Yadi Zhou, Abhijit Sukul, John W Mishler-Elmore, Ahmed Faik, Michael A Held
{"title":"PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum.","authors":"Yadi Zhou, Abhijit Sukul, John W Mishler-Elmore, Ahmed Faik, Michael A Held","doi":"10.1093/pcp/pcac007","DOIUrl":"https://doi.org/10.1093/pcp/pcac007","url":null,"abstract":"<p><p>Global gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to civilization. However, co-expression network tools for these plants are lacking. Here, we have constructed global GCNs for barley and sorghum using existing RNA-seq data sets. Meta-information was manually curated and categorized by tissue type to also build tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus. PlantNexus is freely available at https://plantnexus.ohio.edu/.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"565-572"},"PeriodicalIF":4.9,"publicationDate":"2022-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9214644/pdf/pcac007.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39817412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Letter to the Editor: Expanding the Potential of Plant Interfamily Grafting.","authors":"Yongsheng Liu","doi":"10.1093/pcp/pcac016","DOIUrl":"https://doi.org/10.1093/pcp/pcac016","url":null,"abstract":"","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"448-449"},"PeriodicalIF":4.9,"publicationDate":"2022-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39900147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sayanti De, Jismon Jose, Amita Pal, Swarup Roy Choudhury, Sujit Roy
{"title":"Exposure to Low UV-B Dose Induces DNA Double-Strand Breaks Mediated Onset of Endoreduplication in Vigna radiata (L.) R. Wilczek Seedlings.","authors":"Sayanti De, Jismon Jose, Amita Pal, Swarup Roy Choudhury, Sujit Roy","doi":"10.1093/pcp/pcac012","DOIUrl":"https://doi.org/10.1093/pcp/pcac012","url":null,"abstract":"<p><p>Multiple lines of evidence indicate that solar UV-B light acts as an important environmental signal in plants, regulating various cellular and metabolic activities, gene expression, growth and development. Here, we show that low levels of UV-B (4.0 kJ m-2) significantly influence plant response during early seedling development in the tropical legume crop Vigna radiata (L.) R. Wilczek. Exposure to low doses of UV-B showed relatively less growth inhibition yet remarkably enhanced lateral root formation in seedlings. Both low and high (8.0 kJ m-2) doses of UV-B treatment induced DNA double-strand breaks and activated the SOG1-related ATM-ATR-mediated DNA damage response pathway. These effects led to G2-M-phase arrest with a compromised expression of the key cell cycle regulators, including CDKB1;1, CDKB2;1 and CYCB1;1, respectively. However, along with these effects, imbibitional exposure of seeds to a low UV-B dose resulted in enhanced accumulation of FZR1/CCS52A, E2Fa and WEE1 kinase and prominent induction of endoreduplication in 7-day-old seedlings. Low dose of UV-B mediated phenotypical responses, while the onset of endoreduplication appeared to be regulated at least in part via UV-B induced reactive oxygen species accumulation. Transcriptome analyses further revealed a network of co-regulated genes associated with DNA repair, cell cycle regulation and oxidative stress response pathways that are activated upon exposure to low doses of UV-B.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"463-483"},"PeriodicalIF":4.9,"publicationDate":"2022-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39899680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Takahiro N Uehara, Takashi Nonoyama, Kyomi Taki, Keiko Kuwata, Ayato Sato, Kazuhiro J Fujimoto, Tsuyoshi Hirota, Hiromi Matsuo, Akari E Maeda, Azusa Ono, Tomoaki T Takahara, Hiroki Tsutsui, Takamasa Suzuki, Takeshi Yanai, Steve A Kay, Kenichiro Itami, Toshinori Kinoshita, Junichiro Yamaguchi, Norihito Nakamichi
{"title":"Phosphorylation of RNA Polymerase II by CDKC;2 Maintains the Arabidopsis Circadian Clock Period.","authors":"Takahiro N Uehara, Takashi Nonoyama, Kyomi Taki, Keiko Kuwata, Ayato Sato, Kazuhiro J Fujimoto, Tsuyoshi Hirota, Hiromi Matsuo, Akari E Maeda, Azusa Ono, Tomoaki T Takahara, Hiroki Tsutsui, Takamasa Suzuki, Takeshi Yanai, Steve A Kay, Kenichiro Itami, Toshinori Kinoshita, Junichiro Yamaguchi, Norihito Nakamichi","doi":"10.1093/pcp/pcac011","DOIUrl":"https://doi.org/10.1093/pcp/pcac011","url":null,"abstract":"<p><p>The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"450-462"},"PeriodicalIF":4.9,"publicationDate":"2022-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/48/af/pcac011.PMC9016870.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39954701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"SKIP Regulates ABA Signaling through Alternative Splicing in Arabidopsis.","authors":"Qi Zhang, Wei Zhang, Jianbo Wei, Zhaoxu Gao, Jianing Guan, Zhibo Cui, Xiaoxue Wang","doi":"10.1093/pcp/pcac014","DOIUrl":"https://doi.org/10.1093/pcp/pcac014","url":null,"abstract":"<p><p>Abscisic acid (ABA) plays key roles in plant development and responses to abiotic stresses. A wide number of transcriptional and posttranslational regulatory mechanisms of ABA signaling are known; however, less is known about the regulatory roles of alternative splicing. In this work, we found that SKIP, a splicing factor, positively regulates ABA signaling. SKIP binds to the pre-mRNA of ABA signaling-related genes, such as PYL7, PYL8, ABI1, HAB1 and ABI5, to regulate their splicing. The precursor mRNA alternative splicing of several PYL receptors, PP2C phosphatases and ABF transcriptional factors is disrupted by the skip-1 mutation. The abnormal alternative splicing in skip-1 represses the expression of ABA-positive regulators, including PYLs and ABFs, and activates the expression of ABA-negative regulators, such as PP2Cs, which confers ABA hyposensitive phenotype of skip-1. We also found that ABA-mediated genome-wide alternative splicing and differential gene expression are changed by the skip-1 mutation. The number of the differential splicing events is increased by skip-1; however, the number of differential expressed genes in response to ABA is reduced by skip-1. Our results reveal a principle on how a splicing factor regulates ABA signaling and ABA-mediated genome-wide alternative splicing.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"494-507"},"PeriodicalIF":4.9,"publicationDate":"2022-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39775981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Deding Su, Wei Xiang, Qin Liang, Ling Wen, Yuan Shi, Bangqian Song, Yudong Liu, Zhiqiang Xian, Zhengguo Li
{"title":"Tomato SlBES1.8 Influences Leaf Morphogenesis by Mediating Gibberellin Metabolism and Signaling.","authors":"Deding Su, Wei Xiang, Qin Liang, Ling Wen, Yuan Shi, Bangqian Song, Yudong Liu, Zhiqiang Xian, Zhengguo Li","doi":"10.1093/pcp/pcac019","DOIUrl":"https://doi.org/10.1093/pcp/pcac019","url":null,"abstract":"<p><p>Leaf morphogenetic activity determines its shape diversity. However, our knowledge of the regulatory mechanism in maintaining leaf morphogenetic capacity is still limited. In tomato, gibberellin (GA) negatively regulates leaf complexity by shortening the morphogenetic window. We here report a tomato BRI1-EMS-suppressor 1 transcription factor, SlBES1.8, that promoted the simplification of leaf pattern in a similar manner as GA functions. OE-SlBES1.8 plants exhibited reduced sensibility to exogenous GA3 treatment whereas showed increased sensibility to the application of GA biosynthesis inhibitor, paclobutrazol. In line with the phenotypic observation, the endogenous bioactive GA contents were increased in OE-SlBES1.8 lines, which certainly promoted the degradation of the GA signaling negative regulator, SlDELLA. Moreover, transcriptomic analysis uncovered a set of overlapping genomic targets of SlBES1.8 and GA, and most of them were regulated in the same way. Expression studies showed the repression of SlBES1.8 to the transcriptions of two GA-deactivated genes, SlGA2ox2 and SlGA2ox6, and one GA receptor, SlGID1b-1. Further experiments confirmed the direct regulation of SlBES1.8 to their promoters. On the other hand, SlDELLA physically interacted with SlBES1.8 and further inhibited its transcriptional regulation activity by abolishing SlBES1.8-DNA binding. Conclusively, by mediating GA deactivation and signaling, SlBES1.8 greatly influenced tomato leaf morphogenesis.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"535-549"},"PeriodicalIF":4.9,"publicationDate":"2022-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39901661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"BBX17 Interacts with CO and Negatively Regulates Flowering Time in Arabidopsis thaliana.","authors":"Xiaorui Xu, Jingya Xu, Chen Yuan, Qianqian Chen, Qinggang Liu, Xuming Wang, Cheng Qin","doi":"10.1093/pcp/pcac005","DOIUrl":"https://doi.org/10.1093/pcp/pcac005","url":null,"abstract":"<p><p>Floral transition, the change from vegetative growth to reproductive development, is dramatic in flowering plants. Here, we show that one subgroup III member of the B-box (BBX) family, BBX17, is a repressor of floral transition under long-day conditions. BBX17 contains a B-box domain and a CCT domain. Although the phenotype of the BBX17 loss-of-function plants was comparable to that of wild-type plants, BBX17-overexpression plants displayed a delayed-flowering phenotype under long-day conditions. The delayed-flowering phenotype was not the result of an altered CONSTANS (CO) expression level but rather the repression of the FLOWERING LOCUS T (FT) expression level. BBX17 physically associated with CO and repressed its ability to control FT expression. Furthermore, the BBX17 protein degraded in the dark, but irradiating seedlings with white, blue, red or far-red light stabilized the BBX17 level. We also proved that the degradation of BBX17 was via 26S proteasome and requires COP1. Thus, BBX17 acts as a key factor in the CO-FT regulatory system to control Arabidopsis thaliana flowering.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"401-409"},"PeriodicalIF":4.9,"publicationDate":"2022-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39687600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dawid Perlikowski, Katarzyna Lechowicz, Aleksandra Skirycz, Änna Michaelis, Izabela Pawłowicz, Arkadiusz Kosmala
{"title":"The Role of Triacylglycerol in the Protection of Cells against Lipotoxicity under Drought in Lolium multiflorum/Festucaarundinacea Introgression Forms.","authors":"Dawid Perlikowski, Katarzyna Lechowicz, Aleksandra Skirycz, Änna Michaelis, Izabela Pawłowicz, Arkadiusz Kosmala","doi":"10.1093/pcp/pcac003","DOIUrl":"https://doi.org/10.1093/pcp/pcac003","url":null,"abstract":"<p><p>Triacylglycerol is a key lipid compound involved in maintaining homeostasis of both membrane lipids and free fatty acids (FFA) in plant cells under adverse environmental conditions. However, its role in the process of lipid remodeling has not been fully recognized, especially in monocots, including grass species. For our study, two closely related introgression forms of Lolium multiflorum (Italian ryegrass) and Festuca arundinacea (tall fescue), distinct in their level of drought tolerance, were selected as plant models to study rearrangements in plant lipidome under water deficit and further re-watering. The low drought tolerant (LDT) form revealed an elevated level of cellular membrane damage accompanied by an increased content of polyunsaturated FFA and triacylglycerol under water deficit, compared with the high drought tolerant (HDT) form. However, the LDT introgression form demonstrated also the ability to regenerate its membranes after stress cessation. The obtained results clearly indicated that accumulation of triacylglycerol under advanced drought in the LDT form could serve as a cellular protective mechanism against overaccumulation of toxic polyunsaturated FFA and other lipid intermediates. Furthermore, accumulation of triacylglycerol under drought conditions could serve also as storage of substrates required for further regeneration of membranes after stress cessation. The rearrangements in triacylglycerol metabolism were supported by the upregulation of several genes, involved in a biosynthesis of triacylglycerol. With respect to this process, diacylglycerol O-acyltransferase DGAT2 seems to play the most important role in the analyzed grasses.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"353-368"},"PeriodicalIF":4.9,"publicationDate":"2022-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39793613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Auxin Efflux Transporters OsPIN1c and OsPIN1d Function Redundantly in Regulating Rice (Oryza sativa L.) Panicle Development.","authors":"Jiajun Liu, Xi'an Shi, Zhongyuan Chang, Yanfeng Ding, Chengqiang Ding","doi":"10.1093/pcp/pcab172","DOIUrl":"https://doi.org/10.1093/pcp/pcab172","url":null,"abstract":"<p><p>The essential role of auxin in plant growth and development is well known. Pathways related to auxin synthesis, transport and signaling have been extensively studied in recent years, and the PIN-FORMED (PIN) protein family has been identified as being pivotal for polar auxin transport and distribution. However, research focused on the functional characterization of PIN proteins in rice is still lacking. In this study, we investigated the expression and function of OsPIN1c and OsPIN1d in the japonica rice variety (Nipponbare) using gene knockout and high-throughput RNA sequencing analysis. The results showed that OsPIN1c and OsPIN1d were mainly expressed in young panicles and exhibited a redundant function. Furthermore, OsPIN1c or OsPIN1d loss-of-function mutants presented a mild phenotype compared with the wild type. However, in addition to significantly decreased plant height and tiller number, panicle development was severely disrupted in double-mutant lines of OsPIN1c and OsPIN1d. Severe defects included smaller inflorescence meristem and panicle sizes, fewer primary branches, elongated bract leaves, non-degraded hair and no spikelet growth. Interestingly, ospin1cd-3, a double-mutant line with functional retention of OsPIN1d, showed milder defects than those observed in other mutants. Additionally, several critical regulators of reproductive development, such as OsPID, LAX1, OsMADS1 and OsSPL14/IPA1, were differentially expressed in ospin1c-1 ospin1d-1, supporting the hypothesis that OsPIN1c and OsPIN1d are involved in regulating panicle development. Therefore, this study provides novel insights into the auxin pathways that regulate plant reproductive development in monocots.</p>","PeriodicalId":502140,"journal":{"name":"Plant & Cell Physiology","volume":" ","pages":"305-316"},"PeriodicalIF":4.9,"publicationDate":"2022-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39573482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}