Genomic data mining reveals a rich repertoire of transport proteins in Streptomyces

Abstract

BackgroundStreptomycetes are soil-dwelling Gram-positive bacteria that are best known as the major producers of antibiotics used in the pharmaceutical industry. The evolution of exceptionally powerful transporter systems in streptomycetes has enabled their adaptation to the complex soil environment.ResultsOur comparative genomic analyses revealed that each of the eleven Streptomyces species examined possesses a rich repertoire of from 761-1258 transport proteins, accounting for 10.2 to 13.7 % of each respective proteome. These transporters can be divided into seven functional classes and 171 transporter families. Among them, the ATP-binding Cassette (ABC) superfamily and the Major Facilitator Superfamily (MFS) represent more than 40 % of all the transport proteins in Streptomyces. They play important roles in both nutrient uptake and substrate secretion, especially in the efflux of drugs and toxicants. The evolutionary flexibility across eleven Streptomyces species is seen in the lineage-specific distribution of transport proteins in two major protein translocation pathways: the general secretory (Sec) pathway and the twin-arginine translocation (Tat) pathway.ConclusionsOur results present a catalog of transport systems in eleven Streptomyces species. These expansive transport systems are important mediators of the complex processes including nutrient uptake, concentration balance of elements, efflux of drugs and toxins, and the timely and orderly secretion of proteins. A better understanding of transport systems will allow enhanced optimization of production processes for both pharmaceutical and industrial applications of Streptomyces, which are widely used in antibiotic production and heterologous expression of recombinant proteins.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2899-4) contains supplementary material, which is available to authorized users.

Comprehensive subcellular topologies of polypeptides in Streptomyces

“…Single copies of SecA, SecY, SecE, SecG, that form the core essential Sec translocase [ 16 ], Trigger factor (TF), signal recognition ribonucleoparticle (SRP; Ffh protein component), and the SRP receptor (FtsY protein) were identified. SecD (A0A076M8T9) and SecF (D6EPR3), that are auxiliary components of the translocase, are present both as separate proteins, and in an additional form in which they are fused in a single polypeptide SecDF (D6EKP9), that was previously reported in S. coelicolor [ 44 , 45 ]. Functionally, SecD and SecF, and the fused SecDF may function as membrane-integrated chaperones driving using the proton motive force (PMF) [ 46 ].…”

“…The fourth protein, tyrosinase MelC2, was experimentally shown to be exported in complex with its chaperone MelC1 using the TAT system [ 50 ]. Regarding the structural components of the TAT-secretion system, two functional copies of TatA and one each of TatB and TatC were identified, as seen in S. coelicolor [ 45 , 47 ] (Additional file 6 : Table S6).…”

Streptomyces as a Prominent Resource of Future Anti-MRSA Drugs

“…They also express powerful secretory systems constituting 40% of the ATP-binding cassette (ABC) transporters and MFS (Zhou et al, 2016 ). As a result, they have attracted interest from the biotechnology industry in the production of recombinant proteins.…”

The Cellular Mechanisms that Ensure an Efficient Secretion in Streptomyces

“…The S. coelicolor genome contains two sets of SecD and SecF homologs required for an efficient secretion of some proteins [ 42 ]. Genes homologous to yajC have been identified in eleven Streptomyces genomes [ 43 ] even though a homolog to this does not seem to be present in the S. lividans 66 genome [ 3 ]. The functionality of these genes has not been determined experimentally.…”