In Silico and Transcriptional Analysis of Carbohydrate Uptake Systems of Streptomyces coelicolor A3(2)

Abstract

Streptomyces coelicolor is the prototype for the investigation of antibiotic-producing and differentiating actinomycetes. As soil bacteria, streptomycetes can metabolize a wide variety of carbon sources and are hence vested with various specific permeases. Their activity and regulation substantially determine the nutritional state of the cell and, therefore, influence morphogenesis and antibiotic production. We have surveyed the genome of S. coelicolor A3(2) to provide a thorough description of the carbohydrate uptake systems. Among 81 ATP-binding cassette (ABC) permeases that are present in the genome, we found 45 to encode a putative solute binding protein, an essential feature for carbohydrate permease function. Similarity analysis allowed the prediction of putative ABC systems for transport of cellobiose and cellotriose, ␣-glucosides, lactose, maltose, maltodextrins, ribose, sugar alcohols, xylose, and ␤-xylosides. A novel putative bifunctional protein composed of a substrate binding and a membrane-spanning moiety is likely to account for ribose or ribonucleoside uptake. Glucose may be incorporated by a proton-driven symporter of the major facilitator superfamily while a putative sodium-dependent permease of the solute-sodium symporter family may mediate uptake of galactose and a facilitator protein of the major intrinsic protein family may internalize glycerol. Of the predicted gene clusters, reverse transcriptase PCRs showed active gene expression in 8 of 11 systems. Together with the previously surveyed permeases of the phosphotransferase system that accounts for the uptake of fructose and N-acetylglucosamine, the genome of S. coelicolor encodes at least 53 potential carbohydrate uptake systems.Streptomycetes represent a major fraction of the bacterial soil population (20). They contribute substantially to carbon recycling by degrading a whole variety of biopolymers that stem from dead plant and animal material (16). These organic compounds, which include xylan, chitin, and cellulose, are broken down by exoenzymes. The products are funneled into the cell by specific carbohydrate importers that usually recognize mono-and disaccharides. The recent publication of the genome of the model organism Streptomyces coelicolor A3(2) revealed two interesting features concerning carbon utilization (7), that is, (i) a huge number of 172 genes encoding secreted proteins, such as hydrolases, chitinases, cellulases, lipases, nucleases, and proteases, and (ii) the occurrence of 81 ATPbinding cassette (ABC) permeases that are possibly used for the uptake of sugars, oligopeptides, and nucleosides as well as for drug export (46, 56). The numerousness of exoenzymes and ABC systems is 5-to 10-fold higher than that of other bacteria, underlining the broad metabolic capacity of streptomycetes (7).Canonical carbohydrate-specific ABC systems in gram-positive bacteria are oligoprotein assemblies: a membrane-anchored substrate-binding protein is exposed to the outside of the cell, scavenging for a specific substrate molecule (10) (Fi...

How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria

“…Glucose kinase (443,911) and the accumulation of glycolytic intermediates (694) are implicated in mediating the effect. Although S. coelicolor contains EI, HPr, EIIA Glc (designated EIIA crr ), and EIIBC Glc homologs as well as other sugar-specific EII complexes, PTS proteins do not seem to be involved in CRR in this high-GϩC gram-positive organism (58,629). In contrast to E. coli, the crr gene of S. coelicolor precedes ptsI, and ptsH is located somewhere else on the chromosome.…”

A Genomic View of Sugar Transport inMycobacterium smegmatisandMycobacterium tuberculosis

“…The sequence of the almost finished genome of M. smegmatis mc 2 155 was searched for homologs of well-characterized bacterial sugar transport systems to identify possible carbohydrate uptake systems. Table 1 shows a list of 28 putative carbohydrate permeases: 19 of the ABC family, 3 of the PTS family, 1 of the major intrinsic protein family (MIP), 4 of the major facilitator superfamily (MFS), and one of the sodium solute superfamily (SSS) (6,(47)(48)(49)56).…”

Comparative Genomic Analyses of the Bacterial Phosphotransferase System

“…The biochemical detection of novel PTS proteins in bacteria as diverse as Ancalomicrobium adetum (85), Spirochaeta aurantia (83), Acholeplasma laidlawii (28), Listeria monocytogenes (50), and several antibiotic-producing species of Streptomyces (6,104) suggests the involvement of PTS proteins in cellular processes distinct from those currently recognized. It is worth noting that other families of transport systems, such as the family of ATP-binding cassette (ABC)-type permeases (27) and the major facilitator superfamily (55), apparently do not participate in metabolic and transcriptional regulation to the extent observed for the PTS.…”