Structural basis for the regulation of splicing of a yeast messenger RNA

Eng, Francis J.; Warner, Jonathan R.

doi:10.1016/0092-8674(91)90387-e

Cited by 160 publications

(131 citation statements)

References 48 publications

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“…The YRA1 intron is unusual in size, location within the coding region, and in the sequence of one of the consensus splicing signals (Portman et al+, 1997 (2002) was that cells expressing YRA1 containing the RPL25 intron from the YRA1 promoter had a slight dominantnegative growth defect at 37 8C+ Intriguingly, some of the introns we have tested, notably that of ACT1, could partially complement the growth defect of YRA1-⌬IVS+ It thus seems that the YRA1 intron shares some characteristics that are relevant for autoregulation with a subset of introns from unrelated yeast genes+ These observations will likely facilitate the identification of cisacting regulatory elements in the YRA1 transcript+ For example, like the YRA1 intron, the RPL25 and ACT1 introns are unusually large (414 and 408 nt, respectively), whereas both the UBC8 and YRA1 introns have branchpoint sequences that differ from the normally highly conserved consensus at the first position (CAC UAAC and GACUAAC, respectively)+ In addition, the discrepancies between our findings and those of Rodriguez-Navarro et al+ (2002) might, at least in part, also reflect subtle differences in the experimental details involved, such as different strain backgrounds or plasmid-copy numbers+ Even though we do not know at this point which of the peculiarities of the YRA1 intron mentioned above are involved in autoregulation, each of these characteristics has been shown to be important in the few reports of regulated splicing in yeast+ One prominent example is the meiosis-specific splicing of MER2 premRNA+ During mitotic growth, basal splicing efficiency is lowered by a noncanonical 59 splice site and an unusually large 59 exon (Engebrecht et al+, 1991;Nandabalan & Roeder, 1995)+ Activation of splicing during meiosis requires a splicing enhancer located downstream of the 59 splice site (Spingola & Ares, 2000) and the product of the MER1 gene that is only expressed during meiosis and specifically binds to the MER2 splicing enhancer (Nandabalan & Roeder, 1995;Spingola & Ares, 2000)+ Another well-studied example is the ribosomal protein L30, which regulates splicing of the transcript of its own gene, RPL30+ Binding of L30 to an RNA structure formed by nucleotides surrounding the noncanonical 59 splice site of RPL30 inhibits splicing prior to the first step (Eng & Warner, 1991;Vilardell & Warner, 1994)+ Finally, autoregulation of DBP2, a member of the DEAD-box family of putative RNA helicases, depends on the presence of a 1,002-nt intron, the largest in S. cerevisiae (Barta & Iggo, 1995)+ To our knowledge, YRA1 is the first example of a yeast gene that causes a dramatic growth defect when its intron is removed+ No effect on growth has been observed as a result of DBP2 overexpression from a cDNA copy (Barta & Iggo, 1995)+ Moreover, a cocultivation assay capable of revealing subtle differences in biological fitness was required to show that mutations in RPL30 that abolish autoregulation lead to detectably slower growth only over the course of many generations (Li et al+, 1996)+…”

Section: Expression Of Yra1p Is Regulated On the Level Of Splicingmentioning

confidence: 99%

Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism

Preker

Kim

Guthrie

2002

RNA

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Recent evidence supports the idea that pre-mRNA splicing and mRNA export are mechanistically coupled. In metazoans, this process appears to be mediated by a multicomponent complex, which associates with the spliced RNA upstream of the exon-exon junction. One of these components (Aly/REF) has a homolog in the budding yeast Saccharomyces cerevisiae known as Yra1p. The YRA1 gene is essential for growth and required for mRNA export. Notably, YRA1 is one of the only ;5% intron-containing genes in yeast. Moreover, the YRA1 intron has several unusual features and is conserved in other budding yeast species. Previously, overexpression of intronless YRA1 was shown to be toxic. We show here that overexpression of the intron-containing gene results in increased levels of unspliced pre-mRNA but normal levels of Yra1 protein; conversely, expression of the cDNA results in increased levels of protein and accumulation of nuclear poly(A) 1 RNA. Two additional lines of evidence suggest that expression of Yra1p is autoregulated: First, expression of excess Yra1p from a plasmid reduces the level of tagged, chromosomal Yra1p, and, second, this effect requires wild-type protein. Replacement of the YRA1 intron with that of other S. cerevisiae genes cannot rescue the dominant-negative growth defect of intronless YRA1. We conclude that the level of Yra1p is negatively autoregulated by a mechanism that involves splicing of its unusual intron. Tight control of the levels of Yra1p might be necessary to couple the rates of pre-mRNA splicing and mRNA export.

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Section: Expression Of Yra1p Is Regulated On the Level Of Splicingmentioning

confidence: 99%

Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism

Preker

Kim

Guthrie

2002

RNA

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“…In S. cerevisiae, extraribosomal functions for Rpl2, Rps14, Rpl30, and Rps28 in autoregulation of their own synthesis have been demonstrated (Eng and Warner 1991;Presutti et al 1991;Fewell and Woolford 1999;Badis et al 2004). Two other known cases of extraribosomal functions are for Rps20 and Rpl6, proteins that are capable of influencing Pol III transcription (Hermann-Le Denmat et al 1994;Dieci et al 2009).…”

Section: Functional Specificity Of Rp Paralogs and Extraribosomal Funmentioning

confidence: 99%

Ribosome Deficiency Protects Against ER Stress in Saccharomyces cerevisiae

et al. 2012

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In Saccharomyces cerevisiae, 59 of the 78 ribosomal proteins are encoded by duplicated genes that, in most cases, encode identical or very similar protein products. However, different sets of ribosomal protein genes have been identified in screens for various phenotypes, including life span, budding pattern, and drug sensitivities. Due to potential suppressors of growth rate defects among this set of strains in the ORF deletion collection, we regenerated the entire set of haploid ribosomal protein gene deletion strains in a clean genetic background. The new strains were used to create double deletions lacking both paralogs, allowing us to define a set of 14 nonessential ribosomal proteins. Replicative life-span analysis of new strains corresponding to ORF deletion collection strains that likely carried suppressors of growth defects identified 11 new yeast replicative aging genes. Treatment of the collection of ribosomal protein gene deletion strains with tunicamycin revealed a significant correlation between slow growth and resistance to ER stress that was recapitulated by reducing translation of wild-type yeast with cycloheximide. Interestingly, enhanced tunicamycin resistance in ribosomal protein gene deletion mutants was independent of the unfolded protein response transcription factor Hac1. These data support a model in which reduced translation is protective against ER stress by a mechanism distinct from the canonical ER stress response pathway and further add to the diverse yet specific phenotypes associated with ribosomal protein gene deletions.T HE yeast ribosome consists of two subunits, the 40S (small) and 60S (large), which together contain four discrete rRNA species and 78 ribosomal proteins (RPs). In Saccharomyces cerevisiae, 59 of the 78 ribosomal proteins are encoded by a pair of paralogous genes, most of which arose through a genome-wide duplication event roughly 100 million years ago (Wolfe and Shields 1997). Only 12% of the duplicated genome remains, and of the paralogous gene pairs present, a majority of ribosomal proteins genes (RPGs) are in a class that exhibits little or even decelerated evolution (Kellis et al. 2004). Remarkably, 21 of the 59 RPG pairs encode identical proteins, and the others are highly similar (Supporting Information, Table S1). The prevalence of synthetic lethality among RPG paralogs indicates that the two protein products are generally redundant for at least one essential function (Dean et al. 2008).Despite the significant similarity among RPG paralogs, many reports have described differential effects of deleting only one, and such instances have been observed even in cases where the encoded protein product is identical (Briones et al. 1998). One explanation for this is that the two genes contribute different amounts of protein, and neither is alone sufficient to support wild-type growth. In the case of Rpl16, for example, expression of either RPL16A or RPL16B can rescue the growth defect of cells lacking RPL16B (Rotenberg et al. 1988). Consistently, the RPL16...

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“…In eukarya, it appears that L7Ae homologs have become more specialized. For instance, L30e complexes with 60S rRNA and its own coding mRNA (Eng and Warner 1991), 15.5kD with U4 snRNA ) and box C/D snoRNAs (Watkins et al 2000), and Nhp2 with box H/ACA snoRNAs (Henras et al 2001).…”

Section: Introductionmentioning

confidence: 99%

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

Baird¹,

Zhang²,

Hamma³

et al. 2012

RNA

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The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turnbinding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K d~2 70 nM and~2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.

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Structural basis for the regulation of splicing of a yeast messenger RNA

Cited by 160 publications

References 48 publications

Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism

Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism

Ribosome Deficiency Protects Against ER Stress in Saccharomyces cerevisiae

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

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