Plant Communications最新文献

{"title":"Pangenome and pantranscriptome as the new reference for gene-family characterization: A case study of basic helix-loop-helix (bHLH) genes in barley.","authors":"Cen Tong, Yong Jia, Haifei Hu, Zhanghui Zeng, Brett Chapman, Chengdao Li","doi":"10.1016/j.xplc.2024.101190","DOIUrl":"10.1016/j.xplc.2024.101190","url":null,"abstract":"<p><p>Genome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161-176 bHLHs in 20 barley genomes, which can be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 softcore, 29 shell, and 20 line-specific/cloud bHLHs, revealing the complete profile of bHLH genes in barley. Using a genome-scanning approach, we overcame the genome annotation bias and identified an average of 1.5 un-annotated core bHLHs per barley genome. We found that whole-genome/segmental duplicates are predominant mechanisms contributing to the expansion of most core/softcore bHLHs, whereas dispensable bHLHs are more likely to result from small-scale duplication events. Interestingly, we noticed that the dispensable bHLHs tend to be enriched in the specific subfamilies SF13, SF27, and SF28, implying the potentially biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least 1 intact transposon element (TE) within the 2-kb upstream-to-downstream region. bHLHs with copy-number variations (CNVs) have 1.48 TEs on average, significantly more than core bHLHs without CNVs (1.36), supporting a potential role of TEs in bHLH expansion. Analyses of selection pressure showed that dispensable bHLHs have experienced clear relaxation of selection compared with core bHLHs, consistent with their conservation patterns. We also integrated the pangenome data with recently available barley pantranscriptome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene-family analyses can better describe the previously untapped, genuine evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley. We expect that this study will inspire similar analyses in many other gene families and species.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101190"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632417","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 GAME changer in steroidal metabolite biosynthesis.","authors":"Enzo Lezin, Nicolas Papon, Vincent Courdavault","doi":"10.1016/j.xplc.2024.101201","DOIUrl":"10.1016/j.xplc.2024.101201","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101201"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781803","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":"Distinct features of PsbS essential for mediating plant photoprotection.","authors":"Lili Chen, Melvin Rodriguez-Heredia, Guy T Hanke, Alexander V Ruban","doi":"10.1016/j.xplc.2024.101179","DOIUrl":"10.1016/j.xplc.2024.101179","url":null,"abstract":"<p><p>For optimum photosynthetic productivity, it is crucial for plants to swiftly transition between light-harvesting and photoprotective states as light conditions change in the field. The PsbS protein plays a pivotal role in this process by switching the light-harvesting antenna, light-harvesting complex II (LHCII), into the photoprotective state, energy-dependent chlorophyll fluorescence quenching (qE), to avoid photoinhibition in high-light environments. However, the molecular mechanism by which PsbS acts upon LHCII has remained unclear. In our study, we identified the specific amino acid domains that are essential for PsbS function. Using amino-acid point mutagenesis of PsbS in vivo, we found that the activation of photoprotection involves dynamic changes in the oligomeric state and conformation of PsbS, with two residues, E67 and E173, playing a key role in this process. Further, the replacement of hydrophobic phenylalanine residues in transmembrane helixes II (F83, F84, F87) and IV (F191, F193, F194) with tyrosine revealed that phenylalanine localized in helix IV can play a significant role in hydrophobic interactions of PsbS with LHCII. Removal of the 3₁₀ helix (H3) amino acids I74, Y75, and E76 did not affect the amplitude but strongly delayed the recovery of qE in darkness. Moreover, an AI-assisted protein-folding evolutionary scale model approach (ESMFold) was adopted to intelligently manipulate protein functions in silico and thus streamline and evaluate experimental point mutagenesis strategies. This provides new insights into the molecular architecture of PsbS that are essential for regulating light harvesting in higher plants.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101179"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142548885","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":"Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1.","authors":"Hong Wei, Heyuan Zhu, Wei Ying, Hilde Janssens, Miroslav Kvasnica, Johan M Winne, Yongxiang Gao, Jiří Friml, Qian Ma, Shutang Tan, Xin Liu, Eugenia Russinova, Linfeng Sun","doi":"10.1016/j.xplc.2024.101181","DOIUrl":"10.1016/j.xplc.2024.101181","url":null,"abstract":"<p><p>Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signaling initiation, which requires binding of a BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter ABCB19 functions as a BR exporter and, together with its close homolog ABCB1, positively regulates BR signaling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 can be stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 were determined in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states. In the BL-bound structure, BL is bound to the hydrophobic cavity formed by the transmembrane domain and triggers local conformational changes. Together, our data provide additional insights into ABC transporter-mediated BR export.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101181"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577349","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":"Jasmonic acid plays an important role in mediating retrograde signaling under mitochondrial translational stress to balance plant growth and defense.","authors":"Jiahao Li, Guolong Yu, Xinyuan Wang, Chaocheng Guo, Yudong Wang, Xu Wang","doi":"10.1016/j.xplc.2024.101133","DOIUrl":"10.1016/j.xplc.2024.101133","url":null,"abstract":"<p><p>Proper mitochondrial function is crucial to plant growth and development. Inhibition of mitochondrial translation leads to mitochondrial proteotoxic stress, which triggers a protective transcriptional response that regulates nuclear gene expression, commonly referred to as the mitochondrial unfolded protein response (UPR^mt). Although the UPR^mt has been extensively studied in yeast and mammals, very little is known about the UPR^mt in plants. Here, we show that mitochondrial translational stress inhibits plant growth and development by inducing jasmonic acid (JA) biosynthesis and signaling. The inhibitory effect of mitochondrial translational stress on plant growth was alleviated in the JA-signaling-defective mutants coi1-2, myc2, and myc234. Genetic analysis indicated that Arabidopsis mitochondrial ribosomal protein L1 (MRPL1), a key factor in the UPR^mt, regulates plant growth in a CORONATINE-INSENSITIVE 1 (COI1)-dependent manner. Moreover, under mitochondrial translational stress, MYC2 shows direct binding to G boxes in the ETHYLENE RESPONSE FACTOR 109 (ERF109) promoter. The induction of ERF109 expression enhances hydrogen peroxide production, which acts as a feedback loop to inhibit root growth. In addition, mutation of MRPL1 increases JA accumulation, reduces plant growth, and enhances biotic stress resistance. Overall, our findings reveal that JA plays an important role in mediating retrograde signaling under mitochondrial translational stress to balance plant growth and defense.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101133"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142300594","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":"Functional evolution and diversification of CYP82D subfamily members have shaped flavonoid diversification in the genus Scutellaria.","authors":"Shi Qiu, Jing Wang, Tianlin Pei, Ranran Gao, Chunlei Xiang, Junfeng Chen, Chen Zhang, Ying Xiao, Qing Li, Ziding Wu, Min He, Rong Wang, Qing Zhao, Zhichao Xu, Jiadong Hu, Wansheng Chen","doi":"10.1016/j.xplc.2024.101134","DOIUrl":"10.1016/j.xplc.2024.101134","url":null,"abstract":"<p><p>Flavonoids, the largest class of polyphenols, exhibit substantial structural and functional diversity, yet their evolutionary diversification and specialized functions remain largely unexplored. The genus Scutellaria is notable for its rich flavonoid diversity, particularly of 6/8-hydroxylated variants biosynthesized by the cytochrome P450 subfamily CYP82D. Our study analyzes metabolic differences between Scutellaria baicalensis and Scutellaria barbata, and the results suggest that CYP82Ds have acquired a broad range of catalytic functions over their evolution. By integrating analyses of metabolic networks and gene evolution across 22 Scutellaria species, we rapidly identified 261 flavonoids and delineated five clades of CYP82Ds associated with various catalytic functions. This approach revealed a unique catalytic mode for 6/8-hydroxylation of flavanone substrates and the first instance of 7-O-demethylation of flavonoid substrates catalyzed by a cytochrome P450. Ancestral sequence reconstruction and functional validation demonstrated that gradual neofunctionalization of CYP82Ds has driven the chemical diversity of flavonoids in the genus Scutellaria throughout its evolutionary history. These findings enhance our understanding of flavonoid diversity, reveal the intricate roles of CYP82Ds in Scutellaria species, and highlight the extensive catalytic versatility of cytochrome P450 members within plant taxa.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101134"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142300593","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":"UV-B increases active phytochrome B to suppress thermomorphogenesis and enhance UV-B stress tolerance at high temperatures.","authors":"Geonhee Hwang, Taedong Lee, Jeonghyang Park, Inyup Paik, Nayoung Lee, Yun Ju Kim, Young Hun Song, Woe-Yeon Kim, Eunkyoo Oh","doi":"10.1016/j.xplc.2024.101142","DOIUrl":"10.1016/j.xplc.2024.101142","url":null,"abstract":"<p><p>Plants respond to slight increases in ambient temperature by altering their architecture, a phenomenon collectively termed thermomorphogenesis. Thermomorphogenesis helps mitigate the damage caused by potentially harmful high-temperature conditions and is modulated by multiple environmental factors. Among these factors, ultraviolet-B (UV-B) light has been shown to strongly suppress this response. However, the molecular mechanisms by which UV-B light regulates thermomorphogenesis and the physiological roles of the UV-B-mediated suppression remain poorly understood. Here, we show that UV-B light inhibits thermomorphogenesis through the UV RESISTANCE LOCUS8 (UVR8)-CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1)-phytochrome B (phyB)/LONG HYPOCOTYL IN FAR RED 1 (HFR1) signaling pathway. We found that cop1 mutants maintain high levels of active phyB at high temperatures. Extensive genetic analyses revealed that the increased levels of phyB, HFR1, and CRY1 in cop1 mutants redundantly reduce both the level and the activity of PHYTOCHROME INTERACTING FACTOR4 (PIF4), a key positive regulator in thermomorphogenesis, thereby repressing this growth response. In addition, we found that UV-B light inactivates COP1 to enhance phyB stability and increase its photobody number. The UV-B-stabilized active phyB, in concert with HFR1, inhibits thermomorphogenesis by interfering with PIF4 activity. We further demonstrate that increased levels of active phyB enhance UV-B tolerance by promoting flavonoid biosynthesis and inhibiting thermomorphogenic growth. Taken together, our results elucidate that UV-B increases the levels of active phyB and HFR1 by inhibiting COP1 to suppress PIF4-mediated growth responses, which is crucial for plant tolerance to UV-B stress at high temperatures.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101142"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401931","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":"Assembly of a reference-quality genome and resequencing diverse accessions of Beckmannia syzigachne provide insights into population structure and gene family evolution.","authors":"Yang Han, Jianxiang Wu, Qianhao Zhu, Chuyu Ye, Xinxin Li","doi":"10.1016/j.xplc.2024.101174","DOIUrl":"10.1016/j.xplc.2024.101174","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101174"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480443","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":"Natural variation in OsMADS1 transcript splicing affects rice grain thickness and quality by influencing monosaccharide loading to the endosperm.","authors":"Rongjia Liu, Da Zhao, Pingbo Li, Duo Xia, Qingfei Feng, Lu Wang, Yipei Wang, Huan Shi, Yin Zhou, Fangying Chen, Guangming Lou, Hanyuan Yang, Haozhou Gao, Bian Wu, Junxiao Chen, Guanjun Gao, Qinglu Zhang, Jinghua Xiao, Xianghua Li, Lizhong Xiong, Yibo Li, Zichao Li, Aiqing You, Yuqing He","doi":"10.1016/j.xplc.2024.101178","DOIUrl":"10.1016/j.xplc.2024.101178","url":null,"abstract":"<p><p>Grain size, which encompasses grain length, width, and thickness, is a critical determinant of both grain weight and quality in rice. Despite the extensive regulatory networks known to determine grain length and width, the pathway(s) that regulate grain thickness remain to be clarified. Here, we present the map-based cloning and characterization of qGT3, a major quantitative trait locus for grain thickness in rice that encodes the MADS-domain transcription factor OsMADS1. Our findings demonstrate that OsMADS1 regulates grain thickness by affecting sugar delivery during grain filling, and we show that OsMADS1 modulates expression of the downstream monosaccharide transporter gene MST4. A natural variant leads to alternative splicing and thus to a truncated OsMADS1 protein with attenuated transcriptional repressor activity. The truncated OsMADS1 protein results in increased expression of MST4, leading to enhanced loading of monosaccharides into the developing endosperm and thereby increasing grain thickness and improving grain quality. In addition, our results reveal that NF-YB1 and NF-YC12 interact directly with OsMADS1, acting as cofactors to enhance its transcriptional activity toward MST4. Collectively, these findings reveal a novel molecular mechanism underlying grain thickness regulation that is controlled by the OsMADS1-NF-YB1-YC12 complex and has great potential for synergistic improvement of grain yield and quality in rice.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101178"},"PeriodicalIF":9.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570067","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 basal level of salicylic acid represses the PRT6 N-degron pathway to modulate root growth and stress response in rice.","authors":"Zhuang Xu, Xianqing Jia, Ruili Li, Long Wang, Lei Xu, Keke Yi","doi":"10.1016/j.xplc.2025.101239","DOIUrl":"10.1016/j.xplc.2025.101239","url":null,"abstract":"<p><p>Maintaining a stable basal level of salicylic acid (SA) is crucial for plant growth, development, and stress response, although basal levels of SA vary significantly among plant species. However, the molecular mechanisms by which basal SA regulates plant growth and stress response remain to be clarified. In this study, we performed a genetic screen to identify suppressors of the root growth defect in Osaim1, a rice mutant deficient in basal SA biosynthesis. We found that mutation of the E3 ligase OsPRT6, a key component of the Arg/N-degron pathway, can rescue the root growth defect of Osaim1. Further analysis revealed that OsWRKY62 and OsWRKY76 act as substrates of the OsPRT6 N-degron pathway to modulate root growth. We demonstrated that reducing the basal SA level activates the PRT6 N-degron pathway and that basal SA modulates the stress response in part through the PRT6 N-degron pathway. Importantly, the effects of basal SA levels on the PRT6 N-degron pathway are conserved across plant species. Taken together, these findings reveal a novel regulatory mechanism by which basal SA represses the PRT6 N-degron pathway to modulate root growth and abiotic stress response in rice.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101239"},"PeriodicalIF":9.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973229","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}