A Two-Headed Monster to Avert Disaster: HBS1/SKI7 Is Alternatively Spliced to Build Eukaryotic RNA Surveillance Complexes

Brunkard, Jacob O.; Baker, Barbara

doi:10.3389/fpls.2018.01333

Cited by 14 publications

(19 citation statements)

References 66 publications

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“…This is consistent with published data from other eukaryotes (Kowalinski et al, 2016;Kalisiak et al, 2016;Marshall et al, 2018). The zebrafish ski7specific exon (exon 5) contains the previously annotated Ski7-like motif and the most conserved region of Ski7, the so-called patch 4-like (P4) motif (Kowalinski et al, 2016;Brunkard & Baker, 2018) (Fig. 1C).…”

Section: Ski7 Mrna Is Highly Expressed During the Oocyte-to-embryo Trsupporting

confidence: 91%

“…In this study, we provide the first functional characterization of vertebrate Ski7 and the consequences of its absence. Zebrafish Ski7, similar to its human and plant homologs (Kalisiak et al, 2016;Kowalinski et al, 2016;Brunkard & Baker, 2018), is encoded as an alternative splice isoform of hbs1l. We found that zebrafish ski7 but not hbs1l mRNA is highly expressed in mature eggs and early embryos, which prompted us to investigate Ski7's role during the oocyte-to-embryo transition.…”

Section: Discussionmentioning

confidence: 99%

“…Ski7 is known to interact with the cytoplasmic RNA exosome in yeast (van Hoof et al, 2000), plants (Brunkard & Baker, 2018), and human cells (Kalisiak et al, 2016;Kowalinski et al, 2016) by binding to the cap protein Csl4 via multiple interactions, including its highly conserved P4 motif. However, transcriptomic analyses revealed that components of the zebrafish exosome are relatively lowly expressed during the oocyte-to-embryo transition ( Fig.…”

Section: Zebrafish Ski7 Interacts With the Rna Exosomementioning

confidence: 99%

“…In contrast to yeast, in which Ski7 is encoded by an independent gene locus (Marshall et al, 2013;, the recently identified Ski7 homolog in vertebrates (human HBS1LV3) is encoded by an alternative splice isoform of vertebrate hbs1l (Kowalinski et al, 2016;Marshall et al, 2018;Kalisiak et al, 2016). Vertebrate Ski7 shares the Ski and exosome complex interacting domains of yeast Ski7, yet it lacks the GTPase domain (Marshall et al, 2018;Brunkard & Baker, 2018;Kowalinski et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Quio

Schleiffer

Mechtler

et al. 2020

Preprint

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Post-transcriptional mechanisms are crucial for the regulation of gene expression.These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation.Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte-to-embryo transition. Here, we focused on the auxiliary 3'-to-5' degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults, yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte-toembryo transition, transcriptome profiling identified stage-specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis-regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall, our results provide first insights into the physiological role of vertebrate Ski7 as an important posttranscriptional regulator during the oocyte-to-embryo transition.

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Section: Ski7 Mrna Is Highly Expressed During the Oocyte-to-embryo Trsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Zebrafish Ski7 Interacts With the Rna Exosomementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Quio

Schleiffer

Mechtler

et al. 2020

Preprint

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“…In yeast, the genes encoding Ski7 and Hbs1, which binds to Dom34 (PELOTA in humans and plants) for the release of stalled ribosomes 35 , arose from a whole genome duplication event. In other eukaryotes including mammals and plants, the SKI7 and HBS1 proteins are produced by alternative splicing from a single locus 36–38 .…”

mentioning

confidence: 99%

RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex inArabidopsis

Lange

Ndecky

Gómez-Díaz

et al. 2019

Preprint

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21The RNA exosome is a key 3'-5' exoribonuclease with an evolutionarily conserved structure 22The Ski complex consists of the MTR4-related RNA helicase SKI2, the tetratricopeptide 1 repeat protein SKI3 and two copies of the WD40-repeat protein SKI8 [31][32][33] . Association of the 2 Ski complex with the exosome core complex requires an additional protein, SKI7 34 . In yeast, 3 the genes encoding Ski7 and Hbs1, which binds to Dom34 (PELOTA in humans and plants) 4for the release of stalled ribosomes 35 , arose from a whole genome duplication event. In other 5 eukaryotes including mammals and plants, the SKI7 and HBS1 proteins are produced by 6 alternative splicing from a single locus [36][37][38] . 7The Ski complex is conserved in Arabidopsis thaliana 39 , but its physical association with 8 the exosome core has not been investigated yet. An initial experiment to affinity-capture 9 factors associated with the Arabidopsis exosome identified the homologue of DIS3 and two 10 nuclear RNA helicases, AtMTR4 and its closely related homologue HEN2 23 . In addition, 11Arabidopsis Exo9 systematically co-purified with a 1840 amino acid ARM repeat protein of 12 unknown molecular function named RESURRECTION 1 (RST1) 23 . RST1 was originally 13identified in a genetic screen for factors involved in the biosynthesis of epicuticular waxes 40 . 14 Epicuticular waxes are a protective layer of aliphatic very long chain (VLC) hydrocarbons 15 that cover the outer surface of land plants 41,42 . rst1 mutants have less wax on floral stems than 16 wild-type plants, and about 70% of the seeds produced by rst1 mutants are shrunken due to 17 aborted embryogenesis 40 . The molecular function of RST1 remains unknown. Interestingly, 18 one of the two RRP45 exosome core subunits encoded in the Arabidopsis genome, named 19 RRP45B or CER7 (for ECERIFERUM 7) was also identified in a genetic screen aimed at 20 identifying enzymes or regulators of wax biosynthesis 43 . The wax-deficient phenotype of 21 rrp45b/cer7 mutants (cer7 from now on) is suppressed by mutations in genes encoding RNA 22

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SKI complex: A multifaceted cytoplasmic RNA exosome cofactor in mRNA metabolism with links to disease, developmental processes, and antiviral responses

et al. 2023

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RNA stability and quality control are integral parts of gene expression regulation. A key factor shaping eukaryotic transcriptomes, mainly via 3′–5′ exoribonucleolytic trimming or degradation of diverse transcripts in nuclear and cytoplasmic compartments, is the RNA exosome. Precise exosome targeting to various RNA molecules requires strict collaboration with specialized auxiliary factors, which facilitate interactions with its substrates. The predominant class of cytoplasmic RNA targeted by the exosome are protein‐coding transcripts, which are carefully scrutinized for errors during translation. Normal, functional mRNAs are turned over following protein synthesis by the exosome or by Xrn1 5′–3′‐exonuclease, acting in concert with Dcp1/2 decapping complex. In turn, aberrant transcripts are eliminated by dedicated surveillance pathways, triggered whenever ribosome translocation is impaired. Cytoplasmic 3′–5′ mRNA decay and surveillance are dependent on the tight cooperation between the exosome and its evolutionary conserved co‐factor—the SKI (superkiller) complex (SKIc). Here, we summarize recent findings from structural, biochemical, and functional studies of SKIc roles in controlling cytoplasmic RNA metabolism, including links to various cellular processes. Mechanism of SKIc action is illuminated by presentation of its spatial structure and details of its interactions with exosome and ribosome. Furthermore, contribution of SKIc and exosome to various mRNA decay pathways, usually converging on recycling of ribosomal subunits, is delineated. A crucial physiological role of SKIc is emphasized by describing association between its dysfunction and devastating human disease—a trichohepatoenteric syndrome (THES). Eventually, we discuss SKIc functions in the regulation of antiviral defense systems, cell signaling and developmental transitions, emerging from interdisciplinary investigations.This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes

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A Two-Headed Monster to Avert Disaster: HBS1/SKI7 Is Alternatively Spliced to Build Eukaryotic RNA Surveillance Complexes

Cited by 14 publications

References 66 publications

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex inArabidopsis

SKI complex: A multifaceted cytoplasmic RNA exosome cofactor in mRNA metabolism with links to disease, developmental processes, and antiviral responses

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