The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation

Wen, Jin-Der; Kuo, Syue-Ting; Chou, Hsin‐Hung

doi:10.1080/15476286.2020.1861406

Cited by 27 publications

(22 citation statements)

References 143 publications

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“…The SOP is centred around what worked for E. coli but it is constructed in such a manner that it can also be used as a starting point for improving the expression of FPs in other bacterial species. Since translation by the kingdoms of bacteria and archaea is extremely diverse 33 , we cannot guarantee its general applicability. Even in the well-studied bacterium E. coli, precise predictions about translation rates are difficult—as evidenced by the deviations between the predicted translation rates (Supplementary Table S1 ) and the measured fluorescence (Figs.…”

Section: Discussionmentioning

confidence: 99%

“…Amongst different bacterial species, more factors have to be taken into account (e.g. some species express mainly leaderless mRNAs, some almost none) 33 . The anti-SD sequence is quite strongly conserved, whereas enormous diversity amongst bacterial species SDs exists, which implies that our findings for the alternative RBS found in the first nine codons of mNG (and other non-GFP derived FPs) is relevant for some, but not all bacterial species.…”

Section: Discussionmentioning

confidence: 99%

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Optimising expression of the large dynamic range FRET pair mNeonGreen and superfolder mTurquoise2ox for use in the Escherichia coli cytoplasm

Mertens

Blaauwen

2022

Sci Rep

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The fluorescent proteins superfolder mTurquoise2ox (sfTq2ox) and mNeonGreen function excellently in mammalian cells, but are not well expressed in E. coli when forming the N-terminus of constructs. Expression was increased by decreasing structures at the start of their coding sequences in the mRNA. Unfortunately, the expression of mNeonGreen started from methionine at position ten as optimisation introduced an alternative RBS in the GFP N-terminus of mNeonGreen. The original start-codon was not deleted, which caused the expression of isomers starting at the original start-codon and at the start-codon at the beginning of the GFP N-terminus. By omitting the GFP N-terminus of mNeonGreen and optimising the structure of its mRNA, the expression of a mixture of isomers was avoided, and up to ~ 50-fold higher expression rates were achieved for mNeonGreen. Both fluorescent proteins can now be expressed at readily detectable levels in E. coli and can be used for various purposes. One explored application is the detection of in-cell protein interactions by FRET. mNeonGreen and sfTq2ox form a FRET pair with a larger dynamic range than commonly used donor–acceptor pairs, allowing for an excellent signal-to-noise ratio, which supports the detection of conformational changes that affect the distance between the interacting proteins.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Optimising expression of the large dynamic range FRET pair mNeonGreen and superfolder mTurquoise2ox for use in the Escherichia coli cytoplasm

Mertens

Blaauwen

2022

Sci Rep

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“…Translation initiation of prokaryotic mRNAs (where the SD sequence has not been detected in 5’ UTR) observed in the experiments occurs independently of any interactions with the anti-SD sequence and is mediated by the ribosomal protein bS1. A bioinformatic analysis showed that the stability of the secondary structures of such 5’ UTR sequences was reduced, thus facilitating the formation of the initiation complex and compensating for the lack of SD and anti-SD interactions [ 44 , 45 ].…”

Section: The Variety Of Approaches To Studying the Role Of 5’ Utrs In...mentioning

confidence: 99%

Flow-Seq Method: Features and Application in Bacterial Translation Studies

et al. 2023

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The Flow-seq method is based on using reporter construct libraries, where a certain element regulating the gene expression of fluorescent reporter proteins is represented in many thousands of variants. Reporter construct libraries are introduced into cells, sorted according to their fluorescence level, and then subjected to next-generation sequencing. Therefore, it turns out to be possible to identify patterns that determine the expression efficiency, based on tens and hundreds of thousands of reporter constructs in one experiment. This method has become common in evaluating the efficiency of protein synthesis simultaneously by multiple mRNA variants. However, its potential is not confined to this area. In the presented review, a comparative analysis of the Flow-seq method and other alternative approaches used for translation efficiency evaluation of mRNA was carried out; the features of its application and the results obtained by Flow-seq were also considered.

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“…The relative number of leaderless mRNAs ranges between 1.4 and 72%. The mechanism of mRNA recognition and ribosome association appears to be highly diverse in prokaryotes, and we do not know whether the initiation mechanism influences and correlates with expressome formation ( Wen et al, 2020 ). mRNAs that lack a ribosomal binding site (RBS) can also emerge from RNA processing events at the 5'-end that lead to cleavage of the 5'-UTR ( Qi et al, 2017 ; Figure 2G ).…”

Section: Co-transcriptional Processes and Transcriptomic Features Affecting Transcription-translation Coupling In Archaeamentioning

confidence: 99%

Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World

et al. 2021

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The lack of a nucleus is the defining cellular feature of bacteria and archaea. Consequently, transcription and translation are occurring in the same compartment, proceed simultaneously and likely in a coupled fashion. Recent cryo-electron microscopy (cryo-EM) and tomography data, also combined with crosslinking-mass spectrometry experiments, have uncovered detailed structural features of the coupling between a transcribing bacterial RNA polymerase (RNAP) and the trailing translating ribosome in Escherichia coli and Mycoplasma pneumoniae. Formation of this supercomplex, called expressome, is mediated by physical interactions between the RNAP-bound transcription elongation factors NusG and/or NusA and the ribosomal proteins including uS10. Based on the structural conservation of the RNAP core enzyme, the ribosome, and the universally conserved elongation factors Spt5 (NusG) and NusA, we discuss requirements and functional implications of transcription-translation coupling in archaea. We furthermore consider additional RNA-mediated and co-transcriptional processes that potentially influence expressome formation in archaea.

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The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation

Cited by 27 publications

References 143 publications

Optimising expression of the large dynamic range FRET pair mNeonGreen and superfolder mTurquoise2ox for use in the Escherichia coli cytoplasm

Optimising expression of the large dynamic range FRET pair mNeonGreen and superfolder mTurquoise2ox for use in the Escherichia coli cytoplasm

Flow-Seq Method: Features and Application in Bacterial Translation Studies

Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World

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