smu-1 encodes the Caenorhabditis elegans orthologue of the spliceosomal protein SMU1. The smu-1(mn415) allele was originally identified as a suppressor of synthetic lethality between mec-8 and unc-52 and was mapped to a stop codon at amino acid position 255 in exon 5. Our Sanger sequencing analysis of the smu-1(mn415) allele shows that the stop codon is at amino acid position 257 in exon 6.
","acknowledgements":"We thank all Akay Lab members and the School of Biological Sciences technician team for their support throughout this project. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We thank the WormBase for providing genomic resources (Sternberg et al., 2024).
","authors":[{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","writing_originalDraft"],"email":"Nirmala-Devi-Rajendra-Chauhan.-@uea.ac.uk","firstName":"Nirmala Devi Rajendra ","lastName":"Chauhan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","supervision","writing_reviewEditing"],"email":"Timothy.Pearson@uea.ac.uk","firstName":"Timothy","lastName":"Pearson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","fundingAcquisition","project","resources","writing_reviewEditing","supervision"],"email":"a.akay@uea.ac.uk","firstName":"Alper","lastName":"Akay","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-6825-4443"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"AA and TP are funded by a UKRI Future Leaders Fellowship awarded to AA (MR/S033769/1 and MR/X024261/1).
","image":{"url":"https://portal.micropublication.org/uploads/60c64ed33e4d83ca7091b8d9894e496a.png"},"imageCaption":"(A) Diagram of smu-1 exons 5 and 6. Exon sequences and the corresponding amino acid sequences are shown in letters. The previously reported and the current position of the stop codon are shown with an arrow.
(B) Gel electrophoresis of PCR products around Gln255 in wild-type (WT) and smu-1(mn415) containing SP1792 strain with and without restriction digestion with SspI (-/+ RE).
(C) Sanger sequencing alignment traces of PCR products around Gln255.
(D) Sanger sequencing alignment traces of PCR products around Gln257.
(E) Gel electrophoresis of PCR products around Gln257 in wild-type (WT) and SP1792 strain with and without restriction enzyme digestion with DdeI (-/+RE; the wild-type amplicon has an additional DdeI site observed as a small shift in the WT +RE band). Yellow arrows indicate unspecific / primer dimer bands.
","imageTitle":"smu-1(mn415) has a Gln > STOP mutation in exon 6
","methods":"We used the following strains in this study: N2 Bristol wild type and SP1792 smu-1(mn415) I; unc-52(e669su250) II. C. elegans were maintained on NGM plates at 20℃ and fed E. coli HB101. C. elegans were lysed using the Extract-N-Amp Tissue kit (Sigma, XNAT2). Worms were picked into 10 µl of extraction solution mixed with 2.5 µl of tissue suspension solution. The mixture was heated to 55℃ for 20 min, then to 95℃ for 3 min, and finally mixed with 10 µl of neutralisation solution. For amplification of the Gln255 amplicon, we used the primer set A882 5ʹ-TTTGTAGCCAGTCAACCACTTTC-3ʹ and A883 5ʹ-AGGTACtgtaggtatacggtaag-3ʹ, and for the Gln257 amplicon we used the primer pairs A882 and A904 5ʹ- ACTCGAGTGCCCACGCATTTCC-3ʹ. PCR reactions were carried out using PCRBio TaqMix with an annealing temperature of 62℃. Restriction enzyme digestion with SspI (NEB) and DdeI (NEB) was set up in a 10 µl volume with NEB Cutsmart buffer. PCR products and restriction digests were run on a 1.5% agarose gel in 1XTAE buffer.
","reagents":"","patternDescription":"SMU1/fSAP57 and SMU2/RED are components of the spliceosomal B complex and interact structurally (Hegele et al., 2012; Keiper et al., 2019; Spartz et al., 2004; Zhang et al., 2024). Both proteins are required during B complex activation and for efficient splicing of predominantly short introns (Keiper et al., 2019). Mutations in either gene cause splicing defects in multiple organisms (Chung et al., 2009; Dassah et al., 2009; Keiper et al., 2019; Spartz et al., 2004; Spike et al., 2001; Sugaya et al., 2006). The smu-1(mn415) allele was originally identified as a suppressor of the synthetic lethal mec-8(u218ts); unc-52(e669su250ts) double mutants (Lundquist & Herman, 1994). Later studies showed that smu-1(mn415) and other smu-1 and smu-2 alleles cause alternative splicing of genes harbouring intronic mutations, which contributes to genetic suppression of mutant phenotypes (Dassah et al., 2009; Spartz et al., 2004; Spike et al., 2001).
Molecular characterisation of the smu-1(mn415) allele reported a CAA to TAA transition that converts glutamine 255 in exon 5 into a stop codon (Figure 1A) (Spike et al., 2001). While genotyping the strain SP1792 smu-1(mn415) I; unc-52(e669su250) II, our attempts to use the restriction enzyme SspI, predicted to digest the PCR product around Gln255, failed. Sanger sequencing of the PCR product around Gln255 also didn't reveal any mutations on or around Gln255 (Figure 1B). Gln255 is the last amino acid of exon 5, which is separated from exon 6 by an 847 bp intron (Figure 1A). We also noted that the second amino acid of exon 6 (amino acid 257) is Gln, with the same CAA codon. Therefore, we PCR-amplified and Sanger-sequenced the region around Gln257, which revealed a C to T transition converting Gln257 into a stop codon (Figure 1C). We confirmed that the CAA to TAA mutation at Gln257 is digested by the restriction enzyme DdeI (Figure 1D).
We do not expect the new position of the stop codon in smu-1(mn415) to alter any reported phenotypes. Nevertheless, these results could help other researchers genotype smu-1(mn415) more easily.
","references":[{"reference":"Chung T, Wang D, Kim CS, Yadegari R, Larkins BA. 2009. Plant SMU-1 and SMU-2 Homologues Regulate Pre-mRNA Splicing and Multiple Aspects of Development. Plant Physiology 151: 1498-1512.
","pubmedId":"","doi":"10.1104/pp.109.141705"},{"reference":"Dassah M, Patzek S, Hunt VM, Medina PE, Zahler AM. 2009. A Genetic Screen for Suppressors of a Mutated 5′ Splice Site Identifies Factors Associated With Later Steps of Spliceosome Assembly. Genetics 182: 725-734.
","pubmedId":"","doi":"10.1534/genetics.109.103473"},{"reference":"Hegele A, Kamburov A, Grossmann A, Sourlis C, Wowro S, Weimann M, et al., Stelzl. 2012. Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome. Molecular Cell 45: 567-580.
","pubmedId":"","doi":"10.1016/j.molcel.2011.12.034"},{"reference":"Keiper S, Papasaikas P, Will CL, Valcárcel J, Girard C, Lührmann R. 2019. Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns. Nature Communications 10: 10.1038/s41467-019-11293-8.
","pubmedId":"","doi":"10.1038/s41467-019-11293-8"},{"reference":"Lundquist EA, Herman RK. 1994. The mec-8 gene of Caenorhabditis elegans affects muscle and sensory neuron function and interacts with three other genes: unc-52, smu-1 and smu-2.. Genetics 138: 83-101.
","pubmedId":"","doi":"10.1093/genetics/138.1.83"},{"reference":"Spartz AK, Herman RK, Shaw JE. 2004. SMU-2 and SMU-1, Caenorhabditis elegans Homologs of Mammalian Spliceosome-Associated Proteins RED and fSAP57, Work Together To Affect Splice Site Choice. Molecular and Cellular Biology 24: 6811-6823.
","pubmedId":"","doi":"10.1128/MCB.24.15.6811-6823.2004"},{"reference":"Spike CA, Shaw JE, Herman RK. 2001. Analysis of smu-1, a Gene That Regulates the Alternative Splicing of unc-52 Pre-mRNA in Caenorhabditis elegans. Molecular and Cellular Biology 21: 4985-4995.
","pubmedId":"","doi":"10.1128/MCB.21.15.4985-4995.2001"},{"reference":"Sternberg PW, Van Auken K, Wang Q, Wright A, Yook K, Zarowiecki M, et al., Stein. 2024. WormBase 2024: status and transitioning to Alliance infrastructure. GENETICS 227: 10.1093/genetics/iyae050.
","pubmedId":"","doi":"10.1093/genetics/iyae050"},{"reference":"Sugaya K, Hongo E, Ishihara Y, Tsuji H. 2006. The conserved role of Smu1 in splicing is characterized in its mammalian temperature-sensitive mutant. Journal of Cell Science 119: 4944-4951.
","pubmedId":"","doi":"10.1242/jcs.03288"},{"reference":"Zhang Z, Kumar V, Dybkov O, Will CL, Urlaub H, Stark H, Lührmann R. 2024. Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. The EMBO Journal 43: 10.1038/s44318-024-00052-1.
","pubmedId":"","doi":"10.1038/s44318-024-00052-1"}],"title":"The nonsense mutation of the smu-1(mn415) allele is in exon 6 at Q257, not in exon 5 at Q255
","reviews":[{"reviewer":{"displayName":"Miguel Almeida"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[{"curator":{"displayName":"KJ Yook"},"openAcknowledgement":false,"submitted":null},{"curator":{"displayName":"Stavros Diamantakis"},"openAcknowledgement":false,"submitted":null}]},{"id":"35c8edd0-b6e7-4388-bfce-1b4bf7e2a3fb","decision":"accept","abstract":"smu-1 encodes the Caenorhabditis elegans orthologue of the spliceosomal protein SMU1. The smu-1(mn415) allele was originally identified as a suppressor of synthetic lethality between mec-8 and unc-52 and was mapped to a stop codon at amino acid position 255 in exon 5. Our Sanger sequencing analysis of the smu-1(mn415) allele shows that the stop codon is at amino acid position 257 in exon 6.
","acknowledgements":"We thank all Akay Lab members and the School of Biological Sciences technician team for their support throughout this project. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We thank the WormBase for providing genomic resources (Sternberg et al., 2024).
","authors":[{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","writing_originalDraft"],"email":"Nirmala-Devi-Rajendra-Chauhan.-@uea.ac.uk","firstName":"Nirmala Devi Rajendra ","lastName":"Chauhan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","supervision","writing_reviewEditing"],"email":"Timothy.Pearson@uea.ac.uk","firstName":"Timothy","lastName":"Pearson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","fundingAcquisition","project","resources","writing_reviewEditing","supervision"],"email":"a.akay@uea.ac.uk","firstName":"Alper","lastName":"Akay","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-6825-4443"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"AA and TP are funded by a UKRI Future Leaders Fellowship awarded to AA (MR/S033769/1 and MR/X024261/1).
","image":{"url":"https://portal.micropublication.org/uploads/d720adbd590c89636054534561b1fdd7.png"},"imageCaption":"(A) Diagram of smu-1 exons 5 and 6. Exon sequences and the corresponding amino acid sequences are shown in letters. The previously reported and the current position of the stop codon are shown with an arrow.
(B) Gel electrophoresis of PCR products around Gln255 in wild-type (WT) and smu-1(mn415) containing SP1792 strain with and without restriction digestion with SspI (-/+ RE).
(C) Sanger sequencing alignment traces of PCR products around Gln255.
(D) Sanger sequencing alignment traces of PCR products around Gln257.
(E) Gel electrophoresis of PCR products around Gln257 in wild-type (WT) and SP1792 strain with and without restriction enzyme digestion with DdeI (-/+RE; the wild-type amplicon has an additional DdeI site observed as a small shift in the WT +RE band). Yellow arrows indicate unspecific / primer dimer bands.
","imageTitle":"smu-1(mn415) has a Gln > STOP mutation in exon 6
","methods":"Strains used in this study:
Strain name | Genotype | Source |
N2 Bristol | Wild-type | CGC |
CGC |
C. elegans were maintained on NGM plates at 20℃and fed E. coli HB101. C. elegans were lysed using the Extract-N-Amp Tissue kit (Sigma, XNAT2). Worms were picked into 10 µl of extraction solution mixed with 2.5 µl of tissue suspension solution. The mixture was heated to 55℃ for 20 min, then to 95℃ for 3 min, and finally mixed with 10 µl of neutralisation solution. For amplification of the Gln255 amplicon, we used the primer set A882 5ʹ-TTTGTAGCCAGTCAACCACTTTC-3ʹ and A883 5ʹ-AGGTACtgtaggtatacggtaag-3ʹ, and for the Gln257 amplicon we used the primer pairs A882 and A904 5ʹ-ACTCGAGTGCCCACGCATTTCC-3ʹ. PCR reactions were carried out using PCRBio TaqMix with an annealing temperature of 62℃. Restriction enzyme digestion with SspI (NEB, cuts at 5ʹ…AAT/ATT…3ʹ) and DdeI (NEB) was set up in a 10 µl volume with NEB Cutsmart buffer. PCR products and restriction digests were run on a 1.5% agarose gel in 1XTAE buffer.
","reagents":"","patternDescription":"SMU1/fSAP57 and SMU2/RED are components of the spliceosomal B complex and interact structurally (Hegele et al., 2012; Keiper et al., 2019; Spartz et al., 2004; Zhang et al., 2024). Both proteins are required during B complex activation and for efficient splicing of predominantly short introns (Keiper et al., 2019). Mutations in either gene cause splicing defects in multiple organisms (Chung et al., 2009; Dassah et al., 2009; Keiper et al., 2019; Spartz et al., 2004; Spike et al., 2001; Sugaya et al., 2006). The smu-1(mn415) allele was originally identified as a suppressor of the synthetic lethal mec-8(u218ts); unc-52(e669su250ts) double mutants (Lundquist & Herman, 1994). Later studies showed that smu-1(mn415) and other smu-1 and smu-2 alleles cause alternative splicing of genes harbouring intronic mutations, which contributes to genetic suppression of mutant phenotypes (Dassah et al., 2009; Spartz et al., 2004; Spike et al., 2001).
Molecular characterisation of the smu-1(mn415) allele reported a CAA to TAA transition that converts glutamine 255 in exon 5 into a stop codon (Figure 1A) (Spike et al., 2001). We noted that the Gln255 codon is CAG, not CAA, and therefore assumed the reported stop codon could be TAG rather than TAA. While genotyping the strain SP1792 smu-1(mn415) I; unc-52(e669su250) II, our attempts to use the restriction enzyme SspI (cuts at 5ʹ…AAT/ATT…3ʹ), predicted to digest the PCR product around Gln255, failed. Sanger sequencing of the PCR product around Gln255 also did not reveal any mutations on or around Gln255 (Figure 1B). Gln255 is the last amino acid of exon 5, which is separated from exon 6 by an 847 bp intron (Figure 1A). We also noted that the second amino acid of exon 6 (amino acid 257) is Gln, with the CAA codon. Therefore, we PCR-amplified and Sanger-sequenced the region around Gln257, which revealed a C to T transition converting Gln257 into a TAA stop codon (Figure 1C). We confirmed that the CAA to TAA mutation at Gln257 is digested by the restriction enzyme DdeI (cuts at 5ʹ…C/TNA/G…3ʹ) (Figure 1D).
We do not expect the new position of the stop codon in smu-1(mn415) to alter any reported phenotypes. Nevertheless, these results could help other researchers genotype smu-1(mn415) more easily.
","references":[{"reference":"Chung T, Wang D, Kim CS, Yadegari R, Larkins BA. 2009. Plant SMU-1 and SMU-2 Homologues Regulate Pre-mRNA Splicing and Multiple Aspects of Development. Plant Physiology 151: 1498-1512.
","pubmedId":"","doi":"10.1104/pp.109.141705"},{"reference":"Dassah M, Patzek S, Hunt VM, Medina PE, Zahler AM. 2009. A Genetic Screen for Suppressors of a Mutated 5′ Splice Site Identifies Factors Associated With Later Steps of Spliceosome Assembly. Genetics 182: 725-734.
","pubmedId":"","doi":"10.1534/genetics.109.103473"},{"reference":"Hegele A, Kamburov A, Grossmann A, Sourlis C, Wowro S, Weimann M, et al., Stelzl. 2012. Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome. Molecular Cell 45: 567-580.
","pubmedId":"","doi":"10.1016/j.molcel.2011.12.034"},{"reference":"Keiper S, Papasaikas P, Will CL, Valcárcel J, Girard C, Lührmann R. 2019. Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns. Nature Communications 10: 10.1038/s41467-019-11293-8.
","pubmedId":"","doi":"10.1038/s41467-019-11293-8"},{"reference":"Lundquist EA, Herman RK. 1994. The mec-8 gene of Caenorhabditis elegans affects muscle and sensory neuron function and interacts with three other genes: unc-52, smu-1 and smu-2. Genetics 138: 83-101.
","pubmedId":"","doi":"10.1093/genetics/138.1.83"},{"reference":"Spartz AK, Herman RK, Shaw JE. 2004. SMU-2 and SMU-1, Caenorhabditis elegans Homologs of Mammalian Spliceosome-Associated Proteins RED and fSAP57, Work Together To Affect Splice Site Choice. Molecular and Cellular Biology 24: 6811-6823.
","pubmedId":"","doi":"10.1128/MCB.24.15.6811-6823.2004"},{"reference":"Spike CA, Shaw JE, Herman RK. 2001. Analysis of smu-1, a Gene That Regulates the Alternative Splicing of unc-52 Pre-mRNA in Caenorhabditis elegans. Molecular and Cellular Biology 21: 4985-4995.
","pubmedId":"","doi":"10.1128/MCB.21.15.4985-4995.2001"},{"reference":"Sternberg PW, Van Auken K, Wang Q, Wright A, Yook K, Zarowiecki M, et al., Stein. 2024. WormBase 2024: status and transitioning to Alliance infrastructure. GENETICS 227: 10.1093/genetics/iyae050.
","pubmedId":"","doi":"10.1093/genetics/iyae050"},{"reference":"Sugaya K, Hongo E, Ishihara Y, Tsuji H. 2006. The conserved role of Smu1 in splicing is characterized in its mammalian temperature-sensitive mutant. Journal of Cell Science 119: 4944-4951.
","pubmedId":"","doi":"10.1242/jcs.03288"},{"reference":"Zhang Z, Kumar V, Dybkov O, Will CL, Urlaub H, Stark H, Lührmann R. 2024. Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. The EMBO Journal 43: 10.1038/s44318-024-00052-1.
","pubmedId":"","doi":"10.1038/s44318-024-00052-1"}],"title":"The nonsense mutation of the smu-1(mn415) allele is in exon 6 at Q257, not in exon 5 at Q255
","reviews":[{"reviewer":{"displayName":"Miguel Almeida"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[{"curator":{"displayName":"Stavros Diamantakis"},"openAcknowledgement":true,"submitted":"1792513195751"},{"curator":{"displayName":"KJ Yook"},"openAcknowledgement":false,"submitted":null},{"curator":{"displayName":"Karen Yook (Ad)"},"openAcknowledgement":false,"submitted":"1792556618213"},{"curator":{"displayName":"Karen Yook (Ad)"},"openAcknowledgement":false,"submitted":null},{"curator":{"displayName":"Karen Yook (Ad)"},"openAcknowledgement":false,"submitted":null}]},{"id":"61133a24-7afd-4758-928f-ecc1a328e266","decision":"publish","abstract":"smu-1 encodes the Caenorhabditis elegans orthologue of the spliceosomal protein SMU1. The smu-1(mn415) allele was originally identified as a suppressor of synthetic lethality between mec-8 and unc-52 and was mapped to a stop codon at amino acid position 255 in exon 5. Our Sanger sequencing analysis of the smu-1(mn415) allele shows that the stop codon is at amino acid position 257 in exon 6.
","acknowledgements":"We thank all Akay Lab members and the School of Biological Sciences technician team for their support throughout this project. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We thank the WormBase for providing genomic resources (Sternberg et al., 2024).
","authors":[{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","writing_originalDraft"],"email":"Nirmala-Devi-Rajendra-Chauhan.-@uea.ac.uk","firstName":"Nirmala Devi Rajendra ","lastName":"Chauhan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","supervision","writing_reviewEditing"],"email":"Timothy.Pearson@uea.ac.uk","firstName":"Timothy","lastName":"Pearson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of East Anglia, Norwich, ENG, United Kingdom"],"departments":["School of Biological Sciences"],"credit":["conceptualization","fundingAcquisition","project","resources","writing_reviewEditing","supervision"],"email":"a.akay@uea.ac.uk","firstName":"Alper","lastName":"Akay","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-6825-4443"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"AA and TP are funded by a UKRI Future Leaders Fellowship awarded to AA (MR/S033769/1 and MR/X024261/1).
","image":{"url":"https://portal.micropublication.org/uploads/d720adbd590c89636054534561b1fdd7.png"},"imageCaption":"(A) Diagram of smu-1 exons 5 and 6. Exon sequences and the corresponding amino acid sequences are shown in letters. The previously reported and the current position of the stop codon are shown with an arrow.
(B) Gel electrophoresis of PCR products around Gln255 in wild-type (WT) and smu-1(mn415) containing SP1792 strain with and without restriction digestion with SspI (-/+ RE).
(C) Sanger sequencing alignment traces of PCR products around Gln255.
(D) Sanger sequencing alignment traces of PCR products around Gln257.
(E) Gel electrophoresis of PCR products around Gln257 in wild-type (WT) and SP1792 strain with and without restriction enzyme digestion with DdeI (-/+RE; the wild-type amplicon has an additional DdeI site observed as a small shift in the WT +RE band). Yellow arrows indicate unspecific / primer dimer bands.
","imageTitle":"smu-1(mn415) has a Gln > STOP mutation in exon 6
","methods":"Strains used in this study:
Strain name | Genotype | Source |
N2 Bristol | Wild-type | CGC |
CGC |
C. elegans were maintained on NGM plates at 20℃and fed E. coli HB101. C. elegans were lysed using the Extract-N-Amp Tissue kit (Sigma, XNAT2). Worms were picked into 10 µl of extraction solution mixed with 2.5 µl of tissue suspension solution. The mixture was heated to 55℃ for 20 min, then to 95℃ for 3 min, and finally mixed with 10 µl of neutralisation solution. For amplification of the Gln255 amplicon, we used the primer set A882 5ʹ-TTTGTAGCCAGTCAACCACTTTC-3ʹ and A883 5ʹ-AGGTACtgtaggtatacggtaag-3ʹ, and for the Gln257 amplicon we used the primer pairs A882 and A904 5ʹ-ACTCGAGTGCCCACGCATTTCC-3ʹ. PCR reactions were carried out using PCRBio TaqMix with an annealing temperature of 62℃. Restriction enzyme digestion with SspI (NEB, cuts at 5ʹ…AAT/ATT…3ʹ) and DdeI (NEB) was set up in a 10 µl volume with NEB Cutsmart buffer. PCR products and restriction digests were run on a 1.5% agarose gel in 1X TAE buffer.
","reagents":"","patternDescription":"SMU1/fSAP57 and SMU2/RED are components of the spliceosomal B complex and interact structurally (Hegele et al., 2012; Keiper et al., 2019; Spartz et al., 2004; Zhang et al., 2024). Both proteins are required during B complex activation and for efficient splicing of predominantly short introns (Keiper et al., 2019). Mutations in either gene cause splicing defects in multiple organisms (Chung et al., 2009; Dassah et al., 2009; Keiper et al., 2019; Spartz et al., 2004; Spike et al., 2001; Sugaya et al., 2006). The smu-1(mn415) allele was originally identified as a suppressor of the synthetic lethal mec-8(u218ts); unc-52(e669su250ts) double mutants (Lundquist & Herman, 1994). Later studies showed that smu-1(mn415) and other smu-1 and smu-2 alleles cause alternative splicing of genes harbouring intronic mutations, which contributes to genetic suppression of mutant phenotypes (Dassah et al., 2009; Spartz et al., 2004; Spike et al., 2001).
Molecular characterisation of the smu-1(mn415) allele reported a CAA to TAA transition that converts glutamine 255 in exon 5 into a stop codon (Figure 1A) (Spike et al., 2001). We noted that the Gln255 codon is CAG, not CAA, and therefore assumed the reported stop codon could be TAG rather than TAA. While genotyping the strain SP1792 smu-1(mn415) I; unc-52(e669su250) II, our attempts to use the restriction enzyme SspI (cuts at 5ʹ…AAT/ATT…3ʹ), predicted to digest the PCR product around Gln255, failed. Sanger sequencing of the PCR product around Gln255 also did not reveal any mutations on or around Gln255 (Figure 1B). Gln255 is the last amino acid of exon 5, which is separated from exon 6 by an 847 bp intron (Figure 1A). We also noted that the second amino acid of exon 6 (amino acid 257) is Gln, with the CAA codon. Therefore, we PCR-amplified and Sanger-sequenced the region around Gln257, which revealed a C to T transition converting Gln257 into a TAA stop codon (Figure 1C). We confirmed that the CAA to TAA mutation at Gln257 is digested by the restriction enzyme DdeI (cuts at 5ʹ…C/TNA/G…3ʹ) (Figure 1D).
We do not expect the new position of the stop codon in smu-1(mn415) to alter any reported phenotypes. Nevertheless, these results could help other researchers genotype smu-1(mn415) more easily.
","references":[{"reference":"Chung T, Wang D, Kim CS, Yadegari R, Larkins BA. 2009. Plant SMU-1 and SMU-2 Homologues Regulate Pre-mRNA Splicing and Multiple Aspects of Development. Plant Physiology 151: 1498-1512.
","pubmedId":"","doi":"10.1104/pp.109.141705"},{"reference":"Dassah M, Patzek S, Hunt VM, Medina PE, Zahler AM. 2009. A Genetic Screen for Suppressors of a Mutated 5′ Splice Site Identifies Factors Associated With Later Steps of Spliceosome Assembly. Genetics 182: 725-734.
","pubmedId":"","doi":"10.1534/genetics.109.103473"},{"reference":"Hegele A, Kamburov A, Grossmann A, Sourlis C, Wowro S, Weimann M, et al., Stelzl. 2012. Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome. Molecular Cell 45: 567-580.
","pubmedId":"","doi":"10.1016/j.molcel.2011.12.034"},{"reference":"Keiper S, Papasaikas P, Will CL, Valcárcel J, Girard C, Lührmann R. 2019. Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns. Nature Communications 10: 10.1038/s41467-019-11293-8.
","pubmedId":"","doi":"10.1038/s41467-019-11293-8"},{"reference":"Lundquist EA, Herman RK. 1994. The mec-8 gene of Caenorhabditis elegans affects muscle and sensory neuron function and interacts with three other genes: unc-52, smu-1 and smu-2. Genetics 138: 83-101.
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