Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system.

The adaptation against foreign nucleic acids by the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) depends on the insertion of foreign nucleic acid-derived sequences into the CRISPR array as novel spacers by still unknown mechanism. We identified and characterized in Escherichia coli intermediate states of spacer integration and mapped the integration site at the chromosomal CRISPR array in vivo. The results show that the insertion of new spacers occurs by site-specific nicking at both strands of the leader proximal repeat in a staggered way and is accompanied by joining of the resulting 5'-ends of the repeat strands with the 3'-ends of the incoming spacer. This concerted cleavage-ligation reaction depends on the metal-binding center of Cas1 protein and requires the presence of Cas2. By acquisition assays using plasmid-located CRISPR array with mutated repeat sequences, we demonstrate that the primary sequence of the first repeat is crucial for cleavage of the CRISPR array and the ligation of new spacer DNA.

Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2.

The adaptive immunity of bacteria against foreign nucleic acids, mediated by CRISPR (clustered regularly interspaced short palindromic repeats), relies on the specific incorporation of short pieces of the invading foreign DNA into a special genomic locus, termed CRISPR array. The stored sequences (spacers) are subsequently used in the form of small RNAs (crRNAs) to interfere with the target nucleic acid. We explored the DNA-binding mechanism of the immunization protein Csn2 from the human pathogen Streptococcus agalactiae using different biochemical techniques, atomic force microscopic imaging and molecular dynamics simulations. The results demonstrate that the ring-shaped Csn2 tetramer binds DNA ends through its central hole and slides inward, likely by a screw motion along the helical path of the enclosed DNA. The presented data indicate an accessory function of Csn2 during integration of exogenous DNA by end-joining.

RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants.

The LysR-type transcription factor LeuO is involved in regulation of pathogenicity determinants and stress responses in Enterobacteriaceae, and acts as antagonist of the global repressor H-NS. Expression of the leuO gene is repressed by H-NS, and it is upregulated in stationary phase and under amino acid starvation conditions. Here, we show that the heterodimer of the FixJ/NarL-type transcription regulators RcsB and BglJ strongly activates expression of leuO and that RcsB-BglJ regulates additional loci. Activation of leuO by RcsB-BglJ is independent of the Rcs phosphorelay system. RcsB-BglJ binds to the leuO promoter region and activates one of two leuO promoters mapped in vivo. Moreover, LeuO antagonizes activation of leuO by RcsB-BglJ and acts as negative autoregulator in vivo and in vitro. Further, the H-NS paralogue StpA causes repression of leuO in addition to H-NS. Together, our data suggest a complex arrangement of regulatory elements and they indicate a feedback control mechanism of leuO expression.

RcsB-BglJ-mediated activation of Cascade operon does not induce the maturation of CRISPR RNAs in E. coli K12.

Prokaryotic immunity against foreign nucleic acids mediated by clustered, regularly interspaced, short palindromic repeats (CRISPR) depends on the expression of the CRISPR-associated (Cas) proteins and the formation of small CRISPR RNAs (crRNAs). The crRNA-loaded Cas ribonucleoprotein complexes convey the specific recognition and inactivation of target nucleic acids. In E. coli K12, the maturation of crRNAs and the interference with target DNA is performed by the Cascade complex. The transcription of the Cascade operon is tightly repressed through H-NS-dependent inhibition of the Pcas promoter. Elevated levels of the LysR-type regulator LeuO induce the Pcas promoter and concomitantly activate the CRISPR-mediated immunity against phages. Here, we show that the Pcas promoter can also be induced by constitutive expression of the regulator BglJ. This activation is LeuO-dependent as heterodimers of BglJ and RcsB activate leuO transcription. Each transcription factor, LeuO or BglJ, induced the transcription of the Cascade genes to comparable amounts. However, the maturation of the crRNAs was activated in LeuO but not in BglJ-expressing cells. Studies on CRISPR promoter activities, transcript stabilities, crRNA processing and Cascade protein levels were performed to answer the question why crRNA maturation is defective in BglJ-expressing cells. Our results demonstrate that the activation of Cascade gene transcription is necessary but not sufficient to turn on the CRISPR-mediated immunity and suggest a more complex regulation of the type I-E CRISPR-Cas system in E. coli.

The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae.

The prokaryotic immune system, CRISPR, confers an adaptive and inheritable defense mechanism against invasion by mobile genetic elements. Guided by small CRISPR RNAs (crRNAs), a diverse family of CRISPR-associated (Cas) proteins mediates the targeting and inactivation of foreign DNA. Here, we demonstrate that Csn2, a Cas protein likely involved in spacer integration, forms a tetramer in solution and structurally possesses a ring-like structure. Furthermore, co-purified Ca(2+) was found important for the DNA binding property of Csn2, which contains a helicase fold, with highly conserved DxD and RR motifs found throughout Csn2 proteins. We could verify that Csn2 binds ds-DNA. In addition molecular dynamics simulations suggested a Csn2 conformation that can "sit" on the DNA helix and binds DNA in a groove on the outside of the ring.

Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS.

Inheritable bacterial defence systems against phage infection and foreign DNA, termed CRISPR (clustered regularly interspaced short palindromic repeats), consist of cas protein genes and repeat arrays interspaced with sequences originating from invaders. The Cas proteins together with processed small spacer-repeat transcripts (crRNAs) cause degradation of penetrated foreign DNA by unknown mechanisms. Here, we have characterized previously unidentified promoters of the Escherichia coli CRISPR arrays and cas protein genes. Transcription of precursor crRNA is directed by a promoter located within the CRISPR leader. A second promoter, directing cas gene transcription, is located upstream of the genes encoding proteins of the Cascade complex. Furthermore, we demonstrate that the DNA-binding protein H-NS is involved in silencing the CRISPR-cas promoters, resulting in cryptic Cas protein expression. Our results demonstrate an active involvement of H-NS in the induction of the CRISPR-cas system and suggest a potential link between two prokaryotic defence systems against foreign DNA.

H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO.

The recently discovered prokaryotic CRISPR/Cas defence system provides immunity against viral infections and plasmid conjugation. It has been demonstrated that in Escherichia coli transcription of the Cascade genes (casABCDE) and to some extent the CRISPR array is repressed by heat-stable nucleoid-structuring (H-NS) protein, a global transcriptional repressor. Here we elaborate on the control of the E. coli CRISPR/Cas system, and study the effect on CRISPR-based anti-viral immunity. Transformation of wild-type E. coli K12 with CRISPR spacers that are complementary to phage Lambda does not lead to detectable protection against Lambda infection. However, when an H-NS mutant of E. coli K12 is transformed with the same anti-Lambda CRISPR, this does result in reduced sensitivity to phage infection. In addition, it is demonstrated that LeuO, a LysR-type transcription factor, binds to two sites flanking the casA promoter and the H-NS nucleation site, resulting in derepression of casABCDE12 transcription. Overexpression of LeuO in E. coli K12 containing an anti-Lambda CRISPR leads to an enhanced protection against phage infection. This study demonstrates that in E. coli H-NS and LeuO are antagonistic regulators of CRISPR-based immunity.

6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products.

6S RNA from Escherichia coli is known to bind to RNA polymerase, preventing interaction with many promoters during stationary growth. The resulting repression is released under conditions of nutritional upshift, when the growth situation improves. 6S RNA, which binds to the active site of RNA polymerase, has the particularly interesting feature to act as a template, causing the transcription of defined de novo RNAs (dnRNA) that are complementary to a specific sequence region of the 6S RNA. We analyzed the conditions of dnRNA synthesis and determined their effect on the 6S RNA-mediated inhibition of RNA polymerase in vitro and in vivo. Upon nutritional upshift the RNA polymerase/6S RNA complex induces the rapid synthesis of dnRNAs, which form stable hybrids with the 6S RNA template. The resulting structural change destabilizes the inactivated RNA polymerase complex, causing sigma subunit release. Both dnRNA and 6S RNA are rapidly degraded after complex disintegration. Experiments using the transcriptional inhibitor rifampicin demonstrate that active transcription is required for the disintegration of the RNA polymerase/6S RNA complex. Our results support the conclusion that 6S RNA not only inhibits transcription during stationary growth but also enables cells to resume rapid growth after starvation and help to escape from stationary phase.

Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts.

Escherichia coli 6S RNA represents a non-coding RNA (ncRNA), which, based on the conserved secondary structure and previous functional studies, had been suggested to interfere with transcription. Selective inhibition of sigma-70 holoenzymes, preferentially at extended -10 promoters, but not stationary-phase-specific transcription was described, suggesting a direct role of 6S RNA in the transition from exponential to stationary phase. To elucidate the underlying mechanism, we have analysed 6S RNA interactions with different forms of RNA polymerase by gel retardation and crosslinking. Preferred binding of 6S RNA to Esigma(70) was confirmed, however weaker binding to Esigma(38) was also observed. The crosslinking analysis revealed direct contact between a central 6S RNA sequence element and the beta/beta' and sigma subunits. Promoter complex formation and in vitro transcription analysis with exponential- and stationary-phase-specific promoters and the corresponding holoenzymes demonstrated that 6S RNA interferes with transcription initiation but does not generally distinguish between exponential- and stationary-phase-specific promoters. Moreover, we show for the first time that 6S RNA acts as a template for the transcription of defined RNA molecules in the absence of DNA. In conclusion, this study reveals new aspects of 6S RNA function.

The role of LRP and H-NS in transcription regulation: involvement of synergism, allostery and macromolecular crowding.

LRP has recently been shown to interact with the regulatory regions of bacterial ribosomal RNA promoters. Here we study details of the LRP-rDNA interaction by gel retardation and high-resolution footprinting techniques. We show that a second regulator for rRNA transcription, H-NS, facilitates the formation of a higher-order LRP-nucleoprotein complex, probably acting transiently as a DNA chaperone. The macromolecular crowding substance ectoine stabilizes the formation of this dynamic complex, while the amino acid leucine, as a metabolic effector, has the opposite effect. DNase I and hydroxyl radical footprint experiments with LRP-DNA complexes reveal a periodic change of the target DNA structure, which implies extensive DNA wrapping reaching into the promoter core region. We show furthermore that LRP binding is able to constrain supercoils, providing a link between DNA topology and regulation. The results support the conclusion that the bacterial DNA-binding protein LRP, assisted by H-NS, forms a repressive nucleoprotein structure involved in regulation of rRNA transcription. The formation of this regulatory structure appears to be directly affected by environmental changes.

Posttranslational modification of E. coli histone-like protein H-NS and bovine histones by short-chain poly-(R)-3-hydroxybutyrate (cPHB).

Short-chain poly-(R)-3-hydroxybutyrate (cPHB), a highly flexible, amphiphilic molecule with salt-solvating properties, is a ubiquitous constituent of prokaryotic and eukaryotic cells, wherein it is mainly conjugated to proteins. The solvating properties and cellular distribution of cPHB suggest it may be associated with proteins that bind and/or transfer DNA. Here we examine Escherichia coli protein H-NS and calf thymus histones, H1, H2A, H2B, H3, and H4, for the presence of cPHB. The proteins are related in that all bind to DNA and are implicated in the compact organization of the chromosome. The presence of cPHB in E. coli H-NS was first detected in Western blots of two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of total cell proteins, probed with anti-cPHB IgG, and then by Western blot analysis of the purified protein. Western blot analysis of the calf thymus histones indicated that each contained cPHB. The presence of cPHB in H-NS and histones was confirmed by chemical assay. The in vivo size of conjugated cPHB could not be established due to the lack of standards and degradation of cPHB during protein purification and storage. The molecular characteristics of cPHB and its presence in histone-like and histone proteins of diverse organisms suggest it may play a role in DNA binding and/or DNA organization.

The E. coli anti-sigma factor Rsd: studies on the specificity and regulation of its expression.

BACKGROUND: Among the seven different sigma factors in E. coli σ(70) has the highest concentration and affinity for the core RNA polymerase. The E. coli protein Rsd is regarded as an anti-sigma factor, inhibiting σ(70)-dependent transcription at the onset of stationary growth. Although binding of Rsd to σ(70) has been shown and numerous structural studies on Rsd have been performed the detailed mechanism of action is still unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have performed studies to unravel the function and regulation of Rsd expression in vitro and in vivo. Cross-linking and affinity binding revealed that Rsd is able to interact with σ(70), with the core enzyme of RNA polymerase and is able to form dimers in solution. Unexpectedly, we find that Rsd does also interact with σ(38), the stationary phase-specific sigma factor. This interaction was further corroborated by gel retardation and footprinting studies with different promoter fragments and σ(38)- or σ(70)-containing RNA polymerase in presence of Rsd. Under competitive in vitro transcription conditions, in presence of both sigma factors, a selective inhibition of σ(70)-dependent transcription was prevailing, however. Analysis of rsd expression revealed that the nucleoid-associated proteins H-NS and FIS, StpA and LRP bind to the regulatory region of the rsd promoters. Furthermore, the major promoter P2 was shown to be down-regulated in vivo by RpoS, the stationary phase-specific sigma factor and the transcription factor DksA, while induction of the stringent control enhanced rsd promoter activity. Most notably, the dam-dependent methylation of a cluster of GATC sites turned out to be important for efficient rsd transcription. CONCLUSIONS/SIGNIFICANCE: The results contribute to a better understanding of the intricate mechanism of Rsd-mediated sigma factor specificity changes during stationary phase.

Structural basis for CRISPR RNA-guided DNA recognition by Cascade.

The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA(1)B(2)C(6)D(1)E(1)) and a 61-nucleotide CRISPR RNA (crRNA) with 5'-hydroxyl and 2',3'-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.

Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 - a phasing analysis.

To study the influence of DNA curvature and DNA-binding proteins, which interact with curved DNA on bacterial promoters, we constructed two sets of promoter variants in which a synthetic DNA-bending module was fused at defined distances and angular orientations with respect to the transcription start sites. The distance between the synthetic binding site centre and the transcription start site of the different constructs varied by up to 20 bp, corresponding to almost two complete helical B-DNA turns. The rRNA promoters rrnB P1 and rrnB P2 were selected as target promoters. While in its natural context P1 depends on upstream curved DNA and several transcription factors that bind to this region, promoter P2 is not preceded by curved DNA, nor is it believed to be directly regulated by transcription factors. In vitro transcription measurements of both promoters in the absence of transcription factors varied with the phase of the curved upstream DNA element, underlining the importance of DNA conformation to promoter efficiency. Specific binding of H-NS and LRP to the curved DNA element was demonstrated by gel shift and footprint analysis. Binding affinity was not notably altered for the different distance variants. We demonstrated that the two proteins acted as repressors for both promoters. The extent of H-NS-mediated repression for both promoters did not vary strongly with the phasing of the upstream binding module. In contrast, LRP-dependent repression showed a clear dependence on the angular orientation of the constructs. Phasing-dependent repression is very distinct for P2 but only rudimentary for the P1 promoter.

Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation.

The small bacterial 6S RNA has been recognized as a transcriptional regulator, facilitating the transition from exponential to stationary growth phase by preferentially inhibiting E sigma 70 RNA polymerase holoenzyme transcription. Consistent with this function, the cellular concentration of 6S RNA increases with stationary phase. We have studied the underlying mechanisms responsible for the growth phase-dependent differences in 6S RNA concentration. To this aim, we have analyzed the effects of the typical bacterial growth phase and stress regulators FIS, H-NS, LRP and StpA on 6S RNA expression. Measurements of 6S RNA accumulation in strains deficient in each one of these proteins support their contribution as potential regulators. Specific binding of the four proteins to DNA fragments containing 6S RNA promoters was demonstrated by gel retardation and DNase I footprinting. Moreover, in vitro transcription analysis with both RNA polymerase holoenzymes, E sigma 70 and E sigma 38, demonstrated a direct inhibition of 6S RNA transcription by H-NS, StpA and LRP, while FIS seems to act as a dual regulator. In vitro transcription in the presence of ppGpp indicates that 6S RNA promoters are not stringently regulated. Our results underline that regulation of 6S RNA transcription depends on a complex network, involving a set of bacterial regulators with general importance in the adaptation to changing growth conditions.

The Streptomyces coelicolor GlnR regulon: identification of new GlnR targets and evidence for a central role of GlnR in nitrogen metabolism in actinomycetes.

Streptomyces coelicolor GlnR is a global regulator that controls genes involved in nitrogen metabolism. By genomic screening 10 new GlnR targets were identified, including enzymes for ammonium assimilation (glnII, gdhA), nitrite reduction (nirB), urea cleavage (ureA) and a number of biochemically uncharacterized proteins (SCO0255, SCO0888, SCO2195, SCO2400, SCO2404, SCO7155). For the GlnR regulon, a GlnR binding site which comprises the sequence gTnAc-n(6)-GaAAc-n(6)-GtnAC-n(6)-GAAAc-n(6) has been found. Reverse transcription analysis of S. coelicolor and the S. coelicolor glnR mutant revealed that GlnR activates or represses the expression of its target genes. Furthermore, glnR expression itself was shown to be nitrogen-dependent. Physiological studies of S. coelicolor and the S. coelicolor glnR mutant with ammonium and nitrate as the sole nitrogen source revealed that GlnR is not only involved in ammonium assimilation but also in ammonium supply. blast analysis demonstrated that GlnR-homologous proteins are present in different actinomycetes containing the glnA gene with the conserved GlnR binding site. By DNA binding studies, it was furthermore demonstrated that S. coelicolor GlnR is able to interact with these glnA upstream regions. We therefore suggest that GlnR-mediated regulation is not restricted to Streptomyces but constitutes a regulon conserved in many actinomycetes.

The seven E. coli ribosomal RNA operon upstream regulatory regions differ in structure and transcription factor binding efficiencies.

Ribosomal RNAs in E. coli are transcribed from seven operons, which are highly conserved in their organization and sequence. However, the upstream regulatory DNA regions differ considerably, suggesting differences in regulation. We have therefore analyzed the conformation of all seven DNA elements located upstream of the major E. coli rRNA P1 promoters. As judged by temperature-dependent gel electrophoresis with isolated DNA fragments comprising the individual P1 promoters and the complete upstream regulatory regions, all seven rRNA upstream sequences are intrinsically curved. The degree of intrinsic curvature was highest for the rrnB and rrnD fragments and less pronounced for the rrnA and rrnE operons. Comparison of the experimentally determined differences in curvature with programs for the prediction of DNA conformation revealed a generally high degree of conformity. Moreover, the analysis showed that the center of curvature is located at about the same position in all fragments. The different upstream regions were analyzed for their capacity to bind the transcription factors FIS and H-NS, which are known as antagonists in the regulation of rRNA synthesis. Gel retardation experiments revealed that both proteins interact with the upstream promoter regions of all seven rDNA fragments, with the affinities of the different DNA fragments for FIS and H-NS and the structure of the resulting complexes deviating considerably. FIS binding was non-cooperative, and at comparable protein concentrations the occupancy of the different DNA fragments varied between two and four binding sites. In contrast, H-NS was shown to bind cooperatively and intermediate states of occupancy could not be resolved for each fragment. The different gel electrophoretic mobilities of the individual DNA/protein complexes indicate variable structures and topologies of the upstream activating sequence regulatory complexes. Our results are highly suggestive of differential regulation of the individual rRNA operons.

LRP and H-NS--cooperative partners for transcription regulation at Escherichia coli rRNA promoters.

The synthesis of ribosomal RNAs in bacteria is tightly coupled to changes in the environment. This rapid adaptation is the result of several intertwined regulatory networks. The two proteins FIS and H-NS have previously been described to act as antagonistic transcription factors for rRNA synthesis. Here we provide evidence for another player, the regulatory protein LRP, which binds with high specificity to all seven Escherichia coli rRNA P1 promoter upstream regions (UAS). Comparison of the binding properties of LRP and H-NS, and characterization of the stabilities of the various complexes formed with the rRNA UAS regions revealed different binding modes. Binding studies with LRP and H-NS in combination demonstrated that the two proteins interacted with obvious synergism. The efficiency of LRP binding to the rRNA regulatory region is modified by the presence of the effector amino acid leucine, as has been shown for several other operons regulated by this transcription factor. The effect of LRP on the binding of RNA polymerase to the rrnB P1 promoter and in vitro transcription experiments indicated that LRP acts as a transcriptional repressor, thus resembling the activity of H-NS described previously. The results show for the first time that LRP binds to the regulatory region of bacterial rRNA promoters, and very likely contributes in combination with H-NS to the control of rRNA synthesis. From the known properties of LRP a mechanism can be inferred that couples rRNA synthesis to changes in nutritional quality.

Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1.

The Escherichia coli H-NS protein is a nucleoid-associated protein involved in both transcription regulation and DNA compaction. Each of these processes involves H-NS-mediated bridge formation between adjacent DNA helices. With respect to transcription regulation, preferential binding sites in the promoter regions of different genes have been reported, and generally these regions are curved. Often H-NS binding sites overlap with promoter core regions or with binding sites of other regulatory factors. Not in all cases, however, transcriptional repression is the result of preferential binding by H-NS to promoter regions leading to occlusion of the RNA polymerase. In the case of the rrnB P1, H-NS actually stimulates open complex formation by forming a ternary RNAP.H-NS.DNA complex, while simultaneously stabilizing it to such an extent that promoter clearance cannot occur. To define the mechanism by which H-NS interferes at this step in the initiation pathway, the architecture of the RNAP.H-NS.DNA complex was analyzed by scanning force microscopy (SFM). The SFM images show that the DNA flanking the RNA polymerase in open initiation complexes is bridged by H-NS. On the basis of these data, we present a model for the specific repression of transcription initiation at the rrnB P1 by H-NS.