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So far "broken" mRNAs lacking termination codons [6], [7], and mRNAs possessing inefficient termination codons [8], certain C-terminal codons [9], or containing rare codons [10] have been shown to elicit tmRNA tagging.
The extra nucleotides in the transcript due to an inefficient termination (or the lack of nucleotides due to a premature termination) may influence the folding of the global structure [ 7].
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This is important for chloroplast ncRNA identification, as promoters often share little sequence homology and inefficient transcription termination can result in multiple 3′ ends (Bollenbach et al. 2008; Liere and Borner 2008).
The module which expressed GFP from the pHrpL promoter was assembled upstream of the pBAD-HrpS and pRHAB-HrpR modules to attenuate genetic context-dependent effects that might arise from transcriptional overrun of the stronger pBAD and pRHAB input expression modules as a result of inefficient transcription termination.
Additionally, ribosome pausing at stop codons during inefficient translation termination leads to tmRNASmpB activity in E. coli [19], [20], [21].
Full symmetric transcription of the chloroplast genome is consistent with its well-described inefficient transcription termination, and it implies a heavy reliance on posttranscriptional regulatory mechanisms.
However, ROMA includes other sources of false positives, most importantly read-through transcripts into adjacent genes due to inefficient transcription termination in vitro, as well as ambiguities derived from impure protein preparation or the microarray analysis as such (65).
However, it does play a major role in the evolutionarily related plant chloroplasts, in which it compensates for inefficient transcription termination by removal of antisense RNA (Sharwood et al. 2011).
In this case, the observed minimal transcription is likely a function of the frequency of promoters throughout the plastome and inefficient, stochastic transcription termination in plastids which contribute to transcription of virtually the entire plastome (Hotto et al. 2012; Zhelyazkova et al. 2012).
Co-transcription may be facilitated by close spacing of genes in cpDNA because transcription termination is inefficient [ 57].
Feschotte and Wessler (2001) proposed that capture of host sequences occurs when there is inefficient recognition of the termination signal of a Helitron close to the captured region leading to the transduction of adjacent downstream host sequence and later termination by a random signal.
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