Bacterial Transcription Terminators: The RNA 3 '-End Chronicles

Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Journal of Molecular Biology (Impact Factor: 4.33). 03/2011; 412(5):793-813. DOI: 10.1016/j.jmb.2011.03.036
Source: PubMed


The process of transcription termination is essential to proper expression of bacterial genes and, in many cases, to the regulation of bacterial gene expression. Two types of bacterial transcriptional terminators are known to control gene expression. Intrinsic terminators dissociate transcription complexes without the assistance of auxiliary factors. Rho-dependent terminators are sites of dissociation mediated by an RNA helicase called Rho. Despite decades of study, the molecular mechanisms of both intrinsic and Rho-dependent termination remain uncertain in key details. Most knowledge is based on the study of a small number of model terminators. The extent of sequence diversity among functional terminators and the extent of mechanistic variation as a function of sequence diversity are largely unknown. In this review, we consider the current state of knowledge about bacterial termination mechanisms and the relationship between terminator sequence and steps in the termination mechanism.

Full-text preview

Available from:
    • "This type of termination comprises a short hairpin followed by a U-rich sequence, which in contrast to Rho-dependent terminators do not require any assistance of proteins. As a consequence, intrinsic terminators are much more designable, although details of the molecular mechanism of Rhoindependent termination, despite decades of research, remain unknown (Peters et al., 2011). The ever increasing size of custom biological systems demands however a large set of available terminators. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
    No preview · Article · Oct 2015 · Biotechnology advances
  • Source
    • "There are at least two different ways to terminate transcription in Escherichia coli and other prokaryotes (Richardson, 2003; Peters et al., 2011). Intrinsic termination requires mainly elements located on the mRNA, whereas Rho-dependent termination relies on both mRNA elements and trans-acting factors (Richardson, 2003; Peters et al., 2011). In eukaryotes, two different pathways for transcriptional termination by RNA polymerase II have been proposed: One uses the Nrd1 complex, whereas the other uses 39 cleavage and polyadenylation factors together with Rat1 exonuclease (Rondon et al., 2008; Richard and Manley, 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Although transcription termination is essential to generate functional RNAs, its underlying molecular mechanisms are still poorly understood in plastids of vascular plants. Here, we show that the RNA binding protein RHON1 participates in transcriptional termination of rbcL (encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase) in Arabidopsis thaliana. Inactivation of RHON1 leads to enhanced rbcL read-through transcription and to aberrant accD (encoding β-subunit of the acetyl-CoA carboxylase) transcriptional initiation, which may result from inefficient transcription termination of rbcL. RHON1 can bind to the mRNA as well as to single-stranded DNA of rbcL, displays an RNA-dependent ATPase activity, and terminates transcription of rbcL in vitro. These results suggest that RHON1 terminates rbcL transcription using an ATP-driven mechanism similar to that of Rho of Escherichia coli. This RHON1-dependent transcription termination occurs in Arabidopsis but not in rice (Oryza sativa) and appears to reflect a fundamental difference between plastomes of dicotyledonous and monocotyledonous plants. Our results point to the importance and significance of plastid transcription termination and provide insights into its machinery in an evolutionary context. © 2014 American Society of Plant Biologists. All rights reserved.
    Full-text · Article · Dec 2014 · The Plant Cell
  • Source
    • "This is a unique feature of pol III as other RNA polymerase ternary complexes do not spontaneously disassemble at oligo(T) tracts (Arimbasseri et al., 2013b). Termination by other RNA polymerases requires a terminatorproximal RNA hairpin or other RNA duplex structure in addition to Trich tract, and in some cases use a mechanism that requires accessory factors (Richard and Manley, 2009; Peters et al., 2011; Arimbasseri et al., 2013c). The initial evidence that pol III was sufficient to terminate transcription at an oligo(T) tract without the need for RNA structure and in the absence of accessory factors (Bogenhagen and Brown, 1981; Cozzarelli et al., 1983; Wang and Folk, 1994) was confirmed by studies of bona fide pol III that more directly distinguish pausing and transcript release (Arimbasseri et al., 2014). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to Schizosaccharomyces pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5' and 3' processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3' oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3' oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a 'technical approaches' section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses. Published by Elsevier B.V.
    Full-text · Article · Nov 2014 · Gene
Show more