Transcription–translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits

Fan, H.; Conn, Adam; Williams, Preston; Diggs, Stephen; Hahm, Joseph; Gamper, Howard; Hou, Ya‐Ming; O’Leary, Seán E.; Wang, Yinsheng; Blaha, Gregor

doi:10.1093/nar/gkx719

Cited by 67 publications

(60 citation statements)

References 93 publications

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“…Furthermore, the burst of transcription upon re-aeration is blocked by the presence of CAM, causing up to a four-fold decrease in transcript abundance in the CAM treated cultures when compared to the vehicle treated cultures. This is consistent with the idea that transcription and translation are physically coupled, and blocking translation therefore prevents RNA polymerase from efficiently carrying out transcript elongation, as has been reported for E. coli (72–76).…”

Section: Discussionsupporting

confidence: 91%

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacteria

Vargas-Blanco

Zhou

Zamalloa

et al. 2019

Preprint

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17The success of Mycobacterium tuberculosis (Mtb) as a human pathogen is due in part to its 18 ability to survive stress conditions, such as hypoxia or nutrient deprivation, by entering non-19 growing states. In these low-metabolic states, Mtb can tolerate antibiotics and develop 20 genetically encoded antibiotic resistance, making its metabolic adaptation to stress crucial for 21 survival. Numerous bacteria, including Mtb, have been shown to reduce their rates of mRNA 22 degradation under growth limitation and stress. While the existence of this response appears to 23 be conserved across species, the underlying bacterial mRNA stabilization mechanisms remains 24 65 for other bacteria under stress conditions that slow or halt growth, including carbon deprivation, 66 stationary phase, and temperature shock (4-13). However, the mechanisms responsible for global 67 regulation of mRNA stability in prokaryotes have yet to be elucidated. 68 In better studied bacteria such as E. coli and B. subtilis, the major ribonucleases (RNases) 69 involved in mRNA processing and decay are RNase E and RNase Y, respectively. A 70 conventional model for RNA decay in E. coli start with an endonucleolytic cleavage event 71 usually carried by RNase E in AU-rich regions, particularly in mRNA substrates that possess a 5' 72 monophosphate (14-16). The resulting 5' monophosphorylated fragments are rapidly cleaved by 73 RNase E, resulting in shorter fragments that can be fully degraded by exonucleases such as 74 PNPase, RNase II, and RNase R (17, 18). mRNA degradation seems to be coordinated by 75 formation of a complex known as the degradosome. In E. coli, RNase E serves as the scaffold for 76 this multiprotein complex that comprises RNA helicases, the glycolytic enzyme enolase, and 77 PNPase (19-23). Other organisms that encode RNase E form similar degradosomes (24, 25). In 78 organisms where RNase E is not present, RNase Y and/or RNase J seem to assume the scaffold 79 function (26-28). Mycobacteria encode RNase E, but efforts to define the mycobacterial 80 degradosome have produced inconsistent results (29, 30). It is unclear if degradosome 81 reorganization or dissolution contribute to the global regulation of mRNA degradation under 82 stress conditions in any bacteria. Interestingly, the importance of degradosome formation in E. 83 coli varies depending on the carbon sources provided, suggesting specific links between RNase E 84 degradosomes and metabolic capabilities (31). Furthermore, the chaperones DnaK and CsdA can 85 become degradosome components in E. coli under certain stresses (20, 32, 33). 86Global transcript stabilization in stressed bacteria could plausibly result from reduced RNase 87 abundance, reduced RNase activity, and/or reduced accessibility of transcripts to degradation 88 proteins. In E. coli it has been shown that multiple stressors can upregulate RNase R, possibly as 89 a way to overcome ribosome misassembly (34, 35), and that RNase III levels decrease under 90 cold-shock and stationary phase (36). Surprisin...

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Section: Discussionsupporting

confidence: 91%

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacteria

Vargas-Blanco

Zhou

Zamalloa

et al. 2019

Preprint

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“…E. coli 70S ribosomes were prepared from E. coli strain JE28 (29; grown in media containing 50 g/ml kanamycin to OD600 = 1.0 in a 50 L fermenter, harvested, flash frozen in liquid N 2 , and stored at -80°C), as described (30)(31). , and 30S and 50S subunits were separated by loading an aliquot (250 A 260 units) onto a 36 ml 10-30% sucrose gradient in dissociation buffer and centrifugation (SW28 rotor; 15 h at 20,000 rpm at 4°C).…”

Section: E Coli 70s Ribosomementioning

confidence: 99%

Structural basis of transcription-translation coupling

Wang

Molodtsov

Firlar

et al. 2020

Preprint

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AbstractIn bacteria, transcription and translation are coupled processes, in which movement of RNA polymerase (RNAP) synthesizing mRNA is coordinated with movement of the first ribosome translating mRNA. Coupling is modulated by the transcription factors NusG--which is thought to bridge RNAP and ribosome--and NusA. Here, we report cryo-EM structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P-site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A; previously termed “expressome”). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.One Sentence SummaryCryo-EM defines states that mediate NusG- and NusA-dependent transcription-translation coupling in bacteria

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“…For example, 5’ UTR interactions with cis and trans elements, such as complementary sequences within the UTR or coding sequence, small RNAs (sRNAs), and RNA-binding proteins, can modulate protein synthesis by blocking or improving accessibility to the RBS [6-9]. Importantly, it has been shown in Escherichia coli and other bacteria that transcription and translation are physically coupled, and thus 5’ UTR-mediated modulation of translation could have repercussions on transcription rate as well [10-14]. Translation blocks in M. smegmatis have been shown to decrease transcription as well [15], suggesting that transcription-translation coupling occurs in mycobacteria, although the extent and consequences are unknown.…”

Section: Introductionmentioning

confidence: 99%

The impact of leadered and leaderless gene structures on translation efficiency, transcript stability, and predicted transcription rates inMycobacterium smegmatis

Nguyen

Vargas-Blanco

Roberts

et al. 2019

Preprint

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16Regulation of gene expression is critical for the pathogen Mycobacterium tuberculosis to tolerate 17 stressors encountered during infection, and for non-pathogenic mycobacteria such as 18Mycobacterium smegmatis to survive stressors encountered in the environment. Unlike better 19 studied models, mycobacteria express ~14% of their genes as leaderless transcripts. However, the 20 impacts of leaderless transcript structures on mRNA half-life and translation efficiency in 21 mycobacteria have not been directly tested. For leadered transcripts, the contributions of 5' UTRs 22 to mRNA half-life and translation efficiency are similarly unknown. In both M. tuberculosis and 23 M. smegmatis, the essential sigma factor, SigA, is encoded by an unstable transcript with a 24 relatively short half-life. We hypothesized that sigA's long 5' UTR caused this instability. To test 25 this, we constructed fluorescence reporters and then measured protein abundance, mRNA 26 abundance, and mRNA half-life. From these data we also calculated relative transcription rates. 27We found that the sigA 5' UTR confers an increased transcription rate, a shorter mRNA half-life, 28 and a decreased translation rate compared to a synthetic 5' UTR commonly used in mycobacterial 29 expression plasmids. Leaderless transcripts produced less protein compared to any of the leadered 30 transcripts. However, translation rates were similar to those of transcripts with the sigA 5' UTR, 31 and the protein levels were instead explained by lower transcript abundance. A global comparison 32 of M. tuberculosis mRNA and protein abundances failed to reveal systematic differences in 33 protein:mRNA ratios for natural leadered and leaderless transcripts, consistent with the idea that 34 variability in translation efficiency among mycobacterial genes is largely driven by factors other 35 than leader status. The variability in mRNA half-life and predicted transcription rate among our 36 constructs could not be explained by their different translation efficiencies, indicating that other 37 factors are responsible for these properties and highlighting the myriad and complex roles played 38 by 5' UTRs and other sequences downstream of transcription start sites. 39 40 41 5' UTRs can also regulate gene expression by altering mRNA turnover rates. This can be a 57 consequence of altered translation rates, as impairments to translation often lead to faster mRNA 58 decay [16][17][18][19][20][21][22]. In other cases, mRNA stability is directly affected by sRNA binding to 5' UTRs or 59 by UTR secondary structure [9,[23][24][25][26][27][28]. In E. coli, the half-life of the short-lived transcript bla can 60 be significantly increased when its native 5' UTR is replaced with the 5' UTR of ompA, a long-61 lived transcript [29][30][31]. Conversely, deletion of ompA's native 5' UTR decreased its half-life by 62 5-fold [30]. The longevity conferred by the ompA 5' UTR was attributed to the presence of a non-63 specific stem-loop as well as the specific RBS sequence [30][31][32]. Secondary ...

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Transcription–translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits

Cited by 67 publications

References 93 publications

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacteria

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacteria

Structural basis of transcription-translation coupling

The impact of leadered and leaderless gene structures on translation efficiency, transcript stability, and predicted transcription rates inMycobacterium smegmatis

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