Plant Physiology最新文献_第4页

Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems. 通过费米计算，可以在光合作用系统中快速向下选择目标基因并优化过程。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiaf103

Ratul Chowdhury, Wheaton Schroeder, Debolina Sarkar, Niaz Bahar Chowdhury, Supantha Dey, Rajib Saha

{"title":"Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems.","authors":"Ratul Chowdhury, Wheaton Schroeder, Debolina Sarkar, Niaz Bahar Chowdhury, Supantha Dey, Rajib Saha","doi":"10.1093/plphys/kiaf103","DOIUrl":"10.1093/plphys/kiaf103","url":null,"abstract":"Understanding how photosynthetic organisms including plants and microbes respond to their environment is crucial for optimizing agricultural practices and ensuring food and energy security, particularly in the context of climactic change and sustainability. This perspective embeds back-of-the-envelope calculations across a photosynthetic organism design and scale up workflow. Starting from the whole system level, we provide a recipe to pinpoint key genetic targets, examine the logistics of detailed computational modeling, and explore environmentally driven phenotypes and feasibility as an industrial biofuel production chassis. While complex computer models or high-throughput in vivo studies often dominate scientific inquiry, this perspective highlights the power of simple calculations as a valuable tool for initial exploration and evaluating study feasibility. Fermi calculations are defined as quick, approximate estimations made using back-of-the-envelope calculations and straightforward reasoning to achieve order-of-magnitude accuracy, named after the physicist Enrico Fermi. We show how Fermi calculations, based on fundamental principles and readily available data, can offer a first-pass understanding of metabolic shifts in plants and microbes in response to environmental and genetic changes. We also discuss how Fermi checks can be embedded in data-driven advanced computing workflows to enable bio-aware machine learning. Lastly, an understanding of state of the art is necessary to guide study feasibility and identifying key levers to maximize cost to return ratios. Combining biology- and resource-aware Fermi calculations, this proposed approach enables researchers to prioritize resource allocation, identify gaps in predictions and experiments, and develop intuition about how observed responses of plants differ between controlled laboratory environments and industrial conditions.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12225682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670584","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}

引用次数: 0

The peptide hormone RGF1 modulates PLETHORA2 stability via reactive oxygen species-dependent regulation of a cysteine residue. 肽激素RGF1通过活性氧依赖的半胱氨酸残基调节PLETHORA2的稳定性。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiaf244

Yu-Chun Hsiao, Shiau-Yu Shiue, Ming-Ren Yen, Joon-Keat Lai, Masashi Yamada

{"title":"The peptide hormone RGF1 modulates PLETHORA2 stability via reactive oxygen species-dependent regulation of a cysteine residue.","authors":"Yu-Chun Hsiao, Shiau-Yu Shiue, Ming-Ren Yen, Joon-Keat Lai, Masashi Yamada","doi":"10.1093/plphys/kiaf244","DOIUrl":"10.1093/plphys/kiaf244","url":null,"abstract":"The Root meristem growth factor 1 (RGF1) peptide extends the PLETHORA2 (PLT2) protein gradient by altering the distinct localization of superoxide (O2-) and hydrogen peroxide (H2O2) among the root developmental zones. However, the underlying mechanism through which reactive oxygen species (ROS) regulate PLT2 stability is unclear. Here, we demonstrate that the 212th cysteine of PLT2 is pivotal in modulating PLT2 stability through ROS. The PLT2 protein concentration gradient rapidly decreases in the elongation zone, where H2O2 accumulation initiates. However, substituting the 212th cysteine of PLT2 with serine (PLT2C212S) results in PLT2 being more stable in the elongation zone, more broadly localized by RGF1, and showing robust resistance to H2O2. The sulfenylation of PLT2 was detected following treatment with H2O2 at high concentrations, suggesting that S-sulfenylation of the 212th cysteine controls PLT2 protein stability through local ROS distributions. These findings show that the formation of the PLT2 concentration gradient through ROS depends on a PLT2 sulfenylation mechanism that involves the 212th cysteine.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"198 3","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12225670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560794","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}

引用次数: 0

The xanthophyll cycle balances photoprotection and photosynthetic efficiency in the seawater alga Nannochloropsis oceanica. 海洋纳米绿藻的叶黄素循环平衡光保护和光合效率。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiaf301

Tim Michelberger, Eleonora Mezzadrelli, Alessandra Bellan, Giorgio Perin, Tomas Morosinotto

{"title":"The xanthophyll cycle balances photoprotection and photosynthetic efficiency in the seawater alga Nannochloropsis oceanica.","authors":"Tim Michelberger, Eleonora Mezzadrelli, Alessandra Bellan, Giorgio Perin, Tomas Morosinotto","doi":"10.1093/plphys/kiaf301","DOIUrl":"10.1093/plphys/kiaf301","url":null,"abstract":"Photosynthetic reactions are continuously modulated to respond to highly dynamic environmental conditions. Balancing photosynthesis and photoprotection involves various mechanisms, which differ across phylogenetic groups. One such mechanism that is widespread in photosynthetic eukaryotes is the xanthophyll cycle, which involves the reversible light-dependent conversion between the carotenoids violaxanthin, antheraxanthin, and zeaxanthin. In this study, we investigated the role of the xanthophyll cycle in Nannochloropsis oceanica, a seawater microalga that possesses peculiarly high xanthophyll levels. To this end, we generated and characterized lines with increased levels of the enzymes involved in the xanthophyll cycle, i.e. violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZEP). We demonstrated that the level of VDE and ZEP is the main factor controlling the overall reaction rates and dynamics of the xanthophyll cycle. Subsequent differences in the xanthophyll profile affect the activation of photoprotection mechanisms such as nonphotochemical quenching and tolerance to reactive oxygen species. Interestingly, VDE overexpression enhances high light tolerance, whereas increased ZEP levels facilitate faster recovery after light exposure but also heighten photosensitivity under certain conditions. In addition, light exposure strongly downregulates ZEP activity in Nannochloropsis. Taken together, these findings underscore the critical role of the xanthophyll cycle in regulating photosynthesis in Nannochloropsis. This cycle is not simply a mechanism that responds to excess illumination, but one that balances photoprotection and light-use efficiency under different environmental conditions.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560793","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}

引用次数: 0

The transcriptional repressors IAA5 and IAA29 participate in DNA damage-induced stem cell death in Arabidopsis roots. 转录抑制因子IAA5和IAA29参与拟南芥根系DNA损伤诱导的干细胞死亡。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiaf303

Naoki Takahashi, Nobuo Ogita, Toshiya Koike, Kohei Nishimura, Soichi Inagaki, Ye Zhang, Takumi Higaki, Masaaki Umeda

{"title":"The transcriptional repressors IAA5 and IAA29 participate in DNA damage-induced stem cell death in Arabidopsis roots.","authors":"Naoki Takahashi, Nobuo Ogita, Toshiya Koike, Kohei Nishimura, Soichi Inagaki, Ye Zhang, Takumi Higaki, Masaaki Umeda","doi":"10.1093/plphys/kiaf303","DOIUrl":"10.1093/plphys/kiaf303","url":null,"abstract":"Plants generate organs continuously during postembryonic development. Thus, their ability to preserve stem cells in changing environments is crucial for their survival. Genotoxic stress threatens genome stability in all somatic cells. However, in the meristem, only the stem cells actively die in response to DNA damage, followed by stem cell replenishment that guarantees genome stability in these cells. Cytokinin biosynthesis-induced inhibition of downward auxin flow participates in DNA damage-induced stem cell death in roots. Without this system, stem cell death occurs at a reduced but significant level, suggesting another mechanism governing the DNA damage response in stem cells. Here, we demonstrate that in response to DNA double-strand breaks, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) family members IAA5 and IAA29, encoding negative regulators of auxin signaling, are induced in Arabidopsis (Arabidopsis thaliana) roots. The transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 directly induces their expression as an active response to DNA damage. In the iaa5 iaa29 double mutant, DNA damage-induced stem cell death is greatly suppressed, while it is fully restored by the expression of a stable form of IAA5 in vascular stem cells. Our genetic data reveal that reduced auxin signaling around the stem cell niche, caused by IAA5 and IAA29 induction and enhanced cytokinin biosynthesis, is a prerequisite for cell death induction, thus playing a central role in maintaining genome integrity in root stem cells.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560792","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}

引用次数: 0

B-BOX22 isoforms activate expression of MYBs and elicit blue light-induced flavonoid biosynthesis in soybean. B-BOX22亚型激活MYBs的表达，诱导蓝光诱导的大豆类黄酮生物合成。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiaf302

Junyi Zhan, Haixia Wang, Mengyang Niu, Changjian Bao, Yanning Gong, Gang Hu, Dongqing Xu, Zhenguo Shen, Nana Su

{"title":"B-BOX22 isoforms activate expression of MYBs and elicit blue light-induced flavonoid biosynthesis in soybean.","authors":"Junyi Zhan, Haixia Wang, Mengyang Niu, Changjian Bao, Yanning Gong, Gang Hu, Dongqing Xu, Zhenguo Shen, Nana Su","doi":"10.1093/plphys/kiaf302","DOIUrl":"10.1093/plphys/kiaf302","url":null,"abstract":"Soybean (Glycine max) accumulates a substantial amount of flavonoids, including anthocyanins and flavonols, which play essential roles in both plant growth and human health. While blue light promotes flavonoid biosynthesis, the regulatory circuitry governing this process remains poorly characterized. Here, we demonstrate that blue light stimulates flavonol and anthocyanin accumulation in soybean hypocotyls by inducing the B-box transcription factor GmBBX22. Mechanistically, GmBBX22 transcripts are alternatively spliced under blue light, generating 3 isoforms (designated as X1, X2, and X3). Intriguingly, the truncated isoforms X2 and X3 induce flavonol and anthocyanin biosynthesis through distinct regulatory cascades. Rather than directly targeting the biosynthesis flavonol synthase gene (GmFLS) or dihydroflavonol 4-reductase gene (GmDFR), which encode key enzymes for metabolic flux partitioning between flavonols and anthocyanins, X2 and X3 specifically activate the expression of GmMYB12 and GmMYB90, respectively. Subsequent functional analyses revealed that these MYB transcription factors induce GmFLS and GmDFR expression to coordinate flavonol and anthocyanin accumulation. Collectively, our work delineates a splicing-dependent regulatory module where GmBBX22 isoforms mediate light quality adaptation in soybean through divergent transcriptional programming of flavonoid metabolism.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560789","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}

引用次数: 0

The transcription factor REM16a promotes flowering time in soybean by activating flowering-related genes. 转录因子REM16a通过激活与开花相关的基因来促进大豆的开花时间。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiaf256

Zhikun Wang, Changhuan Du, Qingqing Li, Meng Li, Yuanzhuo Wang, Gege Bao, Yuanyuan Yin, Mingming Yang, Qiang Yang, Pengfei Xu, Shanshan Liu, Bo Song, Shuzhen Zhang

{"title":"The transcription factor REM16a promotes flowering time in soybean by activating flowering-related genes.","authors":"Zhikun Wang, Changhuan Du, Qingqing Li, Meng Li, Yuanzhuo Wang, Gege Bao, Yuanyuan Yin, Mingming Yang, Qiang Yang, Pengfei Xu, Shanshan Liu, Bo Song, Shuzhen Zhang","doi":"10.1093/plphys/kiaf256","DOIUrl":"10.1093/plphys/kiaf256","url":null,"abstract":"The flowering time of soybean [Glycine max (L.) Merr.] is extremely sensitive to photoperiod, which importantly influences its yield potential and restricts the geographical range of soybean cultivars to specific latitudes. Molecular breeding to modulate flowering time and reduce sensitivity to day length is an effective approach to enhance the adaptability and productivity of soybean. Here, we characterized reproductive meristem 16a (GmREM16a), a member of the AP2/B3-like transcription factor family. The GmREM16a protein contains 2 B3 domains, and the expression of its encoding gene is responsive to photoperiod and circadian rhythm. The overexpression of GmREM16a in soybean accelerated flowering by regulating the expression of flowering-related genes. The GmREM16a protein was able to directly bind to the promoters of GmSOC1, GmFT2a, and GmFT5a and upregulate their expression. Yeast two-hybrid screening revealed that GmCSN5 interacts with GmREM16a. GmCSN5 is the fifth subunit of the COP9 signalosome (constitutively photomorphogenic signalosome, CSN) that regulates the activity of CULLIN-RING E3 ubiquitin ligases and regulates protein degradation. Protein degradation assays in vivo and in vitro showed that GmCSN5 promotes the degradation of GmREM16a protein via the ubiquitin-proteasome pathway. Taken together, these findings indicate that the transcription factor GmREM16a promotes flowering by regulating the expression of flowering-related genes. Additionally, GmCSN5 interacts with GmREM16a to regulate its stability in soybean. The GmREM16a-GmSCN5 module may represent a pathway involved in the regulation of flowering time in soybean and is a useful genetic resource for improving the adaptability of soybean through molecular breeding approaches.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144507508","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}

引用次数: 0

Running Fermi calculations as a superpower to gauge reality. 运行费米计算，作为衡量现实的超级能力。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiae347

Edmar R Oliveira-Filho, Rodrigo Campos-Silva, Andrew D Hanson

引用次数: 0

How to eat an idea-A roadmap for translation and impact in plant biology. 如何吃一个想法-一个路线图的翻译和影响在植物生物学。

IF 6.5 1区生物学

Plant Physiology Pub Date : 2025-07-03 DOI: 10.1093/plphys/kiaf178

Johnathan A Napier

引用次数: 0

Seeing is believing: Genome editing made easy with RUBY for educational purposes. 眼见为实：为了教育目的，使用RUBY使基因组编辑变得容易。