Conserved economics of transcription termination in eubacteria

Unniraman, Shyam; Prakash, Ranjana; Nagaraja, Valakunja

doi:10.1093/nar/30.3.675

Cited by 82 publications

(71 citation statements)

References 30 publications

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“…Since this polar effect on gene expression is mediated through an effect on transcription, it closely resembles the process of polarity in bacteria. However, the mechanism responsible for polarity in archaea is unclear since homologues of the bacterial termination factor, Rho, are not evident in the genome of S. solfataricus or other archaea (Santangelo & Reeve, 2006), and bacterial terminators are largely absent (Ermolaeva et al, 2000;Unniraman et al, 2002). While cotranscription can be inferred by detection of transcribed intergenic sequences using RT-PCR, in the case of mer an internal promoter had been proposed that could bypass a requirement for coupled gene expression (Schelert et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

et al. 2013

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Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II), inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously derepresses transcription of a resistance operon, merHAI, through interaction with the MerR transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH nonsense mutant arose through transcriptional polarity, and its metal resistance was restored partially by single copy merH complementation. Since MerH was not required in vitro for MerA-catalysed Hg(II) reduction, MerH may play an alternative role in metal resistance. Inductively coupled plasma-mass spectrometry analysis of the MerH deletion strain following metal challenge indicated that there was prolonged retention of intracellular Hg(II). Finally, a reduced rate of mer operon induction in the merH deletion mutant suggested that the requirement for MerH could result from metal trafficking to the MerR transcription factor.

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Section: Discussionmentioning

confidence: 99%

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

et al. 2013

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“…The efficacy of a given terminator may be influenced by the folding energy of the stem and the identity of the poly(U) trail known to follow the stem-loop structure of transcriptional terminators (9). The GeSTer algorithm identifies both terminators as adopting an L-shape, i.e., containing a poly(U) trail following the stem-loop structure, and those with an I-shape without the poly(U) trail (46). Unniraman and coworkers argue that the significance of the U trail, at least in E. coli, still remains unclear and points to the thr (30) and crp (3) terminators with demonstrable contradistinct dependency of the U-run in transcriptional termination.…”

Section: Discussionmentioning

confidence: 99%

“…The GenBank files of the different genomes were scanned for the presence of transcriptional terminators with a genome scanner for terminators (GeSTer; available at ftp://ftp.bork .embl-heidelberg.de/pub/users/suyama) (46,47). The parameters used were the following: minimum stem length of 4, maximum stem length of 30, minimum bulb length of 3, maximum bulb length of 9, maximum mismatches allowed (i.e., internal loops plus bulges) of 3, maximum distance from open reading frame of 270.…”

Section: Vol 189 2007 Dus Efficiency In Meningococcal Transformatiomentioning

confidence: 99%

New Functional Identity for the DNA Uptake Sequence in Transformation and Its Presence in Transcriptional Terminators

2007

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The frequently occurring DNA uptake sequence (DUS), recognized as a 10-bp repeat, is required for efficient genetic transformation in the human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. Genome scanning for DUS occurrences in three different species of Neisseria demonstrated that 76% of the nearly 2,000 neisserial DUS were found to have two semiconserved base pairs extending from the 5 end of DUS to constitute a 12-mer repeat. Plasmids containing sequential variants of the neisserial DUS were tested for their ability to transform N. meningitidis and N. gonorrhoeae, and the 12-mer was found to outperform the 10-mer DUS in transformation efficiency. Assessment of meningococcal uptake of DNA confirmed the enhanced performance of the 12-mer compared to the 10-mer DUS. An inverted repeat DUS was not more efficient in transformation than DNA species containing a single or direct repeat DUS. Genome-wide analysis revealed that half of the nearly 1,500 12-mer DUS are arranged as inverted repeats predicted to be involved in rho-independent transcriptional termination or attenuation. The distribution of the uptake signal sequence required for transformation in the Pasteurellaceae was also biased towards transcriptional terminators, although to a lesser extent. In addition to assessing the intergenic location of DUS, we propose that the 10-mer identity of DUS should be extended and recognized as a 12-mer DUS. The dual role of DUS in transformation and as a structural component on RNA affecting transcription makes this a relevant model system for assessing significant roles of repeat sequences in biology.Repeat sequences are a prominent feature of all genomes, promoting recombination and other forms of genetic variability (4, 17). The neisserial DNA uptake sequence (DUS), 5Ј-G CCGTCTGAA-3Ј, and the Haemophilus influenzae uptake signal sequence (USS), 5Ј-AAGTGCGGT-3Ј, are required for efficient transformation (12, 23). The recognition of homospecific DNA by means of DUS and USS is a hallmark of transformation in the genus Neisseria (5,15,23,25) and several species in the family Pasteurellaceae (12, 48). A potential DUSor USS-specific DNA-binding receptor is, however, yet to be identified. All neisserial genome sequences available to date accommodate approximately 2,000 copies of DUS per genome, occupying as much as 1% of the chromosomes (32, 42). The extensive analysis on the abundance and distribution of DUS in Neisseria meningitidis Z2491 by Smith and coworkers (36) documented that sequence conservation exists in positions Ϫ1 and Ϫ2 of the 10-mer DUS. The T at Ϫ1 and A at Ϫ2 were found at high frequencies in all DUS. This particular finding has since then been overlooked in neisserial research and also in affinity and transformation studies, and the biological impact of this extended DUS, here termed the 12-mer DUS, has remained unexplored. We show that the two semiconserved residues 5Ј of the 10-mer DUS are both present in 76% of all DUS occurrences in every neisserial genome sequence available, and we dem...

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“…If this is the case, the permeases may be transcriptionally linked to the conserved gene cluster, even though they do not seem to share any functional similarity. Neither the hairpin terminator prediction program TransTerm (10) nor GeSTer (29) predicts a terminator between ftsZ and these genes.…”

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confidence: 99%

Transcriptional Analysis of the Conserved ftsZ Gene Cluster in Mycoplasma genitalium and Mycoplasma pneumoniae

Benders¹,

Powell²,

Hutchison

2005

J Bacteriol

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Several experimental approaches were used to construct a detailed transcriptional profile of the phylogenetically conserved ftsZ cell division gene cluster in both Mycoplasma genitalium and its closest relative, Mycoplasma pneumoniae. We determined initiation and termination points for the cluster, as well as an absolute steady-state RNA level for each gene. Transcription of this cluster in both these organisms was shown to be highly strand specific. While the four genes in this cluster are cotranscribed, their transcription unit also includes two genes of close proximity yet disparate function. A transcription initiation point immediately upstream of these two genes was detected in M. genitalium but not M. pneumoniae. In M. pneumoniae, transcription of the six genes terminates at a poly(U)-tailed hairpin. In M. genitalium, this transcription terminates at two closely spaced points by an unknown mechanism. Real-time reverse transcription-PCR analysis of this cluster in M. pneumoniae shows that mRNA levels for all six genes vary at most fivefold and form a gradient of decreasing quantity with increasing distance from the promoter at the beginning of the cluster. mRNA from coding regions was approximately 20-to 100-fold more abundant than that from intergenic regions. We estimated the most abundant mRNA we detected at 0.6 copy per cell. We conclude that groups of functionally related genes in M. genitalium and M. pneumoniae are often preceded by promoters but rarely followed by terminators. This causes functionally unrelated genes to be commonly cotranscribed in these organisms.

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Conserved economics of transcription termination in eubacteria

Cited by 82 publications

References 30 publications

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

New Functional Identity for the DNA Uptake Sequence in Transformation and Its Presence in Transcriptional Terminators

Transcriptional Analysis of the Conserved ftsZ Gene Cluster in Mycoplasma genitalium and Mycoplasma pneumoniae

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