Histidine 197 in Release Factor 1 Is Essential for A Site Binding and Peptide Release

AbstractArfA rescues ribosomes stalled on truncated mRNAs by recruiting the release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2-Å resolution cryo-EM structures – determined from a single sample – of the 70S ribosome with ArfA∙RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation, hitherto unobserved in 70S termination complexes. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA “senses” the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.

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Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1714554115 ◽

2018 ◽

Vol 115 (3) ◽

pp. E382-E389 ◽

Cited By ~ 7

Author(s):

Thomas Philipp Hoernes ◽

Nina Clementi ◽

Michael Andreas Juen ◽

Xinying Shi ◽

Klaus Faserl ◽

...

Keyword(s):

Stop Codon ◽

Release Factor ◽

Stop Codons ◽

Codon Recognition ◽

Chemically Modified ◽

Peptide Release ◽

Stop Codon Recognition ◽

A Site ◽

Chemical Groups ◽

Insight Into

Termination of protein synthesis is triggered by the recognition of a stop codon at the ribosomal A site and is mediated by class I release factors (RFs). Whereas in bacteria, RF1 and RF2 promote termination at UAA/UAG and UAA/UGA stop codons, respectively, eukaryotes only depend on one RF (eRF1) to initiate peptide release at all three stop codons. Based on several structural as well as biochemical studies, interactions between mRNA, tRNA, and rRNA have been proposed to be required for stop codon recognition. In this study, the influence of these interactions was investigated by using chemically modified stop codons. Single functional groups within stop codon nucleotides were substituted to weaken or completely eliminate specific interactions between the respective mRNA and RFs. Our findings provide detailed insight into the recognition mode of bacterial and eukaryotic RFs, thereby revealing the chemical groups of nucleotides that define the identity of stop codons and provide the means to discriminate against noncognate stop codons or UGG sense codons.

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Conformational control of translation termination on the 70S ribosome

10.1101/226837 ◽

2017 ◽

Cited By ~ 1

Author(s):

Egor Svidritskiy ◽

Andrei A. Korostelev

Keyword(s):

Conformational Changes ◽

Catalytic Domain ◽

Stop Codon ◽

Translation Termination ◽

Release Factor ◽

Codon Recognition ◽

Peptide Release ◽

Stop Codon Recognition ◽

70S Ribosome ◽

A Site

AbstractTranslation termination ensures proper lengths of cellular proteins. During termination, release factor (RF) recognizes a stop codon and catalyzes peptide release. Conformational changes in RF are thought to underlie accurate translation termination. If true, the release factor should bind the A-site codon in inactive (compact) conformation(s), but structural studies of ribosome termination complexes have only captured RFs in an extended, active conformation. Here, we identify a hyper-accurate RF1 variant, and present crystal structures of 70S termination complexes that suggest a structural pathway for RF1 activation. In the presence of blasticidin S, the catalytic domain of RF1 is removed from the peptidyl-transferase center, whereas the codon-recognition domain is fully engaged in stop-codon recognition in the decoding center. RF1 codon recognition induces decoding-center rearrangements that precede accommodation of the catalytic domain. Our findings suggest how structural dynamics of RF1 and the ribosome coordinate stop-codon recognition with peptide release, ensuring accurate translation termination.

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Mechanism of ribosome rescue by ArfA and RF2

eLife ◽

10.7554/elife.23687 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 27

Author(s):

Gabriel Demo ◽

Egor Svidritskiy ◽

Rohini Madireddy ◽

Ruben Diaz-Avalos ◽

Timothy Grant ◽

...

Keyword(s):

Structural Dynamics ◽

Stop Codon ◽

Release Factor ◽

Peptidyl Transferase ◽

Peptidyl Transferase Center ◽

C Terminus ◽

Peptide Release ◽

N Terminus ◽

70S Ribosome ◽

A Site

ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 Å resolution cryo-EM structures – determined from a single sample – of the 70S ribosome with ArfA•RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA ‘senses’ the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.

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Singly Modified Amikacin and Tobramycin Derivatives Show Increased rRNA A-Site Binding and Higher Potency against Resistant Bacteria

ChemMedChem ◽

10.1002/cmdc.201402175 ◽

2014 ◽

Vol 9 (9) ◽

pp. 2164-2171 ◽

Cited By ~ 11

Author(s):

Richard J. Fair ◽

Lisa S. McCoy ◽

Mary E. Hensler ◽

Bernice Aguilar ◽

Victor Nizet ◽

...

Keyword(s):

Resistant Bacteria ◽

A Site ◽

Site Binding

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pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1012612107 ◽

2010 ◽

Vol 108 (1) ◽

pp. 79-84 ◽

Cited By ~ 90

Author(s):

Magnus Johansson ◽

Ka-Weng Ieong ◽

Stefan Trobro ◽

Peter Strazewski ◽

Johan Åqvist ◽

...

Keyword(s):

Ph Value ◽

Ph Dependence ◽

Peptide Bond ◽

Bulk Solution ◽

Peptide Bond Formation ◽

Transfer Rates ◽

Peptidyl Transfer ◽

A Site ◽

Rate Limiting ◽

Site Binding

We studied the pH-dependence of ribosome catalyzed peptidyl transfer from fMet-tRNAfMet to the aa-tRNAs Phe-tRNAPhe, Ala-tRNAAla, Gly-tRNAGly, Pro-tRNAPro, Asn-tRNAAsn, and Ile-tRNAIle, selected to cover a large range of intrinsic pKa-values for the α-amino group of their amino acids. The peptidyl transfer rates were different at pH 7.5 and displayed different pH-dependence, quantified as the pH-value, , at which the rate was half maximal. The -values were downshifted relative to the intrinsic pKa-value of aa-tRNAs in bulk solution. Gly-tRNAGly had the smallest downshift, while Ile-tRNAIle and Ala-tRNAAla had the largest downshifts. These downshifts correlate strongly with molecular dynamics (MD) estimates of the downshifts in pKa-values of these aa-tRNAs upon A-site binding. Our data show the chemistry of peptide bond formation to be rate limiting for peptidyl transfer at pH 7.5 in the Gly and Pro cases and indicate rate limiting chemistry for all six aa-tRNAs.

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Influence of Linker Length and Composition on Enzymatic Activity and Ribosomal Binding of Neomycin Dimers

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00861-15 ◽

2015 ◽

Vol 59 (7) ◽

pp. 3899-3905 ◽

Cited By ~ 16

Author(s):

Derrick Watkins ◽

Sunil Kumar ◽

Keith D. Green ◽

Dev P. Arya ◽

Sylvie Garneau-Tsodikova

Keyword(s):

Enzymatic Activity ◽

Aminoglycoside Antibiotics ◽

Substantial Decrease ◽

Selective Binding ◽

Linker Length ◽

Neomycin B ◽

A Site ◽

Site Binding

ABSTRACTThe human and bacterial A site rRNA binding as well as the aminoglycoside-modifying enzyme (AME) activity against a series of neomycin B (NEO) dimers is presented. The data indicate that by simple modifications of linker length and composition, substantial differences in rRNA selectivity and AME activity can be obtained. We tested five different AMEs with dimeric NEO dimers that were tethered via triazole, urea, and thiourea linkages. We show that triazole-linked dimers were the worst substrates for most AMEs, with those containing the longer linkers showing the largest decrease in activity. Thiourea-linked dimers that showed a decrease in activity by AMEs also showed increased bacterial A site binding, with one compound (compound 14) even showing substantially reduced human A site binding. The urea-linked dimers showed a substantial decrease in activity by AMEs when a conformationally restrictive phenyl linker was introduced. The information learned herein advances our understanding of the importance of the linker length and composition for the generation of dimeric aminoglycoside antibiotics capable of avoiding the action of AMEs and selective binding to the bacterial rRNA over binding to the human rRNA.

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Antimicrobial Activity, AME Resistance, and A-Site Binding Studies of Anthraquinone–Neomycin Conjugates

ACS Infectious Diseases ◽

10.1021/acsinfecdis.6b00176 ◽

2017 ◽

Vol 3 (3) ◽

pp. 206-215 ◽

Cited By ~ 8

Author(s):

Natalya N. Degtyareva ◽

Changjun Gong ◽

Sandra Story ◽

Nathanael S. Levinson ◽

Adegboyega K. Oyelere ◽

...

Keyword(s):

Antimicrobial Activity ◽

Binding Studies ◽

A Site ◽

Site Binding

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Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon

Biochemistry and Cell Biology ◽

10.1139/o95-118 ◽

1995 ◽

Vol 73 (11-12) ◽

pp. 1095-1103 ◽

Cited By ~ 51

Author(s):

Warren P. Tate ◽

Elizabeth S. Poole ◽

Julie A. Horsfield ◽

Sally A. Mannering ◽

Chris M. Brown ◽

...

Keyword(s):

Stop Codon ◽

Stop Signal ◽

Physical Contact ◽

Release Factor ◽

Wide Range ◽

Highly Expressed Genes ◽

Peptidyltransferase Center ◽

A Site ◽

Translational Termination

The translational stop signal and polypeptide release factor (RF) complexed with Escherichia coli ribosomes have been shown to be in close physical contact by site-directed photochemical cross-linking experiments. The RF has a protease-sensitive site in a highly conserved exposed loop that is proposed to interact with the peptidyltransferase center of the ribosome. Loss of peptidyl–tRNA hydrolysis activity and enhanced codon–ribosome binding by the cleaved RF is consistent with a model whereby the RF spans the decoding and peptidyltransferase centers of the ribosome with domains of the RF linked by conformational coupling. The cross-link between the stop signal and RF at the ribosomal decoding site is influenced by the base following the termination codon. This base determines the efficiency with which the stop signal is decoded by the RF in both mammalian and bacterial systems in vivo. The wide range of efficiencies correlates with the frequency with which the signals occur at natural termination sites, with rarely used weak signals often found at recoding sites and strong signals found in highly expressed genes. Stop signals are found at some recoding sites in viruses where −1 frame-shifting occurs, but the generally accepted mechanism of simultaneous slippage from the A and P sites does not explain their presence here. The HIV-1 gag-pol −1 frame shifting site has been used to show that stop signals significantly influence frame-shifting efficiency on prokaryotic ribosomes by a RF-mediated mechanism. These data can be explained by an E/P site simultaneous slippage mechanism whereby the stop codon actually enters the ribosomal A site and can influence the event.Key words: translational stop signal, decoding, release factor, frame-shifting.

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METTL3-Mediated DLGAP1 Antisense RNA 2 Promotes Gastric Cancer Tumorigenesis Through Facilitating C-Myc-Dependent Warburg Effect

10.21203/rs.3.rs-1135467/v1 ◽

2021 ◽

Author(s):

Changshun Yang ◽

Yu Zhang ◽

Xuefei Cheng ◽

Weihua Li

Keyword(s):

Gastric Cancer ◽

Antisense Rna ◽

Warburg Effect ◽

Aerobic Glycolysis ◽

Dependent Manner ◽

Rna Immunoprecipitation ◽

The Stability ◽

A Site ◽

Rip Assay ◽

Site Binding

Abstract Background The critical roles of N6-methyladenosine (m6A) modification have been demonstrated by more and more evidence. However, the cross-talking of m6A and long non-coding RNAs (lncRNAs) in gastric cancer (GC) tumorigenesis is still unclear. Here, our work focused on the functions and molecular mechanism of m6A-modified lncRNA DLGAP1 antisense RNA 2 (DLGAP1-AS2) in GC. Methods LncRNA expression profile data was derived from GEO. M6A profile was screened using Methylated RNA immunoprecipitation sequencing (MeRIP-Seq). The metabolism assays were conducted using quantitative analysis of glucose, lactate, ATP and extracellular acidification rate (ECAR). The m6A level of specific RNA was identified using MeRIP-qPCR. The molecular interaction was detected using RIP assay. Results Microarray analysis found that lncRNA DLGAP1-AS2 up-regulated in GC cells. Clinical data showed that DLGAP1-AS2 high-expression was correlated with advanced pathological stage and poor prognosis. Functionally, DLGAP1-AS2 promoted the Warburg effect (aerobic glycolysis) and knockdown of DLGAP1-AS2 suppressed the tumor growth of GC cells. Mechanistically, m6A methyltransferase METTL3 enhanced the stability of DLGAP1-AS2 via m6A site binding. Moreover, DLGAP1-AS2 interacted with YTHDF1 to enhance the stability of c-Myc mRNA through DLGAP1-AS2/m6A/YTHDF1/c-Myc mRNA. Conclusions In conclusion, our work indicates the functions of m6A-modified DLGAP1-AS2 in the GC aerobic glycolysis, disclosing a potential m6A-dependent manner for GC treatment.

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