Genetic characterization of the araE gene in Salmonella typhimurium lt2

Dietary L-arabinose-induced gut dysbiosis exacerbates Salmonella infection outcome

The gut microbiota is essential for providing colonization resistance against pathogens. Dietary sugars markedly shift the composition of the intestinal microbiota and alter host susceptibility to enteric infections. Here, we demonstrate the effect of L-arabinose on bacterial infection by using a mouse infection model with Salmonella enterica serovar Typhimurium (S. Tm). In the presence of microbiota, L-arabinose induces a dramatic expansion of Enterobacteriaceae, thereby decreasing the microbiota diversity and causing more severe systemic infection. However, L-arabinose supplementation does not alter the disease progression of Salmonella infection in a microbiota-depleted mouse model. More importantly, short-term supplementation of L-arabinose fails to exert anti-diabetic effects in Salmonella-infected hyperglycemia mice and still promotes infection. Overall, our work reveals that a high intake of dietary L-arabinose supports a bloom of Enterobacteriaceae in Salmonella-infected gut, further accelerating the process of systemic infection.IMPORTANCEL-arabinose is a promising natural sweetener and food additive for the regulation of hyperglycemia. Since diabetic subjects are more susceptible to infections, the safety of dietary L-arabinose in diabetic patients experiencing infection remains a concern. Our findings reveal that L-arabinose exacerbates Salmonella infection outcome by inducing gut microbiota dysbiosis in mice. High dietary intake of L-arabinose may be deleterious for diabetic individuals undergoing infection.

L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation

L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.

Virulence Gene Regulation by L-Arabinose in Salmonella enterica

Invasion of the intestinal epithelium is a critical step in Salmonella enterica infection and requires functions encoded in the gene cluster known as Salmonella Pathogenicity Island 1 (SPI-1). Expression of SPI-1 genes is repressed by L-arabinose, and not by other pentoses. Transport of L-arabinose is necessary to repress SPI-1; however, repression is independent of L-arabinose metabolism and of the L-arabinose-responsive regulator AraC. SPI-1 repression by L-arabinose is exerted at a single target, HilD, and the mechanism appears to be post-translational. As a consequence of SPI-1 repression, l-arabinose reduces translocation of SPI-1 effectors to epithelial cells and decreases Salmonella invasion in vitro. These observations reveal a hitherto unknown role of L-arabinose in gene expression control and raise the possibility that Salmonella may use L-arabinose as an environmental signal.

In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter

Using a single-RNA detection technique in live Escherichia coli cells, we measure, for each cell, the waiting time for the production of the first RNA under the control of P_BAD promoter after induction by arabinose, and subsequent intervals between transcription events. We find that the kinetics of the arabinose intake system affect mean and diversity in RNA numbers, long after induction. We observed the same effect on P_lac/ara-1 promoter, which is inducible by arabinose or by IPTG. Importantly, the distribution of waiting times of P_lac/ara-1 is indistinguishable from that of P_BAD, if and only if induced by arabinose alone. Finally, RNA production under the control of P_BAD is found to be a sub-Poissonian process. We conclude that inducer-dependent waiting times affect mean and cell-to-cell diversity in RNA numbers long after induction, suggesting that intake mechanisms have non-negligible effects on the phenotypic diversity of cell populations in natural, fluctuating environments.

The carbon source influences the efflux pump-mediated antimicrobial resistance in clinically important Gram-negative bacteria

OBJECTIVES

Multidrug efflux pumps are proteins known to play an important role in resistance in bacteria. These proteins are located in the inner membrane (IM), together with many other proteins, including inducible permeases that participate in the uptake of non-phosphotransferase system (PTS) carbohydrates (i.e. carbohydrates uptaken by mechanisms other than the PTS). However, lipid bilayer space in the IM is limited. Therefore, we examined whether the overexpression of unrelated IM proteins is able to interfere with the efflux-mediated resistance mechanism, consequently increasing the susceptibility towards different antimicrobial compounds.

METHODS

We cultured bacteria under different conditions that increase the synthesis of unrelated IM proteins, either by using a non-PTS carbohydrate as the sole carbon source or by artificially overexpressing IM proteins, prior to determining the resistance to different antimicrobial compounds by disc diffusion assays.

RESULTS

We observed that efflux-pump-mediated resistance is affected by the carbon source in all the strains tested, exhibiting increased susceptibility when a non-PTS carbohydrate was used as the sole carbon source. Moreover, when we artificially overexpressed an unrelated IM protein, we also observed decreased efflux-mediated resistance.

CONCLUSIONS

These results strongly suggest that overexpression of IM proteins, by using a non-PTS carbohydrate as the sole carbon source, or by artificially introducing a high number of copies of an unrelated IM protein, competes with the antibiotic efflux systems, thereby decreasing the efflux-mediated resistance to different antimicrobial compounds. This sort of competition arises because of the limited available space in the bacterial IM, or by an unknown mechanism.

AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action

This review covers the physiological aspects of regulation of the arabinose operon in Escherichia coli and the physical and regulatory properties of the operon's controlling gene, araC. It also describes the light switch mechanism as an explanation for many of the protein's properties. Although many thousands of homologs of AraC exist and regulate many diverse operons in response to many different inducers or physiological states, homologs that regulate arabinose-catabolizing genes in response to arabinose were identified. The sequence similarities among them are discussed in light of the known structure of the dimerization and DNA-binding domains of AraC.

Broad-host-range expression vectors that carry the L-arabinose-inducible Escherichia coli araBAD promoter and the araC regulator

We describe the development and analysis of broad-host-range (BHR) cloning vectors that carry the araC-PBAD controlled expression cassette from Escherichia coli. These plasmids are designed to facilitate l-arabinose-responsive control of target genes in a variety of Gram-negative bacterial hosts. BHR PBAD::lacZ fusions were used to analyze the utility of this controlled expression system in the plant pathogen Agrobacterium tumefaciens. In A. tumefaciens, the level of control afforded is significant, although less stringent than that observed in E. coli. The BHR PBAD vectors offer a useful alternative to currently used controlled expression systems, and can be employed in conjunction with other regulated promoters to simultaneously regulate expression of multiple genes. Addition of a variety of carbon sources, namely C4 acids and the anti-inducer d-fucose, allows modulation of l-arabinose induction. Activation of PBAD expression in A. tumefaciens requires a plasmid-borne copy of araC, and is not affected by endogenous regulators.

Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources

Duplication-containing cells are selected when growth of Salmonella typhimurium is limited by the availability of any one of several carbon and energy sources. Under conditions of extreme starvation, growth occurs almost exclusively in the duplication-containing fraction of the population. Cells with duplications of one large segment of the chromosome are repeatedly selected regardless of which of these carbon sources limits growth. The duplicated chromosomal segment encodes the transport systems for all of these carbon sources. This duplication is not selected during growth on a carbon source for which the permease is not included within the duplication segment. This suggests that the growth advantage conferred by the duplication may be due to increased transport of the limiting carbon source. Inclusion of the permease alone is not sufficient to explain the growth advantage of the duplications, since other common duplications that include the permease are not selected.

Unmasking of bacteriophage Mu lipopolysaccharide receptors in Salmonella enteritidis confers sensitivity to Mu and permits Mu mutagenesis

The human pathogen Salmonella enteritidis 3b was found to be highly resistant to phage P22 and Mu derivatives. The Mu sensitivity (musA1) allele from Salmonella typhimurium could be transferred to S. enteritidis 3b at low frequency by cotransduction with hisG::Tn10. Sensitivity to Mu resulted in a large reduction in the number of lipopolysaccharide core-region oligosaccharides that were substituted with O-antigen polysaccharide. The residual high-molecular-weight lipopolysaccharide appeared to be a hybrid displaying O antigens which were immunologically related to those of S. typhimurium and not to those of S. enteritidis. Consequently, Mu d1(Ap lac) could then be transduced into Mus strains forming stable lysogens. On temperature induction, Mu transposition could easily be used to generate mutations in genes coding for cell surface antigens including fimbriae, lipopolysaccharide, and flagella.

Reversion and immobilization of phage Mud1 cts (Apr lac) insertion mutations in Salmonella typhimurium

Phage Mud1 cts (Apr lac), or Mud1, insertion mutations may be accompanied by adjacent deletion formation which can complicate use of lac fusions generated with this phage for gene regulatory studies. As for phage Mu insertion mutations, phage Mud1 insertions fail to revert at significant frequency (whether or not accompanied by an adjacent deletion). We describe isolation of revertible (X mutant) derivatives of phage Mud1 in Salmonella typhimurium. The X mutant derivatives allow use of reversion as a simple test to determine whether a Mud1 insertion has occurred precisely without an adjacent deletion that may have fused the lac genes to a promoter outside of the gene of interest. In addition, a simple method for stabilizing Mud1 generated lac fusions against subsequent transposition is described.

Mutations resulting in promoter-like sequences which enhance the expression of araC in Salmonella typhimurium

The araC gene in Salmonella typhimurium is autogeneously regulated. Nine non-self-regulated mutants were isolated by selecting for increased expression of an araC-lacZ fusion in the presence of a repressing AraC protein. S1 mapping experiments demonstrated that the effect of the mutations was to increase the amount of araC mRNA in the cell. The 5'-end of the major araC transcript was the same in the wild-type (wt) and mutant strains. DNA sequence analysis showed that all nine mutations occurred in the araC promoter. Two mutations were a G-to-T transversion at position -25, six were a G-to-T transversion at position -47 and one was a single bp deletion at position -83. The data suggest that the mutations have created a new RNA polymerase binding site which enhances transcription from the wt start point.

Regulation of the araC gene of Escherichia coli: catabolite repression, autoregulation, and effect on araBAD expression

The araC gene encodes a positive regulatory protein required for L-arabinose utilization in Escherichia coli. Transcription from the araC promoter has been shown to be under positive control by cAMP receptor protein and under negative control by its protein product (autoregulation). This work describes the identification of the region of the araC promoter that interacts with the cAMP receptor protein to mediate catabolite repression. A 3-base-pair deletion centered 60 base pairs from the transcriptional initiation site results in a mutant araC promoter that, in the absence of araC protein, reduces transcriptional activity when compared with the wild-type promoter and is unresponsive to various concentrations of intracellular cAMP in vivo. The same deletion results in a lowered affinity of the araC promoter for cAMP receptor protein in vitro. However, this lowered affinity for the mutant araC promoter does not result in substantial reduction of intracellular araC protein because autoregulation of the araC gene dominates catabolite repression. The 3-base-pair deletion in the cAMP receptor protein binding site of the araC promoter does not affect catabolite repression of the adjacent araBAD operon. The implications of these results on current models for expression of the araBAD operon and the araC gene are discussed.

Genetic characterization of Salmonella typhimurium LT2 ara mutations

Seventeen independently isolated L-arabinose utilization-deficient mutants of Salmonella typhimurium LT2 were characterized. Four complementation groups (araA, araB, araC, and araD) were identified and were equivalent to the same genes in the ara system in Escherichia coli. The order of the four genes was determined to be araD-araA-araB-araC-leu. Two transcription units were found: the araBAD operon was transcribed counterclockwise, and the araC gene was transcribed clockwise.

Regulation of proline utilization in Salmonella typhimurium: characterization of put::Mu d(Ap, lac) operon fusions

The genes for proline utilization were fused to the structural genes of the lac operon by use of the hybrid Mu phage derivative Mu d(Ap lac). Stable deletion derivatives of these fusions were selected and used to study the transcriptional regulation of the put genes. Analysis of these fusions showed that the putA gene product, a bifunctional oxidase-dehydrogenase, also serves to negatively control transcription of the putA and putP genes. Transcription of the put genes is repressed only in putA+ strains; this repression is lifted when exogenous proline is supplied. Transcription of the put genes is stimulated by cyclic AMP in putA+ and putA strains. Maximal induction of the put genes in putA+ strains requires oxygen or an alternative electron acceptor. This oxygen effect is mediated by the putA protein since putA mutants show maximal transcription even without an electron acceptor. The orientation of the Mu d(Ap lac) insertions was determined by formation of Hfr's via the lac homology on F'ts114 lac+. The direction of chromosome mobilization by these Mu d(Ap lac)-directed Hfr's demonstrated that the putP and putA genes are divergently transcribed from a central regulatory region lying between them.

Construction and use of pyr::lac fusion strains to study regulation of pyrimidine biosynthesis in Salmonella typhimurium

The technique developed by Rosenfeld and Brenchley [J Bacteriol 144, 848-851 (1980)] has been used to introduce Mu d1 (Apr lac) into Salmonella typhimurium for purposes of constructing pyr::lac fusion strains. A stable pyrB::lac fusion mutant was subsequently derived and used for the genetic characterization of the pyrB gene. The direction of transcription of pyrB was determined to be counterclockwise on the S. typhimurium linkage map and argI was shown to be located clockwise of pyrB. Mutants altered in the regulation of expression of pyrB were isolated and two of the isolates chosen for further study were tentatively categorized as promoter or operator mutants.

Construction from Mu d1 (lac Apr) lysogens of lambda bacteriophage bearing promoter-lac fusions: isolation of lambda ppheA-lac

Bacteriophage Mu d1 (lac Aprr) was used to obtain strains of Escherichia coli K-12 in which the lac genes are expressed from the promoter of pheA, the structural gene for the enzyme chorismate mutase P-prephenate-dehydratase. A derivative of bacteriophage lambda which carries the pheA-lac fusion was prepared; the method used is generally applicable for the construction, from Mu dl lysogens, of specialized transducing lambda phage carrying the promoter-lac fusions. A restriction enzyme cleavage map of lambda ppheA-lac for the enzymes HindIII and PstI is presented.

Regulation of L-arabinose transport in Salmonella typhimurium LT2

The inducible L-arabinose transport system was characterized in Salmonella typhimurium LT2. Only one L-arabinose transport system with a Km of 2 X 10(-4) M was identified. The results suggested that araE may be the only gene which codes for L-arabinose transport activity under the conditions tested. An araE-lac fusion strain was used to study the induction of the araE gene. No araE expression was detected when the L-arabinose concentration was lower than 1 mM. The expression of araE reached a maximum in the presence of 50 mM L-arabinose, and was significantly reduced in the presence of 50 mM L-arabinose, and was significantly reduced in the presence of D-glucose. Expression of the araBAD and araE genes was coordinately regulated. The concentration of L-arabinose that allowed maximum araBAD gene expression was 50-fold lower in an araE+ strain compared to an araE strain.