Ping Zhang, Fei Liu, Mostafa Abdelrahman, Qianqian Song, Fei Wu, Ruishan Li, Min Wu, Luis Herrera-Estrella, Lam-Son Phan Tran, Jin Xu
Cytokinin is central to coordinating plant adaptation to environmental stresses. Here, we first demonstrated the involvement of cytokinin in Arabidopsis responses to arsenite [As(III)] stress. As(III) treatment reduced cytokinin contents, while cytokinin treatment repressed further primary root growth in Arabidopsis plants under As(III) stress. Subsequently, we revealed that the cytokinin signaling members ARR1 and ARR12, the type-B ARABIDOPSIS RESPONSE REGULATORs, participate in cytokinin signaling-mediated As(III) responses in plants as negative regulators. A comprehensive transcriptome analysis of the arr1 and arr12 single and arr1,12 double mutants was then performed to decipher the cytokinin signaling-mediated mechanisms underlying plant As(III) stress adaptation. Results revealed important roles for ARR1 and ARR12 in ion transport, nutrient responses, and secondary metabolite accumulation. Furthermore, using hierarchical clustering and regulatory network analyses, we identified two NODULIN 26-LIKE INTRINSIC PROTEIN (NIP)-encoding genes, NIP1;1 and NIP6;1, potentially involved in ARR1/12-mediated As(III) uptake and transport in Arabidopsis. By analyzing various combinations of arr and nip mutants, including high-order triple and quadruple mutants, we demonstrated that ARR1 and ARR12 redundantly function as negative regulators of As(III) tolerance by acting upstream of NIP1;1 and NIP6;1 to modulate their function in arsenic accumulation. ChIP-qPCR, EMSA, and transient dual-LUC reporter assays revealed that ARR1 and ARR12 transcriptionally activate the expression of NIP1;1 and NIP6;1 by directly binding to their promoters and upregulating their expression, leading to increased arsenic accumulation under As(III) stress. These findings collectively provide insights into cytokinin signaling-mediated plant adaptation to excessive As(III), contributing to the development of crops with low arsenic accumulation.
{"title":"ARR1 and ARR12 modulate arsenite toxicity responses in Arabidopsis roots by transcriptionally controlling the actions of NIP1;1 and NIP6;1.","authors":"Ping Zhang, Fei Liu, Mostafa Abdelrahman, Qianqian Song, Fei Wu, Ruishan Li, Min Wu, Luis Herrera-Estrella, Lam-Son Phan Tran, Jin Xu","doi":"10.1111/tpj.17065","DOIUrl":"https://doi.org/10.1111/tpj.17065","url":null,"abstract":"<p><p>Cytokinin is central to coordinating plant adaptation to environmental stresses. Here, we first demonstrated the involvement of cytokinin in Arabidopsis responses to arsenite [As(III)] stress. As(III) treatment reduced cytokinin contents, while cytokinin treatment repressed further primary root growth in Arabidopsis plants under As(III) stress. Subsequently, we revealed that the cytokinin signaling members ARR1 and ARR12, the type-B ARABIDOPSIS RESPONSE REGULATORs, participate in cytokinin signaling-mediated As(III) responses in plants as negative regulators. A comprehensive transcriptome analysis of the arr1 and arr12 single and arr1,12 double mutants was then performed to decipher the cytokinin signaling-mediated mechanisms underlying plant As(III) stress adaptation. Results revealed important roles for ARR1 and ARR12 in ion transport, nutrient responses, and secondary metabolite accumulation. Furthermore, using hierarchical clustering and regulatory network analyses, we identified two NODULIN 26-LIKE INTRINSIC PROTEIN (NIP)-encoding genes, NIP1;1 and NIP6;1, potentially involved in ARR1/12-mediated As(III) uptake and transport in Arabidopsis. By analyzing various combinations of arr and nip mutants, including high-order triple and quadruple mutants, we demonstrated that ARR1 and ARR12 redundantly function as negative regulators of As(III) tolerance by acting upstream of NIP1;1 and NIP6;1 to modulate their function in arsenic accumulation. ChIP-qPCR, EMSA, and transient dual-LUC reporter assays revealed that ARR1 and ARR12 transcriptionally activate the expression of NIP1;1 and NIP6;1 by directly binding to their promoters and upregulating their expression, leading to increased arsenic accumulation under As(III) stress. These findings collectively provide insights into cytokinin signaling-mediated plant adaptation to excessive As(III), contributing to the development of crops with low arsenic accumulation.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386822","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}
Leaf senescence is a complex developmental process influenced by abscisic acid (ABA) and reactive oxygen species (ROS), both of which increase during senescence. Understanding the regulatory mechanisms of leaf senescence can provide insights into enhancing crop yield and stress tolerance. In this study, we aimed to elucidate the role and mechanisms of rice (Oryza sativa) LONG GRAIN 3 (OsLG3), an APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factor, in orchestrating dark-induced leaf senescence. The transcript levels of OsLG3 gradually increased during dark-induced and natural senescence. Transgenic plants overexpressing OsLG3 exhibited delayed senescence, whereas CRISPR/Cas9-mediated oslg3 mutants exhibited accelerated leaf senescence. OsLG3 overexpression suppressed senescence-induced ABA signaling by downregulating OsABF4 (an ABA-signaling-related gene) and reduced ROS accumulation by enhancing catalase activity through upregulation of OsCATC. In vivo and in vitro binding assays demonstrated that OsLG3 downregulated OsABF4 and upregulated OsCATC by binding directly to their promoter regions. These results demonstrate the critical role of OsLG3 in fine-tuning leaf senescence progression by suppressing ABA-mediated signaling while simultaneously activating ROS-scavenging mechanisms. These findings suggest that OsLG3 could be targeted to enhance crop resilience and longevity.
{"title":"RICE LONG GRAIN 3 delays dark-induced senescence by downregulating abscisic acid signaling and upregulating reactive oxygen species scavenging activity.","authors":"Chaemyeong Lim, Kiyoon Kang, Jisun Lim, Haeun Lee, Sung-Hwan Cho, Nam-Chon Paek","doi":"10.1111/tpj.17061","DOIUrl":"https://doi.org/10.1111/tpj.17061","url":null,"abstract":"<p><p>Leaf senescence is a complex developmental process influenced by abscisic acid (ABA) and reactive oxygen species (ROS), both of which increase during senescence. Understanding the regulatory mechanisms of leaf senescence can provide insights into enhancing crop yield and stress tolerance. In this study, we aimed to elucidate the role and mechanisms of rice (Oryza sativa) LONG GRAIN 3 (OsLG3), an APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factor, in orchestrating dark-induced leaf senescence. The transcript levels of OsLG3 gradually increased during dark-induced and natural senescence. Transgenic plants overexpressing OsLG3 exhibited delayed senescence, whereas CRISPR/Cas9-mediated oslg3 mutants exhibited accelerated leaf senescence. OsLG3 overexpression suppressed senescence-induced ABA signaling by downregulating OsABF4 (an ABA-signaling-related gene) and reduced ROS accumulation by enhancing catalase activity through upregulation of OsCATC. In vivo and in vitro binding assays demonstrated that OsLG3 downregulated OsABF4 and upregulated OsCATC by binding directly to their promoter regions. These results demonstrate the critical role of OsLG3 in fine-tuning leaf senescence progression by suppressing ABA-mediated signaling while simultaneously activating ROS-scavenging mechanisms. These findings suggest that OsLG3 could be targeted to enhance crop resilience and longevity.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386727","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}
Fangyue Zhang, Joel A Biederman, Nathan A Pierce, Daniel L Potts, Sasha C Reed, William K Smith
In the semi-arid grasslands of the southwest United States, annual precipitation is divided between warm-season (July-September) convective precipitation and cool-season (December-March) frontal storms. While evidence suggests shifts in precipitation seasonal distribution, there is a poor understanding of the ecosystem carbon flux responses to cool-season precipitation and the potential legacy effects on subsequent warm-season carbon fluxes. Results from a two-year experiment with three cool-season precipitation treatments (dry, received 5th percentile cool-season total precipitation; normal, 50th; wet, 95th) and constant warm-season precipitation illustrate the direct and legacy effects on carbon fluxes, but in opposing ways. In wet cool-season plots, gross primary productivity (GPP) and ecosystem respiration (ER) were 103% and 127% higher than in normal cool-season plots. In dry cool-season plots, GPP and ER were 47% and 85% lower compared to normal cool-season plots. Unexpectedly, we found a positive legacy effect of the dry cool-season treatment on warm-season carbon flux, resulting in a significant increase in both GPP and ER in the subsequent warm season, compared to normal cool-season plots. Our results reveal positive legacy effects of cool-season drought on warm-season carbon fluxes and highlight the importance of the relatively under-studied cool-growing season and its direct/indirect impact on the ecosystem carbon budget.
{"title":"Direct and Legacy Effects of Varying Cool-Season Precipitation Totals on Ecosystem Carbon Flux in a Semi-Arid Mixed Grassland.","authors":"Fangyue Zhang, Joel A Biederman, Nathan A Pierce, Daniel L Potts, Sasha C Reed, William K Smith","doi":"10.1111/pce.15175","DOIUrl":"https://doi.org/10.1111/pce.15175","url":null,"abstract":"<p><p>In the semi-arid grasslands of the southwest United States, annual precipitation is divided between warm-season (July-September) convective precipitation and cool-season (December-March) frontal storms. While evidence suggests shifts in precipitation seasonal distribution, there is a poor understanding of the ecosystem carbon flux responses to cool-season precipitation and the potential legacy effects on subsequent warm-season carbon fluxes. Results from a two-year experiment with three cool-season precipitation treatments (dry, received 5th percentile cool-season total precipitation; normal, 50th; wet, 95th) and constant warm-season precipitation illustrate the direct and legacy effects on carbon fluxes, but in opposing ways. In wet cool-season plots, gross primary productivity (GPP) and ecosystem respiration (ER) were 103% and 127% higher than in normal cool-season plots. In dry cool-season plots, GPP and ER were 47% and 85% lower compared to normal cool-season plots. Unexpectedly, we found a positive legacy effect of the dry cool-season treatment on warm-season carbon flux, resulting in a significant increase in both GPP and ER in the subsequent warm season, compared to normal cool-season plots. Our results reveal positive legacy effects of cool-season drought on warm-season carbon fluxes and highlight the importance of the relatively under-studied cool-growing season and its direct/indirect impact on the ecosystem carbon budget.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386802","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}
You-Wei Zuo, Miao-Hua Quan, Guang-Hua Liu, Xiao Zhang, Na-Na Long, Shi-Qi You, Yang Peng, Hong-Ping Deng
Lycoris aurea, celebrated for its visually striking flowers and significant medicinal value due to the presence of alkaloids such as lycorine and galanthamine, has intricate yet poorly understood regulatory mechanisms. This study provides a detailed examination of the transcriptomic, metabolomic and ecological dynamics of L. aurea, aiming to elucidate the underlying molecular mechanisms of alkaloid biosynthesis. Our comparative analysis across different ecological settings highlighted key genes involved in alkaloid biosynthesis, such as genes encoding aldehyde dehydrogenase and norbelladine 4'-O-methyltransferase, which were distinctively increased in the high alkaloids-producing group. We identified a total of 6871 differentially expressed genes and 915 metabolites involved in pathways like terpenoid backbone biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. Protein interaction network analysis revealed significant upregulation of photosynthesis, photosystem and photosynthetic membrane pathways in the alkaloids-producing region. Furthermore, our research delineated the interactions among soil microbial communities, genes and plant and soil biochemical properties, noting that bacterial populations correlate with soil properties that favour the activation of metabolic pathways essential for alkaloid production. Collectively, this study advances our understanding of the genetic and metabolic alkaloid biosynthesis pathways in L. aurea, shedding light on the complex interactions that govern alkaloid production.
{"title":"Multi-Omics Analysis Reveals Molecular Responses of Alkaloid Content Variations in Lycoris aurea Across Different Locations.","authors":"You-Wei Zuo, Miao-Hua Quan, Guang-Hua Liu, Xiao Zhang, Na-Na Long, Shi-Qi You, Yang Peng, Hong-Ping Deng","doi":"10.1111/pce.15187","DOIUrl":"https://doi.org/10.1111/pce.15187","url":null,"abstract":"<p><p>Lycoris aurea, celebrated for its visually striking flowers and significant medicinal value due to the presence of alkaloids such as lycorine and galanthamine, has intricate yet poorly understood regulatory mechanisms. This study provides a detailed examination of the transcriptomic, metabolomic and ecological dynamics of L. aurea, aiming to elucidate the underlying molecular mechanisms of alkaloid biosynthesis. Our comparative analysis across different ecological settings highlighted key genes involved in alkaloid biosynthesis, such as genes encoding aldehyde dehydrogenase and norbelladine 4'-O-methyltransferase, which were distinctively increased in the high alkaloids-producing group. We identified a total of 6871 differentially expressed genes and 915 metabolites involved in pathways like terpenoid backbone biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. Protein interaction network analysis revealed significant upregulation of photosynthesis, photosystem and photosynthetic membrane pathways in the alkaloids-producing region. Furthermore, our research delineated the interactions among soil microbial communities, genes and plant and soil biochemical properties, noting that bacterial populations correlate with soil properties that favour the activation of metabolic pathways essential for alkaloid production. Collectively, this study advances our understanding of the genetic and metabolic alkaloid biosynthesis pathways in L. aurea, shedding light on the complex interactions that govern alkaloid production.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379608","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}
Kexin Ning, Xuezhi Li, Jin Yan, Junjie Liu, Zhihua Gao, Wenqiang Tang, Yu Sun
Pollen development and germination are critical for successful generation of offspring in plants, yet they are highly susceptible to heat stress (HS). However, the molecular mechanism underlying this process has not been fully elucidated. In this study, we highlight the essential roles of two mRNA capping enzymes, named Arabidopsis mRNA capping phosphatase (ARCP) 1 and 2, in regulating male and female gamete development. The transmission efficiencies of gametes carrying arcp1 arcp2 from arcp1+/- arcp2-/- and arcp1-/- arcp2+/- mutants are 30% and zero, respectively. These mutants exhibited a significant increase in misshaped pollen, with germination rates approximately half of those in wild type. ARCP1/2 exhibit RNA triphosphatase and RNA guanylyltransferase activities, which are required for proper pollen development. Through RNA-seq analysis, genes involved in pollen development/germination and HS response were identified as downregulated genes in pollen from arcp1+/- arcp2-/- mutant. Furthermore, ARCP2 protein is degraded under HS condition, and inducing the expression of ARCP2 can increase the pollen germination rate under elevated temperature. We propose that HS triggers the degradation of mRNA capping enzymes, which in turn disrupts the transcriptome that required for pollen development and pollen germination and ultimately leads to male sterility.
{"title":"Heat Stress Inhibits Pollen Development by Degrading mRNA Capping Enzyme ARCP1 and ARCP2.","authors":"Kexin Ning, Xuezhi Li, Jin Yan, Junjie Liu, Zhihua Gao, Wenqiang Tang, Yu Sun","doi":"10.1111/pce.15178","DOIUrl":"https://doi.org/10.1111/pce.15178","url":null,"abstract":"<p><p>Pollen development and germination are critical for successful generation of offspring in plants, yet they are highly susceptible to heat stress (HS). However, the molecular mechanism underlying this process has not been fully elucidated. In this study, we highlight the essential roles of two mRNA capping enzymes, named Arabidopsis mRNA capping phosphatase (ARCP) 1 and 2, in regulating male and female gamete development. The transmission efficiencies of gametes carrying arcp1 arcp2 from arcp1<sup>+/-</sup> arcp2<sup>-/-</sup> and arcp1<sup>-/-</sup> arcp2<sup>+/-</sup> mutants are 30% and zero, respectively. These mutants exhibited a significant increase in misshaped pollen, with germination rates approximately half of those in wild type. ARCP1/2 exhibit RNA triphosphatase and RNA guanylyltransferase activities, which are required for proper pollen development. Through RNA-seq analysis, genes involved in pollen development/germination and HS response were identified as downregulated genes in pollen from arcp1<sup>+/-</sup> arcp2<sup>-/-</sup> mutant. Furthermore, ARCP2 protein is degraded under HS condition, and inducing the expression of ARCP2 can increase the pollen germination rate under elevated temperature. We propose that HS triggers the degradation of mRNA capping enzymes, which in turn disrupts the transcriptome that required for pollen development and pollen germination and ultimately leads to male sterility.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379607","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}
Hushuai Nie, Nan Zhao, Bin Li, Kaiyun Jiang, Huijing Li, Jingrou Zhang, Anhui Guo, Jinping Hua
Long non-coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species-specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus-induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682-PAS2-KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long-chain fatty acids.
{"title":"Evolutionary comparison of lncRNAs in four cotton species and functional identification of LncR4682-PAS2-KCS19 module in fiber elongation.","authors":"Hushuai Nie, Nan Zhao, Bin Li, Kaiyun Jiang, Huijing Li, Jingrou Zhang, Anhui Guo, Jinping Hua","doi":"10.1111/tpj.17058","DOIUrl":"https://doi.org/10.1111/tpj.17058","url":null,"abstract":"<p><p>Long non-coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species-specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus-induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682-PAS2-KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long-chain fatty acids.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386824","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 : 2024-10-07DOI: 10.1007/s00249-024-01723-x
Ecren Uzun Yaylacı
This study aimed to calculate the effect of nanopatterns' peak sharpness, width, and spacing parameters on P. aeruginosa and S. aureus cell walls by artificial neural network and finite element analysis. Elastic and creep deformation models of bacteria were developed in silico. Maximum deformation, maximum stress, and maximum strain values of the cell walls were calculated. According to the results, while the spacing of the nanopatterns is constant, it was determined that when their peaks were sharpened and their width decreased, maximum deformation, maximum stress, and maximum strain affecting the cell walls of both bacteria increased. When sharpness and width of the nano-patterns are kept constant and the spacing is increased, maximum deformation, maximum stress, and maximum strain in P. aeruginosa cell walls increase, but a decrease in S. aureus was observed. This study proves that changes in the geometric structures of nanopatterned surfaces can show different effects on different bacteria.
{"title":"Application of artificial neural network for the mechano-bactericidal effect of bioinspired nanopatterned surfaces.","authors":"Ecren Uzun Yaylacı","doi":"10.1007/s00249-024-01723-x","DOIUrl":"https://doi.org/10.1007/s00249-024-01723-x","url":null,"abstract":"<p><p>This study aimed to calculate the effect of nanopatterns' peak sharpness, width, and spacing parameters on P. aeruginosa and S. aureus cell walls by artificial neural network and finite element analysis. Elastic and creep deformation models of bacteria were developed in silico. Maximum deformation, maximum stress, and maximum strain values of the cell walls were calculated. According to the results, while the spacing of the nanopatterns is constant, it was determined that when their peaks were sharpened and their width decreased, maximum deformation, maximum stress, and maximum strain affecting the cell walls of both bacteria increased. When sharpness and width of the nano-patterns are kept constant and the spacing is increased, maximum deformation, maximum stress, and maximum strain in P. aeruginosa cell walls increase, but a decrease in S. aureus was observed. This study proves that changes in the geometric structures of nanopatterned surfaces can show different effects on different bacteria.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mangrove plants, which have evolved to inhabit tidal flats, may adjust their physiological and morphological traits to optimize their growth in saline habitats. Furthermore, the confined distribution of mangroves within warm regions suggests that warm temperature is advantageous to their growth in saline environments. We analyzed growth, morphology and respiratory responses to moderate salinity and temperature in a mangrove species, Rhizophora stylosa. The growth of R. stylosa was accelerated in moderate salinity compared with its growth in fresh water. Under warm conditions, the increased growth is accompanied by increased specific leaf area (SLA) and specific root length. Low temperature resulted in a low relative growth rate due to a low leaf area ratio and small SLA, regardless of salinity. Salinity lowered the ratio of the amounts of alternative oxidase to cytochrome c oxidase in the mitochondrial respiratory chain in leaves. Salinity enhanced the leaf respiration rate for maintenance, but under warm conditions this enhancement was compensated by a low leaf respiration rate for growth. In contrast, salinity enhanced overall leaf respiration rates at low temperature. Our results indicate that under moderate saline conditions R. stylosa leaves require warm temperatures to grow with a high rate of resource acquisition without enhancing respiratory cost.
红树植物进化为滩涂栖息植物,可能会调整其生理和形态特征,以优化其在盐碱生境中的生长。此外,红树林在温暖地区的局限性分布表明,温暖的温度有利于它们在盐碱环境中生长。我们分析了一种红树林物种--Rhizophora stylosa的生长、形态和呼吸对适度盐度和温度的反应。与在淡水中的生长相比,R. stylosa 在中等盐度下的生长速度加快。在温暖条件下,生长速度加快的同时,比叶面积(SLA)和比根长也增加了。无论盐度如何,低温都会导致叶面积比率低和比叶面积小,从而导致相对生长率低。盐度降低了叶片线粒体呼吸链中替代氧化酶与细胞色素 c 氧化酶的数量比。盐度提高了叶片维持的呼吸速率,但在温暖条件下,这种提高被叶片生长的低呼吸速率所补偿。相反,在低温条件下,盐度提高了叶片的整体呼吸速率。我们的研究结果表明,在中度盐度条件下,花叶蓟马叶片需要温暖的温度才能以较高的资源获取率生长,而不会增加呼吸成本。
{"title":"Growth, Morphology and Respiratory Cost Responses to Salinity in the Mangrove Plant Rhizophora Stylosa Depend on Growth Temperature.","authors":"Tomomi Inoue, Tomoko Fujimura, Ko Noguchi","doi":"10.1111/pce.15184","DOIUrl":"https://doi.org/10.1111/pce.15184","url":null,"abstract":"<p><p>Mangrove plants, which have evolved to inhabit tidal flats, may adjust their physiological and morphological traits to optimize their growth in saline habitats. Furthermore, the confined distribution of mangroves within warm regions suggests that warm temperature is advantageous to their growth in saline environments. We analyzed growth, morphology and respiratory responses to moderate salinity and temperature in a mangrove species, Rhizophora stylosa. The growth of R. stylosa was accelerated in moderate salinity compared with its growth in fresh water. Under warm conditions, the increased growth is accompanied by increased specific leaf area (SLA) and specific root length. Low temperature resulted in a low relative growth rate due to a low leaf area ratio and small SLA, regardless of salinity. Salinity lowered the ratio of the amounts of alternative oxidase to cytochrome c oxidase in the mitochondrial respiratory chain in leaves. Salinity enhanced the leaf respiration rate for maintenance, but under warm conditions this enhancement was compensated by a low leaf respiration rate for growth. In contrast, salinity enhanced overall leaf respiration rates at low temperature. Our results indicate that under moderate saline conditions R. stylosa leaves require warm temperatures to grow with a high rate of resource acquisition without enhancing respiratory cost.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386803","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}
Wenwen Liu, Shiyao Xu, Chenggang Ou, Xing Liu, Feiyun Zhuang, Xing Wang Deng
Carrot (Daucus carota) is one of the most popular and nutritious vegetable crops worldwide. However, significant yield losses occur every year due to leaf blight, a disease caused by a fungal pathogen (Alternaria dauci). Past research on resistance to leaf blight disease in carrots has been slow because of the low-quality genome assemblies of both carrot and the pathogen. Here, we report the greatly improved assemblies and annotations of telomere-to-telomere (T2T) reference genomes of carrot DH13M14 (451.04 Mb) and A. dauci A2016 (34.91 Mb). Compared with the previous carrot genome versions, our assembly featured notable improvements in genome size, continuity, and completeness of centromeres and telomeres. In addition, we generated a time course transcriptomic atlas during the infection of carrots by A. dauci and captured their dynamic gene expression reprogramming during the interaction process. During infection, A. dauci genes encoding effectors and enzymes responsible for the degradation of plant cell wall components, e.g., cellulose and pectin, were identified, which appeared to increase pathogenic ability through upregulation. In carrot, the coordinated gene expression of components of pattern- and effector-triggered immunity (PTI and ETI) in response to A. dauci attack was characterized. The biosynthesis or signal transduction of plant hormones, including JA, SA, and ethylene, was also involved in the carrot response to A. dauci. This work provides a foundation for understanding A. dauci pathogenic progression and carrot defense mechanisms to improve carrot resistance to leaf blight disease. The Carrot Database (CDB) developed also provides a useful resource for the carrot community.
胡萝卜(Daucus carota)是全世界最受欢迎、最有营养的蔬菜作物之一。然而,由真菌病原体(Alternaria dauci)引起的叶枯病每年都会造成巨大的产量损失。由于胡萝卜和病原体的基因组组装质量较低,过去对胡萝卜抗叶枯病的研究进展缓慢。在此,我们报告了胡萝卜 DH13M14(451.04 Mb)和 A. dauci A2016(34.91 Mb)的端粒到端粒(T2T)参考基因组的组装和注释的重大改进。与之前的胡萝卜基因组版本相比,我们的组装在基因组大小、连续性以及中心粒和端粒的完整性方面都有显著改进。此外,我们还生成了胡萝卜被杜氏酵母菌感染期间的转录组时间进程图谱,并捕捉了其在相互作用过程中的动态基因表达重编程。在感染过程中,发现了负责降解植物细胞壁成分(如纤维素和果胶)的 A. dauci 基因编码效应因子和酶,这些基因似乎通过上调提高了致病能力。在胡萝卜中,研究人员确定了模式触发免疫和效应触发免疫(PTI 和 ETI)成分的协调基因表达,以应对 A. dauci 的攻击。植物激素(包括 JA、SA 和乙烯)的生物合成或信号转导也参与了胡萝卜对 A. dauci 的反应。这项工作为了解 A. dauci 的致病过程和胡萝卜的防御机制,从而提高胡萝卜对叶枯病的抗性奠定了基础。开发的胡萝卜数据库(CDB)也为胡萝卜界提供了有用的资源。
{"title":"T2T genomes of carrot and Alternaria dauci and their utility for understanding host-pathogen interactions during carrot leaf blight disease.","authors":"Wenwen Liu, Shiyao Xu, Chenggang Ou, Xing Liu, Feiyun Zhuang, Xing Wang Deng","doi":"10.1111/tpj.17049","DOIUrl":"https://doi.org/10.1111/tpj.17049","url":null,"abstract":"<p><p>Carrot (Daucus carota) is one of the most popular and nutritious vegetable crops worldwide. However, significant yield losses occur every year due to leaf blight, a disease caused by a fungal pathogen (Alternaria dauci). Past research on resistance to leaf blight disease in carrots has been slow because of the low-quality genome assemblies of both carrot and the pathogen. Here, we report the greatly improved assemblies and annotations of telomere-to-telomere (T2T) reference genomes of carrot DH13M14 (451.04 Mb) and A. dauci A2016 (34.91 Mb). Compared with the previous carrot genome versions, our assembly featured notable improvements in genome size, continuity, and completeness of centromeres and telomeres. In addition, we generated a time course transcriptomic atlas during the infection of carrots by A. dauci and captured their dynamic gene expression reprogramming during the interaction process. During infection, A. dauci genes encoding effectors and enzymes responsible for the degradation of plant cell wall components, e.g., cellulose and pectin, were identified, which appeared to increase pathogenic ability through upregulation. In carrot, the coordinated gene expression of components of pattern- and effector-triggered immunity (PTI and ETI) in response to A. dauci attack was characterized. The biosynthesis or signal transduction of plant hormones, including JA, SA, and ethylene, was also involved in the carrot response to A. dauci. This work provides a foundation for understanding A. dauci pathogenic progression and carrot defense mechanisms to improve carrot resistance to leaf blight disease. The Carrot Database (CDB) developed also provides a useful resource for the carrot community.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386728","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}
Flowering time is a key agronomic trait that directly affects soybean yield. Both APETALA1 (AP1) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) regulate flowering time in soybean, but their genetic and regulatory relationships have not been clarified. Here, we report that AP1c physically interacted with two SOC1 proteins, SOC1a and SOC1b, and that these SOC1s upregulated the expression of AP1c, promoting flowering. Moreover, AP1c repressed the expression of the SOC1s by directly binding to their promoters, thus preventing plants from flowering too early. These findings indicate that AP1c and SOC1s form a regulatory feedback loop that regulates flowering time. Importantly, we identified an exceptional allele, AP1cG, that was selected for during soybean domestication and promotes the early-flowering phenotype in cultivated soybean. Collectively, our work identifies a previously unknown allelic combination potentially useful for both classical and molecular soybean breeding.
开花时间是直接影响大豆产量的关键农艺性状。APETALA1(AP1)和SUPPRESSOR OF OVEREXPRESSION OF CO 1(SOC1)都调控大豆的花期,但它们之间的遗传和调控关系尚未明确。在这里,我们报告了 AP1c 与两个 SOC1 蛋白(SOC1a 和 SOC1b)的物理相互作用,这些 SOC1 上调 AP1c 的表达,促进开花。此外,AP1c 通过直接与 SOC1s 启动子结合来抑制它们的表达,从而防止植物过早开花。这些发现表明,AP1c 和 SOC1s 形成了一个调节开花时间的反馈回路。重要的是,我们发现了一个在大豆驯化过程中被选择的特殊等位基因 AP1cG,它能促进栽培大豆的早花表型。总之,我们的研究发现了一个以前未知的等位基因组合,它可能对传统大豆育种和分子大豆育种都有用。
{"title":"AP1c and SOC1 Form a Regulatory Feedback Loop to Regulate Flowering Time in Soybean.","authors":"Haiyang Li, Chunmei Liao, Hui Yang, Lingping Kong, Shuangrong Liu, Jin Wei, Haili Chen, Xiaohui Zhao, Baohui Liu, Fanjiang Kong, Liyu Chen","doi":"10.1111/pce.15190","DOIUrl":"https://doi.org/10.1111/pce.15190","url":null,"abstract":"<p><p>Flowering time is a key agronomic trait that directly affects soybean yield. Both APETALA1 (AP1) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) regulate flowering time in soybean, but their genetic and regulatory relationships have not been clarified. Here, we report that AP1c physically interacted with two SOC1 proteins, SOC1a and SOC1b, and that these SOC1s upregulated the expression of AP1c, promoting flowering. Moreover, AP1c repressed the expression of the SOC1s by directly binding to their promoters, thus preventing plants from flowering too early. These findings indicate that AP1c and SOC1s form a regulatory feedback loop that regulates flowering time. Importantly, we identified an exceptional allele, AP1c<sup>G</sup>, that was selected for during soybean domestication and promotes the early-flowering phenotype in cultivated soybean. Collectively, our work identifies a previously unknown allelic combination potentially useful for both classical and molecular soybean breeding.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379605","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}