Prediction driven functional annotation of hypothetical proteins in the major facilitator superfamily of S. aureus NCTC 8325

Abstract

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.

Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

“…CpxR plays essential roles in mediating macrolide (i.e., erythromycin) resistance (Cao et al, 2018). The Bcr/CflA efflux system was identified as a group of antiporters that confer resistance to chloramphenicol, florfenicol, and bicyclomycin by actively transporting these compounds out of the cell (Marklevitz & Harris, 2016). The transposon Tn6678 had two complete inverted repeats of IS110 transposases flanked by 32-bp inverted repeats of ISNme5 at both ends suggesting mobility potential and its potential to transfer antibiotic resistance genes.…”

De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits

“…(E-value≥1e-65; id up to 50%), with no homologs in Botrytis and Sclerotinia spp., was reconstructed only in MFRC. The predicted protein contains domains conserved for MFSs and bacterial Bcr/CflA transporters, which are responsible for drug and antibiotic resistance [ 24 ]. Additional MFSs were over-expressed (T9642, T9594 and T9657) or exclusive (T10106 and T10002).…”

In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato

“…In the last few years, several studies have been done on in silico characterization of an unknown hypothetical proteins/essential genes from pathogenic microbes, that might have a possible role in regulation of metabolic process, or play an indispensable role in microbial pathogenicity ( Ravooru et al, 2014 ; Silva et al, 2015 ; Marklevitz and Harris, 2016 ; Kumar et al, 2017 ; Prava et al, 2018 ). Recently, a hypothetical protein (FcRav2) with ROGDI such as leucine zipper domain, and homologous to yeast Rav2 was reported in F. culmorum .…”