Visualization of the binding site for the transcript cleavage factor GreB on Escherichia coli RNA polymerase

Antibacterial potential and mechanism of action of dithiocyano-methane as a bactericidal agent for farm disinfection

AIMS

This study aimed to investigate the antibacterial ability and action mechanism of dithiocyano-methane against Aeromonas hydrophila, so as to provide a reference for its application in farm disinfection.

METHODS AND RESULTS

After exposing the bacteria to dithiocyano-methane, the minimum inhibitory concentration (MIC), minimum bactericide concentration (MBC), activities of alkaline phosphatase, aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase and electric conductivity in bacterial suspensions were determined, transmission electron microscope images on cellular structure and SDS-PAGE profile of bacterial proteins were analysed and the expression of genes related to the above experimental observations was confirmed by real-time quantitative PCR. The MIC and MBC of dithiocyano-methane against three tested strains was 1·46 and 2·93 mg l^-1 respectively. The results showed that dithiocyano-methane significantly damaged bacterial cell structure, inhibited the biosynthesis of bacterial proteins and changed the integrity and permeability of bacterial cell wall and cell membrane.

CONCLUSIONS

Dithiocyano-methane showed remarkable antibacterial ability against three tested strains, indicating it is a potential effective bactericidal agent for preventing animal diseases resulted from Aer. hydrophila.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our best knowledge, this is the first report to examine the antibacterial ability and action mechanism of dithiocyano-methane against bacteria. The results demonstrate the great potential of dithiocyano-methane as a disinfectant against Aer. hydrophila in settings such as aquaculture ponds and livestock farms.

Mutational analysis of Escherichia coli GreA protein reveals new functional activity independent of antipause and lethal when overexpressed

There is a growing appreciation for the diverse regulatory consequences of the family of proteins that bind to the secondary channel of E. coli RNA polymerase (RNAP), such as GreA, GreB or DksA. Similar binding sites could suggest a competition between them. GreA is characterised to rescue stalled RNAP complexes due to its antipause activity, but also it is involved in transcription fidelity and proofreading. Here, overexpression of GreA is noted to be lethal independent of its antipause activity. A library of random GreA variants has been used to isolate lethality suppressors to assess important residues for GreA functionality and its interaction with the RNA polymerase. Some mutant defects are inferred to be associated with altered binding competition with DksA, while other variants seem to have antipause activity defects that cannot reverse a GreA-sensitive pause site in a fliC::lacZ reporter system. Surprisingly, apparent binding and cleavage defects are found scattered throughout both the coiled-coil and globular domains. Thus, the coiled-coil of GreA is not just a measuring stick ensuring placement of acidic residues precisely at the catalytic centre but also seems to have binding functions. These lethality suppressor mutants may provide valuable tools for future structural and functional studies.

Helical crystallization of soluble and membrane binding proteins

Helical protein arrays offer unique advantages for structure determination by cryo-electron microscopy (cryo-EM). A single image of such an array contains a complete range of equally spaced molecular views of the underlying protein subunits, which allows a low-resolution, isotropic three-dimensional (3D) map to be generated from a single helical tube without tilting the sample in the electron beam as is required for two-dimensional (2D) crystals. Averaging many unit cells from a number of similar tubes can improve the signal-to-noise ratio and consequently, the quality of the 3D map. This approach has yielded reconstructions that approach atomic resolution [Miyazawa et al., 1999, 2003; Sachse et al., 2007; Unwin, 2005; Yonekura et al., 2005]. Proteins that naturally adopt helical protein arrays, such as actin and microtubules, have been studied for decades. The wealth of information on how proteins bind and move along these cytoskeletal tracks, provide cross-talk between tracks, and integrate into the cellular machinery is due, in part, to multiple EM studies of the helical assemblies. Since the majority of proteins do not spontaneously form helical arrays, the power of helical image analysis has only been realized for a small number of proteins. This chapter describes the use of functionalized lipid nanotubes and liposomes as substrates to bind and form helical arrays of soluble and membrane-associated proteins.

Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavage

Transcription elongation in bacteria is promoted by Gre-factors, which stimulate an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase. A GreA paralog, Gfh1, present in Thermus aquaticus and Thermus thermophilus, has the opposite effect on elongation complexes, inhibiting rather than stimulating transcript cleavage. We have determined the 3.3 angstroms-resolution X-ray crystal structure of T.aquaticus Gfh1. The structure reveals an N-terminal and a C-terminal domain with close structural similarity to the domains of GreA, but with an unexpected conformational change in terms of the orientation of the domains with respect to each other. However, structural and functional analysis suggests that when complexed with RNA polymerase, Gfh1 adopts a conformation similar to that of GreA. These results reveal considerable structural flexibility for Gfh1, and for Gre-factors in general, as suggested by structural modeling, and point to a possible role for the conformational switch in Gre-factor and Gfh1 regulation. The opposite functional effect of Gfh1 compared with GreA may be determined by three structural characteristics. First, Gfh1 lacks the basic patch present in Gre-factors that likely plays a role in anchoring the 3'-fragment of the back-tracked RNA. Second, the loop at the tip of the N-terminal coiled-coil is highly flexible and contains extra acidic residues compared with GreA. Third, the N-terminal coiled-coil finger lacks a kink in the first alpha-helix, resulting in a straight coiled-coil compared with GreA. The latter two characteristics suggest that Gfh1 chelates a magnesium ion in the RNA polymerase active site (like GreA) but in a catalytically inactive configuration.

Helical crystallization on nickel-lipid nanotubes: perfringolysin O as a model protein

To facilitate purification and subsequent structural studies of recombinant proteins the most widely used genetically encoded tag is the histidine tag (His-tag) which specifically binds to N-nitrilotriacetic-acid-chelated nickel ions. Lipids derivatized with a nickel-chelating head group can be mixed with galactosylceramide glycolipids to prepare lipid nanotubes that bind His-tagged proteins. In this study, we use His-tagged perfringolysin O (PFO), a soluble toxin secreted by the bacterial pathogen Clostridium perfringens, as a model protein to test the utility of nickel-lipid nanotubes as a tool for structural studies of His-tagged proteins. PFO is a member of the cholesterol dependent cytolysin family (CDC) of oligomerizing, pore-forming toxins found in a variety of Gram-positive bacterial pathogens. CDC pores have been difficult to study by X-ray crystallography because they are membrane associated and vary in size. We demonstrate that both a wild-type and a mutant form of PFO form helical arrays on nickel-lipid containing nanotubes. Cryo-electron microscopy and image analysis of the helical arrays were used to reconstruct a 3D density map of wild-type PFO. This study suggests that the use of nickel-lipid nanotubes may offer a general approach for structural studies of recombinant proteins and may provide insights into the molecular interactions of proteins that have a natural affinity for a membrane surface.

Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase

Prokaryotic transcription elongation factors GreA and GreB stimulate intrinsic nucleolytic activity of RNA polymerase (RNAP). The proposed biological role of Gre-induced RNA hydrolysis includes transcription proofreading, suppression of transcriptional pausing and arrest, and facilitation of RNAP transition from transcription initiation to transcription elongation. Using an array of biochemical and molecular genetic methods, we mapped the interaction interface between Gre and RNAP and identified the key residues in Gre responsible for induction of nucleolytic activity in RNAP. We propose a structural model in which the C-terminal globular domain of Gre binds near the opening of the RNAP secondary channel, the N-terminal coiled-coil domain (NTD) protrudes inside the RNAP channel, and the tip of the NTD is brought to the immediate vicinity of RNAP catalytic center. Two conserved acidic residues D41 and E44 located at the tip of the NTD assist RNAP by coordinating the Mg2+ ion and water molecule required for catalysis of RNA hydrolysis. If so, Gre would be the first transcription factor known to directly participate in the catalytic act of RNAP.

Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase

Bacterial GreA and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase. The structure of Escherichia coli core RNA polymerase bound to GreB was determined by cryo-electron microscopy and image processing of helical crystals to a nominal resolution of 15 A, allowing fitting of high-resolution RNA polymerase and GreB structures. In the resulting model, the GreB N-terminal coiled-coil domain extends 45 A through a channel directly to the RNA polymerase active site. The model leads to detailed insights into the mechanism of Gre factor activity that explains a wide range of experimental observations and points to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNA polymerase active site to catalyze the cleavage reaction. Mutational studies confirm that these positions are critical for Gre factor function.

The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription

Transcription is highly regulated both by protein factors and by specific RNA or DNA sequence elements. Central to this regulation is the ability of RNA polymerase (RNAP) to adopt multiple conformational states during elongation. This review focuses on the mechanism of transcription elongation and the role of different conformational states in the regulation of elongation and termination. The discussion centers primarily on data from structural and functional studies on Escherichia coli RNAP. To introduce the players, a brief introduction to the general mechanism of elongation, the regulatory proteins, and the conformational states is provided. The role of each of the conformational states in elongation is then discussed in detail. Finally, an integrated mechanism of elongation is presented, bringing together the panoply of experiments.

Promoting elongation with transcript cleavage stimulatory factors

Transcript elongation by RNA polymerase is a dynamic process, capable of responding to a number of intrinsic and extrinsic signals. A number of elongation factors have been identified that enhance the rate or efficiency of transcription. One such class of factors facilitates RNA polymerase transcription through blocks to elongation by stimulating the polymerase to cleave the nascent RNA transcript within the elongation complex. These cleavage factors are represented by the Gre factors from prokaryotes, and TFIIS and TFIIS-like factors found in archaea and eukaryotes. High-resolution structures of RNA polymerases and the cleavage factors in conjunction with biochemical investigations and genetic analyses have provided insights into the mechanism of action of these elongation factors. However, there are yet many unanswered questions regarding the regulation of these factors and their effects on target genes.

Characterization of monoclonal antibodies against Escherichia coli core RNA polymerase

Multiple interactions with DNA, RNA and transcription factors occur in a transcription cycle. To survey the proximity of some of these factors to the Escherichia coli RNA polymerase surface, we produced a set of nine monoclonal antibodies (mAbs) against the enzyme. These mAbs, located at different places on the surface of the enzyme, were used in a co-immunopurification assay to investigate interference with the binding of NusA, sigma70, GreB and HepA to core RNA polymerase. One of these mAbs turned out to be the first antibody inhibitor of the binding of NusA and sigma70; it did not affect GreB and HepA interactions. Its epitope was located on the beta' subunit at the C-terminus of region G. The properties of this mAb reinforce the idea that the mutually exclusive binding of NusA and sigma70 to core RNA polymerase is due to, at least partially, overlapping binding sites, rather than allosteric interaction between two distant binding sites. This mAb is also useful to understand the occupancy of sigma70, NusA and Gre proteins on core RNA polymerase.

Bacterial RNA polymerase

The recently determined crystal structure of a bacterial core RNA polymerase (RNAP) provides the first glimpse of this family of evolutionarily conserved cellular RNAPs. Using the structure as a framework, a consistent picture of protein-nucleic acid interactions in transcription complexes has been accumulated from cross-linking experiments. The molecule can be viewed as a molecular machine, with distinct structural features hypothesized to perform specific functions. Comparison with the alpha-carbon backbone of a eukaryotic RNAP reveals close structural similarity.

Function of transcription cleavage factors GreA and GreB at a regulatory pause site

Gre proteins of prokaryotes, and SII proteins of eukaryotes and archaea, are transcription elongation factors that promote an endogenous transcript cleavage activity of RNA polymerases; this process promotes elongation through obstructive regions of DNA, including transcription pauses that act as sites of genetic regulation. We show that a regulatory pause in the early part of the late gene operon of bacteriophage lambda is subject to such cleavage and resynthesis. In cells lacking the cleavage factors GreA and GreB, the pause is prolonged, and RNA polymerase occupies a variant position at the pause site. Furthermore, GreA and GreB are required to mediate efficient function of the lambda gene Q antiterminator at this site. Thus, cleavage factors are necessary for the natural progression of RNA polymerase in vivo.

A structural model of transcription elongation

The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.

Interaction between RNA polymerase and RapA, a bacterial homolog of the SWI/SNF protein family

Recently, we identified a novel Escherichia coli RNA polymerase (RNAP)-associated protein, an ATPase, called RapA (Sukhodolets, M. V. , and Jin, D. J. (1998) J. Biol. Chem. 273, 7018-7023). RapA is a bacterial homolog of SWI2/SNF2. We showed that RapA forms a stable complex with RNAP holoenzyme and that binding to RNAP holoenzyme stimulates the ATPase activity of RapA. We have further analyzed the interactions between purified RapA and the two forms of RNAP: core RNAP and RNAP holoenzyme. We found that RapA interacts with either form of RNAP. However, RapA exhibits higher affinity for core RNAP than for RNAP holoenzyme. Chemical cross-linking of the RNAP-RapA complex indicated that the RapA-binding sites are located at the interface between the alpha and beta' subunits of RNAP. Contrary to previously reported results (Muzzin, O., Campbell, E., A., Xia, L., Severinova, E., Darst, S. A., and Severinov, K. (1998) J. Biol. Chem. 273, 15157-15161), our in vivo analysis of a rapA null mutant suggested that RapA is not likely to be directly involved in DNA repair.

The functional role of basic patch, a structural element of Escherichia coli transcript cleavage factors GreA and GreB

The transcript cleavage factors GreA and GreB of Escherichia coli are involved in the regulation of transcription elongation. The surface charge distribution analysis of their three-dimensional structures revealed that the N-terminal domains of GreA and GreB contain a small and large basic "patch," respectively. To elucidate the functional role of basic patch, mutant Gre proteins were engineered in which the size and charge distribution of basic patch were modified and characterized biochemically. We found that Gre mutants lacking basic patch or carrying basic patch of decreased size bind to RNA polymerase and induce transcript cleavage reaction in minimally backtracked ternary elongation complex (TEC) with the same efficiency as the wild type factors. However, they exhibit substantially lower readthrough and cleavage activities toward extensively backtracked and arrested TECs and display decreased efficiency of photocross-linking to the RNA 3'-terminus. Unlike wild type factors, basic patch-less Gre mutants are unable to complement the thermosensitive phenotype of GreA(-):GreB(-) E. coli strain. The large basic patch is required but not sufficient for the induction of GreB-type cleavage reaction and for the cleavage of arrested TECs. Our results demonstrate that the basic patch residues are not directly involved in the induction of transcript cleavage reaction and suggest that the primary role of basic patch is to anchor the nascent RNA in TEC. These interactions are essential for the readthrough and antiarrest activities of Gre factors and, apparently, for their in vivo functions.

RNA polymerase structure-function: insights into points of transcriptional regulation

The crystal structure of Thermus aquaticus RNA polymerase (RNAP) with 3.3 A resolution has recently been described. The high degree of sequence similarity between T. aquaticus RNAP and the prototypical RNAP from Escherichia coli invites comparison of the new structural data with genetic and biochemical results that defined the interaction sites of E. coli RNAP with transcription regulators.

Mapping interactions of Escherichia coli GreB with RNA polymerase and ternary elongation complexes

Escherichia coli GreA and GreB modulate transcription elongation by interacting with the ternary elongation complex (containing RNA polymerase, DNA template, and RNA transcript) to induce hydrolytic cleavage of the transcript and release of the 3'-terminal fragment. Hydroxyl radical protein footprinting and alanine-scanning mutagenesis were used to investigate the interactions of GreB with RNA polymerase alone and in a ternary elongation complex. A major determinant for binding GreB to both RNA polymerase and the ternary elongation complex was identified. In addition, the hydroxyl radical footprinting indicated major conformational changes of GreB, in terms of reorientations of the N- and C-terminal domains with respect to each other, particularly upon interactions with the ternary elongation complex.

Insights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallography

Our goal is to understand the mechanism of transcription and its regulation. Determining structures of RNA polymerase and transcription complexes is an essential step. Because of their large size and complexity, determination of these structures will require a combination of electron microscopy, biophysical methods, and biochemical methods to identify functionally and structurally relevant subassemblies and domains and x-ray crystallography to determine high-resolution structures of RNA polymerase components and accessory factors. We recently solved the 2.5-A crystal structure of the Escherichia coli RNA polymerase alpha subunit N-terminal domain, which is the first high-resolution structure of a core component required for RNA polymerase assembly and basal transcription. This structure, combined with a new 19-A resolution structure determined by cryo-electron microscopy of helical crystals of E. coli core RNAP embedded in vitreous ice, leads to a model for the organization of the RNAP subunits.