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BioProject

KAP241507

BioProject Title

WSS1A, a DNA-Protein Crosslink Repair Protease, Negatively Regulates Leaf Senescence via Liquid-Liquid Phase Separation and SUMOylation in Arabidopsis (DDBJ: PRJDB37377)

Leaf senescence, the final stage of leaf development, is regulated by a complex interplay of intrinsic genetic programs and environmental cues. Throughout their lifetimes, all living organisms encounter various endogenous and environmental challenges, many of which can cause potentially fatal DNA damage. Among these, DNA-Protein Crosslinks (DPCs) are particularly deleterious, as they impede essential processes such as replication and transcription, compromising genome integrity and ultimately leading to premature aging across diverse organisms. However, the biological significance of DPCs and their repair mechanisms in leaf senescence remains unexplored. In this study, we demonstrate that the accumulation of DPCs by cis-platin (cis-Pt), a well-known DPC inducer, triggers premature leaf senescence in Arabidopsis. We identify Arabidopsis WSS1A, a WLM/Spr-T metalloprotease, as a functional ortholog of yeast Wss1 in DPC repair, playing a negative role in leaf senescence induced by cis-Pt treatment, darkness, and leaf age. WSS1A forms nuclear condensates via liquid-liquid phase separation (LLPS) both in vitro and in vivo, which is cooperatively driven by its N-terminal segment and intrinsically disordered region. Mechanistically, WSS1A non-covalently interacts with SMALL UBIQUITIN MODIFIER 3 (SUMO3) through its SUMO-interacting motif (SIM) and is covalently SUMOylated by SUMO3. Genetic analysis further reveals that WSS1A is epistatic to SUMO3 in regulating cis-Pt-induced leaf senescence. Disrupting the SIM significantly compromises WSS1A condensate dynamics, highlighting its critical role in phase separation. Together, our findings suggest unresolved DPCs as molecular triggers promoting leaf senescence and underscore the importance of efficient DPC repair by WSS1A involving LLPS and SUMOylation in extending leaf longevity.

Common Fields

Common Fields - BioProject, Strategy, Source, Selection, Layout, Instrument, Submission date, Experiments
BioProject	KAP241507
Strategy	RNA-Seq
Source	TRANSCRIPTOMIC
Selection	cDNA
Layout	paired
Instrument	Illumina NovaSeq 6000
Submission date	2025-04-29
Experiments	4

Accession

Accession - RUNs, BIOSAMPLEs
Runs	All runs [4]
BioSamples	All samples [4]

Experiment Metadata

(4 cases)

Experiment Metadata - SUBMISSION ID, EXPERIMENT ID, Identifier, BIOSAMPLE ID, SAMPLE NAME, LIBRARY IDENTIFIER, TITLE, LIBRARY STRATEGY, LIBRARY SOURCE, LIBRARY SELETION, LIBRARY IAYOUT, FLATFORM, INSTRUMENT MODEL
EXPERIMENT ID	Identifier	BIOSAMPLE ID	sample_name	library_name	title	library_strategy	library_source	library_selection	library_layout	platform	instrument_model	library_construction_protocol	Submission dateSubmission date	Registration date
KAE24092868	DRA: DRX857033	KAS24117308	Col_Treat_1DAT_2	Col_Treat_1DAT_2	Illumina NovaSeq 6000 paired Sequencing of pair	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	ILLUMINA	Illumina NovaSeq 6000	Leaves detached from Col plants at 12 DAE were floated on 3 mM MES (pH 5.8) with or without 30 micrometer cis-Pt and incubated at 22 degree C under 16-h light/8-h dark photoperiod for 1 day. The mRNA-seq experiments were performed in two independent biological replicates per treatment (0 and 30 micrometer cis-Pt). Total RNA was isolated from the leaves using QIAzol (QIAGEN, Germany) and its integrity was assessed using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, USA). Total RNA samples with an RNA integrity number (RIN) greater than 7.8 were used for mRNA-seq analysis. Poly(A) mRNA was isolated from the total RNA (2 microgram) and fragmented using Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) with poly-T oligo-attached magnetic beads. After the cDNA synthesis from the RNA fragments using Superscript II reverse transcriptase (InvitrogenTM, USA), strand-specific cDNA libraries were generated by adaptor ligation and sequenced by Illumina NovaSeq 6000 system (Illumina, USA), according to the Illumina Directional RNA-Seq protocol.	2025-04-29	2025-04-25
KAE24092867	DRA: DRX857032	KAS24117307	Col_Treat_1DAT_1	Col_Treat_1DAT_1	Illumina NovaSeq 6000 paired Sequencing of pair	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	ILLUMINA	Illumina NovaSeq 6000	Leaves detached from Col plants at 12 DAE were floated on 3 mM MES (pH 5.8) with or without 30 micrometer cis-Pt and incubated at 22 degree C under 16-h light/8-h dark photoperiod for 1 day. The mRNA-seq experiments were performed in two independent biological replicates per treatment (0 and 30 micrometer cis-Pt). Total RNA was isolated from the leaves using QIAzol (QIAGEN, Germany) and its integrity was assessed using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, USA). Total RNA samples with an RNA integrity number (RIN) greater than 7.8 were used for mRNA-seq analysis. Poly(A) mRNA was isolated from the total RNA (2 microgram) and fragmented using Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) with poly-T oligo-attached magnetic beads. After the cDNA synthesis from the RNA fragments using Superscript II reverse transcriptase (InvitrogenTM, USA), strand-specific cDNA libraries were generated by adaptor ligation and sequenced by Illumina NovaSeq 6000 system (Illumina, USA), according to the Illumina Directional RNA-Seq protocol.	2025-04-29	2025-04-25
KAE24092866	DRA: DRX857031	KAS24117306	Col_Mock_1DAT_2	Col_Mock_1DAT_2	Illumina NovaSeq 6000 paired Sequencing of pair	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	ILLUMINA	Illumina NovaSeq 6000	Leaves detached from Col plants at 12 DAE were floated on 3 mM MES (pH 5.8) with or without 30 micrometer cis-Pt and incubated at 22 degree C under 16-h light/8-h dark photoperiod for 1 day. The mRNA-seq experiments were performed in two independent biological replicates per treatment (0 and 30 micrometer cis-Pt). Total RNA was isolated from the leaves using QIAzol (QIAGEN, Germany) and its integrity was assessed using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, USA). Total RNA samples with an RNA integrity number (RIN) greater than 7.8 were used for mRNA-seq analysis. Poly(A) mRNA was isolated from the total RNA (2 microgram) and fragmented using Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) with poly-T oligo-attached magnetic beads. After the cDNA synthesis from the RNA fragments using Superscript II reverse transcriptase (InvitrogenTM, USA), strand-specific cDNA libraries were generated by adaptor ligation and sequenced by Illumina NovaSeq 6000 system (Illumina, USA), according to the Illumina Directional RNA-Seq protocol.	2025-04-29	2025-04-25
KAE24092865	DRA: DRX857030	KAS24117305	Col_Mock_1DAT_1	Col_Mock_1DAT_1	Illumina NovaSeq 6000 paired Sequencing of pair	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	ILLUMINA	Illumina NovaSeq 6000	Leaves detached from Col plants at 12 DAE were floated on 3 mM MES (pH 5.8) with or without 30 micrometer cis-Pt and incubated at 22 degree C under 16-h light/8-h dark photoperiod for 1 day. The mRNA-seq experiments were performed in two independent biological replicates per treatment (0 and 30 micrometer cis-Pt). Total RNA was isolated from the leaves using QIAzol (QIAGEN, Germany) and its integrity was assessed using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, USA). Total RNA samples with an RNA integrity number (RIN) greater than 7.8 were used for mRNA-seq analysis. Poly(A) mRNA was isolated from the total RNA (2 microgram) and fragmented using Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) with poly-T oligo-attached magnetic beads. After the cDNA synthesis from the RNA fragments using Superscript II reverse transcriptase (InvitrogenTM, USA), strand-specific cDNA libraries were generated by adaptor ligation and sequenced by Illumina NovaSeq 6000 system (Illumina, USA), according to the Illumina Directional RNA-Seq protocol.	2025-04-29	2025-04-25

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