Generally, mRNA secondary structures like hairpin, loop, stem will cause interference with the translation of protein. Given a DNA or RNA sequence, the secondary structure can be predicted and thus the relative translation efficiency (eg, translation initiation rate) can be predicted also. But in bacteria, transcription and translation might occur simultaneously that newly translated mRNA might not have enough time to form the secondary structure before ribosome binds to it. For example, if we have 1000 nt mRNA and we find a stem or haipin at 200 nt, will this affect the translation?To what extend will mRNA structure affect the translation in bacteria?
Bacteria have evolved enough to have RNA helicases - DEAD box proteins which have been shown to unwind double-stranded RNA and also bind to 5'UTRs in E. coli. That clearly indicates that secondary structures in 5'UTR need to be unwound for translation to take place, even in E. coli, especially under stress conditions.
Please consult the following papers:
http://www.sciencedirect.com/science/article/pii/S109727650600116X
http://www.nature.com/scitable/topicpage/riboswitches-a-common-rna-regulatory-element-14262702
Hey Daniel,
Indeed the transcribed mRNA of bacteria (procaryotes in general) has the time to fold up directly after the bases have been transcribed. This serves also a lot of purposes for the bacteria, in controlling gene expression. Especially as procaryotes contain a lot of polycistronic genes. As @Kandasamy already refered, there are quite some examples for riboswitches in procaryotes. But I want also to point out that procaryotes use something called "attenuation" (!) this is a procaryote-specific event, as (as you said) bacteria don't have a spatial separation of transcription and translation. During "attenuation", the procaryotic mRNA is transcribed and forms a stem loop which is then capable of interfering with the RNA-Polymerase. This process has something to do with the control of operons which are encoding for enzymes important for amino acid metabolism (e.g. tryptophan). Depending on the Trp concentration (for instance) in the cell, the mRNA might form different stem loops which result in an premature or normal transcription stop. If you wanna read more about it look for reviews or have a look at the original paper of Yanofsky,1981, Nature. There is also a nice Cell review paper on mRNA structures and their influence on gene expression (for eucaryotes and procaryotes) of Wachter,2014, Cell. But you should find attenuation for Trp, His or Phe also in a lot of text books.
I hope this helped you a bit in answering your question. Best regards, Felix
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