Regulated antisense RNA (asRNA) expression has been employed successfully in Gram-positive bacteria for genome-wide essential gene identification and drug target determination. However, there have been no published reports describing the application of asRNA gene silencing for comprehensive analyses of essential genes in Gram-negative bacteria. In this study, we report the first genome-wide identification of asRNA constructs for essential genes in Escherichia coli. We screened 250,000 library transformants for conditional growth-inhibitory recombinant clones from two shot-gun genomic libraries of E. coli using a paired-termini expression vector (pHN678). After sequencing plasmid inserts of 675 confirmed inducer-sensitive cell clones, we identified 152 separate asRNA constructs of which 134 inserts came from essential genes while 18 originated from non-essential genes (but share operons with essential genes). Among the 79 individual essential genes silenced by these asRNA constructs, 61 genes (77%) engage in processes related to protein synthesis. The cell-based assays of an asRNA clone targeting fusA (encoding elongation factor G) showed that the induced cells were sensitized 12 fold to fusidic acid, a known specific inhibitor. Our results demonstrate the utility of the paired-termini expression vector and feasibility of large-scale gene silencing in E. coli using regulated asRNA expression.
Antibiotic; antisense RNA; Escherichia coli; essential gene; operon
Chlamydia pneumoniaeencodes a functional arginine decarboxylase (ArgDC), AaxB, that activates upon self-cleavage and converts L-arginine to agmatine. In contrast, most Chlamydia trachomatis serovars carry a missense or nonsense mutation in aaxB abrogating activity. The G115R missense mutation was not predicted to impact AaxB functionality, making it unclear if AaxB variations in other Chlamydia species also result in enzyme inactivation. To address the impact of gene polymorphism on functionality, we investigated the activity and production of the Chlamydia AaxB variants. Since ArgDC plays a critical role in the Escherichia coli acid stress response, we studied the ability of these Chlamydia variants to complement an E. coli ArgDC mutant in an acid shock assay. Active AaxB was detected in four additional species: C. caviae, C. pecorum, C. psittaci, and C. muridarum. Of the C. trachomatis serovars, only E appears to encode active enzyme. To determine when functional enzyme is present during the chlamydial developmental cycle, we utilized an anti-AaxB antibody to detect both uncleaved and cleaved enzyme throughout infection. Uncleaved enzyme production peaked around 20 hours post-infection, with optimal cleavage around 44 hours. While the role ArgDC plays in Chlamydia survival or virulence is unclear, our data suggest a niche-specific function.
Chlamydia evolution; arginine decarboxylase; inactivating mutation
Recombineering is a powerful method for DNA manipulation. It has advantages over restriction endonuclease-based methods and is usually rapid. Typically recombineering uses long PCR primers (~65 bases), each of which contains a small region of target homology (~45 bases). We have developed a simple, albeit somewhat less rapid, strategy to create recombineering substrates that can use primers of ≤35 bases for all steps. The regions of homology can be several hundred base pairs in length to (1) increase the chance of obtaining the desired clone and/or (2) allow coliphage-based recombineering in some non-Escherichia coli bacteria. The method uses cloning techniques to construct a template for the generation of the recombineering substrate. Because the template is made from cloned DNA segments, the segments (including those for the homology regions) can be readily changed. During construction of the template plasmid, potential background transformants arising from the vector without insert are significantly reduced by cloning each segment with two restriction endonucleases that produce non-compatible ends. We have used this method to change the bla gene of pACYC177 to aadA, to add the MCS-lacZα region from pBBR1MCS to IncQ plasmid vectors, and to make an oriTIncP-aacC1 cassette and add it to a plasmid.
λ red; recET; genetic engineering; DNA cloning; homologous recombination
We examined intragenomic variation of paralogous 5S rRNA genes to evaluate the concept of ribosomal constraints. In a dataset containing 1168 genomes from 779 unique species, 96 species exhibited >3% diversity. Twenty seven species with >10% diversity contained a total of 421 mismatches between all pairs of the most dissimilar copies of 5S rRNA genes. The large majority (401 of 421) the diversified positions were conserved at the secondary structure level. The high diversity was associated with partial rRNA operon, split operon, or spacer length-related divergence. In total, these findings indicated that there were tight ribosomal constraints on paralogous 5S rRNA genes in a genome despite of the high degree of diversity at the primary structure level.
There is supplementary material.
rRNA diversity; Ribosomal constraints; 5S rRNA
Natural transformation is the main means of horizontal genetic exchange in the obligate human pathogen Neisseria gonorrhoeae. Neisseria spp. have been shown to preferentially take up and transform their own DNA by recognizing a non-palindromic 10 or 12 nucleotide DNA uptake sequence (DUS10 or DUS12). We investigated the ability of the DUS12 to enhance single-stranded DNA (ssDNA) transformation. Given the non-palindromic nature of the DUS12, we tested whether both strands of the DUS equally enhance transformation. Recombinant single-stranded M13 phage harboring transforming DNA with the Watson DUS12, the Crick DUS12, or no DUS (DUS0) were constructed and circular ssDNA was purified. Southern blots of the purified DNA probed with strand-specific oligonucleotide probes showed greater than 10,000:1 ratio of ssDNA to contaminating dsDNA. The Crick strand of the DUS12 enhanced ssDNA transformation 180–470 fold over DUS0 ssDNA whereas the Watson strand of the DUS only modestly enhanced ssDNA transformation in two strains of N. gonorrhoeae. These data confirm that ssDNA efficiently transforms N. gonorrhoeae but that there is a strand preference, and that part of this strand preference is a greater efficiency of the Crick strand of the DUS12 in enhancing transformation.
genetic exchange; pathogen; recombination
In the DNA damage response of most bacteria, UmuD forms part of the error-prone (UmuD′2)C polymerase V, and is activated for this function by self-cleavage after DNA damage. However, the umuD homolog (umuDAb) present throughout the Acinetobacter genus encodes an extra N-terminal region, and in A. baylyi, regulates transcription of DNA-damage induced genes. UmuDAb expressed in cells was correspondingly larger (24 kDa) than the Escherichia coli UmuD (15 kDa). DNA damage from mitomycin C or UV exposure caused UmuDAb cleavage in both E. coli wild type and ΔumuD cells on a timescale resembling UmuD, but did not require UmuD. Like the self-cleaving serine proteases LexA and UmuD, UmuDAb required RecA for cleavage. This cleavage produced a UmuDAb′ fragment of a size consistent with the predicted cleavage site of Ala83-Gly84. Site-directed mutations at Ala83 abolished cleavage, as did mutations at either the Ser119 or Lys156 predicted enzymatic residues. Co-expression of the cleavage site mutant and an enzymatic mutant did not allow cleavage, demonstrating a strictly intramolecular mechanism of cleavage that more closely resembles the LexA-type repressors than UmuD. These data show that UmuDAb undergoes a post-translational, LexA-like cleavage event after DNA damage, possibly to achieve its regulatory action.
DNA damage; serine protease; UmuD; LexA; SOS response
Genetic analysis of Bacteroides fragilis (BF) is hindered due to the lack of efficient transposon mutagenesis methods. Here we describe a simple method for transposon mutagenesis using EZ∷TN5, a commercially available system that we optimized for use in BF638R. The modified EZ∷TN5 transposon contains an E. coli conditional origin of replication, a kanamycin resistance gene for E. coli, an erythromycin resistance gene for BF and 19 basepair transposase recognition sequences on either ends. Electroporation of the transposome (transposon-transposase complex) into BF638R yielded 3.2± 0.35×103 CFU/μg of transposon DNA. Modification of the transposon by the BF638R restriction/modification system increased transposition efficiency 6-fold. Electroporation of the EZ∷TN5 transposome results in a single copy insertion of the transposon evenly distributed across the genome of BF638R and can be used to construct a BF638R transposon library. The transposon was also effective in mutating a BF clinical isolate and a strain of the related species, B. thetaiotaomicron. The EZ∷TN5 based mutagenesis described here is more efficient than other transposon mutagenesis approaches previously reported for BF.
Bacteroides fragilis; transposon mutagenesis; mutant library
Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways.
The Mycoplasma pulmonis Vsa proteins are a family of size- and phase-variable lipoproteins that shield the mycoplasmas from complement and modulate attachment to abiotic surfaces. Mycoplasmas producing a long Vsa protein hemadsorb poorly and yet are proficient at colonizing rats and mice. The effect of the length of the Vsa protein on the attachment of mycoplasmas to epithelial cells has not been previously explored. We find that independent of Vsa isotype, mycoplasmas producing a long Vsa protein with many tandem repeats adhere poorly to murine MLE-12 cells compared to mycoplasmas producing a short Vsa. We also find that mutants lacking the EPS-I polysaccharide of M. pulmonis exhibited decreased adherence to MLE-12 cells even though it has been shown previously that such mutants have an enhanced ability to form a biofilm.
biofilm; colonization; hemadsorption; repetitive proteins; tandem repeats
The Streptococcus mutans ComX-regulon encompasses >200 mostly uncharacterized genes, including cinA. Here we report that cinA is regulated by ComX in the presence of the competence stimulating peptide (CSP), wherein loss of CinA (strain SmuCinA) results in reduced transformability with or without added CSP by 74- and 15-fold, respectively (p<0.003). In CSP-supplemented cultures, a 2-fold increase in cell viability was noted for SmuCinA relative to UA159 (p<0.002), suggesting CinA’s involvement in the CSP-modulated cell killing response. Relative to UA159, loss of CinA also rendered the mutant hypersensitive to killing by methyl methanesulfonate (MMS), which impairs homologous recombination. Despite our use of a non-polar mutagenesis strategy to knockout cinA, which is the first gene of the multicistronic operon harboring cinA, we noted a drastic reduction in recA expression. By using a CinA-complemented mutant, we were able to partially, but not completely restore all phenotypes to UA159 levels. Complementation results suggested that although cinA participates in modulating competence, viability and MMS tolerance, genes downstream of the cinA transcript may also regulate these phenotypes, a finding that warrants further examination. This is the first report that describes a role for S. mutans’ CinA in contending with DNA damage, genetic transformation and cell survival.
Streptococcus mutans; cinA; comX; CSP; genetic competence; cell death
Streptomycetes comprise very important industrial bacteria, producing two-thirds of all clinically relevant secondary metabolites. They are mycelial microorganisms with complex developmental cycles that include programmed cell death (PCD) and sporulation. Industrial fermentations are usually performed in liquid cultures (large bioreactors), conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that there was no differentiation. In this work, we review the current knowledge on Streptomyces pre-sporulation stages of Streptomyces differentiation.
antibiotic; differentiation; programmed cell death; secondary metabolism; sporulation; Streptomyces
Two-component systems are widely used by bacteria to mediate adaptive responses to a variety of environmental stimuli. The CusR/CusS two-component system in Escherichia coli induces expression of genes involved in metal efflux under conditions of elevated Cu(I) and Ag(I) concentrations. As seen in most prototypical two-component systems, signal recognition and transmission is expected to occur by ligand binding in the periplasmic sensor domain of the histidine kinase CusS. Although discussed in the extant literature, little experimental evidence is available to establish the role of CusS in metal homeostasis. In this study, we show that the cusS gene is required for Cu(I) and Ag(I) resistance in E. coli and that CusS is linked to the expression of the cusCFBA genes. These results show a metal dependent mechanism of CusS activation and suggest an absolute requirement for CusS in Cu(I) and Ag(I)-dependent upregulation of cusCFBA expression in E. coli.
Biofilm formation in Vibrio cholerae is in part regulated by norspermidine, a polyamine synthesized by the enzyme carboxynorspermidine decarboxylase (NspC). The absence of norspermidine in the cell leads to a marked reduction in V. cholerae biofilm formation by an unknown mechanism. In this work, we show that overexpression of nspC results in large increases in biofilm formation and vps gene expression as well as a significant decrease in motility. Interestingly, increased NspC levels do not lead to increased concentrations of norspermidine in the cell. Our results show that NspC levels inversely regulate biofilm and motility and implicate the presence of an effective feedback mechanism maintaining norspermidine homeostasis in V. cholerae. Moreover, we provide evidence that NspC and the norspermidine sensor protein, NspS, provide independent and distinct inputs into the biofilm regulatory network.
polyamine; vps gene expression; motility; cadaverine; putrescine; spermidine
The quorum-sensing and CsrA regulons of Vibrios control overlapping cellular functions during growth. Hence, the potential exists for regulatory network interactions between the pathways that enable them to be coordinately controlled. In Vibrio cholerae, CsrA indirectly modulates the activity of LuxO in the quorum-sensing signaling pathway. In this study, it was demonstrated that in Vibrio fischeri, CsrA causes an increase in the transcript levels of a downstream quorum-sensing regulatory gene, luxR, which does not exist in the V. cholerae system. In V. fischeri, the increase in luxR transcripts caused by CsrA does not depend on the LitR transcriptional activator nor does the CsrA effect seem to occur through the global regulator cAMP-CRP. Thus there appears to be more than one mechanism whereby the CsrA and quorum-sensing pathways integrate regulatory outputs in Vibrios.
quorum sensing; factorial design; CsrB; LitR; CRP
Ramoplanin is a lipoglycodepsipeptide antimicrobial active against clinically important Gram-positive bacteria including methicillin resistant Staphylococcus aureus. To proactively examine ramoplanin resistance, we subjected S. aureus NCTC 8325-4 to serial passage in the presence of increasing concentrations of ramoplanin, generating the markedly resistant strain RRSA16. Susceptibility testing of RRSA16 revealed the unanticipated acquisition of cross-resistance to vancomycin and nisin. RRSA16 displayed phenotypes, including a thickened cell wall and reduced susceptibility to Triton X-100 induced autolysis, which are associated with vancomycin intermediate resistant S. aureus strains. Passage of RRSA16 for 18 days in drug-free medium yielded strain R16-18d with restored antibiotic susceptibility. The RRSA16 isolate may be used to identify the genetic and biochemical basis for ramoplanin-resistance and further our understanding of the evolution of antibiotic cross-resistance mechanisms in S. aureus.
ramoplanin; Staphylococcus aureus; vancomycin; VISA; nisin; cross-resistance
Extrachromosomal rDNA circles (ERCs) and recombinant origin-containing plasmids (ARS-plasmids) are thought to reduce replicative life span in the budding yeast Saccharomyces cerevisiae due to their accumulation in yeast cells by an asymmetric inheritance process known as mother cell bias. Most commonly used laboratory yeast strains contain the naturally occurring, high copy number 2-micron circle plasmid. 2-micron plasmids are known to exhibit stable mitotic inheritance, unlike ARS-plasmids and ERCs, but the fidelity of inheritance during replicative aging and cell senescence has not been studied. This raises the question: do 2-micron circles reduce replicative life span? To address this question we have used a convenient method to cure laboratory yeast strains of the 2-micron plasmid. We find no difference in the replicative life spans of otherwise isogenic cir+ and cir0 strains, with and without the 2-micron plasmid. Consistent with this, we find that 2-micron circles do not accumulate in old yeast cells. These findings indicate that naturally occurring levels of 2-micron plasmids do not adversely affect life span, and that accumulation due to asymmetric inheritance is required for reduction of replicative life span by DNA episomes.
DNA episome; Life span; Asymmetric inheritance; Saccharomyces cerevisiae
Various combinations of antibiotics are reported to show synergy to in treating nosocomial infections with multidrug resistant (MDR)-Acinetobacter baumannii (A. baumannii). Here we studied hospital-acquired outbreak strains of MDR-A. baumannii to evaluate optimal combinations of antibiotics. One hundred twenty-one strains were grouped into one major and one minor clonal group based on repetitive-polymerase chain reaction amplification. Twenty representative strains were tested for antibiotic synergy using Etest®. Five strains were further analyzed by analytical isoelectric focusing and PCR to identify β-lactamase resistance genes or other antibiotic resistance determinants. Our investigation showed that the outbreak strains of MDR-A. baumannii belonged to two dominant clones. A combination of colistin and doxycycline showed the best result, being additive or synergistic against 70% of tested strains. Antibiotic additivity was observed more frequently than synergy. Strains possessing the same clonality did not necessarily demonstrate the same response to antibiotic combinations in vitro. We conclude that the effect of antibiotic combinations on our outbreak strains of MDR-A. baumannii seemed strain-specific. The bacterial response to antibiotic combinations is probably a result of complex interactions between multiple concomitant antibiotic resistance determinants in each strain.
Antibiotic combination; Acinetobacter baumannii; multidrug resistance; antibiotic resistance determinants
Streptococcus mutans, a primary dental pathogen, has a remarkable capacity to scavenge nutrients from the oral biofilm for its survival. Cystine is an amino acid dimer formed by the oxidation of two cysteine residues that is required for optimal growth, whereas S. mutans modulates l-cystine uptake via two recently identified transporters designated TcyABC and TcyDEFGH, which have not been fully characterized. Using a non-polar tcyABC-deficient mutant (SmTcyABC), here we report that L-cystine uptake is drastically diminished in the mutant, whereas its ability to grow is severely impaired under l-cystine starvation conditions, relative to wild type. A substrate competition assay showed that l-cystine uptake by the TcyABC transporter was strongly inhibited by dl-cystathionine and l-djenkolic acid and moderately inhibited by S-methyl-l-cysteine and l-cysteine. Using gene expression analysis, we observed that the tcyABC operon was up-regulated under cystine starvation. TcyABC has been shown to be positively regulated by the LysR-type transcriptional regulator CysR. We identified another LysR-type transcriptional regulator that negatively regulates TcyABC with homology to the B. subtilis YtlI regulator, which we termed TcyR. Our study enhances the understanding of l-cystine uptake in S. mutans which allows survival and persistence of this pathogen in the oral biofilm.
Cystine; cysteine; transport; TcyABC; Streptococcus mutans
Nearly all free living bacteria carry toxin-antitoxin (TA) systems on their genomes, through which cell growth and death are regulated. Toxins target a variety of essential cellular functions, including DNA replication, translation, and cell division. Here we identified a novel toxin, YgfX, on the E. coli genome. The toxin, consisting of 135 residues, is composed of the N-terminal membrane domain, which encompasses two transmembrane segments, and the C-terminal cytoplasmic domain. Upon YgfX expression, the cells were initially elongated and then the middle portion of the cells became inflated to form a lemon-shape. YgfX was found to interact with MreB and FtsZ, two essential cytoskeletal proteins in E. coli. The cytoplasmic domain [YgfX(C)], was found to be responsible for the YgfX toxicity, as purified YgfX(C) was found to block polymerization of FtsZ and MreB in vitro. YgfY, located immediately upstream of YgfX, was shown to be the cognate antitoxin. Notably, YgfX is the first membrane associating toxin in bacterial TA systems. We propose to rename the toxin and the antitoxin as CptA and CptB (for Cytoskeleton Polymerization inhibiting Toxin), respectively.
Enterohemorrhagic E. coli (EHEC) is a foodborne pathogen that causes watery diarrhea and hemorrhagic colitis. In this study, we identified StcE, a secreted zinc metalloprotease that contributes to intimate adherence of EHEC to host cells, in culture supernatants of atypical Shigella boydii 13 (Shigella B13) strains. Further examination of the Shigella B13 strains revealed that this cluster of pathogens does not invade but forms pedestals on HEp-2 cells similar to EHEC and enteropathogenic E. coli. This study also demonstrates that atypical Shigella B13 strains are more closely related to attaching and effacing E. coli and that their evolution recapitulates the progression from ancestral E. coli to EHEC.
StcE; E. coli O157:H7; attaching and effacing lesions; Shigella boydii 13
McsA is a key modulator of stress response in Staphylococcus aureus that contains four CXXC potential metal binding motifs at the N-terminal. S. aureus ctsR operon encodes ctsR, clpC and putative mcsA and mcsB genes. The expression of the ctsR operon in S. aureus was shown to be induced in response to various types of heavy metals such as copper and cadmium. McsA was cloned and overexpressed, and purified product was tested for metal binding activity. The protein bound to Cu(II), Zn(II), Co(II) and Cd(II). No binding with any heavy metal except copper was found when we performed site directed mutagenesis of Cys residues of three CXXC motifs of McsA. These data suggest that two conserved cysteine ligands provided by one CXXC motif are required to bind copper ions. In addition, using a bacterial two-hybrid system, McsA was found to be able to bind to McsB and CtsR of S. aureus and the CXXC motif was needed for the binding. This indicates that the Cys residues in the CXXC motif are involved in metal binding and protein interaction.
ctsR regulon; modulator of CtsR; CXXC motifs; cysteine residues; CXXC; metal binding domain; Staphylococcus aureus
Bacterial pathogens face constant challenges from DNA-damaging agents generated by host phagocytes. Although Borrelia burgdorferi appears to have many fewer DNA repair enzymes than pathogens with larger genomes, it does contain homologues of uvrA and uvrB (subunits A and B of excinuclease ABC). As a first step to exploring the physiologic function of uvrABbu and its possible role in survival in the host in the face of DNA damaging agents, a partially deleted uvrA mutant was isolated by targeted inactivation. While growth of this mutant was markedly inhibited by UV irradiation, mitomycin C (MMC) and hydrogen peroxide at doses which lacked effect on wild-type B. burgdorferi, its response to pH 6.0 – 6.8 and reactive nitrogen intermediates was similar to that of the wild-type parental strain. The sensitivity of the inactivation mutant to UV irradiation, MMC and peroxide was complemented by an extrachromosomal copy of uvrABbu. We conclude that uvrABbu is functional in B. burgdorferi.
Borrelia burgdorferi; Lyme disease; uvrA; DNA damage; nucleotide excision repair; UV radiation
Over the years Streptococcus gordonii (sanguis) Challis has become the workhorse of genetic manipulations for the sanguis group of oral streptococci. This is because strain Challis was shown in early studies to be highly naturally competent for transformation. However, Challis is not usually the most appropriate strain to use in studies which focus on oral microbial adherence. We report that other members of the newly reorganized sanguis group, particularly within the species S. crista, display reasonable transformation frequencies, with both plasmid and chromosomal DNA, if transformed at the appropriate time during the growth curve. The ability to transform S. crista may be especially important for genetic studies of biological properties that appear to be limited to these specific streptococcal strains.
Streptococcus crista; Streptococcus gordonii Challis; Transformation; Competence