Editing Stop codon (section)

== Hidden stops ==
[[File:Frameshift deletion (13062713935).jpg|thumb|An example of a single base deletion forming a stop codon.]]
'''Hidden stops''' are non-stop codons that would be read as stop codons if they were [[frameshift]]ed +1 or −1. These prematurely terminate translation if the corresponding frame-shift (such as due to a ribosomal RNA slip) occurs before the hidden stop. It is hypothesised that this decreases resource wastage on nonfunctional proteins and the production of potential [[Cytotoxicity|cytotoxins]]. Researchers at [[Louisiana State University]] propose the ''[[ambush hypothesis]]'', that hidden stops are selected for. Codons that can form hidden stops are used in genomes more frequently compared to synonymous codons that would otherwise code for the same amino acid. Unstable [[Ribosomal RNA|rRNA]] in an organism correlates with a higher frequency of hidden stops.<ref>{{cite journal |pages=701–5 |doi=10.1089/1044549042476910 |title=The Ambush Hypothesis: Hidden Stop Codons Prevent Off-Frame Gene Reading |year=2004 |last1=Seligmann |first1=Hervé |last2=Pollock |first2=David D. |journal=DNA and Cell Biology |volume=23 |issue=10 |pmid=15585128}}</ref>
However, this hypothesis could not be validated with a larger data set.<ref>{{cite journal |pages=1–8 |doi=10.1186/1471-2164-14-418 |title=Ambushing the ambush hypothesis: predicting and evaluating off-frame codon frequencies in Prokaryotic Genomes |year=2013 |last1=Cavalcanti|first1=Andre|last2=Chang |first2=Charlotte H.|last3=Morgens|first3=David W.|journal=BMC Genomics|volume=14 |issue=418 |pmid=23799949 |pmc=3700767 |doi-access=free }}</ref>

Stop-codons and hidden stops together are collectively referred as stop-signals. Researchers at [[University of Memphis]] found that the ratios of the stop-signals on the three reading frames of a genome (referred to as translation stop-signals ratio or TSSR) of genetically related bacteria, despite their great differences in gene contents, are much alike. This nearly identical genomic-TSSR value of genetically related bacteria may suggest that bacterial genome expansion is limited by their unique stop-signals bias of that bacterial species.<ref>{{cite journal |pages= 255–85| doi=10.1080/10590501.2015.1053461 |title=Protein mis-termination initiates genetic diseases, cancers, and restricts bacterial genome expansion |year=2015 |last1=Wong | first1=Tit-Yee|last2=Schwartzbach |first2=Steve|journal=Journal of Environmental Science and Health, Part C |pmid=26087060 |volume=33| issue=3 | bibcode=2015JESHC..33..255W | s2cid=20380447 }}</ref>