Transcription-translation coupling

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Transcription-translation coupling is a mechanism of gene expression regulation in which synthesis of an mRNA (transcription) is affected by its concurrent decoding (translation). In prokaryotes, mRNAs are translated while they are transcribed. This allows communication between RNA polymerase, the multisubunit enzyme that catalyzes transcription, and the ribosome, which catalyzes translation. Coupling involves both direct physical interactions between RNA polymerase and the ribosome ("expressome" complexes), as well as ribosome-induced changes to the structure and accessibility of the intervening mRNA that affect transcription ("attenuation" and "polarity"). [1] [2] [3]

Contents

Significance

Bacteria depend on transcription-translation coupling for genome integrity, termination of transcription and control of mRNA stability. Consequently, artificial disruption of transcription-translation coupling impairs the fitness of bacteria. Without coupling, genome integrity is compromised as stalled transcription complexes interfere with DNA replication and induce DNA breaks. [4] Lack of coupling produces premature transcription termination, likely due to increased binding of termination factor Rho. [5] Degradation of prokaryotic mRNAs is accelerated by loss of coupled translation due to increased availability of target sites of RNase E. [6] It has also been suggested that coupling of transcription with translation is an important mechanism of preventing formation of deleterious R-loops. [7] While transcription-translation coupling is likely prevalent across prokaryotic organisms, not all species are dependent on it. Unlike Escherichia coli , in Bacillus subtilis transcription significantly outpaces translation, and coupling consequently does not occur. [8]

Mechanisms

Translation promotes transcription elongation and regulates transcription termination. Functional coupling between transcription and translation is caused by direct physical interactions between the ribosome and RNA polymerase ("expressome complex"), ribosome-dependent changes to nascent mRNA secondary structure which affect RNA polymerase activity (e.g. "attenuation"), and ribosome-dependent changes to nascent mRNA availability to transcription termination factor Rho ("polarity").

Expressome complex

The expressome is a supramolecular complex consisting of RNA polymerase and a trailing ribosome linked by a shared mRNA transcript. It is supported by the transcription factors NusG and NusA, which interact with both RNA polymerase and the ribosome to couple the complexes together. [9] [10] [11] When coupled by transcription factor NusG, the ribosome binds newly synthesized mRNA and prevents formation of secondary structures that inhibit transcription. [9] Formation of an expressome complex also aids transcription elongation by the trailing ribosome opposing back-tracking of RNA polymerase. [12] [13] Three-dimensional models of ribosome-RNA polymerase expressome complexes have been determined by cryo-electron microscopy. [14] [10] [11] [9]

Ribosome-mediated attenuation

Ribosome-mediated attenuation is a gene expression mechanism in which a transcriptional termination signal is regulated by translation. [15] [16] [17] Attenuation occurs at the start of some prokaryotic operons at sequences called "attenuators", which have been identified in operons encoding amino acid biosynthesis enzymes, pyrimidine biosynthesis enzymes and antibiotic resistance factors. The attenuator functions via a set of mRNA sequence elements that coordinate the status of translation to a transcription termination signal:

Once the start of the leader open reading frame has been transcribed, RNA polymerase pauses due to folding of the nascent mRNA. This programmed arrest of transcription gives time for translation of the leader peptide to commence, and transcription to resume once coupled to translation. The downstream "control region" then modulates the elongation rate of either the ribosome or RNA polymerase. The factor determining this depends on the function of the downstream genes (e.g. the operon encoding enzymes involved in the synthesis of histidine contains a series of histidine codons is the control region). The role of the control region is to modulate whether transcription remains coupled to translation depending on the cellular state (e.g. a low availability of histidine slows translation leading to uncoupling, while high availability of histidine permits efficient translation and maintains coupling). Finally, the transcription terminator sequence is transcribed. Whether transcription is coupled to translation determines whether this stops transcription. The terminator requires folding of the mRNA, and by unwinding mRNA structures the ribosome elects the formation of either of two alternative structures: the terminator, or a competing fold termed the "antiterminator".

For amino acid biosynthesis operons, these allow the gene expression machinery to sense the abundance of the amino acid produced by the encoded enzymes, and adjust the level of downstream gene expression accordingly: transcription occurring only if the amino acid abundance is low and the demand for the enzymes is therefore high. Examples include the histidine (his) [18] [19] and tryptophan (trp) [20] biosynthetic operons.

The term "attenuation" was introduced to describe the his operon. [18] While it is typically used to describe biosynthesis operons of amino acids and other metabolites, programmed transcription termination that does not occur at the end of a gene was first identified in λ phage. [21] The discovery of attenuation was significant as it represented a regulatory mechanism distinct from repression. [22] [23] The trp operon is regulated by both attenuation and repression, and was the first evidence that gene expression regulation mechanisms can be overlapping or redundant. [17]

Polarity

"Polarity" is a gene expression mechanism in which transcription terminates prematurely due to a loss of coupling between transcription and translation. Transcription outpaces translation when the ribosome pauses[ citation needed ] or encounters a premature stop codon. [24] This allows the transcription termination factor Rho to bind the mRNA and terminate mRNA synthesis. Consequently, genes that are downstream in the operon are not transcribed, and therefore not expressed. Polarity serves as mRNA quality control, allowing unused transcripts to be terminated prematurely, rather than synthesized and degraded. [25]

The term "polarity" was introduced to describe the observation that the order of genes within an operon is important: a nonsense mutation within an upstream gene effects the transcription of downstream genes. [24] Furthermore, the position of the nonsense mutation within the upstream gene modulates the "degree of polarity", with nonsense mutations at the start of the upstream genes exerting stronger polarity (more reduced transcription) on downstream genes.

Unlike the mechanism of attenuation, which involves intrinsic termination of transcription at well-defined programmed sites, polarity is Rho-dependent and termination occurs at variable position.

Discovery

The potential for transcription and translation to regulate each other was recognized by the team of Marshall Nirenberg, who discovered that the processes are physically connected through the formation of a DNA-ribosome complex. [26] [27] As part of the efforts of Nirenberg's group to determine the genetic code that underlies protein synthesis, they pioneered the use of cell-free in vitro protein synthesis reactions. Analysis of these reactions revealed that protein synthesis is mRNA-dependent, and that the sequence of the mRNA strictly defines the sequence of the protein product. For this work in breaking in the genetic code, Nirenberg was jointly awarded the Nobel Prize in Physiology or Medicine in 1968. Having established that transcription and translation are linked biochemically (translation depends on the product of transcription), an outstanding question remained whether they were linked physically - whether the newly synthesized mRNA released from the DNA before it is translated, or if can translation occur concurrently with transcription. Electron micrographs of stained cell-free protein synthesis reactions revealed branched assemblies in which strings of ribosomes are linked to a central DNA fibre. [27] DNA isolated from bacterial cells co-sediment with ribosomes, further supporting the conclusion that transcription and translation occur together. [26] Direct contact between ribosomes and RNA polymerase are observable within these early micrographs. [3] The potential for simultaneous regulation of transcription and translation at this junction was noted in Nirenberg's work as early as 1964. [26]

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<span class="mw-page-title-main">Lambda phage</span> Bacteriophage that infects Escherichia coli

Enterobacteria phage λ is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli. It was discovered by Esther Lederberg in 1950. The wild type of this virus has a temperate life cycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase, during which it kills and lyses the cell to produce offspring. Lambda strains, mutated at specific sites, are unable to lysogenize cells; instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell.

In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon.

<span class="mw-page-title-main">RNA polymerase</span> Enzyme that synthesizes RNA from DNA

In molecular biology, RNA polymerase, or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template.

<span class="mw-page-title-main">Rho factor</span> Prokaryotic protein

A ρ factor is a bacterial protein involved in the termination of transcription. Rho factor binds to the transcription terminator pause site, an exposed region of single stranded RNA after the open reading frame at C-rich/G-poor sequences that lack obvious secondary structure.

In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.

<span class="mw-page-title-main">Ribosomal RNA</span> RNA component of the ribosome, essential for protein synthesis in all living organisms

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins by mass.

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Bacterial translation is the process by which messenger RNA is translated into proteins in bacteria.

In genetics, attenuation is a regulatory mechanism for some bacterial operons that results in premature termination of transcription. The canonical example of attenuation used in many introductory genetics textbooks, is ribosome-mediated attenuation of the trp operon. Ribosome-mediated attenuation of the trp operon relies on the fact that, in bacteria, transcription and translation proceed simultaneously. Attenuation involves a provisional stop signal (attenuator), located in the DNA segment that corresponds to the leader sequence of mRNA. During attenuation, the ribosome becomes stalled (delayed) in the attenuator region in the mRNA leader. Depending on the metabolic conditions, the attenuator either stops transcription at that point or allows read-through to the structural gene part of the mRNA and synthesis of the appropriate protein.

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<span class="mw-page-title-main">Termination signal</span>

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<i>trp</i> operon Operon that codes for the components for production of tryptophan

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References

  1. ↑ Artsimovitch, I. (2018). "Rebuilding the bridge between transcription and translation". Molecular Microbiology. 108 (5): 467–472. doi: 10.1111/mmi.13964 . PMC   5980768 . PMID   29608805.
  2. ↑ McGary K. & Nudler, E. (2013). "RNA polymerase and the ribosome: the close relationship". Current Opinion in Microbiology. 16 (2): 112–117. doi:10.1016/j.mib.2013.01.010. PMC   4066815 . PMID   23433801.
  3. 1 2 Klaholz, B. (2017). "The ribosome holds the RNA polymerase on track in bacteria". Trends in Biochemical Sciences. 42 (9): 686–689. doi:10.1016/j.tibs.2017.07.003. PMID   28801047.
  4. ↑ Dutta, D.; Shatalin, K.; Epshtein, V.; Gottesman, M. E. & Nudler, E. (2011). "Linking RNA polymerase backtracking to genome instability in E. coli". Cell. 146 (4): 533–543. doi:10.1016/j.cell.2011.07.034. PMC   3160732 . PMID   21854980.
  5. ↑ Zhu, M.; Mori, M.; Hwa, T. & Dai, X. (2019). "Disruption of transcription-translation coordination in Escherichia coli leads to premature transcriptional termination". Nature Microbiology. 4 (12): 2347–2356. doi:10.1038/s41564-019-0543-1. PMC   6903697 . PMID   31451774.
  6. ↑ Iost, I. & Dreyfus, M. (1995). "The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation". EMBO Journal. 14 (13): 3252–61. doi:10.1002/j.1460-2075.1995.tb07328.x. PMC   394387 . PMID   7542588.
  7. ↑ Gowrishankar, J. & Harinarayanan, R. (2004). "Why is transcription coupled to translation in bacteria?". Molecular Microbiology. 54 (3): 598–603. doi: 10.1111/j.1365-2958.2004.04289.x . PMID   15491353.
  8. ↑ Johnson, G. E.; Lalanne, J.; Peters, M. L. & Li, G. (2020). "Functionally uncoupled transcription-translation in Bacillus subtilis". Nature. 585 (7823): 124–128. Bibcode:2020Natur.585..124J. doi:10.1038/s41586-020-2638-5. PMC   7483943 . PMID   32848247.
  9. 1 2 3 Webster, M. W.; Takacs, M.; Zhu, C.; Vidmar, V.; Eduljee, A.; Abdelkareem, M. & Weixlbaumer, A. (2020). "Structural basis of transcription-translation coupling and collision in bacteria". Science. 369 (6509): 1355–1359. Bibcode:2020Sci...369.1355W. doi: 10.1126/science.abb5036 . PMID   32820062. S2CID   221222557.
  10. 1 2 O'Reilly, F. J.; Xue, L.; Graziadei, A.; Sinn, L.; Lenz, S.; Tegunov, D.; Blötz, C.; Singh, N.; Hagen, W.; Cramer, P.; Stülke, J.; Mahamid, J. & Rappsilber, J. (2020). "In-cell architecture of an actively transcribing-translating expressome". Science. 369 (6503): 554–557. Bibcode:2020Sci...369..554O. doi:10.1126/science.abb3758. hdl: 21.11116/0000-0006-D30E-D . PMC   7115962 . PMID   32732422.
  11. 1 2 Wang, C.; Molodtsov, V.; Firlar, E.; Kaelber, J.; Blaha, G.; Su, M. & Ebright, R. H. (2020). "Structural basis of transcription-translation coupling". Science. 369 (6509): 1359–1365. Bibcode:2020Sci...369.1359W. doi:10.1126/science.abb5317. PMC   7566311 . PMID   32820061. S2CID   221220008.
  12. ↑ Proshkin, S.; Rahmouni, A. R.; Mironov, A. & Nudler, E. (2010). "Cooperation between translating ribosomes and RNA polymerase in transcription elongation". Science. 328 (5977): 504–508. Bibcode:2010Sci...328..504P. doi:10.1126/science.1184939. PMC   2930199 . PMID   20413502.
  13. ↑ Stevenson-Jones, F.; Woodgate, J.; Castro-Roa, D. & Zenkin, N. (2020). "Ribosome reactivates transcription by physically pushing RNA polymerase out of transcription arrest". Proceedings of the National Academy of Sciences. 117 (15): 8462–8467. Bibcode:2020PNAS..117.8462S. doi: 10.1073/pnas.1919985117 . PMC   7165469 . PMID   32238560.
  14. ↑ Kohler, R.; Mooney, R. A.; Mills, D. J.; Landick, R. & Cramer, P. (2017). "Architecture of a transcribing-translating expressome". Science. 356 (6334): 194–197. Bibcode:2017Sci...356..194K. doi:10.1126/science.aal3059. PMC   5528865 . PMID   28408604.
  15. ↑ Turnbough, C. L. (2019). "Regulation of Bacterial Gene Expression by Transcription Attenuation". Microbiology and Molecular Biology Reviews. 83 (3). doi: 10.1128/MMBR.00019-19 . PMC   6710462 . PMID   31270135.
  16. ↑ Yanofsky C (1981). "Attenuation in the control of expression of bacterial operons". Nature. 289 (5800): 751–758. Bibcode:1981Natur.289..751Y. doi:10.1038/289751a0. PMID   7007895. S2CID   4364204.
  17. 1 2 Yanofsky C (2000). "Transcription attenuation: once viewed as a novel regulatory strategy". Journal of Bacteriology. 182 (1): 1–8. doi: 10.1128/jb.182.1.1-8.2000 . PMC   94232 . PMID   10613855.
  18. 1 2 Kasai, T. (1974). "Regulation of the expression of the histidine operon in Salmonella typhimurium". Nature. 249 (5457): 523–527. Bibcode:1974Natur.249..523K. doi:10.1038/249523a0. PMID   4599761. S2CID   472218.
  19. ↑ Johnston, H. M.; Barnes, W. M.; Chumley, F. G.; Bossi, L. & Roth, J. R. (1980). "Model for regulation of the histidine operon of Salmonella". Proceedings of the National Academy of Sciences. 77 (1): 508–512. Bibcode:1980PNAS...77..508J. doi: 10.1073/pnas.77.1.508 . PMC   348301 . PMID   6987654.
  20. ↑ Landick, R.; Carey, J. & Yanofsky, C. (1985). "Translation activates the paused transcription complex and restores transcription of the trp operon leader region". Proceedings of the National Academy of Sciences. 82 (14): 4663–4667. Bibcode:1985PNAS...82.4663L. doi: 10.1073/pnas.82.14.4663 . PMC   390446 . PMID   2991886.
  21. ↑ Luzzati, D. (1970). "Regulation of lambda exonuclease synthesis: role of the N gene product and lambda repressor". Journal of Molecular Biology. 49 (2): 515–519. doi:10.1016/0022-2836(70)90261-5. PMID   4915096.
  22. ↑ Singer, C. E.; Smith, G. R.; Cortese, R. & Ames, B. N. (1972). "Mutant tRNA His ineffective in repression and lacking two pseudouridine modifications". Nature New Biology. 238 (81): 72–74. doi:10.1038/newbio238072a0. PMID   4558263.
  23. ↑ Jackson, E. N. & Yanofsky, C. (1973). "The region between the operator and first structural gene of the tryptophan operon of Escherichia coli may have a regulatory function". Journal of Molecular Biology. 76 (1): 89–101. doi:10.1016/0022-2836(73)90082-x. PMID   4578102.
  24. 1 2 Newton, W. A.; Beckwith, J. R.; Zipser, D. & Brenner, S. (1965). "Nonsense mutants and polarity in the lac operon of Escherichia coli". Journal of Molecular Biology. 14 (1): 290–296. doi:10.1016/s0022-2836(65)80250-9. PMID   5327654.
  25. ↑ Richardson, J. P. (1991). "Preventing the synthesis of unused transcripts by Rho factor". Cell. 64 (6): 1047–1049. doi:10.1016/0092-8674(91)90257-y. PMID   2004415. S2CID   38795667.
  26. 1 2 3 Byrne R (1964). "The In Vitro Formation of a DNA-Ribosome Complex". Proceedings of the National Academy of Sciences. 52 (1): 140–148. Bibcode:1964PNAS...52..140B. doi: 10.1073/pnas.52.1.140 . PMC   300586 . PMID   14192650.
  27. 1 2 Bladen HA (1965). "An electron microscopic study of a DNA-ribosome complex formed in vitro". Journal of Molecular Biology. 11: 78–IN9. doi:10.1016/s0022-2836(65)80172-3. PMID   14255762.
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