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dc.contributor.authorTiruneh, Bayu Sisay
dc.contributor.authorKim, Byung-Hoon
dc.contributor.authorGallie, Daniel R.
dc.contributor.authorRoy, Bijoyita
dc.contributor.authorvon Arnim, Albrecht G.
dc.date2022-08-11T08:09:41.000
dc.date.accessioned2022-08-23T16:40:15Z
dc.date.available2022-08-23T16:40:15Z
dc.date.issued2013-12-30
dc.date.submitted2014-11-14
dc.identifier.citationBMC Biol. 2013 Dec 30;11:123. doi: 10.1186/1741-7007-11-123. <a href="http://dx.doi.org/10.1186/1741-7007-11-123">Link to article on publisher's site</a>
dc.identifier.issn1741-7007 (Linking)
dc.identifier.doi10.1186/1741-7007-11-123
dc.identifier.pmid24377433
dc.identifier.urihttp://hdl.handle.net/20.500.14038/39646
dc.description.abstractBACKGROUND: Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different environmental stresses and genetic lesions in the translation apparatus. To identify additional features of the global landscape of translational control, we used microarray analysis of polysomal as well as non-polysomal mRNAs to examine the defects in translation in a poly(A) binding protein mutant, pab2 pab8, as well as in a mutant of a large ribosomal subunit protein, rpl24b/shortvalve1. RESULTS: The mutation of RPL24B stimulated the ribosome occupancy of mRNAs for nuclear encoded ribosomal proteins. Detailed analysis yielded new insights into the translational regulon containing the ribosomal protein mRNAs. First, the ribosome occupancy defects in the rpl24b mutant partially overlapped with those in a previously analyzed initiation factor mutant, eif3h. Second, a group of mRNAs with incomplete coding sequences appeared to be uncoupled from the regulon, since their dependence on RPL24B differed from regular mRNAs. Third, different sister paralogs of the ribosomal proteins differed in their translation state in the wild-type. Some sister paralogs also differed in their response to the rpl24b mutation. In contrast to rpl24b, the pab2 pab8 mutant revealed few gene specific translational defects, but a group of seed storage protein mRNAs were stimulated in their ribosome occupancy. In the course of this work, while optimizing the statistical analysis of ribosome occupancy data, we collected 12 biological replicates of translation states from wild-type seedlings. We defined 20% of mRNAs as having a high variance in their translation state. Many of these mRNAs were functionally associated with responses to the environment, suggesting that subtle variation in the environmental conditions is sensed by plants and transduced to affect the translational efficiency of hundreds of mRNAs. CONCLUSIONS: These data represent the first genome-wide analysis of translation in a eukaryote defective in the large ribosomal subunit. RPL24 and eIF3h play similar but non-identical roles in eukaryotic translation. The data also shed light on the fine structure of the regulon of ribosomal protein mRNAs.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=24377433&dopt=Abstract">Link to Article in PubMed</a>
dc.rights<p>© 2013 Tiruneh et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<a href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</a>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.</p>
dc.subjectArabidopsis
dc.subjectArabidopsis Proteins
dc.subjectEukaryotic Initiation Factor-3
dc.subjectMicroarray Analysis
dc.subjectMutant Proteins
dc.subjectMutation
dc.subjectOpen Reading Frames
dc.subject*Protein Biosynthesis
dc.subjectRNA, Messenger
dc.subjectRNA, Plant
dc.subjectRibosomal Proteins
dc.subjectGenomics
dc.subjectMicrobiology
dc.titleThe global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant
dc.typeJournal Article
dc.source.journaltitleBMC biology
dc.source.volume11
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=3444&amp;context=oapubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/oapubs/2444
dc.identifier.contextkey6359760
refterms.dateFOA2022-08-23T16:40:15Z
html.description.abstract<p>BACKGROUND: Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different environmental stresses and genetic lesions in the translation apparatus. To identify additional features of the global landscape of translational control, we used microarray analysis of polysomal as well as non-polysomal mRNAs to examine the defects in translation in a poly(A) binding protein mutant, pab2 pab8, as well as in a mutant of a large ribosomal subunit protein, rpl24b/shortvalve1.</p> <p>RESULTS: The mutation of RPL24B stimulated the ribosome occupancy of mRNAs for nuclear encoded ribosomal proteins. Detailed analysis yielded new insights into the translational regulon containing the ribosomal protein mRNAs. First, the ribosome occupancy defects in the rpl24b mutant partially overlapped with those in a previously analyzed initiation factor mutant, eif3h. Second, a group of mRNAs with incomplete coding sequences appeared to be uncoupled from the regulon, since their dependence on RPL24B differed from regular mRNAs. Third, different sister paralogs of the ribosomal proteins differed in their translation state in the wild-type. Some sister paralogs also differed in their response to the rpl24b mutation. In contrast to rpl24b, the pab2 pab8 mutant revealed few gene specific translational defects, but a group of seed storage protein mRNAs were stimulated in their ribosome occupancy. In the course of this work, while optimizing the statistical analysis of ribosome occupancy data, we collected 12 biological replicates of translation states from wild-type seedlings. We defined 20% of mRNAs as having a high variance in their translation state. Many of these mRNAs were functionally associated with responses to the environment, suggesting that subtle variation in the environmental conditions is sensed by plants and transduced to affect the translational efficiency of hundreds of mRNAs.</p> <p>CONCLUSIONS: These data represent the first genome-wide analysis of translation in a eukaryote defective in the large ribosomal subunit. RPL24 and eIF3h play similar but non-identical roles in eukaryotic translation. The data also shed light on the fine structure of the regulon of ribosomal protein mRNAs.</p>
dc.identifier.submissionpathoapubs/2444
dc.contributor.departmentDepartment of Microbiology and Physiological Systems
dc.source.pages123


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