Rational extension of the ribosome biogenesis pathway using network-guided genetics.

Biogenesis of ribosomes is an essential cellular process conserved across all eukaryotes and is known to require >170 genes for the assembly, modification, and trafficking of ribosome components through multiple cellular compartments. Despite intensive study, this pathway likely involves many add...

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Main Authors:	Zhihua Li, Insuk Lee, Emily Moradi, Nai-Jung Hung, Arlen W Johnson, Edward M Marcotte
Format:	article
Language:	EN
Published:	Public Library of Science (PLoS) 2009
Subjects:	Biology (General) QH301-705.5
Online Access:	https://doaj.org/article/dba530d8aa634d3295d41a9626dbda62
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spelling	oai:doaj.org-article:dba530d8aa634d3295d41a9626dbda622021-11-25T05:34:00ZRational extension of the ribosome biogenesis pathway using network-guided genetics.1544-91731545-788510.1371/journal.pbio.1000213https://doaj.org/article/dba530d8aa634d3295d41a9626dbda622009-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19806183/?tool=EBIhttps://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Biogenesis of ribosomes is an essential cellular process conserved across all eukaryotes and is known to require >170 genes for the assembly, modification, and trafficking of ribosome components through multiple cellular compartments. Despite intensive study, this pathway likely involves many additional genes. Here, we employ network-guided genetics-an approach for associating candidate genes with biological processes that capitalizes on recent advances in functional genomic and proteomic studies-to computationally identify additional ribosomal biogenesis genes. We experimentally evaluated >100 candidate yeast genes in a battery of assays, confirming involvement of at least 15 new genes, including previously uncharacterized genes (YDL063C, YIL091C, YOR287C, YOR006C/TSR3, YOL022C/TSR4). We associate the new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export, and we identify genes specifically required for the processing of 5S, 7S, 20S, 27S, and 35S rRNAs. These results reveal new connections between ribosome biogenesis and mRNA splicing and add >10% new genes-most with human orthologs-to the biogenesis pathway, significantly extending our understanding of a universally conserved eukaryotic process.Zhihua LiInsuk LeeEmily MoradiNai-Jung HungArlen W JohnsonEdward M MarcottePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 7, Iss 10, p e1000213 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Zhihua Li Insuk Lee Emily Moradi Nai-Jung Hung Arlen W Johnson Edward M Marcotte Rational extension of the ribosome biogenesis pathway using network-guided genetics.
description	Biogenesis of ribosomes is an essential cellular process conserved across all eukaryotes and is known to require >170 genes for the assembly, modification, and trafficking of ribosome components through multiple cellular compartments. Despite intensive study, this pathway likely involves many additional genes. Here, we employ network-guided genetics-an approach for associating candidate genes with biological processes that capitalizes on recent advances in functional genomic and proteomic studies-to computationally identify additional ribosomal biogenesis genes. We experimentally evaluated >100 candidate yeast genes in a battery of assays, confirming involvement of at least 15 new genes, including previously uncharacterized genes (YDL063C, YIL091C, YOR287C, YOR006C/TSR3, YOL022C/TSR4). We associate the new genes with specific aspects of ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export, and we identify genes specifically required for the processing of 5S, 7S, 20S, 27S, and 35S rRNAs. These results reveal new connections between ribosome biogenesis and mRNA splicing and add >10% new genes-most with human orthologs-to the biogenesis pathway, significantly extending our understanding of a universally conserved eukaryotic process.
format	article
author	Zhihua Li Insuk Lee Emily Moradi Nai-Jung Hung Arlen W Johnson Edward M Marcotte
author_facet	Zhihua Li Insuk Lee Emily Moradi Nai-Jung Hung Arlen W Johnson Edward M Marcotte
author_sort	Zhihua Li
title	Rational extension of the ribosome biogenesis pathway using network-guided genetics.
title_short	Rational extension of the ribosome biogenesis pathway using network-guided genetics.
title_full	Rational extension of the ribosome biogenesis pathway using network-guided genetics.
title_fullStr	Rational extension of the ribosome biogenesis pathway using network-guided genetics.
title_full_unstemmed	Rational extension of the ribosome biogenesis pathway using network-guided genetics.
title_sort	rational extension of the ribosome biogenesis pathway using network-guided genetics.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/dba530d8aa634d3295d41a9626dbda62
work_keys_str_mv	AT zhihuali rationalextensionoftheribosomebiogenesispathwayusingnetworkguidedgenetics AT insuklee rationalextensionoftheribosomebiogenesispathwayusingnetworkguidedgenetics AT emilymoradi rationalextensionoftheribosomebiogenesispathwayusingnetworkguidedgenetics AT naijunghung rationalextensionoftheribosomebiogenesispathwayusingnetworkguidedgenetics AT arlenwjohnson rationalextensionoftheribosomebiogenesispathwayusingnetworkguidedgenetics AT edwardmmarcotte rationalextensionoftheribosomebiogenesispathwayusingnetworkguidedgenetics
_version_	1718414608020013056

Rational extension of the ribosome biogenesis pathway using network-guided genetics.

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