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 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.


Babitzke P and Yanofsky C (1995) Structural features of L‐tryptophan required for activation of TRAP, the trp RNA‐binding attenuation protein of Bacillus subtilis. Journal of Biological Chemistry 270: 12452–12456.

Bechhofer D (1993) 5′ mRNA stabilizers. In: Belasco J and Brawerman G (eds) Control of Messenger RNA Stability, pp. 31–35. San Diego, CA: Academic Press.

Blattner FR, Plunkett G III, Bloch CA, et al. (1997) The complete sequence of Escherichia coli K‐12. Science 277: 1453–1474.

Brenner S, Jacob F and Meselson M (1961) An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 190: 576–581.

Cao G‐J and Sarkar N (1992) Identification of the gene for an Escherichia coli poly(A) polymerase. Proceedings of the National Academy of Sciences of the United States of America 89: 10380–10384.

Carpousis AJ, Van Houwe G, Ehretsmann C and Krisch HM (1994) Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76: 889–900.

Caskey CT, Tompkins R, Scolnick E, Caryk T and Nirenberg M (1968) Sequential translation of trinucleotide codons for the initiation and termination of protein synthesis. Science 162: 135–138.

Condon C (2007) Maturation and degradation of RNA in bacteria. Current Opinion in Microbiology 10: 271–278.

Crick FH, Barnett L, Brenner S and Watts‐Tobin RJ (1961) General nature of the genetic code for proteins. Nature 192: 1227–1232.

Deana A, Celesnik H and Belasco JG (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451: 355–358.

Deutscher MP (1993) Promiscuous exoribonucleases of Escherichia coli. Journal of Bacteriology 175: 4577–4583.

Dunn JJ and Studier FW (1975) Effect of RNAase III, cleavage on translation of bacteriophage T7 messenger RNAs. Journal of Molecular Biology 99: 487–499.

Durand S, Gilet L, Bessieres P, Nicolas P and Condon C (2012) Three essential ribonucleases‐RNase Y, J1, and III‐control the abundance of a majority of Bacillus subtilis mRNAs. PLoS Genetics 8: e1002520.

Emory SA, Bouvet P and Belasco JG (1992) A 5′‐terminal stem‐loop structure can stabilize mRNA in Escherichia coli. Genes and Development 6: 135–148.

Eschbach SH, St‐Pierre P, Penedo JC and Lafontaine DA (2012) Folding of the SAM‐I riboswitch: a tale with a twist. RNA Biology 9: 535–541.

Feng Y, Huang H, Kiao J and Cohen SN (2001) Escherichia coli poly(A) binding proteins that interact with components of degradosomes or impede RNA decay mediated by polynucleotide phosphorylase and RNase E. Journal of Biological Chemistry 276: 31651–31656.

Figaro S, Durand S, Gilet L, et al. (2013) Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence. Journal of Bacteriology 195: 2340–2348.

Gottesman S and Storz G (2011) Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harbor Perspectives in Biology 3. pii: a003798.

Jacob F and Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3: 318–356.

Khemici V, Poljak L, Luisi BF and Carpousis AJ (2008) The RNase E of Escherichia coli is a membrane‐binding protein. Molecular Microbiology 70: 799–813.

Khorana HG (1965) Polynucleotide synthesis and the genetic code. Federation Proceedings 24: 1473–1487.

Kushner SR (2004) mRNA decay in bacteria and eukaryotes: different approaches to a similar problem. IUBMB Life 56: 585–594.

Lehnik‐Habrink M, Pfortner H, Rempeters L, et al. (2010) The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex. Molecular Microbiology 77 (4): 958–971.

Lehnik‐Habrink M, Lewis RJ, Mader U and Stulke J (2012) RNA degradation in Bacillus subtilis: an interplay of essential endo‐ and exoribonucleases. Molecular Microbiology 84: 1005–1017.

Luciano DJ, Vasilyev N, Richards J, Serganov A and Belasco JG (2017) A novel RNA phosphorylation state enables 5′ end‐dependent degradation in Escherichia coli. Molecular Cell 67 (44–54): e46.

Mackie GA (2013) RNase E: at the interface of bacterial RNA processing and decay. Nature Reviews. Microbiology 11: 45–57.

Mathy N, Benard L, Pellegrini O, et al. (2007) 5′‐to‐3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129: 681–692.

Mildenhall KB, Wiese N, Chung D, et al. (2016) RNase E‐based degradosome modulates polyadenylation of mRNAs after Rho‐independent transcription terminators in Escherichia coli. Molecular Microbiology 101: 645–655.

Mizuno T, Chou MY and Inouye M (1984) A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proceedings of the National Academy of Sciences of the United States of America 81: 1966–1970.

Mohanty BK and Kushner SR (1999) Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Molecular Microbiology 34: 1094–1108.

Mohanty BK and Kushner SR (2000a) Polynucleotide phosphorylase functions both as a 3′–5′ exonuclease and a poly(A) polymerase in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 97: 11966–11971.

Mohanty BK and Kushner SR (2000b) Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Molecular Microbiology 36: 982–994.

Mohanty BK, Maples VF and Kushner SR (2004) The Sm‐like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Molecular Microbiology 54: 905–920.

Mohanty BK and Kushner SR (2016) Regulation of mRNA decay in bacteria. Annual Review of Microbiology 70: 25–44.

Nudler E and Mironov AS (2004) The riboswitch control of bacterial metabolism. Trends in Biochemical Sciences 29: 11–17.

Pobre V and Arraiano CM (2015) Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli. BMC Genomics 16: 72.

Portier C, Dondon L, Grunberg‐Manago M and Regnier P (1987) The first step in the functional inactivation of the Escherichia coli polynucleotide phosphorylase messenger is ribonuclease III processing at the 5′ end. EMBO Journal 6: 2165–2170.

Py B, Higgins CF, Krisch HM and Carpousis AJ (1996) A DEAD‐box RNA helicase in the Escherichia coli RNA degradosome. Nature 381: 169–172.

Richards J, Liu Q, Pellegrini O, et al. (2011) An RNA pyrophosphohydrolase triggers 5′‐exonucleolytic degradation of mRNA in Bacillus subtilis. Molecular Cell 43: 940–949.

Schweisguth DC, Chelladurai BS, Nicholson AW and Moore PB (1994) Structural characterization of a ribonuclease III processing signal. Nucleic Acids Research 22: 604–612.

Shine J and Dalgarno L (1974) The 3′‐terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proceedings of the National Academy of Sciences of the United States of America 71: 1342–1346.

Spickler C and Mackie GA (2000) Action of RNase II and polynucleotide phosphorylase against RNAs containing stem‐loops of defined structure. Journal of Bacteriology 182: 2422–2427.

Stead MB, Marshburn S, Mohanty BK, Mitra J, et al. (2010) Analysis of E. coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Research 39: 3188–3203.

Stern MJ, Ames GF‐L, Smith NH, Robinson EC and Higgins CF (1984) Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37: 1015–1026.

Watson JD and Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171: 737–738.

Yanofsky C (1981) Attenuation in the control of expression of bacterial operons. Nature 289: 751–758.

Yao S, Richards J, Belasco JG and Bechhofer DH (2011) Decay of a model mRNA in Bacillus subtilis by a combination of RNase J1 5′ exonuclease and RNase Y endonuclease activities. Journal of Bacteriology 193: 6384–6386.

Further Reading

Arraiano CM, Andrade JM, Dominques S, et al. (2010) The critical role of RNA degradation in the control of gene expression. FEMS Microbiology Reviews 34: 883–923.

Denoyers G, Bouchard M‐P and Massé E (2013) New insights into small RNA‐dependent translation regulation in prokaryotes. Trends in Genetics 29: 92–98.

Lehnik‐Habrink M, Lewis RJ, Mader U and Stulke J (2012) RNA degradation in Bacillus subtilis: an interplay of essential endo‐ and exoribonucleases. Molecular Microbiology 84: 1005–1017.

Mackie GA (2013) RNase E: at the interface of bacterial RNA processing and decay. Nature Reviews Microbiology 11: 45–57.

Mohanty BK and Kushner SR (2010) Bacterial/archaeal/organellar polyadenylation. WIREs RNA 2: 256–276.

Mohanty BK and Kushner SR (2016) Regulation of mRNA decay in bacteria. Annual Review of Microbiology 70: 25–44.

Serganov A and Nudler E (2013) A decade of riboswitches. Cell 152: 17–24.

Snyder L, Peters JE, Henkin TM and Champness W (2013) Molecular Genetics of Bacteria. Washington, DC: ASM Press.

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Kushner, Sidney R(Jan 2018) Messenger RNA in Prokaryotes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000874.pub4]