NanoRNAs: A Class of Small RNAs That Can Prime Transcription Initiation in Bacteria

Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
Journal of Molecular Biology (Impact Factor: 4.33). 06/2011; 412(5):772-81. DOI: 10.1016/j.jmb.2011.06.015
Source: PubMed


It has been widely assumed that all transcription in cells occur using NTPs only (i.e., de novo). However, it has been known for several decades that both prokaryotic and eukaryotic RNA polymerases can utilize small (2 to ∼5 nt) RNAs to prime transcription initiation in vitro, raising the possibility that small RNAs might also prime transcription initiation in vivo. A new study by Goldman et al. has now provided the first evidence that priming with so-called "nanoRNAs" (i.e., 2 to ∼5 nt RNAs) can, in fact, occur in vivo. Furthermore, this study provides evidence that altering the extent of nanoRNA-mediated priming of transcription initiation can profoundly influence global gene expression. In this perspective, we summarize the findings of Goldman et al. and discuss the prospect that nanoRNA-mediated priming of transcription initiation represents an underappreciated aspect of gene expression in vivo.

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    • "We argue that βW183 may be the key in preventing the formation of such alternative transcripts by limiting the transcriptional activity of the RPi during the various stages of DNA scrunching. Also, biasing towards RPi-dependent transcription by providing promoters with variable non-template strand lengths allowed the βW183 mutants to produce a larger number of short abortive RNAs in RPi (Figure 5C), which—along with intermediates of RNA degradation (41,42), products of RNA cleavage during elongation (43,44) and products of cyclic dinculeotide degradation (45–48) are one source of bacterial nano-RNAs (49–51). Such transcripts with a length of 2 to ∼5 nt can significantly alter the intracellular gene expression profile by (i) competing with nucleotides as primers for transcription initiations and extending the 5′ end of the resulting transcripts; (ii) changing the position where transcription begins (52); and (iii) affecting the phosphorylation state—and accordingly the stability of a transcript—by changing the 5′ end (48,53). "
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    ABSTRACT: The formation of the open promoter complex (RPo) in which the melted DNA containing the transcription start site is located at the RNA polymerase (RNAP) catalytic centre is an obligatory step in the transcription of DNA into RNA catalyzed by RNAP. In the RPo, an extensive network of interactions is established between DNA, RNAP and the σ-factor and the formation of functional RPo occurs via a series of transcriptional intermediates (collectively ‘RPi’). A single tryptophan is ideally positioned to directly engage with the flipped out base of the non-template strand at the +1 site. Evidence suggests that this tryptophan (i) is involved in either forward translocation or DNA scrunching and (ii) in σ54-regulated promoters limits the transcription activity of at least one intermediate complex (RPi) before the formation of a fully functional RPo. Limiting RPi activity may be important in preventing the premature synthesis of abortive transcripts, suggesting its involvement in a general mechanism driving the RPi to RPo transition for transcription initiation.
    Full-text · Article · Apr 2013 · Nucleic Acids Research
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    • "The term ''nanoRNA'' refers to RNA transcripts 2 to ;4 nt in length (Mechold et al. 2007). NanoRNAs can, in principle, be generated via a number of distinct cellular processes, including RNA degradation and abortive transcription initiation (for review, see Nickels and Dove 2011). Nevertheless, whether nanoRNAs can accumulate to sufficient concentrations to exert functional roles under physiological conditions has not been established. "
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    ABSTRACT: Prokaryotic and eukaryotic RNA polymerases can use 2- to ∼4-nt RNAs, "nanoRNAs," to prime transcription initiation in vitro. It has been proposed that nanoRNA-mediated priming of transcription can likewise occur under physiological conditions in vivo and influence transcription start site selection and gene expression. However, no direct evidence of such regulation has been presented. Here we demonstrate in Escherichia coli that nanoRNAs prime transcription in a growth phase-dependent manner, resulting in alterations in transcription start site selection and changes in gene expression. We further define a sequence element that determines, in part, whether a promoter will be targeted by nanoRNA-mediated priming. By establishing that a significant fraction of transcription initiation is primed in living cells, our findings contradict the conventional model that all cellular transcription is initiated using nucleoside triphosphates (NTPs) only. In addition, our findings identify nanoRNAs as a previously undocumented class of regulatory small RNAs that function by being directly incorporated into a target transcript.
    Full-text · Article · Jul 2012 · Genes & development
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    ABSTRACT: Processive RNases are unable to degrade efficiently very short oligonucleotides, and they are complemented by specific enzymes, nanoRNases, that assist in this process. We previously identified NrnA (YtqI) from Bacillus subtilis as a bifunctional protein with the ability to degrade nanoRNA (RNA oligos ≤5 nucleotides) and to dephosphorylate 3'-phosphoadenosine 5'-phosphate (pAp) to AMP. While the former activity is analogous to that of oligoribonuclease (Orn) from Escherichia coli, the latter corresponds to CysQ. NrnA homologs are widely present in bacterial and archaeal genomes. They are found preferably in genomes that lack Orn or CysQ homologs. Here, we characterize NrnA homologs from important human pathogens, Mpn140 from Mycoplasma pneumoniae, and Rv2837c from Mycobacterium tuberculosis. Like NrnA, these enzymes degrade nanoRNA and dephosphorylate pAp in vitro. However, they show dissimilar preferences for specific nanoRNA substrate lengths. Whereas NrnA prefers RNA 3-mers with a 10-fold higher specific activity compared to 5-mers, Rv2837c shows a preference for nanoRNA of a different length, namely, 2-mers. Mpn140 degrades Cy5-labeled nanoRNA substrates in vitro with activities varying within one order of magnitude as follows: 5-mer>4-mer>3-mer>2-mer. In agreement with these in vitro activities, both Rv2837c and Mpn140 can complement the lack of their functional counterparts in E. coli: CysQ and Orn. The NrnA homolog from Streptococcus mutans, SMU.1297, was previously shown to hydrolyze pAp and to complement an E. coli cysQ mutant. Here, we show that SMU.1297 can complement an E. coli orn(-) mutant, suggesting that having both pAp-phosphatase and nanoRNase activity is a common feature of NrnA homologs.
    Full-text · Article · Nov 2011 · RNA
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