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The Arabidopsis thaliana core splicing factor PORCUPINE/SmE1 requires intron-mediated expression
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). (Markus Schmid)ORCID-id: 0000-0002-3262-0859
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden. (Markus Schmid)ORCID-id: 0000-0001-6058-6830
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). (Markus Schmid)ORCID-id: 0000-0002-5799-7572
Department of Biology, Aarhus University, Aarhus C, Denmark; Royal Botanic Gardens, Kew, Richmond, Surrey, UK. (Wolf Eiserhardt)ORCID-id: 0000-0002-8136-5233
Visa övriga samt affilieringar
2025 (Engelska)Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 20, nr 3, artikel-id e0318163Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress.

Ort, förlag, år, upplaga, sidor
Public Library of Science (PLoS), 2025. Vol. 20, nr 3, artikel-id e0318163
Nyckelord [en]
Arabidopsis thaliana, alternative RNA splicing, temperature signaling, SmE, PORCUPINE (PCP)
Nationell ämneskategori
Biokemi Molekylärbiologi Evolutionsbiologi
Identifikatorer
URN: urn:nbn:se:umu:diva-234799DOI: 10.1371/journal.pone.0318163ISI: 001456749600044PubMedID: 40138296Scopus ID: 2-s2.0-105001186937OAI: oai:DiVA.org:umu-234799DiVA, id: diva2:1933481
Forskningsfinansiär
Knut och Alice Wallenbergs Stiftelse, KAW 2018.0202Forskningsrådet Formas, 2023-01077Tillgänglig från: 2025-01-31 Skapad: 2025-01-31 Senast uppdaterad: 2025-04-15Bibliografiskt granskad
Ingår i avhandling
1. Broken Sm-ring: a quest to the source of the cold sensitivity of the A. thaliana SmE1 splicing mutant
Öppna denna publikation i ny flik eller fönster >>Broken Sm-ring: a quest to the source of the cold sensitivity of the A. thaliana SmE1 splicing mutant
2025 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Alternativ titel[sv]
Den trasiga Sm-ringen : jakten på ursprunget till köldkänsligheten hos splitsningsmutanten SmE1 i A. thaliana
Abstract [en]

Temperature is an important signal that informs plants about their surroundings and daily and seasonal changes. In temperate climates, temperature variation throughout the year can reach up to 40°C, and usually, it is the cold that acts as a limiting factor for successful growth and development. The cold response is a multifaceted process that affects all levels of the organization, from molecular to organismal. There is an intertwined network of transcriptional changes, cold-triggered splicing events, and unspecific stress responses.

The aim of this thesis was to investigate the role of PORCUPINE (PCP/SmE1), a component of the core splicing complex called Sm-ring, in cold signaling and its connection to co-occurring events in the model plant Arabidopsis thaliana. Despite the functional redundancy of PCP and its homolog PORCUPINE-LIKE (PCPL/SmE2), their roles diverge due to the differential gene regulation in response to temperature. We showed a correlation between the level of the PCP transcript and plant phenotype and linked PCP expression to its introns. Then, we compared the transcriptome of the knockout PCP mutant, pcp-1, to other temperature-sensitive splicing mutants and showed a pool of differential splicing events that were PCP-specific. Some of these events were linked to the core components of the cold response. We hypothesized that at least part of the pleiotropic effects of the PCP loss in A. thaliana occur due to the misregulated splicing of these genes. We also identified a plausible connection between splicing and transcription through PCP as a component of the Sm-ring and an RNA Polymerase II regulator, CDKC;2. Here we found that the loss of CDKC;2 in the pcp-1 background rescued the cold-sensitive pcp-1 phenotype and restored transcriptional kinetics to the wild-type levels. Finally, we hypothesize that a broken Sm-ring requires an appropriate attenuation of the transcription rates to perform the splicing successfully.

Taken together, the work in this thesis demonstrates the complexity of the cold response mechanisms in A. thaliana and the central role of splicing components, such as PCP, for temperature acclimatization.

Ort, förlag, år, upplaga, sidor
Umeå: Umeå University, 2025. s. 62
Nyckelord
Arabidopsis thaliana, temperature, cold response, splicing, splicing mutants, Sm-ring, transcription
Nationell ämneskategori
Biokemi Molekylärbiologi Botanik
Forskningsämne
molekylärbiologi
Identifikatorer
urn:nbn:se:umu:diva-234806 (URN)9789180705691 (ISBN)9789180705707 (ISBN)
Disputation
2025-02-28, Stora hörsalen (KBE303), KBC-huset, Linnaeus väg 6, 09:00 (Engelska)
Opponent
Handledare
Tillgänglig från: 2025-02-07 Skapad: 2025-02-02 Senast uppdaterad: 2025-02-20Bibliografiskt granskad

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Dikaya, VarvaraRojas-Murcia, NelsonBenstein, Ruben MaximilianSchmid, Markus

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Dikaya, VarvaraRojas-Murcia, NelsonBenstein, Ruben MaximilianEiserhardt, Wolf L.Schmid, Markus
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