{"title":"Mitochondrial DNA and the largest nuclear-mitochondrial DNA in Arabidopsis can be separated by their methylation levels.","authors":"Yuyang Zhong, Miki Okuno, Nobuhiro Tsutsumi, Shin-Ichi Arimura","doi":"10.1093/plphys/kiaf069","DOIUrl":"10.1093/plphys/kiaf069","url":null,"abstract":"<p><p>Methylation of cytosines in plant mitochondrial DNA (mtDNA) has been a controversial issue. Results supporting mtDNA methylation may have been subject to contamination due to the presence of nuclear sequences originating from the mitochondrial genome called nuclear mitochondrial insertions (NUMT). In Arabidopsis (Arabidopsis thaliana) Columbia 0 (Col-0), the largest NUMT, located on Chromosome 2, is nearly twice the size of the entire mitochondrial genome and exhibits a sequence almost identical to the mitochondrial genome, albeit with shuffling and repeats. In the presence of such high similarity, it is challenging to eliminate interference when determining mtDNA methylation levels. Here, we applied a methyl-CpG-binding domain (MBD) protein-based affinity assay to separate total DNA, applied next-generation sequencing to the pre- and postseparation DNA samples, and examined the single nucleotide polymorphism (SNP) sites between NUMT and mtDNA. The results revealed successful separation of methylated and non-methylated DNA within the total DNA, with simultaneous separation achieved between NUMT DNA and mtDNA. These results suggest that our method can achieve separation based on the differential methylation levels of the whole lengths of NUMT and mtDNAs. The bisulfite sequencing results for the postseparation DNA samples suggest that mtDNA exhibits not only a lack of CpG methylation but also an absence of CHH and CHG methylation. In contrast, the NUMT shows high levels of methylation across all 3 contexts, at least in the Col-0 accession.</p>","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The tomato SBP-box protein SlCNR negatively regulates genes involved in fruit cutin deposition.","authors":"Di Chen, Hua Huang, Qiaoli Zhang, Tingting Hu, Zongyan Sun, Tingyu Wang, Xue Chen, Rongrong Nie, Leilei Zhou, Daqi Fu, Hongliang Zhu, Guozheng Qin, Benzhong Zhu, Guiqin Qu","doi":"10.1093/plphys/kiaf099","DOIUrl":"10.1093/plphys/kiaf099","url":null,"abstract":"<p><p>Cutin serves as the foundational structure of the plant cuticle and plays a crucial role in determining fruit development and quality. However, the transcriptional regulation of cutin deposition by fruit-specific transcription factors remains largely unknown. This study delves into the regulatory role of the tomato (Solanum lycopersicum) SBP-box protein Colorless Non-Ripening (SlCNR), primarily expressed in fruits, in cutin formation. We found that clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9-induced slcnr mutants exhibited thicker cuticles and elevated contents in total cutin and cutin monomers compared with wild-type fruits, whereas SlCNR overexpression (OE) lines displayed the opposite tendency. Transcriptome-wide RNA sequencing identified differentially expressed genes in SlCNR OE fruits. Further validation by gene expression, DNA binding, and transcriptional activity assays revealed that SlCNR directly binds to and represses the transcription of 13 genes associated with cutin synthesis, export, and assembly, including glycerol-3-phosphate acyltransferase 4/6, ATP-binding cassette transporter subfamily G protein 36/42, and cutin synthase. In addition, SlCNR directly bound to and repressed the transcription activities of the promoter of NON-RIPENING like-1, which encodes a positive regulator of cutin deposition. Thus, SlCNR emerged as a negative transcription regulator of cutin content and cuticle thickness, ultimately affecting fruit firmness and cuticle permeability. This study sheds light on the molecular mechanisms governing cutin deposition through transcriptional regulatory networks, highlighting the role of SlCNR as an important player in fruit cuticle development.</p>","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant PhysiologyPub Date : 2025-03-01DOI: 10.1093/plphys/kiaf065
Moona Rahikainen
{"title":"Oiling the wheels of growth: TOR kinase promotes lipid synthesis in plants.","authors":"Moona Rahikainen","doi":"10.1093/plphys/kiaf065","DOIUrl":"10.1093/plphys/kiaf065","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11887541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"GT1 and ZmHB13/VRL1 regulate flower sexual differentiation by modulating jasmonate biosynthesis and signaling in maize.","authors":"Yateng Yuan, Xiaotong Ou, Minhao Yao, Pinle Wang, Chunlian Li, Guisen Zhang, Mengqi He, Heying Li, Xin Xu, Zhuojun Zhong, Yun Lu, Xiaojun Lai, Chen Zou, Jie Shen, Tianyu Zhang, Defan Liu, Yaoyao Li, Haiyang Wang, Dexin Kong, Qing Liu","doi":"10.1093/plphys/kiaf075","DOIUrl":"10.1093/plphys/kiaf075","url":null,"abstract":"<p><p>As a typical monoecious plant, maize (Zea mays L.) produces unisexual male and female flowers comprising tassels and ears, respectively. However, the molecular mechanisms underlying unisexual flower development remain largely unclear. Here, we identify a pair of homeodomain-leucine zipper (HD-ZIP) transcription factors, Grassy tiller1 (GT1) and ZmHB13 (also termed VRS1-like1, VRL1), which act synergistically to control carpel development in maize. Mutations in GT1, but not ZmHB13/VRL1, cause defects in carpel abortion in the tassels, resulting in feminized tassels. The gt1 Zmhb13 double mutants show a notably more severe phenotype and a defect in the abortion of the lower floret in the ear spikelet, resulting in extra fertile flowers and seed setting. We demonstrate that GT1 and ZmHB13/VRL1 bind directly to the promoters of 2 jasmonate (JA) biosynthesis genes, ZmLOX3 and ZmOPR7, and upregulate their expression in the developing flowers. The application of methyl jasmonate (MeJA) rescues the feminized tassel phenotype of the gt1 Zmhb13 double mutants. Additionally, GT1 and ZmHB13/VRL1 interact with the key JA-pathway repressors ZmJAZ4 and ZmJAZ26, thus releasing the key JA-pathway activators ZmMYC2a and ZmMYC2b to activate the downstream JA signaling processes. Our findings indicate that GT1 and ZmHB13/VRL1 function synergistically to regulate maize carpel development through modulating JA biosynthesis and signaling.</p>","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant PhysiologyPub Date : 2025-03-01DOI: 10.1093/plphys/kiaf042
Marta Hoffman-Sommer, Natalia Piłka, Anna Anielska-Mazur, Julita Nowakowska, Małgorzata Kozieradzka-Kiszkurno, Cezary Pączkowski, Małgorzata Jemioła-Rzemińska, Kamil Steczkiewicz, Yasin Dagdas, Ewa Swiezewska
{"title":"The TRAPPC8/TRS85 subunit of the Arabidopsis TRAPPIII tethering complex regulates endoplasmic reticulum function and autophagy.","authors":"Marta Hoffman-Sommer, Natalia Piłka, Anna Anielska-Mazur, Julita Nowakowska, Małgorzata Kozieradzka-Kiszkurno, Cezary Pączkowski, Małgorzata Jemioła-Rzemińska, Kamil Steczkiewicz, Yasin Dagdas, Ewa Swiezewska","doi":"10.1093/plphys/kiaf042","DOIUrl":"10.1093/plphys/kiaf042","url":null,"abstract":"<p><p>Transport protein particle (TRAPP) tethering complexes are known for their function as Rab GTPase exchange factors. Two versions of the complex are considered functionally separate: TRAPPII, an activator of the Rab11 family (RabA in plants) GTPases that function in post-Golgi sorting, and TRAPPIII, activating Rab1 family (RabD in plants) members that regulate endoplasmic reticulum (ER)-to-Golgi trafficking and autophagy. In Arabidopsis (Arabidopsis thaliana), the TRAPPIII complex has been identified and its subunit composition established, but little is known about its functions. Here, we found that binary subunit interactions of the plant TRAPPIII complex are analogous to those of metazoan TRAPPIII, with the 2 large subunits TRAPPC8 and TRAPPC11 linking the TRAPP core and the small C12 to C13 dimer. To gain insight into the functions of TRAPPIII in plants, we characterized 2 A. thaliana trappc8 mutants. These mutants display abnormalities in plant morphology, particularly in flower and seed development. They also exhibit autophagic defects, a constitutive ER stress response, and elevated levels of the ER lipid dolichol (Dol), which is an indispensable cofactor in protein glycosylation. These results indicate that plant TRAPPC8 is involved in multiple cellular trafficking events and suggest a link between ER stress responses and Dol levels.</p>","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"197 3","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A NAC transcription factor and a MADS-box protein antagonistically regulate sucrose accumulation in strawberry receptacles.","authors":"Kun Xiao, Junmiao Fan, Xiaoyi Bi, Xiaoyu Tu, Xinyu Li, Minghao Cao, Zheng Liu, Anqi Lin, Chong Wang, Pengbo Xu, Hongli Lian","doi":"10.1093/plphys/kiaf043","DOIUrl":"https://doi.org/10.1093/plphys/kiaf043","url":null,"abstract":"<p><p>Sugar accumulation during fruit ripening is an essential physiological change that influences fruit quality. While NAC transcription factors are recognized for their role in modulating strawberry (Fragaria × ananassa) fruit ripening, their specific contributions to sugar accumulation have remained largely unexplored. This study identified FvNAC073, a NAC transcription factor, as a key regulator that not only exhibits a gradual increase in gene expression during fruit ripening but also enhances the accumulation of sucrose. Further investigation showed that FvNAC073 positively regulates the expression of sucrose-6-phosphate synthase 1 (FvSPS1), a gene associated with sucrose synthesis, and negatively regulates sucrose synthase 2 (FvSUS2), which is involved in sucrose breakdown, through direct promoter binding. Additionally, we uncovered that FvCMB1L, a MADS-box protein, exhibits high gene expression levels at the premature fruit stage and acts to repress FvSPS1 while activating FvSUS2, thus negatively affecting sucrose accumulation. Notably, we demonstrated a competitive interaction between FvNAC073 and FvCMB1L in binding to the promoters of FvSPS1 and FvSUS2, resulting in antagonistic regulation of these genes. This intricate dynamic between FvCMB1L and FvNAC073 elucidates a mechanism for balancing sugar content during strawberry fruit development. Our findings offer insights into the complex regulatory network governing sucrose accumulation in strawberries, highlighting the potential for targeted genetic interventions to enhance fruit quality.</p>","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"197 3","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}