Messenger RNA in Prokaryotes

Abstract

Messenger ribonucleic acids (mRNAs) are molecules that represent the intermediate step in the conversion of genetic information carried in a cell's DNA (deoxyribonucleic acid) 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 good ribosome‐binding site (RBS) and appropriate spacing between the RBS and the translation start codon, control how effectively the information they contain is translated into functional proteins and play a role in the stability of the mRNAs. 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 bacteria is carried out by a series of nucleases that can initiate the degradation of the RNA molecule by cleaving at internal sites or by 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 bacteria, mRNAs must have a ribosome‐binding site (RBS) that is properly space upstream from the translation start site.
  • Secondary and tertiary structures of an mRNA can affect both its stability and functionality.
  • The physical location of an mRNA within a cell will affect its stability.
  • Riboswitches help control the expression of a large number of genes.
  • The translation and stability of many mRNAs is regulated by small regulatory RNAs (sRNAs).
  • mRNAs are degraded by a variety of pathways that utilise many different ribonucleases.
  • For many mRNAs decay is carried out by multiprotein complexes in both Gram‐negative and Gram‐positive bacteria.
  • Polyadenylation of mRNAs, particularly in Gram‐negative bacteria, stimulate their degradation.

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

Figure 1. Diagrammatic representation of a polycistronic mRNA (messenger ribonucleic acid). 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. Since 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 S‐adenosyl methionine (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‐ 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). Before RNase E binding, a combination of the RppH protein (RNA pyrophosphohydralase) and an as yet unidentified phosphatase convert the terminal triphosphate into a phosphomonoester in a two‐step reaction, thereby stimulating RNase E binding. In some cases, RNase E 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. Yellow square, RNase G cleavage site; magenta oval, RNase E cleavage site; orange pacman, RNase II, RNase R or polynucleotide phosphorylase.
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(Jan 2018) Messenger RNA in Prokaryotes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000874.pub4]