BglG, the transcriptional antiterminator of the bgl system, interacts with the beta' subunit of the Escherichia coli RNA polymerase

MinD-RNase E interplay controls localization of polar mRNAs in E. coli

The E. coli transcriptome at the cell's poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.

Validation of Predicted Virulence Factors in Listeria monocytogenes Identified Using Comparative Genomics

Listeria monocytogenes is an intracellular facultative pathogen that causes listeriosis, a foodborne zoonotic infection. There are differences in the pathogenic potential of L. monocytogenes subtypes and strains. Comparison of the genome sequences among L. monocytogenes pathogenic strains EGD-e and F2365 with nonpathogenic L. innocua CLIP1182 and L. monocytogenes strain HCC23 revealed a set of proteins that were present in pathogenic strains and had no orthologs among the nonpathogenic strains. Among the candidate virulence factors are five proteins: putrescine carbamoyltransferase; InlH/InlC2 family class 1 internalin; phosphotransferase system (PTS) fructose transporter subunit EIIC; putative transketolase; and transcription antiterminator BglG family. To determine if these proteins have a role in adherence and invasion of intestinal epithelial Caco-2 cells and/or contribute to virulence, five mutant strains were constructed. F2365ΔinlC2, F2365Δeiic, and F2365Δtkt exhibited a significant (p < 0.05) reduction in adhesion to Caco-2 cells compared to parent F2365 strain. The invasion of F2365ΔaguB, F2365ΔinlC2, and F2365ΔbglG decreased significantly (p < 0.05) compared with the parent strain. Bacterial loads in mouse liver and spleen infected by F2365 was significantly (p < 0.05) higher than it was for F2365ΔaguB, F2365ΔinlC2, F2365Δeiic, F2365Δtkt, and F2365ΔbglG strains. This study demonstrates that aguB, inlC2, eiic, tkt, and bglG play a role in L. monocytogenes pathogenicity.

Characterization of D-Arabitol as Newly Discovered Carbon Source of Bacillus methanolicus

Bacillus methanolicus is a Gram-positive, thermophilic, methanol-utilizing bacterium. As a facultative methylotroph, B. methanolicus is also known to utilize D-mannitol, D-glucose and, as recently discovered, sugar alcohol D-arabitol. While metabolic pathways for utilization of methanol, mannitol and glucose are known, catabolism of arabitol has not yet been characterized in B. methanolicus. In this work we present the elucidation of this hitherto uncharted pathway. In order to confirm our predictions regarding genes coding for arabitol utilization, we performed differential gene expression analysis of B. methanolicus MGA3 cells grown on arabitol as compared to mannitol via transcriptome sequencing (RNA-seq). We identified a gene cluster comprising eight genes that was up-regulated during growth with arabitol as a sole carbon source. The RNA-seq results were subsequently confirmed via qRT-PCR experiments. The transcriptional organization of the gene cluster identified via RNA-seq was analyzed and it was shown that the arabitol utilization genes are co-transcribed in an operon that spans from BMMGA3_RS07325 to BMMGA3_RS07365. Since gene deletion studies are currently not possible in B. methanolicus, two complementation experiments were performed in an arabitol negative Corynebacterium glutamicum strain using the four genes discovered via RNA-seq analysis as coding for a putative PTS for arabitol uptake (BMMGA3_RS07330, BMMGA3_RS07335, and BMMGA3_RS07340 renamed to atlABC) and a putative arabitol phosphate dehydrogenase (BMMGA3_RS07345 renamed to atlD). C. glutamicum is a natural D-arabitol utilizer that requires arabitol dehydrogenase MtlD for arabitol catabolism. The C. glutamicum mtlD deletion mutant was chosen for complementation experiments. Heterologous expression of atlABCD as well as the arabitol phosphate dehydrogenase gene atlD from B. methanolicus alone restored growth of the C. glutamicum ΔmtlD mutant with arabitol. Furthermore, D-arabitol phosphate dehydrogenase activities could be detected in crude extracts of B. methanolicus and these were higher in arabitol-grown cells than in methanol- or mannitol-grown cells. Thus, B. methanolicus possesses an arabitol inducible operon encoding, amongst others, a putative PTS system and an arabitol phosphate dehydrogenase for uptake and activation of arabitol as growth substrate.

Comparative genomic and metabolic analysis of three Lactobacillus paracasei cheese isolates reveals considerable genomic differences in strains from the same niche

Background

Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. In this study, we compared the genome sequences of three L. paracasei strains isolated from mature Cheddar cheeses, two of which (DPC4206 and DPC4536) shared the same genomic fingerprint by PFGE, but demonstrated varying metabolic capabilities.

Results

Genome sizes varied from 2.9 Mbp for DPC2071, to 3.09 Mbp for DPC4206 and 3.08 Mpb for DPC4536. The presence of plasmids was a distinguishing feature between the strains with strain DPC2071 possessing an unusually high number of plasmids (up to 11), while DPC4206 had one plasmid and DPC4536 harboured no plasmids. Each of the strains possessed specific genes not present in the other two analysed strains. The three strains differed in their abundance of sugar-converting genes, and in the types of sugars that could be used as energy sources. Genes involved in the metabolism of sugars not usually connected with the dairy niche, such as myo-inositol and pullulan were also detected, but strains did not utilise these sugars. The genetic content of the three strains differed in regard to specific genes for arginine and sulfur-containing amino acid metabolism and genes contributing to resistance to heavy metal ions. In addition, variability in the presence of phage remnants and phage protection systems was evident.

Conclusions

The findings presented in this study confirm a considerable level of heterogeneity of Lactobacillus paracasei strains, even between strains isolated from the same niche.

A Search for Ribonucleic Antiterminator Sites in Bacterial Genomes: Not Only Antitermination?

BglG/LicT-like proteins are transcriptional antiterminators that prevent termination of transcription at intrinsic terminators by binding to ribonucleic antiterminator (RAT) sites and stabilizing an RNA conformation which is mutually exclusive with the terminator structure. The known RAT sites, which are located in intergenic regions of sugar utilization operons, show low sequence conservation but significant structural analogy. To assess the prevalence of RATs in bacterial genomes, we employed bioinformatic tools that describe RNA motifs based on both sequence and structural constraints. Using descriptors with different stringency, we searched the genomes of Escherichiacoli K12, uropathogenic E. coli and Bacillus subtilis for putative RATs. Our search identified all known RATs and additional putative RAT elements. Surprisingly, most putative RATs do not overlap an intrinsic terminator and many reside within open reading frames (ORFs). The ability of one of the putative RATs, which is located within an antiterminator-encoding ORF and does not overlap a terminator, to bind to its cognate antiterminator protein in vitro and in vivo was confirmed experimentally. Our results suggest that the capacity of RAT elements has been exploited during evolution to mediate activities other than antitermination, for example control of transcription elongation or of RNA stability.

PafR, a novel transcription regulator, is important for pathogenesis in uropathogenic Escherichia coli

The metV genomic island in the chromosome of uropathogenic Escherichia coli (UPEC) encodes a putative transcription factor and a sugar permease of the phosphotransferase system (PTS), which are predicted to compose a Bgl-like sensory system. The presence of these two genes, hereby termed pafR and pafP, respectively, has been previously shown to correlate with isolates causing clinical syndromes. We show here that deletion of both genes impairs the ability of the resulting mutant to infect the CBA/J mouse model of ascending urinary tract infection compared to that of the parent strain, CFT073. Expressing the two genes in trans in the two-gene knockout mutant complemented full virulence. Deletion of either gene individually generated the same phenotype as the double knockout, indicating that both pafR and pafP are important to pathogenesis. We screened numerous environmental conditions but failed to detect expression from the promoter that precedes the paf genes in vitro, suggesting that they are in vivo induced (ivi). Although PafR is shown here to be capable of functioning as a transcriptional antiterminator, its targets in the UPEC genome are not known. Using microarray analysis, we have shown that expression of PafR from a heterologous promoter in CFT073 affects expression of genes related to bacterial virulence, biofilm formation, and metabolism. Expression of PafR also inhibits biofilm formation and motility. Taken together, our results suggest that the paf genes are implicated in pathogenesis and that PafR controls virulence genes, in particular biofilm formation genes.

High-mobility-group a-like CarD binds to a DNA site optimized for affinity and position and to RNA polymerase to regulate a light-inducible promoter in Myxococcus xanthus

The CarD-CarG complex controls various cellular processes in the bacterium Myxococcus xanthus including fruiting body development and light-induced carotenogenesis. The CarD N-terminal domain, which defines the large CarD_CdnL_TRCF protein family, binds to CarG, a zinc-associated protein that does not bind DNA. The CarD C-terminal domain resembles eukaryotic high-mobility-group A (HMGA) proteins, and its DNA binding AT hooks specifically recognize the minor groove of appropriately spaced AT-rich tracts. Here, we investigate the determinants of the only known CarD binding site, the one crucial in CarD-CarG regulation of the promoter of the carQRS operon (P(QRS)), a light-inducible promoter dependent on the extracytoplasmic function (ECF) σ factor CarQ. In vitro, mutating either of the 3-bp AT tracts of this CarD recognition site (TTTCCAGAGCTTT) impaired DNA binding, shifting the AT tracts relative to P(QRS) had no effect or marginally lowered DNA binding, and replacing the native site by the HMGA1a binding one at the human beta interferon promoter (with longer AT tracts) markedly enhanced DNA binding. In vivo, however, all of these changes deterred P(QRS) activation in wild-type M. xanthus, as well as in a strain with the CarD-CarG pair replaced by the Anaeromyxobacter dehalogenans CarD-CarG (CarD(Ad)-CarG(Ad)). CarD(Ad)-CarG(Ad) is functionally equivalent to CarD-CarG despite the lower DNA binding affinity in vitro of CarD(Ad), whose C-terminal domain resembles histone H1 rather than HMGA. We show that CarD physically associates with RNA polymerase (RNAP) specifically via interactions with the RNAP β subunit. Our findings suggest that CarD regulates a light-inducible, ECF σ-dependent promoter by coupling RNAP recruitment and binding to a specific DNA site optimized for affinity and position.

Mutations in β' subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance

Transcription activator C employs a unique mechanism to activate mom gene of bacteriophage Mu. The activation process involves, facilitating the recruitment of RNA polymerase (RNAP) by altering the topology of the promoter and enhancing the promoter clearance by reducing the abortive transcription. To understand the basis of this multi-step activation mechanism, we investigated the nature of the physical interaction between C and RNAP during the process. A variety of assays revealed that only DNA-bound C contacts the β' subunit of RNAP. Consistent to these results, we have also isolated RNAP mutants having mutations in the β' subunit which were compromised in C-mediated activation. Mutant RNAPs show reduced productive transcription and increased abortive initiation specifically at the C-dependent mom promoter. Positive control (pc) mutants of C, defective in interaction with RNAP, retained the property of recruiting RNAP to the promoter but were unable to enhance promoter clearance. These results strongly suggest that the recruitment of RNAP to the mom promoter does not require physical interaction with C, whereas a contact between the β' subunit and the activator, and the subsequent allosteric changes in the active site of the enzyme are essential for the enhancement of promoter clearance.

Spatial and temporal organization of the E. coli PTS components

The phosphotransferase system (PTS) controls preferential use of sugars in bacteria. It comprises of two general proteins, enzyme I (EI) and HPr, and various sugar-specific permeases. Using fluorescence microscopy, we show here that EI and HPr localize near the Escherichia coli cell poles. Polar localization of each protein occurs independently, but HPr is released from the poles in an EI- and sugar-dependent manner. Conversely, the β-glucoside-specific permease, BglF, localizes to the cell membrane. EI, HPr and BglF control the β-glucoside utilization (bgl) operon by modulating the activity of the BglG transcription factor; BglF inactivates BglG by membrane sequestration and phosphorylation, whereas EI and HPr activate it by an unknown mechanism in response to β-glucosides availability. Using biochemical, genetic and imaging methodologies, we show that EI and HPr interact with BglG and affect its subcellular localization in a phosphorylation-independent manner. Upon sugar stimulation, BglG migrates from the cell periphery to the cytoplasm through the poles. Hence, the PTS components appear to control bgl operon expression by ushering BglG between the cellular compartments. Our results reinforce the notion that signal transduction in bacteria involves dynamic localization of proteins.

The bgl sensory system: a transmembrane signaling pathway controlling transcriptional antitermination

The bgl system represents a family of sensory systems composed of membrane-bound sugar-sensors and transcriptional antiterminators, which regulate expression of genes involved in sugar utilization in response to the presence of the corresponding sugar in the growth medium. The BglF sensor catalyzes different activities depending on its stimulation state: in its non-stimulated state, it phosphorylates the BglG transcriptional regulator, thus inactivating it; in the presence of the stimulating sugar, it transports the sugar and phosphorylates it and also activates BglG by dephosphorylation, leading to bgl operon expression. The sugar stimulates BglF by inducing a change in its membrane topology. BglG exists in several conformations: a dimer, which is active, and compact and non-compact monomers, which are inactive. BglF modulates the transition of BglG from one conformation to another, depending on sugar availability. The two Bgl proteins form a pre-complex at the membrane that dissociates upon stimulation, enabling BglG to exert its effect on transcription.

Modulation of monomer conformation of the BglG transcriptional antiterminator from Escherichia coli

The BglG protein positively regulates expression of the bgl operon in Escherichia coli by binding as a dimer to the bgl transcript and preventing premature termination of transcription in the presence of beta-glucosides. BglG activity is negatively controlled by BglF, the beta-glucoside phosphotransferase, which reversibly phosphorylates BglG according to beta-glucoside availability, thus modulating its dimeric state. BglG consists of an RNA-binding domain and two homologous domains, PRD1 and PRD2. Based on structural studies of a BglG homologue, the two PRDs fold similarly, and the interactions within the dimer are PRD1-PRD1 and PRD2-PRD2. We have recently shown that the affinity between PRD1 and PRD2 of BglG is high, and a fraction of the BglG monomers folds in the cell into a compact conformation, in which PRD1 and PRD2 are in close proximity. We show here that both BglG forms, the compact and noncompact, bind to the active site-containing domain of BglF, IIB(bgl), in vitro. The interaction of BglG with IIB(bgl) or BglF is mediated by PRD2. Both BglG forms are detected as phosphorylated proteins after in vitro phosphorylation with IIB(bgl) and are dephosphorylated by BglF in vitro in the presence of beta-glucosides. Nevertheless, genetic evidence indicates that the interaction of IIB(bgl) and BglF with the compact form is seemingly less favorable. Using in vivo cross-linking, we show that BglF enhances folding of BglG into a compact conformation, whereas the addition of beta-glucosides reduces the amount of this form. Based on these results we suggest a model for the modulation of BglG conformation and activity by BglF.

Interactions between the PTS regulation domains of the BglG transcriptional antiterminator from Escherichia coli

The E. coli BglG protein inhibits transcription termination within the bgl operon in the presence of beta-glucosides. BglG represents a family of transcriptional antiterminators that bind to RNA sequences, which partially overlap rho-independent terminators, and prevent termination by stabilizing an alternative structure of the transcript. The activity of BglG is determined by its dimeric state, which is modulated by reversible phosphorylation catalyzed by BglF, a PTS permease. Only the non-phosphorylated BglG dimer binds to RNA and allows read-through of transcription. BglG is composed of three domains: an RNA-binding domain followed by two domains, PRD1 and PRD2 (PTS regulation domains), which are similar in their sequence and folding. Based on the three-dimensional structure of dimeric LicT, a BglG homologue from Bacillus subtilis, the interactions within the dimer are PRD1-PRD1 and PRD2-PRD2. We have shown before that PRD2 mediates homodimerization very efficiently. Using genetic systems and in vitro techniques that assay and characterize protein-protein interactions, we show here that the PRD1 dimerizes very slowly, but once it does, the homodimers are stable. These results support our model that formation of BglG dimers initiates with PRD2 dimerization followed by zipping up of two BglG monomers to create the active RNA-binding domain. Moreover, our results demonstrate that PRD1 and PRD2 heterodimerize efficiently in vitro and in vivo. The affinity among the PRDs is in the following order: PRD2-PRD2 > PRD1-PRD2 > PRD1-PRD1. The interaction between PRD1 and PRD2 offers an explanation for the requirement of conserved residues in PRD1 for the phosphorylation of PRD2 by BglF.

Transcription attenuation

In this review, we describe a variety of mechanisms that bacteria use to regulate transcription elongation in order to control gene expression in response to changes in their environment. Together, these mechanisms are known as attenuation and antitermination, and both involve controlling the formation of a transcription terminator structure in the RNA transcript prior to a structural gene or operon. We examine attenuation and antitermination from the point of view of the different biomolecules that are used to influence the RNA structure. Attenuation of many amino acid biosynthetic operons, particularly in enteric bacteria, is controlled by ribosomes translating leader peptides. RNA-binding proteins regulate attenuation, particularly in gram-positive bacteria such as Bacillus subtilis. Transfer RNA is also used to bind to leader RNAs and influence transcription antitermination in a large number of amino acyl tRNA synthetase genes and several biosynthetic genes in gram-positive bacteria. Finally, antisense RNA is involved in mediating transcription attenuation to control copy number of several plasmids.

Analysis of cis- and trans-acting factors involved in regulation of the Streptococcus mutans fructanase gene (fruA)

There are two primary levels of control of the expression of the fructanase gene (fruA) of Streptococcus mutans: induction by levan, inulin, or sucrose and repression in the presence of glucose and other readily metabolized sugars. The goals of this study were to assess the functionality of putative cis-acting regulatory elements and to begin to identify the trans-acting factors involved in induction and catabolite repression of fruA. The fruA promoter and its derivatives generated by deletions and/or site-directed mutagenesis were fused to a promoterless chloramphenicol acetyltransferase (CAT) gene as a reporter, and strains carrying the transcriptional fusions were then analyzed for CAT activities in response to growth on various carbon sources. A dyadic sequence, ATGACA(TC)TGTCAT, located at -72 to -59 relative to the transcription initiation site was shown to be essential for expression of fruA. Inactivation of the genes that encode fructose-specific enzymes II resulted in elevated expression from the fruA promoter, suggesting negative regulation of fruA expression by the fructose phosphotransferase system. Mutagenesis of a terminator-like structure located in the 165-base 5' untranslated region of the fruA mRNA or insertional inactivation of antiterminator genes revealed that antitermination was not a mechanism controlling induction or repression of fruA, although the untranslated leader mRNA may play a role in optimal expression of fructanase. Deletion or mutation of a consensus catabolite response element alleviated glucose repression of fruA, but interestingly, inactivation of the ccpA gene had no discernible effect on catabolite repression of fruA. Accumulating data suggest that expression of fruA is regulated by a mechanism that has several unique features that distinguish it from archetypical polysaccharide catabolic operons of other gram-positive bacteria.

Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator

The transcriptional antiterminator protein LicT regulates the expression of Bacillus subtilis operons involved in beta-glucoside metabolism. It belongs to a newly characterized family of bacterial regulators whose activity is controlled by the phosphoenolpyruvate:sugar phosphotransferase system (PTS). LicT contains an N-terminal RNA-binding domain (56 residues), and a PTS regulation domain (PRD, 221 residues) that is phosphorylated on conserved histidines in response to substrate availability. Replacement of both His207 and His269 with a negatively charged residue (aspartic acid) led to a highly active LicT variant that no longer responds to either induction or catabolite repression signals from the PTS. In contrast to wild type, the activated mutant form of the LicT regulatory domain crystallized easily and provided the first structure of a PRD, determined at 1.55 A resolution. The structure is a homodimer, each monomer containing two analogous alpha-helical domains. The phosphorylation sites are totally buried at the dimer interface and hence inaccessible to phosphorylating partners. The structure suggests important tertiary and quaternary rearrangements upon LicT activation, which could be communicated from the protein C-terminal end up to the RNA-binding domain.

The Escherichia coli antiterminator protein BglG stabilizes the 5'region of the bgl mRNA

The beta-glucoside utilization (bgl) genes of Escherichia coli are positively regulated by the product of the bglG gene, which functions as an antiterminator by binding to specific sequences present within the bgl mRNA. BglG is inactivated by phosphorylation in the absence of beta-glucosides by BglF, the bgl-specific component of the phosphotransferase system (PTS). Here, we present evidence for an additional function for BglG, namely the stabilization of the 5' end of the bgl mRNA. Half-life measurements of the promoter-proximal region of the bgl mRNA indicate a five fold enhancement of stability in the presence of active (unphosphorylated) BglG. This enhancement is lost when the binding of BglG to mRNA is prevented by deletion of the binding site. Interestingly, stabilization by BglG does not extend to downstream sequences. The enhanced stability of the upstream sequences suggest that BglG remains bound to its target on the mRNA even after the downstream sequences have been degraded. Implications of these observations for the mechanism of positive regulation of the operon by BglG are discussed.

Efficient transcriptional antitermination from the Escherichia coli cytoplasmic membrane

The BglG protein is a transcriptional antiterminator acting within the beta-glucoside operon of Escherichia coli by binding to a specific sequence motif in the growing mRNA. Binding of BglG prevents formation of the terminator stem-loop structure, thereby causing the RNA polymerase to continue transcription. Activity of BglG is modulated in a complex way by antagonistically acting phosphorylations in response to the availability of beta-glucosidic substrates and to the catabolic state of the cell. The enzymes responsible for these phosphorylations are members of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) that represents a central carbohydrate uptake and signal transduction system. As these enzymes are believed to all form higher-order complexes associated with the cytoplasmic membrane, we tested whether or not BglG would remain active when artificially anchored to its presumptive site of regulation, the inner membrane. We show that the membrane-anchored protein indeed efficiently catalyzes transcriptional antitermination. Moreover, the membrane-attached BglG remains regulated by the PTS. Thus, a membrane-bound regulatory RNA binding protein can potentially interact fast enough with its target within the nascent transcript and cause the transcriptional machinery to proceed, before transcriptional termination would occur. Consequently, there is no principal necessity for an RNA-binding transcriptional regulator like BglG to leave the inner membrane, a potential regulatory site, and migrate to the site of transcription, the nucleoid.

Interim report on genomics of Escherichia coli

We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.

Transcription termination control in bacteria

Transcription termination is a dynamic process and is subject to control at a number of levels. New information about the molecular mechanisms of transcription elongation and termination, as well as new insights into protein-RNA interactions, are providing a framework for increased understanding of the molecular details of transcription termination control.