title: The identification of oppA gene homologues as part of the oligopeptide transport system in mycoplasmas.
abstract: The lack of an annotated oppA gene as part of many oligopeptide permease (opp) operons has questioned the necessity of the oligopeptide-binding domain (OppA) as a part of the Opp transport system in mycoplasmas. This study investigated the occurrence of an oppA gene as part of the oppBCDF operon in 42 mycoplasma genomes. Except for hemoplasma, all mycoplasmas were found to possess one or more copies of the oppBCDF operon and with the help of similarity searches their oppA genes could be identified. Phylogenetic analysis of the combined OppABCDF amino acid sequences allowed them to be grouped into three types. Each type has a unique set of conserved motifs, which are likely to reflect substrate preference and adaption strategies. Our approach allowed the identification of oppA gene homologues for all mycoplasma opp operons and thereby provides a method for re-evaluating the current annotation of oppA genes in mycoplasma genomes.
authors.affiliation: Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
authors.forename: Martha
authors.initials: M
authors.lastname: Wium
authors.affiliation: Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Electronic address: annelise@sun.ac.za.
authors.forename: Annelise
authors.initials: A
authors.lastname: Botes
authors.affiliation: Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
authors.forename: Dirk U
authors.initials: DU
authors.lastname: Bellstedt
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D001715:Bird Diseases / Q000382:microbiology; D002352:Carrier Proteins / Q000235:genetics* / Q000378:metabolism*; D004269:DNA, Bacterial / Q000235:genetics; D008074:Lipoproteins / Q000235:genetics* / Q000378:metabolism*; D009174:Mycoplasma / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D009175:Mycoplasma Infections / Q000382:microbiology; D009876:Operon; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D020310:Struthioniformes
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D004269:DNA, Bacterial; D008074:Lipoproteins; D012336:RNA, Ribosomal, 16S; C046506:oligopeptide-binding protein, bacteria
keywords: ABC transporters; Mycoplasma; Oligopeptide permease transport; OppA; opp operon