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Molecular basis of mRNA delivery to the bacterial ribosome by bS1 protein and RNA polymerase

ABSTRACT: The initiation of translation begins with formation of a ribosome-mRNA complex. In bacteria, the 30S ribosomal subunit is recruited to many mRNAs through both base pairing with the Shine Dalgarno (SD) sequence and RNA-binding by ribosomal protein bS1. Translation can initiate on mRNAs that are being transcribed, and RNA polymerase (RNAP) can promote recruitment of the pioneering 30S. Here we have examined ribosome recruitment to mRNAs using cryogenic electron microscopy (cryo-EM), single-molecule fluorescence co-localization, and whole-cell cross-linking mass spectrometry. Structures of 30S-mRNA complexes show that bS1 delivers the mRNA to the ribosome for SD duplex formation and initial 30S subunit activation. RNAP associates flexibly with the 30S platform during nascent mRNA delivery and accelerates their association in a bS1-dependent manner in vitro. Collectively, our data provide a mechanistic framework for how the SD duplex, ribosomal proteins and RNAP cooperate in 30S recruitment to mRNAs and thereby establish transcription-translation coupling.

ORGANISM(S): Escherichia Coli

SUBMITTER: Juri Rappsilber

PROVIDER: PXD048229 | JPOST Repository | Fri Nov 15 00:00:00 GMT 2024

REPOSITORIES: jPOST

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			Action	DRS
	B210625_02_Lumos_KC_IN_120_RpoB_PD_7p5_scaleup_pepSEC_5_rep1.raw	Raw
	B210625_03_Lumos_KC_IN_120_RpoB_PD_7p5_scaleup_pepSEC_5_rep2.raw	Raw
	B210625_04_Lumos_KC_IN_120_RpoB_PD_7p5_scaleup_pepSEC_6_rep1.raw	Raw
	B210625_05_Lumos_KC_IN_120_RpoB_PD_7p5_scaleup_pepSEC_6_rep2.raw	Raw
	B210625_06_Lumos_KC_IN_120_RpoB_PD_7p5_scaleup_pepSEC_7_rep1.raw	Raw

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Project description:Firczuk2013 - Eukaryotic mRNA translation machinery This is a model of Saccharomyces cerevisiae mRNA translation which includes the initiation, elongation and termination phases. The model is for 20 condon mRNAs. The building of a multi-factor complex in initiation and also the different processes in elongation and termination are modelled in detail. The model takes into account that ribosomes cover more than one codon of mRNA so that the movement of ribosomes are effectively blocked by other ribosomes several codons downstream. It is assumed that 15 codons are occupied by each ribosome. This blocking effect is considered in reaction R18 in initiation and also reaction R26, the reaction where translocation of ribosomes takes place in elongation. The kinetic functions of these two reactions are based on MacDonald et al. 1968 and Heinrich & Rapaport 1980. All other kinetic functions follow mass-action kinetics. The concentrations of transfer RNA species (Met-tRNA, aa-tRNA and tRNA in the model) are kept constant, while the other species' concentrations can change in the course of the simulation. The model describes the translation of a short mRNA with 20 codons. Therefore, all reactions in the elongation cycle (R22, R23, R25, R26, R28 and R29) and the corresponding species are replicated accordingly to model the species with ribosomes bound at different positions. In summary, the model contains 165 different species and 141 reactions. The value of the 56 rate constant parameters were estimated by fitting the model against a series of experimental data consisting of modulation of the various translation factors (Figures 2, 3 and S3). Overall the parameter estimation was carried out over 212 different data points (steady states). This model is described in the article: An in vivo control map for the eukaryotic mRNA translation machinery Helena Firczuk, Shichina Kannambath, Jürgen Pahle, Amy Claydon, Robert Beynon, John Duncan, Hans Westerhoff, Pedro Mendes and John EG McCarthy Molecular Systems Biology. 9:635 Abstract: Rate control analysis defines the in vivo control map governing yeast protein synthesis and generates an extensively parameterized digital model of the translation pathway. Among other non-intuitive outcomes, translation demonstrates a high degree of functional modularity and comprises a non-stoichiometric combination of proteins manifesting functional convergence on a shared maximal translation rate. In exponentially growing cells, polypeptide elongation (eEF1A, eEF2, and eEF3) exerts the strongest control. The two other strong control points are recruitment of mRNA and tRNAi to the 40S ribosomal subunit (eIF4F and eIF2) and termination (eRF1; Dbp5). In contrast, factors that are found to promote mRNA scanning efficiency on a longer than-average 5′untranslated region (eIF1, eIF1A, Ded1, eIF2B, eIF3, and eIF5) exceed the levels required for maximal control. This is expected to allow the cell to minimize scanning transition times, particularly for longer 5′UTRs. The analysis reveals these and other collective adaptations of control shared across the factors, as well as features that reflect functional modularity and system robustness. Remarkably, gene duplication is implicated in the fine control of cellular protein synthesis. This model is hosted on BioModels Database and identified by: BIOMD0000000457 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Molecular basis of mRNA delivery to the bacterial ribosome by bS1 protein and RNA polymerase

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