Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor

Abstract

BackgroundTwo of the largest fully sequenced prokaryotic genomes are those of the actinobacterium, Streptomyces coelicolor (Sco), and the δ-proteobacterium, Myxococcus xanthus (Mxa), both differentiating, sporulating, antibiotic producing, soil microbes. Although the genomes of Sco and Mxa are the same size (~9 Mbp), Sco has 10% more genes that are on average 10% smaller than those in Mxa.ResultsSurprisingly, Sco has 93% more identifiable transport proteins than Mxa. This is because Sco has amplified several specific types of its transport protein genes, while Mxa has done so to a much lesser extent. Amplification is substrate- and family-specific. For example, Sco but not Mxa has amplified its voltage-gated ion channels but not its aquaporins and mechano-sensitive channels. Sco but not Mxa has also amplified drug efflux pumps of the DHA2 Family of the Major Facilitator Superfamily (MFS) (49 versus 6), amino acid transporters of the APC Family (17 versus 2), ABC-type sugar transport proteins (85 versus 6), and organic anion transporters of several families. Sco has not amplified most other types of transporters. Mxa has selectively amplified one family of macrolid exporters relative to Sco (16 versus 1), consistent with the observation that Mxa makes more macrolids than does Sco.ConclusionsExcept for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently. A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives. The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene amplification.

Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production

“…This culminated in adding 43 new transport reactions and updating 39 of the 262 existing reactions in Sco-GEM ( Figure 1F, Table S4). The majority of the transporters comprises primary active transport proteins and secondary carriers (46%), in accordance with previous work (Getsin et al, 2013). Most primary active transporters are ATP-binding cassette (ABC) transporters (30%), while proton symports (30%) dominate the secondary carriers.…”

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

“…Classification of a putative transporter into a family or subfamily according to the TC system allows for the prediction of substrate types and transport direction with confidence [13, 17, 41]. …”

A MarR Family Transcriptional Regulator, DptR3, Activates Daptomycin Biosynthesis and Morphological Differentiation in Streptomyces roseosporus

“…SCO1144, the orf16 homolog gene in S. coelicolor, encodes a protein belonging to a lipid exporter family in the ABC-type export system. The substrates of this exporter family include lipoproteins, lipopolysaccharides, lipid A, multiple drugs, and peptides (35). Another possibility is that the orf16 product is involved in the expulsion of harmful or toxic by-products generated from the biosynthesis of daptomycin or that it has an effect on daptomycin resistance through the expulsion of daptomycin.…”