Novel phosphotransferase system genes revealed by genome analysis – the complete complement of PTS proteins encoded within the genome of Bacillus subtilis

Reizer, Jonathan; Bachem, Steffi; Reizer, Aiala; Arnaud, Maryvonne; Saier, Milton H.; Stülke, Jörg

doi:10.1099/00221287-145-12-3419

Cited by 105 publications

(100 citation statements)

References 63 publications

(22 reference statements)

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“…In CD630, gntR was upstream of genes encoding the mannose-specific phosphotransferase system (PTS) (Sebaihia et al, 2006). The mannose PTS is involved in sugar transport and global regulation of gene expression, in a number of Gram-positive genera (Abranches et al, 2003;Arous et al, 2004;Chaillou et al, 2001;Reizer et al, 1999), including the regulation of energy metabolism and virulence genes in Streptococcus mutans (Abranches et al, 2006). Hypothetically, integration of wC2 into CD630 could lead to significant changes in the C. difficile phenotype through mannose PTS deregulation.…”

Section: Discussionmentioning

confidence: 99%

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

et al. 2007

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The complete genome sequence of Clostridium difficile phage wC2 and comparisons to wCD119 and inducible prophages of CD630 The complete genomic sequence of a previously characterized temperate phage of Clostridium difficile, wC2, is reported. The genome is 56 538 bp and organized into 84 putative ORFs in six functional modules. The head and tail structural proteins showed similarities to that of C. difficile phage wCD119 and Streptococcus pneumoniae phage EJ-1, respectively. Homologues of structural and replication proteins were found in prophages 1 and 2 of the sequenced C. difficile CD630 genome. A putative holin appears unique to the C. difficile phages and was functional when expressed in Escherichia coli. Nucleotide sequence comparisons of wC2 to wCD119 and the CD630 prophage sequences showed relatedness between wC2 and the prophages, but less so to wCD119. wC2 integrated into a gene encoding a putative transcriptional regulator of the gntR family. wC2, wCD119 and CD630 prophage 1 genomes had a Cdu1-attP-integrase arrangement, suggesting that the pathogenicity locus (PaLoc) of C. difficile, flanked by cdu1, has phage origins. The attP sequences of wC2, wCD119 and CD630 prophages were dissimilar. wC2-related sequences were found in 84 % of 37 clinical C. difficile isolates and typed reference strains. INTRODUCTIONClostridium difficile has emerged as an important intestinal pathogen since the 1970s, continuing to plague hospital settings worldwide and causing recent epidemics in the USA and Canada (Loo et al., 2005;Warny et al., 2005). The major virulence factors of C. difficile are toxins A and B encoded by tcdA and tcdB respectively, which are located on a 19 kb genomic region termed the pathogenicity locus (PaLoc) (Braun et al., 1996;Hammond & Johnson, 1995). The toxins are positively regulated by TcdR (Mani & Dupuy, 2001;Rupnik et al., 2005) and are negatively regulated by TcdC (Hundsberger et al., 1997;Matamouros et al., 2006); they are encoded by tcdR and tcdC respectively, also on the PaLoc. Another toxin-associated gene, tcdE, appears phage related but its function is unknown (Tan et al., 2001). C. difficile acquires antibiotic resistance and virulence genes through plasmids and transposons (Bruggemann, 2005) shown to significantly contribute to genome plasticity (Sebaihia et al., 2006). It is possible that phages also contribute to variance in virulence-associated genes (Lemee et al., 2005) and to the emergence of outbreak strains . However, the prevalence of phage genes within C. difficile genomes is not known. In comparison to phages of Escherichia coli, Staphylococcus aureus and Lactobacillus species, the study of clostridial phages is in its infancy. Only one phage specific for C. difficile, temperate phage wCD119, has been sequenced , while two putative prophage sequences were detected in the recently sequenced genome of C. difficile CD630 (Sebaihia et al., 2006).

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Section: Discussionmentioning

confidence: 99%

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

et al. 2007

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“…The Bacillus subtilis genome encodes 15 PTS proteins with different sugar specificities (31), one of which is also adjacent to a 1-pfk enzyme. PTS transport systems are linked with uptake of monomeric substrates, whereas ABC transport systems are required for the transport of larger substrates, as shown for L. acidophilus (29).…”

Section: Discussionmentioning

confidence: 99%

Substrate-driven gene expression in Roseburia inulinivorans : Importance of inducible enzymes in the utilization of inulin and starch

Scott

Martin

Chassard

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

121

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Roseburia inulinivorans is a recently identified motile representative of the Firmicutes that contributes to butyrate formation from a variety of dietary polysaccharide substrates in the human large intestine. Microarray analysis was used here to investigate substratedriven gene-expression changes in R. inulinivorans A2-194. A cluster of fructo-oligosaccharide/inulin utilization genes induced during growth on inulin included one encoding a β-fructofuranosidase protein that was prominent in the proteome of inulin-grown cells. This cluster also included a 6-phosphofructokinase and an ABC transport system, whereas a distinct inulin-induced 1-phosphofructokinase was linked to a fructose-specific phosphoenolpyruvatedependent sugar phosphotransferase system (PTS II transport enzyme). Real-time PCR analysis showed that the β-fructofuranosidase and adjacent ABC transport protein showed greatest induction during growth on inulin, whereas the 1-phosphofructokinase enzyme and linked sugar phosphotransferase transport system were most strongly up-regulated during growth on fructose, indicating that these two clusters play distinct roles in the use of inulin. The R. inulinivorans β-fructofuranosidase was overexpressed in Escherichia coli and shown to hydrolyze fructans ranging from inulin down to sucrose, with greatest activity on fructo-oligosaccharides. Genes induced on starch included the major extracellular α-amylase and two distinct α-glucanotransferases together with a gene encoding a flagellin protein. The latter response may be concerned with improving bacterial access to insoluble starch particles.anaerobic gut bacteria | differential gene expression | fructooligosaccharides | butyrate | prebiotic P lant cell wall polysaccharides, storage polysaccharides such as resistant starch and inulin, and many oligosaccharides of plant origin remain undigested in the upper gastrointestinal tract and become important substrates for the growth of colonic bacteria. Prebiotics are defined as dietary substrates that reach the colon where they selectively stimulate the growth of beneficial gut bacteria (1), with the most widely used prebiotics being the fructans inulin and fructo-oligosaccharides (FOS). Inulin is a linear polymer [degree of polymerization (DP) = 3-60] of β-2,1-linked fructose monomers with a terminal glucose residue, whereas FOS have the same backbone but a maximal chain length of 8 monomeric units. The increasing use of prebiotics to enhance gut health is driving research into their mode of action. Many studies have shown that both inulin and FOS selectively stimulate the growth of potentially beneficial gut bacteria such as bifidobacteria and lactobacilli (reviewed in ref.2). However, only a few studies have considered the potential for stimulation of other bacterial groups that may also be beneficial (3-6).The bifidogenic dose of inulin has been defined as 5-8 g/d (7), yet the effect of such supplementation on other beneficial groups of gut bacteria and the differences relating to different compositions of inulin...

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“…In contrast, many other microorganisms including the actinomycetes Corynebacterium diphtheriae and Mycobacterium smegmatis, some mycoplasmae, and low-GC Gram-positive bacteria such as Bacillus subtilis possess no crr gene. These have crr homologues as part of sugar-specific enzyme IIABC permeases that solely appear to fulfil transport function (F. Titgemeyer, unpublished data; [30][31][32]). For Gramnegative species a multiple role of IIA Glc has been documented and proposed [9,13,14,29].…”

Section: Discussionmentioning

confidence: 99%

The phosphotransferase system of Streptomyces coelicolor

Kamionka

Parche

Nothaft

et al. 2002

European Journal of Biochemistry

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We have investigated the crr gene of Streptomyces coelicolor that encodes a homologue of enzyme IIA Glucose of Escherichia coli, which, as a component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) plays a key role in carbon regulation by triggering glucose transport, carbon catabolite repression, and inducer exclusion. As in E. coli, the crr gene of S. coelicolor is genetically associated with the ptsI gene that encodes the general phosphotransferase enzyme I. The gene product IIA Crr was overproduced, purified, and polyclonal antibodies were obtained. Western blot analysis revealed that IIA Crr is expressed in vivo. The functionality of IIA Crr was demonstrated by phosphoenolpyruvate-dependent phosphorylation via enzyme I and the histidine-containing phosphoryl carrier protein HPr. Phosphorylation was abolished when His72, which corresponds to the catalytic histidine of E. coli IIA Glucose , was mutated. The capacity of IIA Crr to operate in sugar transport was shown by complementation of the E. coli glucose-PTS. The striking functional resemblance between IIA Crr and IIA Glucose was further demonstrated by its ability to confer inducer exclusion of maltose to E. coli. A specific interaction of IIA Crr with the maltose permease subunit MalK from Salmonella typhimurium was uncovered by surface plasmon resonance. These data suggest that this IIA Glucose -like protein may be involved in carbon metabolism in S. coelicolor.Keywords: inducer exclusion; protein phosphorylation; protein-protein interaction; Streptomyces; surface plasmon resonance.Streptomycetes undergo global changes in gene expression and enzyme activities in response to developmental stages, secondary metabolite production (antibiotics), carbon utilization, and stress conditions [1][2][3][4][5]. The focus of our research is the regulation of carbon source utilization (C-regulation) and how this influences the other abovementioned processes.Streptomyces coelicolor metabolizes a wide variety of nutrients. Their utilization is subject to C-regulation, in which glucose kinase appears to be of significant importance [6,7]. However, the signal transduction pathways are poorly understood. In many other bacteria, components of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) trigger C-regulation by mechanisms known as carbon catabolite repression and inducer exclusion [8,9]. One key element in Escherichia coli is enzyme IIA Glucose (IIA Glc ). IIA Glc becomes phosphorylated by the general PTS proteins, which are histidine-containing phosphoryl carrier protein (HPr) and enzyme I (EI). In turn, it phosphorylates the sugar-specific PTS permeases that catalyse the uptake of glucose, trehalose, and sucrose [8,10,11]. Mutations in the respective gene crr exhibit a pleiotropic catabolite repression resistant phenotype [12]. The underlying mechanisms are that unphosphorylated IIA Glc inhibits a set of catabolic enzymes and sugar permeases including the MalK subunit of the maltose permease by protein-protein interac...

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Novel phosphotransferase system genes revealed by genome analysis – the complete complement of PTS proteins encoded within the genome of Bacillus subtilis

Cited by 105 publications

References 63 publications

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

Substrate-driven gene expression in Roseburia inulinivorans : Importance of inducible enzymes in the utilization of inulin and starch

The phosphotransferase system of Streptomyces coelicolor

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