Pub Date : 2024-09-27DOI: 10.1038/s41477-024-01805-w
Takashi Akagi, Shigeo S. Sugano
In contrast to the recent progress in the genome sequencing of plant sex chromosomes, the functional contribution of the genes in sex chromosomes remains little known1. They were classically thought to be related to sexual dimorphism, which is beneficial to male or female functions, including segregation ratios. Here we focused on the functional evolution of the sex ratio distortion-related locus Half Male Sterile/Inviable (HaMSter), which is located in the short sex-linked region in diploid persimmon (Diospyros lotus). The expression of HaMSter, encoding a plant1589-like undefined protein, is necessary for production of viable seeds. Notably, only X-allelic HaMSter is substantially expressed and half of the maternal X alleles of HaMSter is randomly inactivated, which results in sex ratio distortion in seeds. Genome-wide DNA methylome analyses revealed endosperm-specific DNA hypermethylation, especially in the X-linked region. The maintenance/release of this hypermethylation is linked to inactivation/activation of HaMSter expression, respectively, which determines the sex ratio distortion pattern. The sex ratio is often not even in plants, and its molecular mechanisms have been little known. The study found that an X chromosome-encoded gene, named HaMSter in persimmon, influences sex ratio distortion via seed viability through a regulatory mechanism involving random DNA methylation.
与植物性染色体基因组测序的最新进展相比，人们对性染色体基因的功能贡献仍然知之甚少1。人们通常认为它们与性二态性有关，而性二态性有利于雄性或雌性的功能，包括分离比。在此，我们重点研究了性比畸变相关位点半雄不育/不育（HaMSter）的功能进化，该位点位于二倍体柿子（Diospyros lotus）的短性连锁区。HaMSter编码一种类似植物1589的未定义蛋白质，它的表达是产生可存活种子的必要条件。值得注意的是，只有X等位基因HaMSter大量表达，而HaMSter的母本X等位基因有一半随机失活，从而导致种子的性别比例失调。全基因组 DNA 甲基化分析显示，胚乳特异性 DNA 高甲基化，尤其是在 X 连锁区域。这种高甲基化的维持/释放分别与 HaMSter 表达的失活/活化有关，从而决定了性比畸变模式。
{"title":"Random epigenetic inactivation of the X-chromosomal HaMSter gene causes sex ratio distortion in persimmon","authors":"Takashi Akagi, Shigeo S. Sugano","doi":"10.1038/s41477-024-01805-w","DOIUrl":"10.1038/s41477-024-01805-w","url":null,"abstract":"In contrast to the recent progress in the genome sequencing of plant sex chromosomes, the functional contribution of the genes in sex chromosomes remains little known1. They were classically thought to be related to sexual dimorphism, which is beneficial to male or female functions, including segregation ratios. Here we focused on the functional evolution of the sex ratio distortion-related locus Half Male Sterile/Inviable (HaMSter), which is located in the short sex-linked region in diploid persimmon (Diospyros lotus). The expression of HaMSter, encoding a plant1589-like undefined protein, is necessary for production of viable seeds. Notably, only X-allelic HaMSter is substantially expressed and half of the maternal X alleles of HaMSter is randomly inactivated, which results in sex ratio distortion in seeds. Genome-wide DNA methylome analyses revealed endosperm-specific DNA hypermethylation, especially in the X-linked region. The maintenance/release of this hypermethylation is linked to inactivation/activation of HaMSter expression, respectively, which determines the sex ratio distortion pattern. The sex ratio is often not even in plants, and its molecular mechanisms have been little known. The study found that an X chromosome-encoded gene, named HaMSter in persimmon, influences sex ratio distortion via seed viability through a regulatory mechanism involving random DNA methylation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 11","pages":"1643-1651"},"PeriodicalIF":15.8,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325578","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}
Pub Date : 2024-09-26DOI: 10.1038/s41477-024-01808-7
Young Geun Mok, Sunghyun Hong, Da In Seo, Seunghee Choi, Hee Kyoung Kim, Da Mon Jin, JungEun Joanna Lee, Jin-Soo Kim
CRISPR-free, protein-only cytosine base editors (CBEs) or adenine base editors, composed of DNA-binding proteins such as zinc finger proteins or transcription activator-like effectors (TALEs) and nucleobase cytosine or adenine deaminases, respectively, enable organellar DNA editing in cultured cells, animals and plants1–4. TALE-linked double-stranded DNA deaminase toxin A (DddAtox)-derived CBEs (DdCBEs) and TALE-linked adenine deaminases (TALEDs) install C-to-T and A-to-G single-nucleotide conversions, respectively, in mitochondria and chloroplasts5–9. Interestingly, whereas TALEDs exclusively induce A-to-G conversions without C-to-T conversions in mammalian mitochondrial DNA10, they often install unwanted C-to-T edits in addition to intended A-to-G edits in plastid DNA7,9,11,12. Here we show that uracil DNA glycosylase (UDG)-fused TALEDs (UDG-TALEDs) minimize C-to-T conversions without reducing the A-to-G editing efficiency and install a mutation in the chloroplast psbA gene that encodes a single-amino-acid substitution (S264G), which confers herbicide resistance in the resulting plants. Uracil DNA glycosylase-fused TALE-linked deaminases achieve precision A-to-G base editing without bystander C-to-T editing in chloroplast DNA to create herbicide-resistant plants with a heritable homoplasmic mutation in the psbA gene.
无 CRISPR 的纯蛋白质胞嘧啶碱基编辑器（CBEs）或腺嘌呤碱基编辑器分别由 DNA 结合蛋白（如锌指蛋白或转录激活剂样效应物（TALEs））和核碱基胞嘧啶或腺嘌呤脱氨酶组成，可在培养细胞、动物和植物中进行细胞器 DNA 编辑1,2,3,4。与 TALE 链接的双链 DNA 脱氨酶毒素 A（DddAtox）衍生的 CBEs（DdCBEs）和与 TALE 链接的腺嘌呤脱氨酶（TALEDs）分别在线粒体和叶绿体中进行 C 到 T 和 A 到 G 的单核苷酸转换5,6,7,8,9。有趣的是，在哺乳动物线粒体 DNA 中，TALED 只诱导 A 到 G 的转换，而不诱导 C 到 T 的转换10，但在质体 DNA 中，TALED 除了诱导预期的 A 到 G 的转换外，还经常诱导不需要的 C 到 T 的转换7,9,11,12。在这里，我们展示了尿嘧啶 DNA 糖基化酶（UDG）融合的 TALEDs（UDG-TALEDs）在不降低 A-G 编辑效率的情况下最大程度地减少了 C-T 转换，并在叶绿体 psbA 基因中安装了一个编码单氨基酸置换（S264G）的突变，从而使产生的植株具有除草剂抗性。
{"title":"Herbicide-resistant plants produced by precision adenine base editing in plastid DNA","authors":"Young Geun Mok, Sunghyun Hong, Da In Seo, Seunghee Choi, Hee Kyoung Kim, Da Mon Jin, JungEun Joanna Lee, Jin-Soo Kim","doi":"10.1038/s41477-024-01808-7","DOIUrl":"10.1038/s41477-024-01808-7","url":null,"abstract":"CRISPR-free, protein-only cytosine base editors (CBEs) or adenine base editors, composed of DNA-binding proteins such as zinc finger proteins or transcription activator-like effectors (TALEs) and nucleobase cytosine or adenine deaminases, respectively, enable organellar DNA editing in cultured cells, animals and plants1–4. TALE-linked double-stranded DNA deaminase toxin A (DddAtox)-derived CBEs (DdCBEs) and TALE-linked adenine deaminases (TALEDs) install C-to-T and A-to-G single-nucleotide conversions, respectively, in mitochondria and chloroplasts5–9. Interestingly, whereas TALEDs exclusively induce A-to-G conversions without C-to-T conversions in mammalian mitochondrial DNA10, they often install unwanted C-to-T edits in addition to intended A-to-G edits in plastid DNA7,9,11,12. Here we show that uracil DNA glycosylase (UDG)-fused TALEDs (UDG-TALEDs) minimize C-to-T conversions without reducing the A-to-G editing efficiency and install a mutation in the chloroplast psbA gene that encodes a single-amino-acid substitution (S264G), which confers herbicide resistance in the resulting plants. Uracil DNA glycosylase-fused TALE-linked deaminases achieve precision A-to-G base editing without bystander C-to-T editing in chloroplast DNA to create herbicide-resistant plants with a heritable homoplasmic mutation in the psbA gene.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 11","pages":"1652-1658"},"PeriodicalIF":15.8,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321828","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}
Pub Date : 2024-09-24DOI: 10.1038/s41477-024-01800-1
Xiang Lu, Yao He, Jin-Qiao Guo, Yue Wang, Qian Yan, Qing Xiong, Hui Shi, Qingqing Hou, Junjie Yin, Yi-Bang An, Yi-Di Chen, Cheng-Shuang Yang, Ye Mao, Xiaobo Zhu, Yongyan Tang, Jiali Liu, Yu Bi, Li Song, Long Wang, Yihua Yang, Min He, Weitao Li, Xuewei Chen, Jing Wang
Messenger RNA modifications play pivotal roles in RNA biology, but comprehensive landscape changes of epitranscriptomes remain largely unknown in plant immune response. Here we report translational reprogramming directed by ac4C mRNA modification upon pathogen challenge. We first investigate the dynamics of translatomes and epitranscriptomes and uncover that the change in ac4C at single-base resolution promotes translational reprogramming upon Magnaporthe oryzae infection. Then by characterizing the specific distributions of m1A, 2’O-Nm, ac4C, m5C, m6A and m7G, we find that ac4Cs, unlike other modifications, are enriched at the 3rd position of codons, which stabilizes the Watson–Crick base pairing. Importantly, we demonstrate that upon pathogen infection, the increased expression of the ac4C writer OsNAT10/OsACYR (N-ACETYLTRANSFERASE FOR CYTIDINE IN RNA) promotes translation to facilitate rapid activation of immune responses, including the enhancement of jasmonic acid biosynthesis. Our study provides an atlas of mRNA modifications and insights into ac4C function in plant immunity. By characterizing the dynamics of epitranscriptomes and translatomes upon Magnaporthe oryzae infection, the authors uncover that ac4C enriched in the 3rd nt of codons improves translation of mRNA to enhance rice resistance against M. oryzae.
{"title":"Dynamics of epitranscriptomes uncover translational reprogramming directed by ac4C in rice during pathogen infection","authors":"Xiang Lu, Yao He, Jin-Qiao Guo, Yue Wang, Qian Yan, Qing Xiong, Hui Shi, Qingqing Hou, Junjie Yin, Yi-Bang An, Yi-Di Chen, Cheng-Shuang Yang, Ye Mao, Xiaobo Zhu, Yongyan Tang, Jiali Liu, Yu Bi, Li Song, Long Wang, Yihua Yang, Min He, Weitao Li, Xuewei Chen, Jing Wang","doi":"10.1038/s41477-024-01800-1","DOIUrl":"10.1038/s41477-024-01800-1","url":null,"abstract":"Messenger RNA modifications play pivotal roles in RNA biology, but comprehensive landscape changes of epitranscriptomes remain largely unknown in plant immune response. Here we report translational reprogramming directed by ac4C mRNA modification upon pathogen challenge. We first investigate the dynamics of translatomes and epitranscriptomes and uncover that the change in ac4C at single-base resolution promotes translational reprogramming upon Magnaporthe oryzae infection. Then by characterizing the specific distributions of m1A, 2’O-Nm, ac4C, m5C, m6A and m7G, we find that ac4Cs, unlike other modifications, are enriched at the 3rd position of codons, which stabilizes the Watson–Crick base pairing. Importantly, we demonstrate that upon pathogen infection, the increased expression of the ac4C writer OsNAT10/OsACYR (N-ACETYLTRANSFERASE FOR CYTIDINE IN RNA) promotes translation to facilitate rapid activation of immune responses, including the enhancement of jasmonic acid biosynthesis. Our study provides an atlas of mRNA modifications and insights into ac4C function in plant immunity. By characterizing the dynamics of epitranscriptomes and translatomes upon Magnaporthe oryzae infection, the authors uncover that ac4C enriched in the 3rd nt of codons improves translation of mRNA to enhance rice resistance against M. oryzae.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1548-1561"},"PeriodicalIF":15.8,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142313712","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}
Pub Date : 2024-09-23DOI: 10.1038/s41477-024-01796-8
Anchilie F. Mangilet, Joachim Weber, Sandra Schüler, Manon Adler, Eneza Yoeli Mjema, Paula Heilmann, Angie Herold, Monique Renneberg, Luise Nagel, Irina Droste-Borel, Samuel Streicher, Thomas Schmutzer, Gregor Rot, Boris Macek, Cornelius Schmidtke, Sascha Laubinger
The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP and revealed a tight link to mRNA cleavage and polyadenylation factors. Interestingly, we found that the U1 snRNP protects mRNAs against premature cleavage and polyadenylation within introns—a mechanism known as telescripting in metazoans—while also influencing alternative polyadenylation site selection in 3′-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3′-end processing in Arabidopsis, laying the groundwork for understanding non-canonical functions of plant U1 snRNPs. Researchers found that a plant U1 snRNP complex associates with 200 proteins and conducts splicing-independent roles by safeguarding RNAs against premature cleavage and polyadenylation, similar to a process known as telescripting in metazoans.
{"title":"The Arabidopsis U1 snRNP regulates mRNA 3′-end processing","authors":"Anchilie F. Mangilet, Joachim Weber, Sandra Schüler, Manon Adler, Eneza Yoeli Mjema, Paula Heilmann, Angie Herold, Monique Renneberg, Luise Nagel, Irina Droste-Borel, Samuel Streicher, Thomas Schmutzer, Gregor Rot, Boris Macek, Cornelius Schmidtke, Sascha Laubinger","doi":"10.1038/s41477-024-01796-8","DOIUrl":"10.1038/s41477-024-01796-8","url":null,"abstract":"The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP and revealed a tight link to mRNA cleavage and polyadenylation factors. Interestingly, we found that the U1 snRNP protects mRNAs against premature cleavage and polyadenylation within introns—a mechanism known as telescripting in metazoans—while also influencing alternative polyadenylation site selection in 3′-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3′-end processing in Arabidopsis, laying the groundwork for understanding non-canonical functions of plant U1 snRNPs. Researchers found that a plant U1 snRNP complex associates with 200 proteins and conducts splicing-independent roles by safeguarding RNAs against premature cleavage and polyadenylation, similar to a process known as telescripting in metazoans.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1514-1531"},"PeriodicalIF":15.8,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01796-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276827","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}
Pub Date : 2024-09-19DOI: 10.1038/s41477-024-01793-x
Yetong Qi, Jiahui Wu, Zhu Yang, Hongjun Li, Lang Liu, Haixia Wang, Xinyuan Sun, Xinya Wu, Jiahui Nie, Jing Zhou, Meng Xu, Xintong Wu, Susan Breen, Ruimin Yu, Dong Cheng, Qingguo Sun, Huishan Qiu, Yingtao Zuo, Petra C. Boevink, Paul R. J. Birch, Zhendong Tian
Chloroplasts regulate plant development and immunity. Here we report that potato chloroplast elongation factors StTuA and StTuB, targeted by Phytophthora infestans RXLR effector Pi22926, positively regulate immunity and growth. Plants expressing Pi22926, or silenced for TuA/B, show increased P. infestans susceptibility and decreased photosynthesis, plant growth and tuber yield. By contrast, StTuA/B overexpression reduces susceptibility, elevates chloroplast-derived reactive oxygen species production and increases photosynthesis and potato tuber yield by enhancing chloroplast protein translation. Another plant target of Pi22926, StMAP3Kβ2, interacts with StTuB, phosphorylating it to promote its translocation into chloroplasts. However, Pi22926 attenuates StTuB association with StMAP3Kβ2 and phosphorylation. This reduces StTuB translocation into chloroplasts, leading to its proteasome-mediated turnover in the cytoplasm. We uncover new mechanisms by which a pathogen effector inhibits immunity by disrupting key chloroplast functions. This work shows that StTuA/B break the growth–immunity trade-off, promoting both disease resistance and yield, revealing the enormous potential of chloroplast biology in crop breeding. Enhanced expression of chloroplast elongation factors StTuA/B increases potato disease resistance and photosynthesis, while oomycete effector Pi22926 inhibits their entry into the chloroplasts by disrupting their phosphorylation by StMAP3Kβ2.
{"title":"Chloroplast elongation factors break the growth–immunity trade-off by simultaneously promoting yield and defence","authors":"Yetong Qi, Jiahui Wu, Zhu Yang, Hongjun Li, Lang Liu, Haixia Wang, Xinyuan Sun, Xinya Wu, Jiahui Nie, Jing Zhou, Meng Xu, Xintong Wu, Susan Breen, Ruimin Yu, Dong Cheng, Qingguo Sun, Huishan Qiu, Yingtao Zuo, Petra C. Boevink, Paul R. J. Birch, Zhendong Tian","doi":"10.1038/s41477-024-01793-x","DOIUrl":"10.1038/s41477-024-01793-x","url":null,"abstract":"Chloroplasts regulate plant development and immunity. Here we report that potato chloroplast elongation factors StTuA and StTuB, targeted by Phytophthora infestans RXLR effector Pi22926, positively regulate immunity and growth. Plants expressing Pi22926, or silenced for TuA/B, show increased P. infestans susceptibility and decreased photosynthesis, plant growth and tuber yield. By contrast, StTuA/B overexpression reduces susceptibility, elevates chloroplast-derived reactive oxygen species production and increases photosynthesis and potato tuber yield by enhancing chloroplast protein translation. Another plant target of Pi22926, StMAP3Kβ2, interacts with StTuB, phosphorylating it to promote its translocation into chloroplasts. However, Pi22926 attenuates StTuB association with StMAP3Kβ2 and phosphorylation. This reduces StTuB translocation into chloroplasts, leading to its proteasome-mediated turnover in the cytoplasm. We uncover new mechanisms by which a pathogen effector inhibits immunity by disrupting key chloroplast functions. This work shows that StTuA/B break the growth–immunity trade-off, promoting both disease resistance and yield, revealing the enormous potential of chloroplast biology in crop breeding. Enhanced expression of chloroplast elongation factors StTuA/B increases potato disease resistance and photosynthesis, while oomycete effector Pi22926 inhibits their entry into the chloroplasts by disrupting their phosphorylation by StMAP3Kβ2.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1576-1591"},"PeriodicalIF":15.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245257","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}
Pub Date : 2024-09-19DOI: 10.1038/s41477-024-01809-6
The language of science preserves reminders of its chequered history, sometimes resulting in unintended consequences and offence.
科学的语言保留了其坎坷历史的记忆，有时会造成意想不到的后果和冒犯。
{"title":"Naming conventions","authors":"","doi":"10.1038/s41477-024-01809-6","DOIUrl":"10.1038/s41477-024-01809-6","url":null,"abstract":"The language of science preserves reminders of its chequered history, sometimes resulting in unintended consequences and offence.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 9","pages":"1269-1269"},"PeriodicalIF":15.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01809-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245252","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}
Biodiversity is increasingly threatened by local extinction under global climate change. This may reflect direct effects of climate on poorly adapted native species or increased impacts of exotic species in these conditions, but their relative importance is poorly understood. By examining global occurrence records of 142 plant species found in the Yangtze River Valley, we found that the climatic niches of exotic species differed from those of natives, mainly reflecting exotics being most common in warmer, drier and more isothermal climates in their native ranges. These differences in climatic niches, especially temperature, predicted invasion intensity in 459 plots along a 1,800-km transect in the Yangtze River Valley. On the basis of this strong match between model predictions and field survey results, we predict that invasions will probably be more intense in future climatic conditions, especially from warming at the coldest sites. The direct negative effect of warming on native diversity was larger than the indirect effects mediated through increased invasions. However, moderate invasion increased communities’ overall species diversity. More broadly, our study highlights the role of exotic species in the ecological response of regional biodiversity to global climate change. Exotic species benefit from differing climatic niches, compensating for native species loss due to climate mismatch and driving biodiversity toward climatic equilibrium under climate change.
{"title":"Deterministic responses of biodiversity to climate change through exotic species invasions","authors":"Pengdong Chen, Changchao Shen, Zhibin Tao, Wenchao Qin, Wei Huang, Evan Siemann","doi":"10.1038/s41477-024-01797-7","DOIUrl":"10.1038/s41477-024-01797-7","url":null,"abstract":"Biodiversity is increasingly threatened by local extinction under global climate change. This may reflect direct effects of climate on poorly adapted native species or increased impacts of exotic species in these conditions, but their relative importance is poorly understood. By examining global occurrence records of 142 plant species found in the Yangtze River Valley, we found that the climatic niches of exotic species differed from those of natives, mainly reflecting exotics being most common in warmer, drier and more isothermal climates in their native ranges. These differences in climatic niches, especially temperature, predicted invasion intensity in 459 plots along a 1,800-km transect in the Yangtze River Valley. On the basis of this strong match between model predictions and field survey results, we predict that invasions will probably be more intense in future climatic conditions, especially from warming at the coldest sites. The direct negative effect of warming on native diversity was larger than the indirect effects mediated through increased invasions. However, moderate invasion increased communities’ overall species diversity. More broadly, our study highlights the role of exotic species in the ecological response of regional biodiversity to global climate change. Exotic species benefit from differing climatic niches, compensating for native species loss due to climate mismatch and driving biodiversity toward climatic equilibrium under climate change.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1464-1472"},"PeriodicalIF":15.8,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01797-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236221","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}
SUMOylation—the attachment of a small ubiquitin-like modifier (SUMO) to target proteins—plays roles in controlling plant growth, nutrient signalling and stress responses. SUMOylation studies in plants are scarce because identifying SUMOylated proteins and their sites is challenging. To date, only around 80 SUMOylation sites have been identified. Here we introduce lysine-null SUMO1 into the Arabidopsis sumo1 sumo2 mutant and establish a two-step lysine-null SUMO enrichment method. We identified a site-specific SUMOylome comprising over 2,200 SUMOylation sites from 1,300 putative acceptors that function in numerous nuclear processes. SUMOylation marks occur on several motifs, differing from the canonical ψKxE motif in distant eukaryotes. Quantitative comparisons demonstrate that SUMOylation predominantly enhances the stability of SUMO1 acceptors. Our study delivers a highly sensitive and efficient method for site-specific SUMOylome studies and provides a comprehensive catalogue of Arabidopsis SUMOylation, serving as a valuable resource with which to further explore how SUMOylation regulates protein function. This study establishes an efficient method for site-specific SUMOylation proteomics, achieving a comprehensive SUMOylome comprising over 2,200 SUMOylation sites, which could serve as a useful tool and valuable resource for future research in plants.
{"title":"Highly sensitive site-specific SUMOylation proteomics in Arabidopsis","authors":"Tian Sang, Yaping Xu, Guochen Qin, Shasha Zhao, Chuan-Chi Hsu, Pengcheng Wang","doi":"10.1038/s41477-024-01783-z","DOIUrl":"10.1038/s41477-024-01783-z","url":null,"abstract":"SUMOylation—the attachment of a small ubiquitin-like modifier (SUMO) to target proteins—plays roles in controlling plant growth, nutrient signalling and stress responses. SUMOylation studies in plants are scarce because identifying SUMOylated proteins and their sites is challenging. To date, only around 80 SUMOylation sites have been identified. Here we introduce lysine-null SUMO1 into the Arabidopsis sumo1 sumo2 mutant and establish a two-step lysine-null SUMO enrichment method. We identified a site-specific SUMOylome comprising over 2,200 SUMOylation sites from 1,300 putative acceptors that function in numerous nuclear processes. SUMOylation marks occur on several motifs, differing from the canonical ψKxE motif in distant eukaryotes. Quantitative comparisons demonstrate that SUMOylation predominantly enhances the stability of SUMO1 acceptors. Our study delivers a highly sensitive and efficient method for site-specific SUMOylome studies and provides a comprehensive catalogue of Arabidopsis SUMOylation, serving as a valuable resource with which to further explore how SUMOylation regulates protein function. This study establishes an efficient method for site-specific SUMOylation proteomics, achieving a comprehensive SUMOylome comprising over 2,200 SUMOylation sites, which could serve as a useful tool and valuable resource for future research in plants.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 9","pages":"1330-1342"},"PeriodicalIF":15.8,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236222","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}
Pub Date : 2024-09-17DOI: 10.1038/s41477-024-01789-7
Kenneth D. Birnbaum, Siobhan M. Brady, Kimberley L. Gallagher, Jee Jung, Olivier Pourquié, Ben Scheres, Rachel Shahan, Rosangela Sozzani, Lucia Strader
An archetype of collaboration, community development and vision, who made fundamental contributions to biology through his studies on the often-unseen part of the plant, the root.
{"title":"Philip Benfey (1953–2023)","authors":"Kenneth D. Birnbaum, Siobhan M. Brady, Kimberley L. Gallagher, Jee Jung, Olivier Pourquié, Ben Scheres, Rachel Shahan, Rosangela Sozzani, Lucia Strader","doi":"10.1038/s41477-024-01789-7","DOIUrl":"10.1038/s41477-024-01789-7","url":null,"abstract":"An archetype of collaboration, community development and vision, who made fundamental contributions to biology through his studies on the often-unseen part of the plant, the root.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1436-1438"},"PeriodicalIF":15.8,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01789-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235097","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}
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