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An AI-powered Knowledge Hub for Potato Functional Genomics. 马铃薯功能基因组学的人工智能知识中心。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-13 DOI: 10.1016/j.xplc.2026.101730
Jinye Li, Yudong Jia, Futing Li, Xiaoqi Su, Jilin Luo, Yarui Dong, Chunyan Sun, Qinghan Cui, Li Wang, Axiu Li, Yi Shang, Sanwen Huang, Yujuan Zhu, Yuxin Jia
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引用次数: 0
Rhizobial effector NopM mediates the ubiquitination of the Nod factor receptor NFR5 and promotes rhizobial symbiosis in Lotus japonicus. 根瘤菌效应物NopM介导Nod因子受体NFR5的泛素化,促进莲藕根瘤菌共生。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-13 DOI: 10.1016/j.xplc.2026.101717
Yanan Wang, Hanbin Bao, Yutao Lei, Zhongmin Zou, Lifa Yuan, Haoxing Li, Hui Zhu, Dawei Xin, Christian Staehelin, Yangrong Cao

Bacterial pathogens and most nitrogen-fixing rhizobia employ type III effectors (T3Es) as potent tools to manipulate plant signaling pathways, thereby facilitating infection and colonization. However, how rhizobial T3Es regulate legume symbiosis remains elusive. Here, we show that NopM, a T3E from Sinorhizobium fredii NGR234, contributes to infection and nodulation in Lotus japonicus Gifu. The loss of nopM in an NGR234ΔnopT mutant reduced infection and nodulation in L. japonicus, and expression of NopM under the control of L. japonicus NIN promoter enhanced these processes. NopM associated with the NF receptors NFR1 and NFR5 and physically interacted with their cytosolic domains in vitro, and selectively mediated ubiquitination of NFR5. Expression of NopM in hairy roots of NFR5-HA transgenic plants correlated with increased NFR5 protein abundance relative to the inactive NopM variant. Taken together, our work suggests that NopM-dependent effects on symbiosis are associated with increased NFR5 abundance, expanding our understanding of rhizobial T3E functionality and the co-evolution of legume-rhizobium symbiosis.

细菌病原体和大多数固氮根瘤菌使用III型效应物(T3Es)作为操纵植物信号通路的有效工具,从而促进感染和定植。然而,根瘤菌T3Es如何调节豆科植物的共生关系仍然是一个谜。本研究表明,来自fredii Sinorhizobium NGR234的T3E NopM参与了荷花歧阜的感染和结瘤。在NGR234ΔnopT突变体中,nopM的缺失减少了日本乳菇的感染和结瘤,而在日本乳菇NIN启动子的控制下,nopM的表达增强了这些过程。在体外实验中,NopM与NF受体NFR1和NFR5相关,并与它们的胞质结构域相互作用,选择性介导NFR5的泛素化。NFR5- ha转基因植株毛状根中NopM的表达与NFR5蛋白丰度的增加相关。综上所述,我们的研究表明,nopm对共生的依赖效应与NFR5丰度的增加有关,这扩大了我们对根瘤菌T3E功能和豆科植物-根瘤菌共生共同进化的理解。
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引用次数: 0
Multi-omics and functional analyses of Aesculus wilsonii uncover moretane- and oleanane-type triterpenoid biosynthesis. 多组学和功能分析揭示了多烷型和齐墩烷型三萜的生物合成。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-13 DOI: 10.1016/j.xplc.2026.101715
Yipeng Zhang, Xueting Zhao, Shengqiu Feng, Qinglin Cheng, Jiale Zhao, Fengfeng Li, Keyue Wang, Xiaoxing Hou, Shaofang He, Jing Xing, Duanyang Weng, Shumei Zhong, Beibei Luo, Yuanlong Liu, Xuekui Wang, De-Yu Xie, Zhinan Mei, Shaohua Shu

Aesculus wilsonii, a medicinal tree used in Traditional Chinese Medicine, is rich in aescin and other structurally diverse triterpenoids, yet the biosynthetic mechanism of this diversity remains poorly understood. In this study, we employed integrated omics analyses and functional characterization to elucidate triterpenoid biosynthesis in A. wilsonii. Metabolic profiling annotated 135 triterpenoids that were classified into nine skeleton types, including one previously uncharacterized scaffold. A near telomere-to-telomere genome assembly together with seven transcriptomes enabled comprehensive analysis of genome organization and evolution and determined four triterpenoid biosynthetic gene clusters (TBGC-1 to TBGC-4). Comparative genomics and co-expression analyses identified A. wilsonii-specific cytochrome P450 genes. The functional characterization of seven in yeast together with β-amyrin synthase and cytochrome P450 reductase revealed two CYP716A enzymes from TBGC-2 that catalyzed distinct oxidative reactions. AwCYP716A1278 converted 2,3-oxidosqualene to 21β-hydroxyl-β-amyrin, whereas AwCYP716A277 produced 28-hydroxyl-β-amyrin and oleanolic acid, two oleanane-type triterpenoids. Molecular docking and mutational analyses revealed amino acid residues critical for product specificity. Moreover, functional characterization of a neofunctionalized oxidosqualene cyclase, AwOSC13 from TBGC-4, uncovered a unknown pathway leading to hop-17(21)-en-3β-ol and an uncharacterized triterpenoid. Structural elucidation using NMR and MS identified this compound as moretenol. Heterologous expression of AwOSC13 in tobacco successfully reconstituted the pathway in planta. Together, these findings reveal how biosynthetic gene clusters and enzyme diversification shape triterpenoid metabolism in A. wilsonii and provide valuable resources for discovering and engineering bioactive plant natural products.

七叶神树(Aesculus wilsonii)是一种富含七叶神素和其他结构多样的三萜化合物的中药药用树种,但这种多样性的生物合成机制尚不清楚。在这项研究中,我们采用了综合组学分析和功能表征来阐明金银花三萜的生物合成。代谢分析注释了135种三萜,分为9种骨架类型,包括一种以前未表征的支架。近端粒到端粒基因组组装以及7个转录组使基因组组织和进化进行了全面分析,并确定了4个三萜生物合成基因簇(TBGC-1至TBGC-4)。比较基因组学和共表达分析鉴定了拟南芥特异性细胞色素P450基因。通过与β-amyrin合成酶和细胞色素P450还原酶的功能表征,发现TBGC-2中有两种CYP716A酶催化了不同的氧化反应。AwCYP716A1278将2,3-氧化角鲨烯转化为21β-羟基-β-amyrin,而AwCYP716A277则产生28-羟基-β-amyrin和齐墩果酸,这是两种齐墩果酸型三萜。分子对接和突变分析揭示了对产品特异性至关重要的氨基酸残基。此外,对来自TBGC-4的氧化角鲨烯环化酶AwOSC13的功能表征揭示了通向啤酒花-17(21)-en-3β-醇和未知三萜的未知途径。经核磁共振和质谱分析,该化合物为moretenol。AwOSC13在烟草中的异源表达成功地重建了这一途径。综上所述,这些发现揭示了生物合成基因簇和酶多样化如何塑造了威尔逊ii的三萜代谢,并为发现和设计具有生物活性的植物天然产物提供了宝贵的资源。
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引用次数: 0
Simultaneous defects in chloroplast development and division cause leaf variegation in Arabidopsis. 拟南芥叶片杂色是由叶绿体发育和分裂同时缺陷引起的。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-12 Epub Date: 2025-10-14 DOI: 10.1016/j.xplc.2025.101564
Wenjuan Wu, Wei Guo, Haojie Zhu, Di Li, Zhiyi Zhang, Danni Lin, Meiying Qu, Zhenjia Yu, Jirong Huang

Chloroplast biogenesis is essential not only for photosynthesis but also for the synthesis of many metabolites critical for plant growth and human nutrition. Leaf variegation provides a powerful model for dissecting the process of chloroplast biogenesis, which encompasses both chloroplast development and division. Here, we show that the Arabidopsis thaliana leaf variegation mutant var2, defective in the thylakoid protease FtsH2, exhibits severe defects in chloroplast biogenesis. Confocal and ultrastructural analyses revealed that chloroplast development is delayed yet prolonged in the green sectors of var2, leading to increased cellular heterogeneity in chloroplast number and size. Strikingly, plastid-free cells were observed in white sectors, indicating impaired chloroplast division. Consistent with this, loss of the chloroplast division factors Paralog of Accumulation and Replication of Chloroplasts 6 (PARC6) or Plastid Division 1 (PDV1) exacerbated var2 variegation, whereas overexpression of PDV1 or PDV2 suppressed it. Similarly, chloroplast division was compromised in the variegated mutant immutans, whereas the virescent mutant clpr4, which exhibits increased chloroplast number, rescued leaf variegation phenotype of var2. Furthermore, VAR2-regulated chloroplast development and division are mediated by Constitutively Photomorphogenic 1 (COP1) and autophagy-related ATG8a, respectively. Collectively, our findings demonstrate that leaf variegation arises from simultaneous defects in chloroplast development and division, unveiling a coordinated regulatory mechanism that maintains chloroplast homeostasis.

叶绿体的生物发生不仅对光合作用至关重要,而且对许多对植物生长和人体营养至关重要的代谢物的合成也至关重要。叶片杂色为研究叶绿体的发育和分裂提供了一个强有力的模型。在这里,我们发现拟南芥叶片杂交突变体var2在类囊体蛋白酶FtsH2中存在缺陷,在叶绿体生物发生中表现出严重缺陷。共聚焦和超微结构分析表明,在var2的绿色部分,叶绿体发育延迟或延长,导致叶绿体数量和大小的细胞异质性增加。引人注目的是,白色部门中存在无质体细胞,表明叶绿体分裂受损。与此一致的是,叶绿体分裂因子——叶绿体积累和复制平行体6 (paruc6)或质体分裂1 (PDV1)的缺失加剧了var2的变异,而PDV1或PDV2的过表达则抑制了var2的变异。同样,斑变突变体的叶绿体分裂受到损害,叶绿体数量增加的翠绿色突变体clpr4可以挽救var2的叶片斑变。此外,var2调节的叶绿体发育和分裂分别由组成型光形态发生1 (COP1)和自噬相关的ATG8a介导。总的来说,我们的研究结果表明,叶片杂色是由叶绿体发育和分裂的同步缺陷引起的,揭示了维持叶绿体稳态的协调调节机制。
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引用次数: 0
A transposon insertion in the 5' UTR of OsPT1 reprograms its expression pattern and promotes cadmium accumulation in rice grains. 一个转座子插入到OsPT1的5' UTR中,重新编程了其表达模式,导致水稻籽粒中镉的高积累。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-12 Epub Date: 2025-10-15 DOI: 10.1016/j.xplc.2025.101566
Shasha Peng, Dan Wang, Jinling Liu, Su Jiang, Yuchen Xu, Yufei Deng, Xiaolong Zhou, Fangzhi Hu, Zhuo Liu, Ye Peng, Hejun Ao, Yinghui Xiao, Jiurong Wang, Junliang Zhao, Bin Liu, Keke Yi, Lianyang Bai, Guo-Liang Wang, Houxiang Kang

Cadmium (Cd) accumulation in rice grains presents a serious risk to human health; however, the mechanisms underlying this process remain incompletely understood. In this study, a genome-wide association analysis identified 29 loci associated with grain Cd content (LAGCCs). Among these, one of the most strongly associated loci, LAGCC4, contains the transporter gene OsPT1, whose haplotypes show a strong correlation with Cd content in rice grains. A transposon, H-MITE, inserts into the 5' untranslated region (UTR) of OsPT1, altering its expression pattern and leading to increased Cd accumulation. Furthermore, we identified the transcription factor OsbHLH35, which specifically binds to the OsPT1H-MITE promoter to regulate its transcription in response to Cd stress. Targeted knockout of either OsPT1H-MITE or OsbHLH35 via CRISPR-Cas9 gene editing significantly reduced grain Cd content, with reductions ranging from 61.7% to 80.6%. This study reveals a previously unrecognized mechanism contributing to high Cd accumulation in rice and identifies genetic targets for breeding rice varieties with reduced Cd content.

稻米中镉的积累对人类健康构成严重威胁,但其潜在机制尚不完全清楚。在这里,我们进行了一项全基因组关联研究,确定了29个与谷物Cd含量(lagcc)相关的位点。其中一个最重要的相关位点LAGCC4包含转运基因OsPT1,其单倍型与水稻中镉含量密切相关。转座子H-MITE插入OsPT1的5'非翻译区,改变其表达模式,导致Cd积累增加。我们进一步确定了一个转录因子OsbHLH35,它特异性地结合OsPT1H-MITE启动子来调节其在Cd胁迫下的转录。通过CRISPR/Cas9基因编辑敲除OsPT1H-MITE或OsbHLH35基因均可显著降低籽粒Cd含量,降低幅度在61.7% ~ 80.6%之间。我们的研究揭示了水稻高Cd积累的一个未知机制,并确定了培育低Cd含量水稻品种的目标。
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引用次数: 0
The wheat Yr6 locus, allelic to Pm5, harbors an NLR gene pair conferring stripe rust resistance. 含有NLR基因对的小麦Yr6位点Pm5等位基因赋予小麦抗条锈病能力。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-12 Epub Date: 2025-09-30 DOI: 10.1016/j.xplc.2025.101541
Weihang Sun, Haitao Dong, Shengjie Liu, Shengwei Ma, Qingdong Zeng, Jihu Li, Ke Ke, Wenjie Yue, Wenjing Zhang, Xinrui Fang, Jinyu Han, Xinying Zhou, Jiwen Zhao, Guanghao Guo, Genying Li, Xinyou Cao, Weijun Zheng, Chunlian Li, Zhensheng Kang, Dejun Han, Zhiyong Liu, Gang Li, Xiaojie Wang, Jianhui Wu
{"title":"The wheat Yr6 locus, allelic to Pm5, harbors an NLR gene pair conferring stripe rust resistance.","authors":"Weihang Sun, Haitao Dong, Shengjie Liu, Shengwei Ma, Qingdong Zeng, Jihu Li, Ke Ke, Wenjie Yue, Wenjing Zhang, Xinrui Fang, Jinyu Han, Xinying Zhou, Jiwen Zhao, Guanghao Guo, Genying Li, Xinyou Cao, Weijun Zheng, Chunlian Li, Zhensheng Kang, Dejun Han, Zhiyong Liu, Gang Li, Xiaojie Wang, Jianhui Wu","doi":"10.1016/j.xplc.2025.101541","DOIUrl":"10.1016/j.xplc.2025.101541","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101541"},"PeriodicalIF":11.6,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208195","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
Unidirectional genomic introgression facilitates the colonization of an invasive orchid in arid, metal-enriched sedimentary habitats. 单向基因组渗入促进了入侵兰花在干旱富金属沉积栖息地的定植。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-12 Epub Date: 2025-10-13 DOI: 10.1016/j.xplc.2025.101561
Zhenbin Jiao, Zhiyao Ren, Chao Hu, Xiaokai Ma, Guo-Qiang Zhang, Li-Jun Chen, Gang Wei, Dong-Hui Peng, Siren Lan, Yi-Bo Luo, Zhong-Jian Liu

Genes that introgress between species can influence the evolutionary and ecological fate of recipients exposed to novel environments. However, key questions on the patterns and molecular mechanisms of introgression in perennial herbaceous plants, which enable distantly related invasive species to thrive in extreme habitats, remain largely unanswered. Here, we report unidirectional introgression from the local species Dendrobium huoshanense to the distantly related invasive species Dendrobium catenatum (Dendrobium officinale) in lithophytic habitats of eastern China. The introgressed regions, which comprise approximately 1% of the genome, contain genes that regulate responses to drought, cold, and metal-ion stresses. Notably, introgressed loci such as CDPK, HHP, PIF, BRI1, and FY show distinct selection signatures and differential expression compared with their paralogs, each playing a distinct role in drought and cold-stress responses. In addition, CIPK23, PDR9, and HAM demonstrate differential expression relative to their paralogous genes and alleles within introgressed loci, indicating their potential involvement in responses to metal-ion stress. Introgression thus facilitates the colonization of arid, metal-enriched sedimentary habitats by D. catenatum. These findings enhance our understanding of Orchidaceae evolution and reveal the evolutionary role of unidirectional introgression in the adaptation of perennial herbaceous plants to extreme environments.

基因在物种间的渗入可以影响新环境下接受者的进化和生态命运。然而,关于多年生草本植物的入侵模式和分子机制的关键问题,使远亲入侵物种能够在极端生境中茁壮成长,仍然没有很大的答案。本文报道了中国东部岩生生境中本地物种霍山石斛(Dendrobium hooshanense)向远亲入侵物种D. catenatum (D. officinale)的单向渗透。基因渗入区约占基因组的1%,包含调控对干旱、寒冷和金属离子胁迫反应的基因。值得注意的是,CDPK、HHP、PIF、BRI1和FY等基因座与同类基因座相比,表现出不同的选择特征和差异表达,在干旱和寒冷胁迫响应中发挥着不同的作用。此外,CIPK23、PDR9和HAM在其渗入位点内的同源基因和等位基因中表现出差异表达,表明它们可能参与对金属离子胁迫的反应。这种渗入有利于在干旱、富金属的沉积生境中定植。本研究结果有助于加深对兰科植物进化的认识,并阐明了单向渗入在多年生草本植物极端环境适应中的进化作用。
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引用次数: 0
Plant-derived vaccines: Advances in delivery approaches. 植物源性疫苗:递送方法的进展
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-12 Epub Date: 2025-12-16 DOI: 10.1016/j.xplc.2025.101676
Hai-Ping Diao, Yong-Feng Guo, Yong Chen, Inhwan Hwang, Shi-Jian Song
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引用次数: 0
Genome-based mutant RNA mapping identifies an NLR pair underlying Yr6-mediated stripe rust resistance in wheat. 基于基因组的突变体RNA定位(GMRM)鉴定了小麦中与yr6介导的条锈病抗性相关的NLR对。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-12 Epub Date: 2025-09-30 DOI: 10.1016/j.xplc.2025.101542
Shuo Huang, Lu Zhang, Jiabao Liang, Yi Ouyang, Yurong Yan, Huike Ju, Yaxin Wang, Hao Zhang, Taiguo Liu, Chunlei Tang, Xiaojie Wang, Yajun Wang
{"title":"Genome-based mutant RNA mapping identifies an NLR pair underlying Yr6-mediated stripe rust resistance in wheat.","authors":"Shuo Huang, Lu Zhang, Jiabao Liang, Yi Ouyang, Yurong Yan, Huike Ju, Yaxin Wang, Hao Zhang, Taiguo Liu, Chunlei Tang, Xiaojie Wang, Yajun Wang","doi":"10.1016/j.xplc.2025.101542","DOIUrl":"10.1016/j.xplc.2025.101542","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101542"},"PeriodicalIF":11.6,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208149","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
Residue P132 of PsbS plays an important role in regulating the dynamics of non-photochemical quenching in Arabidopsis. PsbS残基P132在拟南芥非化学猝灭动力学调控中起重要作用。
IF 11.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-12 Epub Date: 2025-10-31 DOI: 10.1016/j.xplc.2025.101582
Linxiong Mao, Yingjie Wang, Runrui Yu, Yajun Lin, Pengfei Zhou, Meixia Ruan, Huiqiong Zheng, Na Li, Yuxiang Weng, Minrui Fan, Xin-Guang Zhu

Increasing the dynamics of non-photochemical quenching (NPQ) under changing light levels represents a promising strategy for improving photosynthetic light-use efficiency for greater crop yields. PsbS plays a crucial role in modulating both the capacity and dynamics of NPQ. Nevertheless, the specific mechanisms by which PsbS mediates functional state transitions and the detailed molecular interactions involved in NPQ are still not fully understood. In this study, we identified an amino acid residue, P132, in Arabidopsis thaliana PsbS (AtPsbS) whose substitution with alanine (P132A) causes rapid NPQ induction under low light and significantly reduces the rate of NPQ relaxation in the dark. Our findings suggest that the AtPsbSP132A mutation keeps PsbS in a loose dimer state that is prone to dissociation and hence causes a reduced proportion of dimers and altered NPQ dynamics. Our study also shows that the AtPsbSP132A+E122Q+E226Q mutant, which lacks protonation-sensing amino acids, may partially induce NPQ even in the absence of protonation, indicating that the structural features of PsbS may independently influence NPQ. Data from this study provide strong evidence that the structural features of PsbS affect NPQ induction and point to a significant role of the PsbS sequence in NPQ dynamics, in addition to the commonly assumed importance of PsbS levels and protonation of E122 and E226 in PsbS. In other words, the protonation sites (i.e., E122 and E226) and the amino acid residues that alter the structural characteristics of the PsbS protein both have an important effect on its NPQ function.

增加非光化学猝灭(NPQ)对光照水平变化的动态响应是提高光合光利用效率以提高作物产量的一种有前途的策略。psb在调节NPQ的容量和动态方面起着至关重要的作用。然而,PsbS介导功能状态转变的具体机制以及NPQ中涉及的详细分子相互作用仍未完全了解。在本研究中,我们在拟南芥PsbS (AtPsbS)中发现了一个氨基酸残基P132,它被丙氨酸(P132A)取代,可以在弱光下快速诱导NPQ,并显著降低NPQ在黑暗下的弛化速度。我们的研究结果表明,AtPsbSP132A突变使PsbS处于松散的二聚体状态,容易解体,从而导致二聚体比例下降和NPQ动力学改变。此外,我们的研究还表明,AtPsbSP132A+E122Q+E226Q突变体缺乏质子感应氨基酸,即使在没有质子化的情况下,也可能部分诱导NPQ的产生,这表明PsbS的结构特征可能独立影响NPQ。本研究的数据有力地支持了PsbS的结构特征影响NPQ的形成,并指出PsbS序列在NPQ动力学中的重要作用,除了通常认为PsbS水平和PsbS中E122和E226的质子化的重要性之外。换句话说,质子化位点(即E122和E226)和改变PsbS蛋白结构特征的氨基酸残基都在影响其NPQ功能中起关键作用。
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引用次数: 0
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Plant Communications
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