechanism of pathogenesis, and identification of therapeutic targets. However, to understand bacterial pathogenesis it requires proper function annotation of its proteins. The genome of Staphylococcus aureus N315 consists of 2533 proteins. Among these, 1577 are without any known function and known as 'hypothetical proteins'. We analyzed it and classified it into 92 families using bioinformatic tools like CDD-BLAST, INTERPROSCAN and PFAM by searching sequence databases for the presence of enzymatic conserved domains in the hypothetical proteins. And further two families were selected (nucleases and DNA, RNA polymerases) for further detail analysis. These enzymatic data for hypothetical proteins can be used for understanding of functional, structural, evolutionary and metabolic development of Staphylococcus aureus and its life cycle along with their role in pathogenicity and for drug targeting.
opportunistic organism that has emerged as one of the predominant pathogens in community and healthcare- associated infections with limited and less effective options for treatment in the face of a rising trend in the emergence of resistant strains. This fact has necessitated the search for alternative targets for development of new drugs. In this present study, a subtractive genomic (proteome) approach was used to identify potential drug targets in methicillin resistant Staphylococcus aureus using strain 252 (MSRA252). The complete proteome of MSRA 252 obtained from Uniprot database was subjected to CD-hit suite for clustering; NCBI BlastP suite against the human proteome to exclude homologous proteins; and sequence homology with Database of Essential Genes(DEG) to determine the indispensability of the proteins for the bacteria survival. The essential proteins were further analyzed to predict the metabolic pathways they were involved in using KEGG automatic annotation server (KAAS) and their subcellular locations using, Uniprot and PsortB suite subsequently. The sequence sorting, segregation and formatting was carried out using UFS Sequence Analysis Application after each successive step. The study identified 291 essential non homologous proteins to human out of 2640. Further analysis with KAAS revealed that 114 (33 predicted membrane-associated) of the essential non homologous proteins were involved in different metabolic pathways in the organism and 60 of these were implicated in pathways unique to the bacteria relative to human (host). The study revealed a number of putative, essential non homologous protein candidates that could be further explored for the development of alternative treatments and vaccines for methicillin resistant Staphylococcus aureus infections
Bioinformation, 2017
Antibiotic resistant Staphylococcus aureus is a major public health concern effecting millions of people annually. Medical science has documented completely untreatable S. aureus infections. These strains are appearing in the community with increasing frequency. New diagnostic and therapeutic options are needed to combat this deadly infection. Interestingly, around 50% of the proteins in S. aureus are annotated as hypothetical. Methods to select hypothetical proteins related to antibiotic resistance have been inadequate. This study uses differential gene expression to identify hypothetical proteins related to antibiotic resistant phenotype strain variations. We apply computational tools to predict physiochemical properties, cellular location, sequence-based homologs, domains, 3D modeling, active site features, and binding partners. Nine of 23 hypothetical proteins were <100 residues, unlikely to be functional proteins based on size. Of the 14 differentially expressed hypothetical proteins examined, confident predictions on function could not be made. Most identified domains had unknown functions. Six hypothetical protein models had >50% confidence over >20% residues. These findings indicate the method of hypothetical protein identification is sufficient; however, current scientific knowledge is inadequate to properly annotate these proteins. This process should be repeated regularly until entire genomes are clearly and accurately annotated.
Biopolymers & Cell, 2019
Aim. To identify novel putative drug targets of methicillin-resistant S. aureus (MRSA) through subtractive proteome analysis. Methods. Identification of non-homologous proteins in the human proteome, search of MRSA essential genes and evaluation of drug target novelty were performed using a protein BLAST server. Unique metabolic pathways identification was carried out using data and tools from KEGG (Kyoto Encyclopedia of Genes and Genomes). Prediction of sub-cellular proteins localization was performed using combination of PSORT v. 3.0.2, CELLO v. 2.5, iLoc-Gpos, and Pred-Lipo tools. Homology modeling was performed using SWISS-MODEL, Phyre2, I-TASSER web-servers and the MODELLER software. Results. Proteomes of six annotated methicillin-resistant strains : MRSA ATCC BAA-1680, H-EMRSA-15, LA MRSA ST398, MRSA 252, MRSA ST772, UTSW MRSA 55 were initially analyzed. The proteome analysis of the MRSA strains in several consequent steps allowed to identify two molecular targets: diadenylate cyclase and D-alanyl-lipoteichoic acid biosynthesis (DltB) protein which meet the requirements of being essential, membrane-bound, non-homologous to human proteome, involved in unique metabolic pathways and new in terms of not having approved drugs. Using the homology modeling approach, we have built three-dimensional structures of these proteins and predicted their ligand-binding sites. Conclusions. We used classical bioinformatics approaches to identify two molecular targets of MRSA :diadenylate cyclase and DltB which can be used for further rational drug design in order to find novel therapeutic agents for treatment of multidrug resistant staphylococcal infection. K e y w o r d s: molecular drug targets; methicillin-resistant Staphylococcus aureus; MRSA; subtractive proteome analysis.
2016
Vancomycin-resistant Staphylococcus aureus (VRSA) is a Gram-positive, facultative aerobic bacterium which is evolved from the extensive exposure of Vancomycin to Methicillin resistant S. aureus (MRSA) that had become the most common cause of hospital and community-acquired infections. Due to the emergence of different antibiotic resistance strains, there is an exigency to develop novel drug targets to address the provocation of multidrug-resistant bacteria. In this study, in-silico genome subtraction methodology was used to design potential and pathogen specific drug targets against VRSA. Our study divulged 1987 proteins from the proteome of 34,549 proteins, which have no homologues in human genome after sequential analysis through CD-HIT and BLASTp. The high stringency analysis of the remaining proteins against database of essential genes (DEG) resulted in 169 proteins which are essential for S. aureus. Metabolic pathway analysis of human host and pathogen by KAAS at the KEGG server sorted out 19 proteins involved in unique metabolic pathways. 26 human non-homologous membrane-bound essential proteins including 4 which were also involved in unique metabolic pathway were deduced through PSORTb, CELLO v.2.5, ngLOC. Functional classification of uncharacterized proteins through SVMprot derived 7 human non-homologous membrane-bound hypothetical essential proteins. Study of potential drug target against Drug Bank revealed pbpA-penicillin-binding protein 1 and hypothetical protein MQW_01796 as the best drug target candidate. 2D structure was predicted by PRED-TMBB, 3D structure and functional analysis was also performed. Protein–protein interaction network of potential drug target proteins was analyzed by using STRING. The identified drug targets are expected to have great potential for designing novel drugs against VRSA infections and further screening of the compounds against these new targets may result in the discovery of novel therapeutic compounds that can be effective against Vancomycin resistant S. aureus.