Plant CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae276
Qi He, Hao Wu, Longjun Zeng, Caiyun Yin, Li Wang, Yiqing Tan, Wanqing Lv, Zhiqiang Liao, Xuelian Zheng, Shuting Zhang, Qinqin Han, Danning Wang, Yong Zhang, Guosheng Xiong, Quan Wang
{"title":"OsKANADI1 and OsYABBY5 regulate rice plant height by targeting GIBERELLIN 2-OXIDASE6.","authors":"Qi He, Hao Wu, Longjun Zeng, Caiyun Yin, Li Wang, Yiqing Tan, Wanqing Lv, Zhiqiang Liao, Xuelian Zheng, Shuting Zhang, Qinqin Han, Danning Wang, Yong Zhang, Guosheng Xiong, Quan Wang","doi":"10.1093/plcell/koae276","DOIUrl":"10.1093/plcell/koae276","url":null,"abstract":"<p><p>Plant height is an important agronomic characteristic of rice (Oryza sativa L.). Map-based cloning analyses of a natural semi-dwarf rice mutant with inwardly curled leaves found in the field revealed that the defects were due to a mutation of a SHAQKYF-class MYB family transcription factor, OsKANADI1 (OsKAN1). OsKAN1 directly bound to the OsYABBY5 (OsYAB5) promoter to repress its expression and interacted with OsYAB5 to form a functional OsKAN1-OsYAB5 complex. GIBERELLIN 2-OXIDASE6 (OsGA2ox6), encoding an enzyme in the gibberellin (GA) catabolic pathway, was activated by OsYAB5. Furthermore, the OsKAN1-OsYAB5 complex suppressed the inhibitory effect of OsKAN1 toward OsYAB5 and inhibited OsYAB5-induced OsGA2ox6 expression. The proOsKAN1:OsYAB5 transgenic plants were taller than wild-type plants, whereas oskan1 proOsKAN1:OsYAB5 plants exhibited a severe dwarf phenotype due to the absence of the OsKAN1-OsYAB5 complex. The OsKAN1-OsYAB5 complex modulated OsGA2ox6 expression, thereby regulating the levels of bioactive gibberellins and, consequently, plant height. This study elucidated the mechanism underlying the effect of the OsKAN1-OsYAB5-OsGA2ox6 regulatory pathway on plant height at different positions in rice stems and provided insights on stem development and candidate genes for the aerial architecture improvement of crop plants.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142392432","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae295
Lijuan Zhou, Ying Du, Manqi Zhang, Jincheng Li, Yue Zhao, Xuechun Hu, Kunrong He, Fuliang Cao, Yajin Ye
{"title":"REGULATOR OF FATTY ACID SYNTHESIS proteins regulate de novo fatty acid synthesis by modulating hetACCase distribution.","authors":"Lijuan Zhou, Ying Du, Manqi Zhang, Jincheng Li, Yue Zhao, Xuechun Hu, Kunrong He, Fuliang Cao, Yajin Ye","doi":"10.1093/plcell/koae295","DOIUrl":"10.1093/plcell/koae295","url":null,"abstract":"<p><p>In plants, heteromeric acetyl-CoA carboxylase (hetACCase) initiates de novo fatty acid synthesis (FAS) by generating malonyl-CoA in the first committed step of this process. hetACCase activity is precisely regulated to meet the cellular demand for acyl chains during the plant life cycle. In this study, we performed a systematic coexpression analysis of hetACCase and its regulators in Arabidopsis (Arabidopsis thaliana) to better understand the regulatory mechanism of hetACCase. Our analysis uncovered REGULATOR OF FATTY ACID SYNTHESIS 1 (RFS1), whose expression is positively correlated with that of other regulators of hetACCase. The RFS gene family encodes two plastid inner envelope membrane proteins with undiscovered roles. Further analysis revealed that RFS1 colocalizes and directly interacts with CARBOXYLTRANSFERASE INTERACTOR 1 (CTI1). CRISPR/Cas9-mediated knockouts of RFSs exhibit enhanced hetACCase activity, higher FAS rates, and increased fatty acid contents, with particularly marked accumulation of absolute triacylglycerol levels in leaves, similar to cti mutants. The mutations of rfs and cti alter the plastid membrane distribution pattern of α-CT, leading to reduced hetACCase activity on the membrane, which could potentially be the original mechanism through which RFSs restrain hetACCase activity. Thus, we reveal a unique regulatory module that regulates de novo FAS and a genetic locus that may contribute to breeding of improved oil crops.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569414","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}
{"title":"Evolution and functional divergence of glycosyltransferase genes shaped the quality and cold tolerance of tea plants.","authors":"Jingming Wang, Yutong Hu, Danyang Guo, Ting Gao, Tianqi Liu, Jieyang Jin, Mingyue Zhao, Keke Yu, Wei Tong, Honghua Ge, Yuting Pan, Mengting Zhang, Mengqian Lu, Tingting Jing, Wenkai Du, Xiaoyan Tang, Chenjie Zhao, Wei Zhao, Zhijie Bao, Wilfried Schwab, Enhua Xia, Chuankui Song","doi":"10.1093/plcell/koae268","DOIUrl":"10.1093/plcell/koae268","url":null,"abstract":"<p><p>Plant uridine diphosphate-dependent glycosyltransferases (UGTs) play a key role in plant growth and metabolism. Here, we examined the evolutionary landscape among UGTs in 28 fully sequenced species from early algae to angiosperms. Our findings revealed a distinctive expansion and contraction of UGTs in the G and H groups in tea (Camellia sinensis), respectively. Whole-genome duplication and tandem duplication events jointly drove the massive expansion of UGTs, and the interplay of natural and artificial selection has resulted in marked functional divergence within the G group of the sinensis-type tea population. In Cluster II of group G, differences in substrate selection (e.g. abscisic acid) of the enzymes encoded by UGT genes led to their functional diversification, and these genes influence tolerance to abiotic stresses such as low temperature and drought via different modes of positive and negative regulation, respectively. UGTs in Cluster III of the G group have diverse aroma substrate preferences, which contribute a diverse aroma spectrum of the sinensis-type tea population. All Cluster III genes respond to low-temperature stress, whereas UGTs within Cluster III-1, shaped by artificial selection, are unresponsive to drought. This suggests that artificial selection of tea plants focused on improving quality and cold tolerance as primary targets.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375792","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae288
Xutong Wang, Jingbo Duan, Chancelor B Clark, Wanjie Feng, Jianxin Ma
{"title":"Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.","authors":"Xutong Wang, Jingbo Duan, Chancelor B Clark, Wanjie Feng, Jianxin Ma","doi":"10.1093/plcell/koae288","DOIUrl":"10.1093/plcell/koae288","url":null,"abstract":"<p><p>Alternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes. However, the extent to which it affects the products of gene expression and how it evolves and is regulated remain unknown. Here, we report genome-wide identification and analysis of transcription start sites (TSSs) in various soybean (Glycine max) tissues using a survey of transcription initiation at promoter elements with high-throughput sequencing (STRIPE-seq). We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in canonical regulatory regions and 43.5% from start codons to 3' untranslated regions, which were responsible for changes in open reading frames of 24,131 genes. Strikingly, 6,845 genes underwent ATI within coding sequences (CDSs). These CDS-TSRs were tissue-specific, did not have TATA-boxes typical of canonical promoters, and were embedded in nucleosome-free regions flanked by nucleosomes with enhanced levels of histone marks potentially associated with intragenic transcriptional initiation, suggesting that ATI within CDSs was epigenetically tuned and associated with tissue-specific functions. Overall, duplicated genes possessed more TSRs, exhibited lower degrees of tissue specificity, and underwent stronger purifying selection than singletons. This study highlights the significance of ATI and the genomic and epigenomic factors shaping the distribution of ATI in CDSs in a paleopolyploid eukaryote.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625404","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae306
Laura Arribas-Hernández
{"title":"Multitasker Argonaute leaves no stone unturned.","authors":"Laura Arribas-Hernández","doi":"10.1093/plcell/koae306","DOIUrl":"10.1093/plcell/koae306","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644316","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae252
Noah Sprent, C Y Maurice Cheung, Sanu Shameer, R George Ratcliffe, Lee J Sweetlove, Nadine Töpfer
{"title":"Metabolic modeling reveals distinct roles of sugars and carboxylic acids in stomatal opening as well as unexpected carbon fluxes.","authors":"Noah Sprent, C Y Maurice Cheung, Sanu Shameer, R George Ratcliffe, Lee J Sweetlove, Nadine Töpfer","doi":"10.1093/plcell/koae252","DOIUrl":"10.1093/plcell/koae252","url":null,"abstract":"<p><p>Guard cell metabolism is crucial for stomatal dynamics, but a full understanding of its role is hampered by experimental limitations and the flexible nature of the metabolic network. To tackle this challenge, we constructed a time-resolved stoichiometric model of guard cell metabolism that accounts for energy and osmolyte requirements and which is integrated with the mesophyll. The model resolved distinct roles for starch, sugars, and malate in guard cell metabolism and revealed several unexpected flux patterns in central metabolism. During blue light-mediated stomatal opening, starch breakdown was the most efficient way to generate osmolytes with downregulation of glycolysis allowing starch-derived glucose to accumulate as a cytosolic osmolyte. Maltose could also accumulate as a cytosolic osmoticum, although this made the metabolic system marginally less efficient. The metabolic energy for stomatal opening was predicted to be derived independently of starch, using nocturnally accumulated citrate which was metabolized in the tricarboxylic acid cycle to malate to provide mitochondrial reducing power for ATP synthesis. In white light-mediated stomatal opening, malate transferred reducing equivalents from guard cell photosynthesis to mitochondria for ATP production. Depending on the capacity for guard cell photosynthesis, glycolysis showed little flux during the day but was crucial for energy metabolism at night. In summary, our analyses have corroborated recent findings in Arabidopsis guard cell research, resolved conflicting observations by highlighting the flexibility of guard cell metabolism, and proposed new metabolic flux modes for further experimental testing.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381501","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae305
Raul Sanchez-Muñoz
{"title":"The older the wiser, unless you are a banana: The NAP1-MADS1 network in the regulation of banana ripening.","authors":"Raul Sanchez-Muñoz","doi":"10.1093/plcell/koae305","DOIUrl":"10.1093/plcell/koae305","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648446","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae308
Sébastien Bélanger, Junpeng Zhan, Yunqing Yu, Blake C Meyers
{"title":"Comparative RNA profiling identifies stage-specific phasiRNAs and coexpressed Argonaute genes in Bambusoideae and Pooideae species.","authors":"Sébastien Bélanger, Junpeng Zhan, Yunqing Yu, Blake C Meyers","doi":"10.1093/plcell/koae308","DOIUrl":"10.1093/plcell/koae308","url":null,"abstract":"<p><p>Phased, small interfering RNAs (PhasiRNAs) play a crucial role in supporting male fertility in grasses. Earlier work in maize (Zea mays) and rice (Oryza sativa)-and subsequently many other plant species-identified premeiotic 21-nucleotide (nt) and meiotic 24-nt phasiRNAs. More recently, a group of premeiotic 24-nt phasiRNAs was discovered in the anthers of 2 Pooideae species, barley (Hordeum vulgare) and bread wheat (Triticum aestivum). Whether premeiotic 24-nt phasiRNAs and other classes of reproductive phasiRNAs are conserved across Pooideae species remains unclear. We conducted comparative RNA profiling of 3 anther stages in 6 Pooideae species and 1 Bambusoideae species. We observed complex temporal accumulation patterns of 21-nt and 24-nt phasiRNAs in Pooideae and Bambusoideae grasses. In Bambusoideae, 21-nt phasiRNAs accumulated during meiosis, whereas 24-nt phasiRNAs were present in both premeiotic and postmeiotic stages. We identified premeiotic 24-nt phasiRNAs in all 7 species examined. These phasiRNAs exhibit distinct biogenesis mechanisms and potential Argonaute effectors compared to meiotic 24-nt phasiRNAs. We show that specific Argonaute genes coexpressed with stage-specific phasiRNAs are conserved across Bambusoideae and Pooideae species. Our degradome analysis identified a set of conserved miRNA target genes across species, while 21-nt phasiRNA targets were species-specific. Cleavage of few targets was observed for 24-nt phasiRNAs. In summary, this study demonstrates that premeiotic 24-nt phasiRNAs are present across Bambusoideae and Pooideae families, and the temporal accumulation of other classes of 21-nt and 24-nt phasiRNA differs between bamboo and Pooideae species. Furthermore, targets of the 3 classes of phasiRNAs may be rapidly evolving or undetectable.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668710","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae312
Guangling Wang, Zhiyue Wu, Bo Sun
{"title":"KNUCKLES regulates floral meristem termination by controlling auxin distribution and cytokinin activity.","authors":"Guangling Wang, Zhiyue Wu, Bo Sun","doi":"10.1093/plcell/koae312","DOIUrl":"10.1093/plcell/koae312","url":null,"abstract":"<p><p>The termination of floral meristem (FM) activity is essential for the normal development of reproductive floral organs. During this process, KNUCKLES (KNU), a C2H2-type zinc finger protein, crucially regulates FM termination by directly repressing the expression of both the stem cell identity gene WUSCHEL (WUS) and the stem cell marker gene CLAVATA3 (CLV3) to abolish the WUS-CLV3 feedback loop required for FM maintenance. In addition, phytohormones auxin and cytokinin are involved in FM regulation. However, whether KNU modulates auxin and cytokinin activities for FM determinacy control remains unclear. Here, we show that the auxin distribution and the cytokinin activity mediated by KNU in Arabidopsis (Arabidopsis thaliana) promote the termination of FM during stage 6 of flower development. Mutation of KNU leads to altered distribution of auxin and cytokinin in the FM of a stage 6 floral bud. Moreover, KNU directly represses the auxin transporter gene PIN-FORMED1 (PIN1) and the cytokinin biosynthesis gene ISOPENTENYLTRANSFERASE7 (IPT7) via mediating H3K27me3 deposition on these 2 loci to regulate auxin and cytokinin activities. Our study presents a molecular regulatory network that elucidates how the transcriptional repressor KNU integrates and modulates the activities of auxin and cytokinin, thus securing the timed FM termination.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687666","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 CellPub Date : 2024-12-23DOI: 10.1093/plcell/koae293
Jing Li, Brandon Le, Xufeng Wang, Ye Xu, Suikang Wang, Hao Li, Lei Gao, Beixin Mo, Lin Liu, Xuemei Chen
{"title":"ALTERED MERISTEM PROGRAM1 impairs RNA silencing by repressing the biogenesis of a subset of inverted repeat-derived siRNAs.","authors":"Jing Li, Brandon Le, Xufeng Wang, Ye Xu, Suikang Wang, Hao Li, Lei Gao, Beixin Mo, Lin Liu, Xuemei Chen","doi":"10.1093/plcell/koae293","DOIUrl":"10.1093/plcell/koae293","url":null,"abstract":"<p><p>RNA silencing negatively regulates gene expression at the transcriptional and posttranscriptional levels through DNA methylation, histone modification, mRNA cleavage, and translational inhibition. Small interfering RNAs (siRNAs) of 21 to 24 nucleotides are processed from double-stranded RNAs by Dicer-like (DCL) enzymes and play essential roles in RNA silencing in plants. Here, we demonstrated that ALTERED MERISTEM PROGRAM1 (AMP1) and its putative paralog LIKE AMP1 (LAMP1) impair RNA silencing by repressing the biogenesis of a subset of inverted repeat (IR)-derived siRNAs in Arabidopsis (Arabidopsis thaliana). AMP1 and LAMP1 inhibit Pol II-dependent IR gene transcription by suppressing ARGONAUTE 1 (AGO1) protein levels. Genetic analysis indicates that AMP1 acts upstream of RNA polymerase IV subunit 1 (NRPD1), RNA-dependent RNA polymerase 2 (RDR2), and DCL4, which are required for IR-induced RNA silencing. We also show that AMP1 and LAMP1 inhibit siRNA-mediated silencing in a different mechanism from that of AGO4 and DCL3. Together, these results reveal two previously unknown players in siRNA biogenesis from IRs-AGO1, which promotes IR transcription, and AMP1, which inhibits IR transcription indirectly through the repression of AGO1 expression.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576547","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}