Insertion of DNA activates the cryptic bgl operon in E. coli K12

Investigating How Genomic Contexts Impact IS5 Transposition Within the Escherichia coli Genome

Insertions of the transposable element IS5 into its target sites in response to stressful environmental conditions, DNA structures, and DNA-binding proteins are well studied, but how the genomic contexts near IS5's native loci impact its transpositions is largely unknown. Here, by examining the roles of all 11 copies of IS5 within the genome of E. coli strain BW25113 in transposition, we reveal that the most significant copy of IS5 is one nested within and oriented in the same direction as the nmpC gene, while two other copies of IS5 harboring point mutations are hardly transposed. Transposition activity is heavily reliant on the upstream nmpC promoter that drives IS5 transposase gene ins5A, with more transpositions resulting from greater promoter activity. The IS5 element at nmpC but not at other loci transcribed detectable amounts of ins5A mRNA. By increasing expression of the ins5CB operon harbored in IS5, we demonstrate that Ins5B and Ins5C appear to exert a stimulatory role in IS5 transposition, suggesting that the downstream genomic regions near the native loci are involved in overall IS5 transposition as well. Using a strain that carries IS5 only at the nmpC locus, we confirm that IS5 primarily uses a copy/paste mechanism for transposition, although we cannot rule out the cut/paste mechanism.

H-NS is a bacterial transposon capture protein

The histone-like nucleoid structuring (H-NS) protein is a DNA binding factor, found in gammaproteobacteria, with functional equivalents in diverse microbes. Universally, such proteins are understood to silence transcription of horizontally acquired genes. Here, we identify transposon capture as a major overlooked function of H-NS. Using genome-scale approaches, we show that H-NS bound regions are transposition "hotspots". Since H-NS often interacts with pathogenicity islands, such targeting creates clinically relevant phenotypic diversity. For example, in Acinetobacter baumannii, we identify altered motility, biofilm formation, and interactions with the human immune system. Transposon capture is mediated by the DNA bridging activity of H-NS and, if absent, more ubiquitous transposition results. Consequently, transcribed and essential genes are disrupted. Hence, H-NS directs transposition to favour evolutionary outcomes useful for the host cell.

The effect of DNA-binding proteins on insertion sequence element transposition upstream of the bgl operon in Escherichia coli

The bglGFB operon in Escherichia coli K-12 strain BW25113, encoding the proteins necessary for the uptake and metabolism of β-glucosides, is normally not expressed. Insertion of either IS1 or IS5 upstream of the bgl promoter activates expression of the operon only when the cell is starving in the presence of a β-glucoside, drastically increasing transcription and allowing the cell to survive and grow using this carbon source. Details surrounding the exact mechanism and regulation of the IS insertional event remain unclear. In this work, the role of several DNA-binding proteins in how they affect the rate of insertion upstream of bgl are examined via mutation assays and protocols measuring transcription. Both Crp and IHF exert a positive effect on insertional Bgl+ mutations when present, active, and functional in the cell. Our results characterize IHF's effect in conjunction with other mutations, show that IHF's effect on IS insertion into bgl also affects other operons, and indicate that it may exert its effect by binding to and altering the DNA conformation of IS1 and IS5 in their native locations, rather than by directly influencing transposase gene expression. In contrast, the cAMP-CRP complex acts directly upon the bgl operon by binding upstream of the promoter, presumably altering local DNA into a conformation that enhances IS insertion.

Genetic context effects can override canonical cis regulatory elements in Escherichia coli

Recent experiments have shown that in addition to control by cis regulatory elements, the local chromosomal context of a gene also has a profound impact on its transcription. Although this chromosome-position dependent expression variation has been empirically mapped at high-resolution, the underlying causes of the variation have not been elucidated. Here, we demonstrate that 1 kb of flanking, non-coding synthetic sequences with a low frequency of guanosine and cytosine (GC) can dramatically reduce reporter expression compared to neutral and high GC-content flanks in Escherichia coli. Natural and artificial genetic context can have a similarly strong effect on reporter expression, regardless of cell growth phase or medium. Despite the strong reduction in the maximal expression level from the fully-induced reporter, low GC synthetic flanks do not affect the time required to reach the maximal expression level after induction. Overall, we demonstrate key determinants of transcriptional propensity that appear to act as tunable modulators of transcription, independent of regulatory sequences such as the promoter. These findings provide insight into the regulation of naturally occurring genes and an independent control for optimizing expression of synthetic biology constructs.

Pleiotropic Effects of Hfq on the Cytochrome c Content and Pyomelanin Production in Shewanella oneidensis

Shewanella oneidensis is the best understood model microorganism for the study of diverse cytochromes (cytos) c that support its unparallel respiratory versatility. Although RNA chaperone Hfq has been implicated in regulation of cyto c production, little is known about the biological pathways that it affects in this bacterium. In this study, from a spontaneous mutant that secretes pyomelanin and has a lowered cyto c content, we identified Hfq to be the regulator that critically associates with both phenotypes in S. oneidensis. We found that expression of the key genes in biosynthesis and degradation of heme is differentially affected by Hfq at under- and overproduced levels, and through modulating heme levels, Hfq influences the cyto c content. Although Hfq in excess results in overproduction of the enzymes responsible for both generation and removal of homogentisic acid (HGA), the precursor of pyomelanin, it is compromised activity of HmgA that leads to excretion and polymerization of HGA to form pyomelanin. We further show that Hfq mediates HmgA activity by lowering intracellular iron content because HmgA is an iron-dependent enzyme. Overall, our work highlights the significance of Hfq-mediated posttranscriptional regulation in the physiology of S. oneidensis, unraveling unexpected mechanisms by which Hfq affects cyto c biosynthesis and pyomelanin production. IMPORTANCE In bacteria, Hfq has been implicated in regulation of diverse biological processes posttranslationally. In S. oneidensis, Hfq affects the content of cytos c that serve as the basis of its respiratory versatility and potential application in bioenergy and bioremediation. In this study, we found that Hfq differentially regulates heme biosynthesis and degradation, leading to altered cyto c contents. Hfq in excess causes a synthetic effect on HmgA, an enzyme responsible for pyomelanin formation. Overall, the data presented manifest that the biological processes in a given bacterium regulated by Hfq are highly complex, amounting to required coordination among multiple physiological aspects to allow cells to respond to environmental changes promptly.

Effects of Global and Specific DNA-Binding Proteins on Transcriptional Regulation of the E. coli bgl Operon

Using reporter gene (lacZ) transcriptional fusions, we examined the transcriptional dependencies of the bgl promoter (Pbgl) and the entire operon regulatory region (Pbgl-bglG) on eight transcription factors as well as the inducer, salicin, and an IS5 insertion upstream of Pbgl. Crp-cAMP is the primary activator of both Pbgl and the bgl operon, while H-NS is a strong dominant operon repressor but only a weak repressor of Pbgl. H-NS may exert its repressive effect by looping the DNA at two binding sites. StpA is a relatively weak repressor in the absence of H-NS, while Fis also has a weak repressive effect. Salicin has no effect on Pbgl activity but causes a 30-fold induction of bgl operon expression. Induction depends on the activity of the BglF transporter/kinase. IS5 insertion has only a moderate effect on Pbgl but causes a much greater activation of the bgl operon expression by preventing the full repressive effects of H-NS and StpA. While several other transcription factors (BglJ, RcsB, and LeuO) have been reported to influence bgl operon transcription when overexpressed, they had little or no effect when present at wild type levels. These results indicate the important transcriptional regulatory mechanisms operative on the bgl operon in E. coli.

Frequency, composition and mobility of Escherichia coli-derived transposable elements in holdings of plasmid repositories

By providing the scientific community with uniform and standardized resources of consistent quality, plasmid repositories play an important role in enabling scientific reproducibility. Plasmids containing insertion sequence elements (IS elements) represent a challenge from this perspective, as they can change the plasmid structure and function. In this study, we conducted a systematic analysis of a subset of plasmid stocks distributed by plasmid repositories (The Arabidopsis Biological Resource Center and Addgene) which carry unintended integrations of bacterial mobile genetic elements. The integration of insertion sequences was most often found in, but not limited to, pBR322-derived vectors, and did not affect the function of the specific plasmids. In certain cases, the entire stock was affected, but the majority of the stocks tested contained a mixture of the wild-type and the mutated plasmids, suggesting that the acquisition of IS elements likely occurred after the plasmids were acquired by the repositories. However, comparison of the sequencing results of the original samples revealed that some plasmids already carried insertion mutations at the time of donation. While an extensive BLAST analysis of 47 877 plasmids sequenced from the Addgene repository uncovered IS elements in only 1.12%, suggesting that IS contamination is not widespread, further tests showed that plasmid integration of IS elements can propagate in conventional Escherichia coli hosts over a few tens of generations. Use of IS-free E. coli hosts prevented the emergence of IS insertions as well as that of small indels, suggesting that the use of IS-free hosts by donors and repositories could help limit unexpected and unwanted IS integrations into plasmids.

Insertion Sequence (IS) Element-Mediated Activating Mutations of the Cryptic Aromatic β-Glucoside Utilization (BglGFB) Operon Are Promoted by the Anti-Terminator Protein (BglG) in Escherichia coli

The cryptic β-glucoside GFB (bglGFB) operon in Escherichia coli (E. coli) can be activated by mutations arising under starvation conditions in the presence of an aromatic β-glucoside. This may involve the insertion of an insertion sequence (IS) element into a "stress-induced DNA duplex destabilization" (SIDD) region upstream of the operon promoter, although other types of mutations can also activate the bgl operon. Here, we show that increased expression of the bglG gene, encoding a well-characterized transcriptional antiterminator, dramatically increases the frequency of both IS-mediated and IS-independent Bgl⁺ mutations occurring on salicin- and arbutin-containing agar plates. Both mutation rates increased with increasing levels of bglG expression but IS-mediated mutations were more prevalent at lower BglG levels. Mutations depended on the presence of both BglG and an aromatic β-glucoside, and bglG expression did not influence IS insertion in other IS-activated operons tested. The N-terminal mRNA-binding domain of BglG was essential for mutational activation, and alteration of BglG's binding site in the mRNA nearly abolished Bgl⁺ mutant appearances. Increased bglG expression promoted residual bgl operon expression in parallel with the increases in mutation rates. Possible mechanisms are proposed explaining how BglG enhances the frequencies of bgl operon activating mutations.

Transporters of glucose and other carbohydrates in bacteria

Glucose arguably is the most important energy carrier, carbon source for metabolites and building block for biopolymers in all kingdoms of life. The proper function of animal organs and tissues depends on the continuous supply of glucose from the bloodstream. Most animals can resorb only a small number of monosaccharides, mostly glucose, galactose and fructose, while all other sugars oligosaccharides and dietary fibers are degraded and metabolized by the microbiota of the lower intestine. Bacteria, in contrast, are omnivorous. They can import and metabolize structurally different sugars and, as a consortium of different species, utilize almost any sugar, sugar derivative and oligosaccharide occurring in nature. Bacteria have membrane transport systems for the uptake of sugars against steep concentration gradients energized by ATP, the proton motive force and the high energy glycolytic intermediate phosphoenolpyruvate (PEP). Different uptake mechanisms and the broad range of overlapping substrate specificities allow bacteria to quickly adapt to and colonize changing environments. Here, we review the structures and mechanisms of bacterial representatives of (i) ATP-dependent cassette (ABC) transporters, (ii) major facilitator (MFS) superfamily proton symporters, (iii) sodium solute symporters (SSS) and (iv) enzyme II integral membrane subunits of the bacterial PEP-dependent phosphotransferase system (PTS). We give a short overview on the distribution of transporter genes and their phylogenetic relationship in different bacterial species. Some sugar transporters are hijacked for import of bacteriophage DNA and antibacterial toxins (bacteriocins) and they facilitate the penetration of polar antibiotics. Finally, we describe how the expression and activity of certain sugar transporters are controlled in response to the availability of sugars and how the presence and uptake of sugars may affect pathogenicity and host-microbiota interactions.

Catabolism of aromatic β-glucosides by bacteria can lead to antibiotics resistance

Antimicrobial resistance is a serious public health threat worldwide today. Escherichia coli is known to resist low doses of antibiotics in the presence of sodium salicylate and related compounds by mounting non-heritable transient phenotypic antibiotic resistance (PAR). In the present study, we demonstrate that Bgl⁺ bacterial strains harboring a functional copy of the β-glucoside (bgl) operon and are actively hydrolyzing plant-derived aromatic β-glucosides such as salicin show PAR to low doses of antibiotics. The aglycone released during metabolism of aromatic β-glucosides is responsible for conferring this phenotype by de-repressing the multiple antibiotics resistance (mar) operon. We also show that prolonged exposure of Bgl⁺ bacteria to aromatic β-glucosides in the presence of sub-lethal doses of antibiotics can lead to a significant increase in the frequency of mutants that show heritable resistance to higher doses of antibiotics. Although heritable drug resistance in many cases is known to reduce the fitness of the carrier strain, we did not see a cost associated with resistance in the mutants, most of which carry clinically relevant mutations. These findings indicate that the presence of the activated form of the bgl operon in the genome facilitates the survival of bacteria in environments in which both aromatic β-glucosides and antibiotics are present.

Carbohydrate Transport by Group Translocation: The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System

The Bacterial Phosphoenolpyruvate (PEP) : Sugar Phosphotransferase System (PTS) mediates the uptake and phosphorylation of carbohydrates, and controls the carbon- and nitrogen metabolism in response to the availability of sugars. PTS occur in eubacteria and in a few archaebacteria but not in animals and plants. All PTS comprise two cytoplasmic phosphotransferase proteins (EI and HPr) and a species-dependent, variable number of sugar-specific enzyme II complexes (IIA, IIB, IIC, IID). EI and HPr transfer phosphorylgroups from PEP to the IIA units. Cytoplasmic IIA and IIB units sequentially transfer phosphates to the sugar, which is transported by the IIC and IICIID integral membrane protein complexes. Phosphorylation by IIB and translocation by IIC(IID) are tightly coupled. The IIC(IID) sugar transporters of the PTS are in the focus of this review. There are four structurally different PTS transporter superfamilies (glucose, glucitol, ascorbate, mannose) . Crystal structures are available for transporters of two superfamilies: bcIIC^mal (MalT, 5IWS, 6BVG) and bcIIC^chb (ChbC, 3QNQ) of B. subtilis from the glucose family, and IIC^asc (UlaA, 4RP9, 5ZOV) of E. coli from the ascorbate superfamily . They are homodimers and each protomer has an independent transport pathway which functions by an elevator-type alternating-access mechanism. bcIIC^mal and bcIIC^chb have the same fold, IIC^asc has a completely different fold. Biochemical and biophysical data accumulated in the past with the transporters for mannitol (IICBA^mtl) and glucose (IICB^glc) are reviewed and discussed in the context of the bcIIC^mal crystal structures. The transporters of the mannose superfamily are dimers of protomers consisting of a IIC and a IID protein chain. The crystal structure is not known and the topology difficult to predict. Biochemical data indicate that the IICIID complex employs a different transport mechanism . Species specific IICIID serve as a gateway for the penetration of bacteriophage lambda DNA across, and insertion of class IIa bacteriocins into the inner membrane. PTS transporters are inserted into the membrane by SecYEG translocon and have specific lipid requirements. Immunoelectron- and fluorescence microscopy indicate a non-random distribution and supramolecular complexes of PTS proteins.

Silent but deadly: IS200 promotes pathogenicity in Salmonella Typhimurium

Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA). This sRNA represses expression of genes encoded within Salmonella Pathogenicity Island 1 (SPI-1), and accordingly limits invasion into non-phagocytic cells in vitro. We present new data here that shows IS200 elements are important for colonization of the mouse gastrointestinal tract. We discuss our previous and current findings in the context of transposon biology and suggest that otherwise 'silent' transposons may in fact play an important role in controlling host gene expression.

Hopping into a hot seat: Role of DNA structural features on IS5-mediated gene activation and inactivation under stress

Insertion sequence elements (IS elements) are proposed to play major roles in shaping the genetic and phenotypic landscapes of prokaryotic cells. Recent evidence has raised the possibility that environmental stress conditions increase IS hopping into new sites, and often such hopping has the phenotypic effect of relieving the stress. Although stress-induced targeted mutations have been reported for a number of E. coli genes, the glpFK (glycerol utilization) and the cryptic bglGFB (β-glucoside utilization) systems are among the best characterized where the effects of IS insertion-mediated gene activation are well-characterized at the molecular level. In the glpFK system, starvation of cells incapable of utilizing glycerol leads to an IS5 insertion event that activates the glpFK operon, and enables glycerol utilization. In the case of the cryptic bglGFB operon, insertion of IS5 (and other IS elements) into a specific region in the bglG upstream sequence has the effect of activating the operon in both growing cells, and in starving cells. However, a major unanswered question in the glpFK system, the bgl system, as well as other examples, has been why the insertion events are promoted at specific locations, and how the specific stress condition (glycerol starvation for example) can be mechanistically linked to enhanced insertion at a specific locus. In this paper, we show that a specific DNA structural feature (superhelical stress-induced duplex destabilization, SIDD) is associated with "stress-induced" IS5 insertion in the glpFK, bglGFB, flhDC, fucAO and nfsB systems. We propose a speculative mechanistic model that links specific environmental conditions to the unmasking of an insertional hotspot in the glpFK system. We demonstrate that experimentally altering the predicted stability of a SIDD element in the nfsB gene significantly impacts IS5 insertion at its hotspot.

The impact of insertion sequences on bacterial genome plasticity and adaptability

Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.

Comprehensive analysis of type 1 fimbriae regulation in fimB-null strains from the multidrug resistant Escherichia coli ST131 clone

Uropathogenic Escherichia coli (UPEC) of sequence type 131 (ST131) are a pandemic multidrug resistant clone associated with urinary tract and bloodstream infections. Type 1 fimbriae, a major UPEC virulence factor, are essential for ST131 bladder colonization. The globally dominant sub-lineage of ST131 strains, clade C/H30-R, possess an ISEc55 insertion in the fimB gene that controls phase-variable type 1 fimbriae expression via the invertible fimS promoter. We report that inactivation of fimB in these strains causes altered regulation of type 1 fimbriae expression. Using a novel read-mapping approach based on Illumina sequencing, we demonstrate that 'off' to 'on' fimS inversion is reduced in these strains and controlled by recombinases encoded by the fimE and fimX genes. Unlike typical UPEC strains, the nucleoid-associated H-NS protein does not strongly repress fimE transcription in clade C ST131 strains. Using a genetic screen to identify novel regulators of fimE and fimX in the clade C ST131 strain EC958, we defined a new role for the guaB gene in the regulation of type 1 fimbriae and in colonisation of the mouse bladder. Our results provide a comprehensive analysis of type 1 fimbriae regulation in ST131, and highlight important differences in its control compared to non-ST131 UPEC.

Control of Transposon-Mediated Directed Mutation by the Escherichia coli Phosphoenolpyruvate:Sugar Phosphotransferase System

The phosphoenolpyruvate:sugar phosphotransferase system (PTS) has been shown to control transport, cell metabolism and gene expression. We here present results supporting the novel suggestion that in certain instances it also regulates the mutation rate. Directed mutations are defined as mutations that occur at higher frequencies when beneficial than when neutral or detrimental. To date, the occurrence of directed point mutations has not been documented and confirmed, but a few examples of transposon-mediated directed mutations have been reported. Here we focus on the first and best-studied example of directed mutation, which involves the regulation of insertion sequence-5 hopping into a specific site upstream of the glpFK glycerol utilization operon in Escherichia coli. This insertional event specifically activates expression of the glpFK operon, allowing the growth of wild-type cells with glycerol as a carbon source in the presence of nonmetabolizable glucose analogues which normally block glycerol utilization. The sugar-transporting PTS controls this process by regulating levels of cytoplasmic glycerol-3-phosphate and cyclic (c)AMP as established in previous publications. Direct involvement of the glycerol repressor, GlpR, and the cAMP receptor protein, Crp, in the regulation of transposon-mediated directed mutation has been demonstrated.

Regulation of gene expression: cryptic β-glucoside (bgl) operon of Escherichia coli as a paradigm

Bacteria have evolved various mechanisms to extract utilizable substrates from available resources and consequently acquire fitness advantage over competitors. One of the strategies is the exploitation of cryptic cellular functions encoded by genetic systems that are silent under laboratory conditions, such as the bgl (β-glucoside) operon of E. coli. The bgl operon of Escherichia coli, involved in the uptake and utilization of aromatic β-glucosides salicin and arbutin, is maintained in a silent state in the wild type organism by the presence of structural elements in the regulatory region. This operon can be activated by mutations that disrupt these negative elements. The fact that the silent bgl operon is retained without accumulating deleterious mutations seems paradoxical from an evolutionary view point. Although this operon appears to be silent, specific physiological conditions might be able to regulate its expression and/or the operon might be carrying out function(s) apart from the utilization of aromatic β-glucosides. This is consistent with the observations that the activated operon confers a Growth Advantage in Stationary Phase (GASP) phenotype to Bgl⁺ cells and exerts its regulation on at least twelve downstream target genes.

The multifaceted benefits of protein co-expression in Escherichia coli

We report here that the expression of protein complexes in vivo in Escherichia coli can be more convenient than traditional reconstitution experiments in vitro. In particular, we show that the poor solubility of Escherichia coli DNA polymerase III ε subunit (featuring 3'-5' exonuclease activity) is highly improved when the same protein is co-expressed with the α and θ subunits (featuring DNA polymerase activity and stabilizing ε, respectively). We also show that protein co-expression in E. coli can be used to efficiently test the competence of subunits from different bacterial species to associate in a functional protein complex. We indeed show that the α subunit of Deinococcus radiodurans DNA polymerase III can be co-expressed in vivo with the ε subunit of E. coli. In addition, we report on the use of protein co-expression to modulate mutation frequency in E. coli. By expressing the wild-type ε subunit under the control of the araBAD promoter (arabinose-inducible), and co-expressing the mutagenic D12A variant of the same protein, under the control of the lac promoter (inducible by isopropyl-thio-β-D-galactopyranoside, IPTG), we were able to alter the E. coli mutation frequency using appropriate concentrations of the inducers arabinose and IPTG. Finally, we discuss recent advances and future challenges of protein co-expression in E. coli.

A dual reporter system for detecting RNA interactions in bacterial cells

Detecting RNA-partner interactions in cells is often difficult due to a lack of suitable tools. Here we describe a dual reporter system capable of detecting intracellular interactions in which one of the partners is an RNA. The system utilizes two fluorescent proteins with similar maturation rates but distinct spectral properties, specifically cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). By placing the CFP gene upstream and the YFP gene downstream of an RNA gene of interest, the production of YFP becomes sensitive to RNA-partner interaction, whereas the synthesis of CFP is not disturbed. Therefore, the RNA-partner interaction can be simply measured by the change in the ratio of fluorescence of YFP over CFP. The utility of our approach is demonstrated through verification of three known RNA-partner interactions in the model bacterium Escherichia coli. Our two-reporter strategy should be broadly useful to the study of RNA-targeted interactions in bacteria.

Elevated recombinant clyA gene expression in the uropathogenic Escherichia coli strain 536, a clue to explain pathoadaptive mutations in a subset of extraintestinal E. coli strains

Background

Analysis of the Escherichia coli collection of reference strains (ECOR) for the presence of the gene locus clyA, which encodes the pore-forming protein ClyA (cytolysin A), revealed that a non-functional clyA locus is common among certain extraintestinal pathogenic E. coli (ExPEC). In fact, all 15 ECOR group B2 strains and several additionally examined extraintestinal pathogenic (uropathogenic (UPEC) and neonatal meningitis (NBM)) E. coli strains contained various ΔclyA alleles.

Results

There are at least four different variants of ΔclyA, suggesting that such deletions in clyA have arisen at more than one occasion. On the basis of this occurrence of the truncated clyA genes, we considered that there may be a patho-adaptive selection for deletions in clyA in extraintestinal pathogenic E. coli. In E. coli K-12 the clyA gene has been viewed as “cryptic” since it is tightly silenced by the nucleoid structuring protein H-NS. We constructed a restored clyA⁺ locus in derivatives of the UPEC strain 536 for further investigation of this hypothesis and, in particular, how the gene would be expressed. Our results show that the level of clyA⁺ expression is highly increased in the UPEC derivatives in comparison with the non-pathogenic E. coli K-12. Transcription of the clyA⁺ gene was induced to even higher levels when the SfaX regulatory protein was overproduced. The derivative with a restored clyA⁺ locus displayed a somewhat slower growth than the parental UPEC strain 536 when a sub-inhibitory concentration of the antimicrobial peptide Polymyxin B was added to the growth medium.

Conclusions

Taken together, our findings show that the clyA⁺ locus is expressed at an elevated level in the UPEC strain and we conclude that this is at least in part due to the effect of the SfaX/PapX transcriptional regulators.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0216-4) contains supplementary material, which is available to authorized users.

Mutations upregulating the flhDC operon of Escherichia coli K-12

Bacterial motility is governed by the flhDC master operon that is under the control of factors like OmpR, LrhA, HdfR, and H-NS. Previously, derivatives of the wild-type MG1655 strain of E. coli K-12 with enhanced motility were found to contain insertion sequences (ISs) in the regulatory region of the flhDC operon. Here, we report that not only integrations of IS insertion sequences into the regulatory region of the flhDC operon, but also a missense mutation in the lrhA gene enhances motility by relieving transcriptional repression of the flhDC operon. Two novel IS insertions were found upstream of flhDC. So far, the relationships between the trans- acting factors and the cis-acting regulatory sequences associated with the flhDC operon have not been clearly established. In this study, it was found that effects of the cis- and trans-acting mutations were acting in parallel, suggesting their apparently independent regulation of flagellar expression.

Bacteriophage recombineering in the lytic state using the lambda red recombinases

Bacteriophages, the historic model organisms facilitating the initiation of molecular biology, are still important candidates of numerous useful or promising biotechnological applications. Development of generally applicable, simple and rapid techniques for their genetic engineering is therefore a validated goal. In this article, we report the use of bacteriophage recombineering with electroporated DNA (BRED), for the first time in a coliphage. With the help of BRED, we removed a copy of mobile element IS1, shown to be active, from the genome of P1vir, a coliphage frequently used in genome engineering procedures. The engineered, IS-free coliphage, P1virdeltaIS, displayed normal plaque morphology, phage titre, burst size and capacity for generalized transduction. When performing head-to-head competition experiments, P1vir could not outperform P1virdeltaIS, further indicating that the specific copy of IS1 plays no direct role in lytic replication. Overall, P1virdeltaIS provides a genome engineering vehicle free of IS contamination, and BRED is likely to serve as a generally applicable tool for engineering bacteriophage genomes in a wide range of taxa.

Mutations at several loci cause increased expression of ribonucleotide reductase in Escherichia coli

Production of deoxyribonucleotides for DNA synthesis is an essential and tightly regulated process. The class Ia ribonucleotide reductase (RNR), the product of the nrdAB genes, is required for aerobic growth of Escherichia coli. In catalyzing the reduction of ribonucleotides, two of the cysteines of RNR become oxidized, forming a disulfide bond. To regenerate active RNR, the cell uses thioredoxins and glutaredoxins to reduce the disulfide bond. Strains that lack thioredoxins 1 and 2 and glutaredoxin 1 do not grow because RNR remains in its oxidized, inactive form. However, suppressor mutations that lead to RNR overproduction allow glutaredoxin 3 to reduce sufficient RNR for growth of these mutant strains. We previously described suppressor mutations in the dnaA and dnaN genes that had such effects. Here we report the isolation of new mutations that lead to increased levels of RNR. These include mutations that were not known to influence production of RNR previously, such as a mutation in the hda gene and insertions in the nrdAB promoter region of insertion elements IS1 and IS5. Bioinformatic analysis raises the possibility that IS element insertion in this region represents an adaptive mechanism in nrdAB regulation in E. coli and closely related species. We also characterize mutations altering different amino acids in DnaA and DnaN from those isolated before.

Transposon-mediated adaptive and directed mutations and their potential evolutionary benefits

Transposons, mobile genetic elements that can hop from one chromosomal location to another, are known to be both beneficial and deleterious to the cell that bears them. Their value in accelerating evolutionary adaptation is well recognized. We herein summarize published research dealing with these elements and then move on to review our own research efforts which focus on a small transposon that can induce mutations under the control of host factors in a process that phenotypically and mechanistically conforms to the definition of 'directed mutation'. Directed mutations occur at higher frequencies when they are beneficial, being induced by the stress condition that they relieve. Here, we review evidence for transposon-mediated directed mutation in Escherichia coli. Deletion mutants in the crp gene can not grow on glycerol (Glp(-)); however, these cells mutate specifically to efficient glycerol utilization (Glp(+)) at rates that are greatly enhanced by the presence of glycerol or the loss of the glycerol repressor (GlpR). These rates are greatly depressed by glucose or by glpR overexpression. Of the four tandem GlpR-binding sites (O1-O4) in the control region of the glpFK operon, O4 (downstream) specifically controls glpFK expression while O1 (upstream) controls mutation rate. Mutation is due to insertion of the small transposon IS5 into a specific site just upstream of the glpFK promoter. Mutational control by the glycerol regulon repressor GlpR is independent of the selection and assay procedures, and IS5 insertion into other gene activation sites is unaffected by the presence of glycerol or the loss of GlpR. The results establish the principle of transposon-mediated directed mutation, identify a protein responsible for its regulation, and define essential aspects of the mechanism.

H-NS mediates the dissociation of a refractory protein-DNA complex during Tn10/IS10 transposition

Tn10/IS10 transposition takes place in the context of a protein–DNA complex called a transpososome. During the reaction, the transpososome undergoes several conformational changes. The host proteins IHF and H-NS, which also are global regulators of gene expression, play important roles in directing these architectural changes. IHF binds tightly to only one of two transposon ends within the transpososome, folding this end into a DNA loop structure. Unfolding this DNA loop is necessary for excising the transposon from flanking donor DNA and preventing integration of the transposon into itself. We show here that efficient DNA loop unfolding relies on the continuity of the flanking donor DNA on the side of the transpososome opposite to the folded transposon end. We also show this same donor DNA is a preferred binding site for H-NS, which promotes opening of the IHF-loop, which is required for productive target interactions. This is counter to the usual mode of H-NS action, which is repressive due to its propensity to coat DNA. The interplay between IHF and H-NS likely serves to couple the rate of transposition to the host cell physiology as both of these proteins are integrated into cellular stress response pathways.

Partial functional replacement of CymA by SirCD in Shewanella oneidensis MR-1

The gammaproteobacterium Shewanella oneidensis MR-1 utilizes a complex electron transfer network composed primarily of c-type cytochromes to respire under anoxic conditions a variety of compounds, including fumarate, nitrate, and dimethyl sulfoxide (DMSO), in addition to the minerals Fe(III) and Mn(IV). Central to several respiratory pathways is CymA, a cytoplasmic membrane-bound tetraheme c-type cytochrome that functions as the major hydroquinone dehydrogenase. To investigate functional redundancy and plasticity in S. oneidensis MR-1 electron transport, we isolated ΔcymA suppressor mutants and characterized one biochemically and genetically. Interestingly, in the characterized ΔcymA suppressor mutant, respiration of fumarate, ferric citrate, and DMSO was restored but that of nitrate was not. The suppression was found to be due to transcriptional activation of sirC and sirD, encoding a periplasmic iron sulfur protein and an integral membrane hydroquinone dehydrogenase, respectively. Biochemical in vitro reconstitution experiments confirmed electron transport between formate and fumarate via fumarate reductase by suppressor membrane fractions. The suppression was found to be caused by insertion of an ISSod1 element upstream of the sirCD transcriptional start site, generating a novel, constitutively active hybrid promoter. This work revealed that adaptation of an alternative electron transfer pathway from quinol to terminal oxidoreductases independent of CymA occurs rapidly in S. oneidensis MR-1.

BglJ-RcsB heterodimers relieve repression of the Escherichia coli bgl operon by H-NS

RcsB is the response regulator of the complex Rcs two-component system, which senses perturbations in the outer membrane and peptidoglycan layer. BglJ is a transcriptional regulator whose constitutive expression causes activation of the H-NS- and StpA-repressed bgl (aryl-β,D-glucoside) operon in Escherichia coli. RcsB and BglJ both belong to the LuxR-type family of transcriptional regulators with a characteristic C-terminal DNA-binding domain. Here, we show that BglJ and RcsB interact and form heterodimers that presumably bind upstream of the bgl promoter, as suggested by mutation of a sequence motif related to the consensus sequence for RcsA-RcsB heterodimers. Heterodimerization of BglJ-RcsB and relief of H-NS-mediated repression of bgl by BglJ-RcsB are apparently independent of RcsB phosphorylation. In addition, we show that LeuO, a pleiotropic LysR-type transcriptional regulator, likewise binds to the bgl upstream regulatory region and relieves repression of bgl independently of BglJ-RcsB. Thus, LeuO can affect bgl directly, as shown here, and indirectly by activating the H-NS-repressed yjjQ-bglJ operon, as shown previously. Taken together, heterodimer formation of RcsB and BglJ expands the role of the Rcs two-component system and the network of regulators affecting the bgl promoter.

Microbial degradation of halogenated compounds

The mode of degradation of various halogenated compounds in isolated pure cultures and the disposition of the degradative genes have been studied. In many cases the degradative genes are found to be clustered on plasmids and appear to be under positive control. Genetic selection in vivo and genetic manipulations in vitro have allowed construction of strains having wider biodegradative potentials than their natural counterparts. Molecular cloning of the degradative gene clusters for halogenated compounds in vectors with a broad host range also allows the transfer of such genes to a large number of Gram-negative bacteria. The application of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading microorganisms has demonstrated the effectiveness of this strain in removing large amounts of 2,4,5-T from contaminated soil within a short period, and such soil has been shown to support the growth of plants normally sensitive to low concentrations of 2,4,5-T. The two major challenges that must be addressed in the near future are the development of appropriate microbial technology for the decontamination of soil containing hazardous halogenated compounds, and the promulgation of appropriate regulations to ensure the safety and well-being of the public during the application of genetically improved strains in an open environment.

Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications

Background

Evolvability is an intrinsic feature of all living cells. However, newly emerging, evolved features can be undesirable when genetic circuits, designed and fabricated by rational, synthetic biological approaches, are installed in the cell. Streamlined-genome E. coli MDS42 is free of mutation-generating IS elements, and can serve as a host with reduced evolutionary potential.

Results

We analyze an extreme case of toxic plasmid clone instability, and show that random host IS element hopping, causing inactivation of the toxic cloned sequences, followed by automatic selection of the fast-growing mutants, can prevent the maintenance of a clone developed for vaccine production. Analyzing the molecular details, we identify a hydrophobic protein as the toxic byproduct of the clone, and show that IS elements spontaneously landing in the cloned fragment relieve the cell from the stress by blocking transcription of the toxic gene. Bioinformatics analysis of sequence reads from early shotgun genome sequencing projects, where clone libraries were constructed and maintained in E. coli, suggests that such IS-mediated inactivation of ectopic genes inhibiting the growth of the E. coli cloning host might happen more frequently than generally anticipated, leading to genomic instability and selection of altered clones.

Conclusions

Delayed genetic adaptation of clean-genome, IS-free MDS42 host improves maintenance of unstable genetic constructs, and is suggested to be beneficial in both laboratory and industrial settings.

Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol

Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source, l-1,2-propanediol (l-1,2-PDO), for approximately 700 generations. We found that (i) experimental evolution of E. coli for approximately 700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to use l-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h(-1); (ii) six mutations detected by whole-genome resequencing accumulated in the evolved E. coli mutant over the course of adaptive evolution on l-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS5 was inserted between two fuc regulons; (iv) two major mutations (mutations in fucO and its promoter) involved in l-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.

Precise excision of IS5 from the intergenic region between the fucPIK and the fucAO operons and mutational control of fucPIK operon expression in Escherichia coli

Excision of transposable genetic elements from host DNA occurs at low frequencies and is usually imprecise. A common insertion sequence element in Escherichia coli, IS5, has been shown to provide various benefits to its host by inserting into specific sites. Precise excision of this element had not previously been demonstrated. Using a unique system, the fucose (fuc) regulon, in which IS5 insertion and excision result in two distinct selectable phenotypes, we have demonstrated that IS5 can precisely excise from its insertion site, restoring the wild-type phenotype. In addition to precise excision, several "suppressor" insertion, deletion, and point mutations restore the wild-type Fuc(+) phenotype to various degrees without IS5 excision. The possible bases for these observations are discussed.

A novel mechanism of transposon-mediated gene activation

Transposable Insertion Sequences (IS elements) have been shown to provide various benefits to their hosts via gene activation or inactivation under stress conditions by appropriately inserting into specific chromosomal sites. Activation is usually due to derepression or introduction of a complete or partial promoter located within the element. Here we define a novel mechanism of gene activation by the transposon IS5 in Escherichia coli. The glycerol utilization operon, glpFK, that is silent in the absence of the cAMP-Crp complex, is activated by IS5 when inserted upstream of its promoter. High-level expression is nearly constitutive, only mildly dependent on glycerol, glucose, GlpR, and Crp, and allows growth at a rate similar to or more rapid than that of wild-type cells. Expression is from the glpFK promoter and dependent on (1) the DNA phase, (2) integration host factor (IHF), and (3) a short region at the 3′ end of IS5 harboring a permanent bend and an IHF binding site. The lacZYA operon is also subject to such activation in the absence of Crp. Thus, we have defined a novel mechanism of gene activation involving transposon insertion that may be generally applicable to many organisms.

Transposons are “jumping genes” that can move from one location within a genome to another. Insertion of a transponson changes the DNA sequence and therefore gives rise to mutations that can activate or inactivate gene expression. Here, we demonstrate for the first time that one such transposon, Insertion Sequence 5 (IS5), when positioned upstream of a metabolic operon (glpFK) of E. coli, can activate the otherwise cryptic expression of the operon. This effect is due solely to a short region at the 3′ end of IS5 that harbors a permanent bend and an overlapping nucleoid protein binding site, both of which are required for maximal gene expression. We demonstrate the importance of phasing and conclude that DNA looping probably plays a role. We also show that another operon, the E. coli lactose operon (lacZYA), can be similarly activated by IS5. Although this is the first study to show that unique sequences within a transposon are necessary and sufficient to activate a downstream silent promoter, similar mechanisms of gene activation may occur for other operons.

A mechanism of transposon-mediated directed mutation

Directed mutation is a proposed process that allows mutations to occur at higher frequencies when they are beneficial. Until now, the existence of such a process has been controversial. Here we describe a novel mechanism of directed mutation mediated by the transposon, IS5 in Escherichia coli. crp deletion mutants mutate specifically to glycerol utilization (Glp(+)) at rates that are enhanced by glycerol or the loss of the glycerol repressor (GlpR), depressed by glucose or glpR overexpression, and RecA-independent. Of the four tandem GlpR binding sites (O1-O4) upstream of the glpFK operon, O4 specifically controls glpFK expression while O1 primarily controls mutation rate in a process mediated by IS5 hopping to a specific site on the E. coli chromosome upstream of the glpFK promoter. IS5 insertion into other gene activation sites is unaffected by the presence of glycerol or the loss of GlpR. The results establish an example of transposon-mediated directed mutation, identify the protein responsible and define the mechanism involved.

Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon

The asc operon of Escherichia coli is one of the cryptic genetic systems for beta-D-galactoside utilization as a carbon source. The ascFB genes for beta-D-galactoside transport and catabolism are repressed by the AscG regulator. After genomic SELEX screening, AscG was found to recognize and bind the consensus palindromic sequence TGAAACC-GGTTTCA. AscG binding was detected at two sites upstream of the ascFB promoter and at three sites upstream of the prpBC operon for propionate catabolism. In an ascG-disrupted mutant, transcription of ascFB was enhanced, in agreement with the repressor model of AscG. This repression was indicated to be due to interference of binding of cyclic AMP-CRP to the CRP box, which overlaps with the AscG-binding site 1, as well as binding of RNA polymerase to the promoter. Under conditions of steady-state E. coli growth in a rich medium, the intracellular level of AscG stayed constant at a level supposedly leading to tight repression of the ascFB operon. The level of prpR, encoding the activator of prpBCDE, was also increased in the absence of AscG, indicating the involvement of AscG in repression of prpR. Taken together, these data suggest a metabolic link through interplay between the asc and prp operons.

Fate of the H-NS-repressed bgl operon in evolution of Escherichia coli

In the enterobacterial species Escherichia coli and Salmonella enterica, expression of horizontally acquired genes with a higher than average AT content is repressed by the nucleoid-associated protein H-NS. A classical example of an H-NS–repressed locus is the bgl (aryl-β,D-glucoside) operon of E. coli. This locus is “cryptic,” as no laboratory growth conditions are known to relieve repression of bgl by H-NS in E. coli K12. However, repression can be relieved by spontaneous mutations. Here, we investigated the phylogeny of the bgl operon. Typing of bgl in a representative collection of E. coli demonstrated that it evolved clonally and that it is present in strains of the phylogenetic groups A, B1, and B2, while it is presumably replaced by a cluster of ORFans in the phylogenetic group D. Interestingly, the bgl operon is mutated in 20% of the strains of phylogenetic groups A and B1, suggesting erosion of bgl in these groups. However, bgl is functional in almost all B2 isolates and, in approximately 50% of them, it is weakly expressed at laboratory growth conditions. Homologs of bgl genes exist in Klebsiella, Enterobacter, and Erwinia species and also in low GC-content Gram-positive bacteria, while absent in E. albertii and Salmonella sp. This suggests horizontal transfer of bgl genes to an ancestral Enterobacterium. Conservation and weak expression of bgl in isolates of phylogenetic group B2 may indicate a functional role of bgl in extraintestinal pathogenic E. coli.

Horizontal gene transfer, an important mechanism in bacterial adaptation and evolution, requires mechanisms to avoid uncontrolled and possibly disadvantageous expression of the transferred genes. Recently, it was shown that the protein H-NS selectively silences genes gained by horizontal transfer in enteric bacteria. Regulated expression of these genes can then evolve and be integrated into the regulatory network of the new host. Our analysis of the catabolic bgl (aryl-β,D-glucoside) operon, which is silenced by H-NS in E. coli, provides a snapshot on the evolution of such a locus. Genes of the bgl operon were presumably gained by horizontal transfer from Gram-positive bacteria to ancestral enteric bacteria. In E. coli, the bgl operon co-evolved with the diversification of the species into four phylogenetic groups. In one phylogenetic group the bgl operon is functional. However, in two other phylogenetic groups, bgl accumulates disrupting mutations, and it is absent in the fourth group. This indicates that the H-NS–silenced bgl operon evolved differently in E. coli and is presumably positively selected in one phylogenetic group, while it is neutrally or negatively selected in the other groups.

Characterization of a beta-glucoside operon (bgc) prevalent in septicemic and uropathogenic Escherichia coli strains

Escherichia coli strains, in general, do not ferment cellobiose and aryl-beta-D-glucosidic sugars, although "cryptic" beta-d-glucoside systems have been characterized. Here we describe an additional cryptic operon (bgc) for the utilization of cellobiose and the aryl-beta-d-glucosides arbutin and salicin at low temperature. The bgc operon was identified by the characterization of beta-glucoside-positive mutants of an E. coli septicemia strain (i484) in which the well-studied bgl (aryl-beta-d-glucoside) operon was deleted. These bgc* mutants appeared after 5 days of incubation on salicin indicator plates at 28 degrees C. The bgc operon codes for proteins homologous to beta-glucoside/cellobiose-specific phosphoenolpyruvate-dependent phosphotransfer system permease subunits IIB (BgcE), IIC (BgcF), and IIA (BgcI); a porin (BgcH); and a phospho-beta-D-glucosidase (BgcA). Next to the bgc operon maps the divergent bgcR gene, which encodes a GntR-type transcriptional regulator. Expression of the bgc operon is dependent on the cyclic-AMP-dependent regulator protein CRP and positively controlled by BgcR. In the bgc* mutants, a single nucleotide exchange enhances the activity of the bgc promoter, rendering it BgcR independent. Typing of a representative collection of E. coli demonstrated the prevalence of bgc in strains of phylogenetic group B2, representing mainly extraintestinal pathogens, while it is rare among commensal E. coli strains. The bgc locus is also present in the closely related species Escherichia albertii. Further, bioinformatic analyses demonstrated that homologs of the bgc genes exist in the enterobacterial Klebsiella, Enterobacter, and Citrobacter spp. and also in gram-positive bacteria, indicative of horizontal gene transfer events.

RepPop: a database for repetitive elements in Populus trichocarpa

BACKGROUND

Populus trichocarpa is the first tree genome to be completed, and its whole genome is currently being assembled. No functional annotation about the repetitive elements in the Populus trichocarpa genome is currently available.

RESULTS

We predicted 9,623 repetitive elements in the Populus trichocarpa genome, and assigned functions to 3,075 of them (31.95%). The 9,623 repetitive elements cover approximately 40% of the current (partially) assembled genome. Among the 9,623 repetitive elements, 668 have copies only in the contigs that have not been assigned to one of the 19 chromosome while the rest all have copies in the partially assembled chromosomes.

CONCLUSION

All the predicted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.

Genetic basis of evolutionary adaptation by Escherichia coli to stressful cycles of freezing, thawing and growth

Microbial evolution experiments offer a powerful approach for coupling changes in complex phenotypes, including fitness and its components, with specific mutations. Here we investigate mutations substituted in 15 lines of Escherichia coli that evolved for 1000 generations under freeze-thaw-growth (FTG) conditions. To investigate the genetic basis of their improvements, we screened many of the lines for mutations involving insertion sequence (IS) elements and identified two genes where multiple lines had similar mutations. Three lines had IS150 insertions in cls, which encodes cardiolipin synthase, and 8 lines had IS150 insertions in the uspA-uspB intergenic region, encoding two universal stress proteins. Another line had an 11-bp deletion mutation in the cls gene. Strain reconstructions and competitions demonstrated that this deletion is beneficial under the FTG regime in its evolved genetic background. Further experiments showed that this cls mutation helps maintain membrane fluidity after freezing and thawing and improves freeze-thaw (FT) survival. Reconstruction of isogenic strains also showed that the IS150 insertions in uspA/B are beneficial under the FTG regime. The evolved insertions reduce uspB transcription and increase both FT survival and recovery, but the physiological mechanism for this fitness improvement remains unknown.

Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea

Background

Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool.

Results

In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a) the activities of IS elements heavily depend on the environments where the host organisms live; (b) the number of recently active IS elements in a genome tends to increase with the genome size; (c) the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d) IS movements show no tendency to disrupt operonic structures.

Conclusion

This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.

Stress-induced mutagenesis in bacteria

Bacteria spend their lives buffeted by changing environmental conditions. To adapt to and survive these stresses, bacteria have global response systems that result in sweeping changes in gene expression and cellular metabolism. These responses are controlled by master regulators, which include: alternative sigma factors, such as RpoS and RpoH; small molecule effectors, such as ppGpp; gene repressors such as LexA; and, inorganic molecules, such as polyphosphate. The response pathways extensively overlap and are induced to various extents by the same environmental stresses. These stresses include nutritional deprivation, DNA damage, temperature shift, and exposure to antibiotics. All of these global stress responses include functions that can increase genetic variability. In particular, up-regulation and activation of error-prone DNA polymerases, down-regulation of error-correcting enzymes, and movement of mobile genetic elements are common features of several stress responses. The result is that under a variety of stressful conditions, bacteria are induced for genetic change. This transient mutator state may be important for adaptive evolution.