Structure of prokaryotic mRNAs

The polycistronic structure of prokaryotic mRNA presents another intriguing prospect. In some cases, a downstream cistron lacking a strong (or exposed) RBS is... 

See also Structure of Prokaryotic mRNAs, Structure of tRNAs, Ribosomes, Initiation of Translation, Elongation of Translation, Termination of Translation... 

See also mRNA Turnover, Ribozymes (from Chapter 11), Structure of tRNAs (from Chapter 27), Structure of Prokaryotic mRNAs (from Chapter 27)... 

Structures of prokaryotic and eukaryotic primary transcripts (mRNAs). Prokaryotic mRNAs are polygenic, do not contain introns or exons, and are short lived in the cell. Eukaryotic mRNAs are monogenic, contain introns and exons, and usually are long lived in the cell. 

What are the major differences in the synthesis and structure of prokaryotic and eukaryotic mRNAs ... 

Initiation The components of the translation system are assembled, and mRNA associates with the small ribosomal subunit. The process requires initiation factors. In prokaryotes,a purine-rich region (the Shine-Dalgarno sequence) of the mRNA base-pairs with a complementary sequence on 16S rRNA, resulting in the positioning of the mRNA so that translation can begin. The 5 -cap on eukaryotic mRNA is used to position that structure on the ribosome. The initiation codon is 5 -AUG-3. ... 

The cap protects the 5 end of the primary transcript against attack by ribonu-cleases that have specificity for 3 5 phosphodiester bonds and so cannot hydrolyze the 5 5 bond in the cap structure. In addition, the cap plays a role in the initiation step of protein synthesis in eukaryotes. Only RNA transcripts from eukaryotic protein-coding genes become capped prokaryotic mRNA and eukaryotic rRNA and tRNAs are uncapped. 

Kozak M (2005), Regulation of translation via mRNA structure in prokaryotes and eukaryotes, Gene 361 13-37. 

Gene expression can also be regulated at the level of translation. In prokaryotes, many operons important in amino acid biosynthesis are regulated by attenuation, a process that depends on the formation of alternative structures in mRNA, one of which favors transcriptional termination. Attenuation is mediated by the translation of a leader region of mRNA. A ribosome stalled by the absence of an aminoacyl-tRNA needed to translate the leader mRNA alters the structure of mRNA so that RNA polymerase transcribes the operon beyond the attenuator site. 

Whereas the structure of mRNA determines its susceptibility to degradative enzymes, the detailed mechanisms are complex. In prokaryotes, the enzymes involved include two endonucleases (RNase E and RNase III) and two exonucleases (polynucleotide phosphorylase and RNase II). Other nucleases may be active in particular cases such as phage infection. In eukaryotes, a major pathway involves removal of the 3 poly(A) tail (deadenylation), followed by removal of the 5 cap, which renders the mRNA susceptible to rapid endonucleolytic degradation in the 5 3 ... 

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