Functional Divergence in the Growing Family of RNA Polymerases

In plants, unorthodox multisubunit RNA polymerases (RNAPs) play key roles in small interfering RNA (siRNA) genesis and function. In a recent issue of Molecular Cell, Ream et al. (2009) established a 12-subunit composition for Arabidopsis RNAPIV and RNAPV. Subunit and sequence divergence between RNAPIV-V and RNAPI-III suggests significant functional deviation of these intriguing RNAPs

CoSMoS Unravels Mysteries of Transcription Initiation

Using a fluorescence method called colocalization single-molecule spectroscopy (CoSMoS), Friedman and Gelles dissect the kinetics of transcription initiation at a bacterial promoter. Ultimately, CoSMoS could greatly aid the study of the effects of DNA sequence and transcription factors on both prokaryotic and eukaryotic promoters

The elemental mechanism of transcriptional pausing.

Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged by backtracking or nascent RNA hairpins are recognized, the fundamental mechanism of the elemental pause is less well-defined. Here we report a mechanistic dissection that establishes the elemental pause signal (i) is multipartite; (ii) causes a modest conformational shift that puts γ-proteobacterial RNAP in an off-pathway state in which template base loading but not RNA translocation is inhibited; and (iii) allows RNAP to enter pretranslocated and one-base-pair backtracked states easily even though the half-translocated state observed in paused cryo-EM structures rate-limits pause escape. Our findings provide a mechanistic basis for the elemental pause and a framework to understand how pausing is modulated by sequence, cellular conditions, and regulators

Genome-wide mapping of the distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis chromosome using chromatin immunoprecipitation sequencing

CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis [6]. We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli [3], however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 [5] as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164)

Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria.

Bacterial H-NS forms nucleoprotein filaments that spread on DNA and bridge distant DNA sites. H-NS filaments co-localize with sites of Rho-dependent termination in Escherichia coli, but their direct effects on transcriptional pausing and termination are untested. In this study, we report that bridged H-NS filaments strongly increase pausing by E. coli RNA polymerase at a subset of pause sites with high potential for backtracking. Bridged but not linear H-NS filaments promoted Rho-dependent termination by increasing pause dwell times and the kinetic window for Rho action. By observing single H-NS filaments and elongating RNA polymerase molecules using atomic force microscopy, we established that bridged filaments surround paused complexes. Our results favor a model in which H-NS-constrained changes in DNA supercoiling driven by transcription promote pausing at backtracking-susceptible sites. Our findings provide a mechanistic rationale for H-NS stimulation of Rho-dependent termination in horizontally transferred genes and during pervasive antisense and noncoding transcription in bacteria

The leucine binding proteins of Escherichia coli as models for studying the relationships between protein structure and function

The genes encoding the leucine binding proteins in E coli have been cloned and their DNA sequences have been determined. One of the binding proteins (LIV-BP) binds leucine, isoleucine, valine, threonine, and alanine, whereas the oilier (LS-BP) binds only the D- and L-isomers of leucine. These proteins bind their solutes as they enter the periplasm, then interact with three membrane components, livH, livG, and livM, to achieve the translocation of the solute across the bacterial cell membrane. Another feature of the binding proteins is that they must be secreted into the periplasmic space where they carry out their function. The amino acid sequence of the two binding proteins is 80% homologous, indicating that they arc the products of an ancestral gene duplication. Because of these characteristics of the leucine binding proteins, we are using them as models for studying the relationships between protein structure and function.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38447/1/240290305_ftp.pd

The in vitro synthesis and processing of the branched-chain amino acid binding proteins

The synthesis of the leucine-specific and LIV-binding proteins was examined in vitro in a coupled transcription/translation system using the hybrid plasmids pOX7 and pOX13 as templates. Plasmid pOX7 contains the livK gene coding for the leucine-specific binding protein, and pOX13 contains the liv J gene coding for the LIV-binding protein. Both binding proteins were synthesized in vitro as precursor forms with molecular weights approximately 2,500 greater than their respective mature forms. Conversion of the precursor forms to their mature forms occurred during post-translational incubation following synthesis in the presence of membrane. The precursor of the LIV-binding protein was processed more rapidly than the leucine-specific binding protein precursor. Processing activity could be removed from the in vitro synthesis system by centrifugation, suggesting that the processing activity was membrane associated. Restoration of post-translational processing activity was achieved by adding inside-out membrane vesicles to membrane-depleted reaction mixtures.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38208/1/400140305_ftp.pd

Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain

Additional file 3. Fermentation profiles of Y133 and Y133-IIL in the presence of 1 % [BMIM]Cl at pH 6.5 and pH 5.0, and either aerobic or anaerobic conditions (n = 3, Mean ± S.E, except n = 2 for Y133 pH 6.5 anaerobic 72 h)

The bridge helix coordinates movements of modules in RNA polymerase

The RNA polymerase 'bridge helix' is a metastable α-helix that spans the leading edge of the enzyme active-site cleft. A new study published in BMC Biology reveals surprising tolerance to helix-disrupting changes in a region previously thought crucial for translocation, and suggests roles for two hinge-like segments of the bridge helix in coordinating modules that move during the nucleotide-addition cycle

Regulation of high-affinity leucine transport in escherichia coli

Leucine is transported into E coli by two osmotic shock-sensitive, high-affinity systems (LIV-I and leucine-specific systems) and one membrane bound, low-affinity system (LIV-II). Expression of the high-affinity transport systems is altered by mutations in liv R and 1st R , genes for negatively acting regulatory elements, and by mutations in rho , the gene for transcription termination. All four genes for high-affinity leucine transport ( livJ, livK, livH , and livG ) are closely linked and have been cloned on a plasmid vector, pOX1. Several subcloned fragments of this plasmid have been prepared and used in complementation and regulation studies. The results of these studies suggest that livJ and livK are separated by approximately one kilobase and give a gene order of livJ–livK–livH. livJ and livK appear to be regulated in an interdependent fashion; livK is expressed maximally when the livJ gene is inactivated by mutation or deletion. The results support the existence of separate promoters for the livJ and livK genes. The effects of mutations in the rho and livR genes are additive on one another and therefore appear to be involved in independent regulatory mechanisms. Mutations in the rho gene affect both the LIV-I and leucinespecific transport systems by increasing the expression of livJ and livK , genes for the LIV-specific and leucine-specific binding proteins, respectively.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38209/1/400140410_ftp.pd