Nucleoli: Composition, Function, and Dynamics

Shaw, Peter; Brown, John W.

doi:10.1104/pp.111.188052

Cited by 107 publications

(125 citation statements)

References 82 publications

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“…Several splicing factors were also found in the nucleolus (Lorkovi c et al, 2004;Pendle et al, 2005;Tillemans et al, 2006), and the nucleolus and Cajal bodies are known to function in U1 snRNP maturation (Lorkovi c and Barta, 2008) in Arabidopsis. These findings strongly suggest that, as in animals, the nucleolus is involved in snRNP biogenesis, and possibly in spliceosome formation, in plants (Shaw and Brown, 2012). A lot of rearrangements of RNA-RNA and RNA-protein are included in these processes, and RNA helicases should mediate at least a subset of them.…”

Section: Discussionmentioning

confidence: 79%

“…The nucleolus is the site of ribosome biogenesis, including transcription of rRNA genes, rRNA maturation, and ribosome assembly (reviewed in Shaw and Brown, 2012), and some DExD/ H-box proteins are known to function in rRNA maturation (Tanner and Linder, 2001). To test the possibility that RID1 is also involved in rRNA maturation, we performed RNA gel blot analysis with a probe specific for the internal transcribed spacer region 1 of rRNA.…”

Section: Subcellular Localization Of Rid1mentioning

confidence: 99%

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Arabidopsis ROOT INITIATION DEFECTIVE1, a DEAH-Box RNA Helicase Involved in Pre-mRNA Splicing, Is Essential for Plant Development

2013

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ORCID ID: 0000-0001-5429-3310 (M.O.).Pre-mRNA splicing is a critical process in gene expression in eukaryotic cells. A multitude of proteins are known to be involved in pre-mRNA splicing in plants; however, the physiological roles of only some of these have been examined. Here, we investigated the developmental roles of a pre-mRNA splicing factor by analyzing root initiation defective1-1 (rid1-1), an Arabidopsis thaliana mutant previously shown to have severe defects in hypocotyl dedifferentiation and de novo meristem formation in tissue culture under high-temperature conditions. Phenotypic analysis in planta indicated that RID1 is differentially required during development and has roles in processes such as meristem maintenance, leaf morphogenesis, and root morphogenesis. RID1 was identified as encoding a DEAH-box RNA helicase implicated in pre-mRNA splicing. Transient expression analysis using intron-containing reporter genes showed that pre-mRNA splicing efficiency was affected by the rid1 mutation, which supported the presumed function of RID1 in pre-mRNA splicing. Our results collectively suggest that robust levels of pre-mRNA splicing are critical for several specific aspects of plant development.

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Section: Discussionmentioning

confidence: 79%

Section: Subcellular Localization Of Rid1mentioning

confidence: 99%

Arabidopsis ROOT INITIATION DEFECTIVE1, a DEAH-Box RNA Helicase Involved in Pre-mRNA Splicing, Is Essential for Plant Development

2013

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“…7). Inside the nucleolus, TEV P1 specifically localizes in the granular component, where final processing of preribosomal particles takes place (55). In fact, TEV P1 nucleolar localization is similar to that of a genuine ribosomal protein (Fig.…”

Section: Discussionmentioning

confidence: 88%

Tobacco etch virus Protein P1 Traffics to the Nucleolus and Associates with the Host 60S Ribosomal Subunits during Infection

Martínez

Daròs

2014

J Virol

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The genus Potyvirus comprises a large group of positive-strand RNA plant viruses whose genome encodes a large polyprotein processed by three viral proteinases. P1 protein, the most amino-terminal product of the polyprotein, is an accessory factor stimulating viral genome amplification whose role during infection is not well understood. We infected plants with Tobacco etch virus (TEV; genus Potyvirus) clones in which P1 was tagged with a fluorescent protein to track its expression and subcellular localization or with an affinity tag to identify host proteins involved in complexes in which P1 also takes part during infection. Our results showed that TEV P1 exclusively accumulates in infected cells at an early stage of infection and that the protein displays a dynamic subcellular localization, trafficking in and out of the nucleus and nucleolus during infection. Inside the nucleolus, P1 particularly targets the dense granular component. Consistently, we found functional nucleolar localization and nuclear export signals in TEV P1 sequence. Our results also indicated that TEV P1 physically interacts with the host 80S cytoplasmic ribosomes and specifically binds to the 60S ribosomal subunits during infection. In vitro translation assays of reporter proteins suggested that TEV P1 stimulates protein translation, particularly when driven from the TEV internal ribosome entry site. These in vitro assays also suggested that TEV helper-component proteinase (HC-Pro) inhibits protein translation. Based on these findings, we propose that TEV P1 stimulates translation of viral proteins in infected cells. IMPORTANCEIn this work, we researched the role during infection of tobacco etch virus P1 protease. P1 is the most mysterious protein of potyviruses, a relevant group of RNA viruses infecting plants. Our experiments showed that the viral P1 protein exclusively accumulates in infected cells at an early stage of infection and moves in and out of the nucleus of infected cells, particularly targeting the nucleolus. Our experiments also showed that P1 protein binds host ribosomes during infection. Based on these findings and other in vitro experiments we propose that P1 protein stimulates translation of viral proteins during infection.

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“…However, poorly represented or even entirely absent rDNA sequences seem to be a common issue in many currently assembled genomes (Treangen and Salzberg 2012), which might hamper the discovery of 5S rRNA variants. A recent review emphasized our lack of knowledge regarding full rRNA sequences in higher eukaryotes, because of the imperfection of modern technology for highly repetitive sequence analysis, and doubted whether all the rDNA repeats are intact functional genes or what other functional sequences are interspersed with them (Shaw and Brown 2012). For example, the 5S rRNA of zebrafish (Danio rerio) has not been thoroughly described, despite being one of the most versatile model organisms (Dooley 2000;Briggs 2002;Langheinrich et al 2002;Veldman and Lin 2008;Norton and Bally-Cuif 2010).…”

Section: Introductionmentioning

confidence: 99%

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

Locati

Pagano

Ensink

et al. 2016

RNA

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5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal-and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci.

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Nucleoli: Composition, Function, and Dynamics

Cited by 107 publications

References 82 publications

Arabidopsis ROOT INITIATION DEFECTIVE1, a DEAH-Box RNA Helicase Involved in Pre-mRNA Splicing, Is Essential for Plant Development

Arabidopsis ROOT INITIATION DEFECTIVE1, a DEAH-Box RNA Helicase Involved in Pre-mRNA Splicing, Is Essential for Plant Development

Tobacco etch virus Protein P1 Traffics to the Nucleolus and Associates with the Host 60S Ribosomal Subunits during Infection

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

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