St Andrews Research Repository

St Andrews University Home
View Item 
  •   St Andrews Research Repository
  • Biology (School of)
  • Biology
  • Biology Theses
  • View Item
  •   St Andrews Research Repository
  • Biology (School of)
  • Biology
  • Biology Theses
  • View Item
  •   St Andrews Research Repository
  • Biology (School of)
  • Biology
  • Biology Theses
  • View Item
  • Login
JavaScript is disabled for your browser. Some features of this site may not work without it.

2A-induced ribosome stalling

Thumbnail
View/Open
ValèrieOdonPhDThesis.pdf (6.362Mb)
Appendix 1a pSTA1.pdf (249.5Kb)
Appendix 1b pJC3.pdf (167.6Kb)
figure 4.3 testing consensuses variants.pdf (178.6Kb)
figure 4.4 the translation of hybrids.pdf (176.2Kb)
figure 4.5 translation of TaV and DHV hybrids.pdf (180.0Kb)
figure 4.6 mutations to TaV 2A consensus.pdf (221.8Kb)
figure 4.7 N terminal truncation of ADRV and IFV 2A.pdf (240.2Kb)
figure 4.8 Ala scan of TaV upstream context.pdf (188.4Kb)
figure 4.9 Ala scan of FMDV 2A upstream context.pdf (244.6Kb)
figure 4.10 other mutations of the upstream contexts.pdf (254.9Kb)
figure 4.13 mutations of TaV Arg 1 and or 5.pdf (216.0Kb)
figure 4.14 Gly and Pro mutations of the upstream context of TaV 2A.pdf (181.4Kb)
figure 4.15 proline disruption of DHV20 FMDV and TaV 2As.pdf (175.2Kb)
figure 4.16 Leu substitutions for DHV TaV and FMDV2As.pdf (137.1Kb)
FMDV 2A codon usage at the A site.pdf (149.4Kb)
puromycin release.pdf (161.0Kb)
TaV P20 mutants.pdf (139.6Kb)
Appendix 4a Amphioxus sequences.pdf (127.7Kb)
Appendix 4b 2A from Saccoglossus kowalevskii.pdf (90.94Kb)
Date
25/06/2014
Author
Odon, Valèrie
Supervisor
Ryan, Martin Denis
Funder
Biotechnology and Biological Sciences Research Council (BBSRC)
Keywords
2A peptide
Elongation arrest
Nascent peptide
Ribosome stalling
Exit tunnel
2A-like sequences
Non-LTR retrotransposons
Branchiostoma floridae
Saccoglossus kowalevskii
Metadata
Show full item record
Altmetrics Handle Statistics
Altmetrics DOI Statistics
Abstract
Originally 2A was characterised in foot-and-mouth disease virus. Site directed mutagenesis identified a C-terminus consensus motif [D(V/I)ExNPGP] and it is proposed that 2A interacts with the exit tunnel of the ribosome in a way that a specific peptide bond is skipped between the last glycine of 2A and the proline of 2B, thus providing a discontinuity in translation, resulting in release of discrete proteins from one single ORF. 2A was also identified in other picornaviruses, positive, single and double-stranded RNA insect viruses and mammalian rotaviruses. A motif present at the C-terminus of the 2A oligopeptide [D(V/I)ExNPGP] is very highly, though not completely conserved . The sequence upstream of this motif shows, however, no apparent conservation between 2As of different viruses. In this study, extensive site-directed mutagenesis were performed on several 2A sequences and a series of ‘hybrid’ 2As comprising different consensus motifs juxtaposed with different upstream contexts were created as part of a detailed analysis of the mechanism of 2A-mediated ribosome stalling. The results demonstrated that a minimal region of twenty to twenty-three amino acids interacts with the exit tunnel of the ribosome to bring about a pause in processivity, alter the peptidyl transferase centre geometry and restrict the ribosome A site via two distinctive stalling mechanisms. Other molecular analyses tested here will require further optimisations or alternative methods: a visual method to explore the dynamics of re-initiation of translation from proline codon, purification of the translation-regulating factors and structural resolution of 2A sequences. Previously, cellular 2As were identified in non-LTR retrotransposons of trypanosomes. It is reported here as part of two other cellular organisms Saccoglossus kowalevskii (acorn worm) and Branchiostoma floridae (amphioxus). In the acorn worm, the nucleotides sequences corresponding to 2A motifs were part of the untranslated genome. In amphioxus, three 2A elements were identified in hypothetical proteins, and at the N-terminus of twenty non-LTR retrotransposons.
DOI
https://doi.org/10.17630/10023-4894
Type
Thesis, PhD Doctor of Philosophy
Collections
  • Biology Theses
URI
http://hdl.handle.net/10023/4894

Items in the St Andrews Research Repository are protected by copyright, with all rights reserved, unless otherwise indicated.

Advanced Search

Browse

All of RepositoryCommunities & CollectionsBy Issue DateNamesTitlesSubjectsClassificationTypeFunderThis CollectionBy Issue DateNamesTitlesSubjectsClassificationTypeFunder

My Account

Login

Open Access

To find out how you can benefit from open access to research, see our library web pages and Open Access blog. For open access help contact: openaccess@st-andrews.ac.uk.

Accessibility

Read our Accessibility statement.

How to submit research papers

The full text of research papers can be submitted to the repository via Pure, the University's research information system. For help see our guide: How to deposit in Pure.

Electronic thesis deposit

Help with deposit.

Repository help

For repository help contact: Digital-Repository@st-andrews.ac.uk.

Give Feedback

Cookie policy

This site may use cookies. Please see Terms and Conditions.

Usage statistics

COUNTER-compliant statistics on downloads from the repository are available from the IRUS-UK Service. Contact us for information.

© University of St Andrews Library

University of St Andrews is a charity registered in Scotland, No SC013532.

  • Facebook
  • Twitter