Messenger RNA in Prokaryotes


Messenger ribonucleic acids (mRNAs) are molecules that represent the intermediate step in the conversion of genetic information carried in a cell's deoxyribonucleic acid (DNA) into functional proteins. They are synthesised by the enzyme RNA polymerase, which recognises specific sequences in the DNA (promoters) to initiate the process called transcription. Downstream sequences, called terminators, provide the signals for transcription to stop. Structural features of mRNAs, such as the presence of a strong ribosome‐binding site (RBS) and appropriate spacing between the RBS and the translation start codon, control both how effectively the information they contain is translated into functional proteins and how rapidly they are decayed. The steady‐state level of each mRNA, which is determined by the rate of its synthesis versus the rate of its decay, helps regulate how much protein is synthesised from each mRNA. mRNA decay in prokaryotes is carried out by a series of nucleases that can either degrade the RNA molecule by cleaving at internal sites or removing one nucleotide at a time from either the 5′ or 3′ terminus.

Key Concepts:

  • RNA is distinguished from DNA by the presence of ribose instead of deoxyribose and uracil instead of thymine.

  • Messenger RNAs are required for converting the genetic information in the DNA into functional proteins.

  • More than one protein can be encoded in a single mRNA.

  • In prokaryotes mRNAs must have a ribosome binding site in order to be translated.

  • Secondary and tertiary structures within an mRNA affect its stability and functionality.

  • Riboswitches help regulate the expression of a large number of genes.

  • mRNAs are degraded by a variety of ribonucleases.

  • mRNA decay is carried out by multiprotein complexes in bacteria.

  • Polyadenylation of mRNAs in bacteria stimulate their degradation.

  • The translation and stability of many mRNAs are regulated by sRNAs.

Keywords: transcription; translation; ribonucleases; polyadenylation; decay; riboswitch; small regulatory RNA

Figure 1.

Diagrammatic representation of a polycistronic mRNA. This polycistronic mRNA contains the coding sequences for three different genes that have originated from a single transcription start site upstream of Gene 1. Each gene has its own ribosome‐binding site (RBS) as well as a translation start and translation stop. The intercistronic spacer region (dotted line) can vary in length from −1 nucleotide to approximately 40 nucleotides in length.

Figure 2.

Structural features of an mRNA molecule that can affect its stability. (a) Rho‐independent transcription terminators result in the formation of a stem–loop structure in an mRNA molecule by the pairing of complementary nucleotides. As the formation of the double‐stranded region generates a structure that is energetically more stable than the single‐stranded molecule, the stem–loop will rapidly form in vivo. (b) Diagrammatic representation of an mRNA molecule showing possible stability elements at both the 5′ and 3′ ends. In addition, upward arrows indicate the presence of endonucleolytic cleavage sites that would lead to the functional inactivation of the mRNA. The relative positions of the RBS, the translation start and the translation stop are also indicated.

Figure 3.

Structures associated with the SAM regulated riboswitch from the Gram‐positive bacteria Enterococcuc faecalis. A two‐dimensional representation of the SAM‐regulated riboswitch is shown. In the absence of SAM, the RBS is exposed and translation can occur. In the presence of SAM, a reorganisation of the 5′ leader region takes place such that the RBS is now paired with nucleotides in the anti‐RBS such that translation cannot be initiated. Riboswitches can exert anywhere from 2‐fold to >100‐fold levels of control.

Figure 4.

Model for mRNA decay in E. coli. For most mRNAs in E. coli, RNase E will initiate decay by first binding to the 5′ end of the transcript, probably as part of the multiprotein complex called the degradosome (not shown here for the sake of simplicity). However, before RNase E binding, the RppH protein (RNA pyrophosphohydralase) converts the terminal triphosphate into a phosphomonester, thereby stimulating RNase E binding. In some cases, it will attack an mRNA at an internal location in the absence of binding to the 5′ terminus. Once the initial cleavage takes place, RNase E and/or RNase G can continue degrading the mRNA, moving in a 5′→3′ direction. The endonucleolytic cleavage products are subsequently degraded in the 3′→5′ direction by either polynucleotide phosphorylase, RNase II or RNase R. For those species that have secondary structures at their 3′ termini, poly(A) polymerase adds A residues to enhance the binding of the 3′→5′ exonucleases.

Figure 5.

Structure of MicF sRNA. The nucleotide sequence of the 93‐nucleotide MicF sRNA. The residues shown in red can pair with complementary bases in the 5′ region of the OmpF mRNA leading to the downregulation of OmpF protein synthesis.



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Kushner, Sidney R(May 2014) Messenger RNA in Prokaryotes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000874.pub3]