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The COP1W467 tryptophan residue in the WD40 domain is essential for light- and temperature-mediated hypocotyl growth and flowering in Arabidopsis
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70051
Bidhan Chandra Malakar, Cristian M. Escudero, Vishmita Sethi, Gouranga Upadhyaya, Sreeramaiah N. Gangappa, Javier F. Botto

COP1 is the essential protein that integrates various environmental and hormonal cues to control plant growth and development at multiple levels. COP1 is a RING-finger-type E3 ubiquitin ligase that acts as a potent repressor of photomorphogenesis and flowering by targeting numerous substrates for ubiquitination and promoting their proteolysis via the 26S proteasome system. The WD40 repeat domain with conserved amino acid residues was shown to be essential for interacting with its targets. However, the role of these amino acids in regulating hypocotyl growth and flowering in response to varying light and temperatures remains unknown. Here, we show that tryptophan amino acid at the position 467 residue (COP1W467) is relevant in mediating the interaction with its targets to regulate the COP1-mediated proteolysis. The COP1W467 plays a critical role in inducing growth responses in shade light by interacting and degrading HY5, a crucial negative regulator of shade-avoidance response (SAR). Moreover, COP1W467 integrates warm ambient temperature signals to promote hypocotyl growth by increasing PIF4 and decreasing HY5 protein stability. Finally, we found that COP1W467 is important in inhibiting flowering under a short-day photoperiod, likely through interacting with CO for degradation. Together, this study highlights that the COP1W467 residue is essential to regulate seedling photomorphogenesis, SAR, thermomorphogenesis and flowering for the fine adjustment of plant growth and development under dynamic light and temperature conditions.

{"title":"The COP1W467 tryptophan residue in the WD40 domain is essential for light- and temperature-mediated hypocotyl growth and flowering in Arabidopsis","authors":"Bidhan Chandra Malakar,&nbsp;Cristian M. Escudero,&nbsp;Vishmita Sethi,&nbsp;Gouranga Upadhyaya,&nbsp;Sreeramaiah N. Gangappa,&nbsp;Javier F. Botto","doi":"10.1111/tpj.70051","DOIUrl":"https://doi.org/10.1111/tpj.70051","url":null,"abstract":"<div>\u0000 \u0000 <p>COP1 is the essential protein that integrates various environmental and hormonal cues to control plant growth and development at multiple levels. COP1 is a RING-finger-type E3 ubiquitin ligase that acts as a potent repressor of photomorphogenesis and flowering by targeting numerous substrates for ubiquitination and promoting their proteolysis via the 26S proteasome system. The WD40 repeat domain with conserved amino acid residues was shown to be essential for interacting with its targets. However, the role of these amino acids in regulating hypocotyl growth and flowering in response to varying light and temperatures remains unknown. Here, we show that tryptophan amino acid at the position 467 residue (COP1<sup>W467</sup>) is relevant in mediating the interaction with its targets to regulate the COP1-mediated proteolysis. The COP1<sup>W467</sup> plays a critical role in inducing growth responses in shade light by interacting and degrading HY5, a crucial negative regulator of shade-avoidance response (SAR). Moreover, COP1<sup>W467</sup> integrates warm ambient temperature signals to promote hypocotyl growth by increasing PIF4 and decreasing HY5 protein stability. Finally, we found that COP1<sup>W467</sup> is important in inhibiting flowering under a short-day photoperiod, likely through interacting with CO for degradation. Together, this study highlights that the COP1<sup>W467</sup> residue is essential to regulate seedling photomorphogenesis, SAR, thermomorphogenesis and flowering for the fine adjustment of plant growth and development under dynamic light and temperature conditions.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481571","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
A self-amplifying NO-H2S loop mediates melatonin-induced CBF-responsive pathway and cold tolerance in watermelon
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70025
Yanliang Guo, Jiayue Li, Lingling Liu, Jiahe Liu, Wanbang Yang, Yi Chen, Chao Li, Li Yuan, Chunhua Wei, Jianxiang Ma, Yong Zhang, Jianqiang Yang, Feishi Luan, Xian Zhang, Hao Li

Melatonin is a pivotal bioactive molecule that enhances plant cold stress tolerance, but the precise mechanisms remain enigmatic. Here, we have discovered that overexpressing melatonin biosynthetic gene ClCOMT1 or applying exogenous melatonin activates the C-repeat binding factor (CBF)-responsive pathway and enhances watermelon cold tolerance. This enhancement is accompanied by elevated levels of nitric oxide (NO) and hydrogen sulfide (H2S), along with upregulation of nitrate reductase 1 (ClNR1) and L-cysteine desulfhydrase (ClLCD) genes involved in NO and H2S generation respectively. Conversely, knockout of ClCOMT1 exhibits contrasting effects compared to its overexpression. Furthermore, application of sodium nitroprusside (SNP, a NO donor) and NaHS (a H2S donor) promotes the accumulation of H2S and NO, respectively, activating the CBF pathway and enhancing cold tolerance. However, knockout of ClNR1 or ClLCD abolished melatonin-induced H2S or NO production respectively and abrogated melatonin-induced CBF pathway and cold tolerance. Conversely, supplementation with SNP and NaHS restored the diminished cold response caused by ClCOMT1 deletion. Additionally, deletion of either ClNR1 or ClLCD eliminated NaHS- or SNP-induced cold response, respectively. Overall, these findings suggest a reciprocal positive-regulatory loop between ClNR1-mediated NO and ClLCD-mediated H2S, which plays a crucial role in mediating the melatonin-induced enhancement of cold tolerance.

{"title":"A self-amplifying NO-H2S loop mediates melatonin-induced CBF-responsive pathway and cold tolerance in watermelon","authors":"Yanliang Guo,&nbsp;Jiayue Li,&nbsp;Lingling Liu,&nbsp;Jiahe Liu,&nbsp;Wanbang Yang,&nbsp;Yi Chen,&nbsp;Chao Li,&nbsp;Li Yuan,&nbsp;Chunhua Wei,&nbsp;Jianxiang Ma,&nbsp;Yong Zhang,&nbsp;Jianqiang Yang,&nbsp;Feishi Luan,&nbsp;Xian Zhang,&nbsp;Hao Li","doi":"10.1111/tpj.70025","DOIUrl":"https://doi.org/10.1111/tpj.70025","url":null,"abstract":"<div>\u0000 \u0000 <p>Melatonin is a pivotal bioactive molecule that enhances plant cold stress tolerance, but the precise mechanisms remain enigmatic. Here, we have discovered that overexpressing melatonin biosynthetic gene <i>ClCOMT1</i> or applying exogenous melatonin activates the C-repeat binding factor (CBF)-responsive pathway and enhances watermelon cold tolerance. This enhancement is accompanied by elevated levels of nitric oxide (NO) and hydrogen sulfide (H<sub>2</sub>S), along with upregulation of <i>nitrate reductase 1</i> (<i>ClNR1</i>) and <i>L-cysteine desulfhydrase</i> (<i>ClLCD</i>) genes involved in NO and H<sub>2</sub>S generation respectively. Conversely, knockout of <i>ClCOMT1</i> exhibits contrasting effects compared to its overexpression. Furthermore, application of sodium nitroprusside (SNP, a NO donor) and NaHS (a H<sub>2</sub>S donor) promotes the accumulation of H<sub>2</sub>S and NO, respectively, activating the CBF pathway and enhancing cold tolerance. However, knockout of <i>ClNR1</i> or <i>ClLCD</i> abolished melatonin-induced H<sub>2</sub>S or NO production respectively and abrogated melatonin-induced CBF pathway and cold tolerance. Conversely, supplementation with SNP and NaHS restored the diminished cold response caused by <i>ClCOMT1</i> deletion. Additionally, deletion of either <i>ClNR1</i> or <i>ClLCD</i> eliminated NaHS- or SNP-induced cold response, respectively. Overall, these findings suggest a reciprocal positive-regulatory loop between <i>ClNR1</i>-mediated NO and <i>ClLCD</i>-mediated H<sub>2</sub>S, which plays a crucial role in mediating the melatonin-induced enhancement of cold tolerance.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481575","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 mixed auto-/allooctoploid genome of Japanese knotweed (Reynoutria japonica) provides insights into its polyploid origin and invasiveness
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70005
Fanhong Wang, Minghao Li, Ze Liu, Wei Li, Qiang He, Longsheng Xing, Yao Xiao, Meijia Wang, Yu Wang, Cailian Du, Hongyu Zhang, Yue Zhou, Huilong Du

Reynoutria japonica Houtt. (Polygonaceae), a traditional Chinese medicine, is one of the top 100 most destructive invasive species worldwide due to its aggressive growth and strong adaptability. Here, we report an 8.04 Gb chromosome-scale assembly of R. japonica with 88 chromosomes across eight homologous sets. Through a combined phylogenetic and genomic analysis, we demonstrate that R. japonica is a mixed auto-/allooctoploid (AAAABBBB). Subgenome A (SubA) exhibited a close phylogenetic relationship with the related species Fallopia multiflora. We also unveiled the origin and evolutionary history of octoploid R. japonica based on resequencing data from Reynoutria species with different ploidy. Comparative genomics analysis revealed the genetic basis of R. japonica's invasivity and adaptability. The auxin response factor (ARF) gene family was significantly expanded in R. japonica, and these genes were highly expressed in rhizomes. We also investigated the collaboration and differentiation of the duplicated genes resulting from auto- and allo-polyploidization at the genomic variation, gene family evolution, and gene expression levels in R. japonica. Transcriptomic analysis of stem internodes and apices at different developmental stages revealed that the octuplication and significant expansion of the SAUR19 and SAUR63 subfamilies due to tandem replication in SubA, and the high expression of these genes in stems, likely contribute to the rapid growth of R. japonica. Our study provides important clues into adaptive evolution and polyploidy dominant traits in invasive plants, and will also provide important guidance for the breeding of polyploid crops.

{"title":"The mixed auto-/allooctoploid genome of Japanese knotweed (Reynoutria japonica) provides insights into its polyploid origin and invasiveness","authors":"Fanhong Wang,&nbsp;Minghao Li,&nbsp;Ze Liu,&nbsp;Wei Li,&nbsp;Qiang He,&nbsp;Longsheng Xing,&nbsp;Yao Xiao,&nbsp;Meijia Wang,&nbsp;Yu Wang,&nbsp;Cailian Du,&nbsp;Hongyu Zhang,&nbsp;Yue Zhou,&nbsp;Huilong Du","doi":"10.1111/tpj.70005","DOIUrl":"https://doi.org/10.1111/tpj.70005","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Reynoutria japonica</i> Houtt. (Polygonaceae), a traditional Chinese medicine, is one of the top 100 most destructive invasive species worldwide due to its aggressive growth and strong adaptability. Here, we report an 8.04 Gb chromosome-scale assembly of <i>R. japonica</i> with 88 chromosomes across eight homologous sets. Through a combined phylogenetic and genomic analysis, we demonstrate that <i>R. japonica</i> is a mixed auto-/allooctoploid (AAAABBBB). Subgenome A (SubA) exhibited a close phylogenetic relationship with the related species <i>Fallopia multiflora</i>. We also unveiled the origin and evolutionary history of octoploid <i>R. japonica</i> based on resequencing data from <i>Reynoutria</i> species with different ploidy. Comparative genomics analysis revealed the genetic basis of <i>R. japonica</i>'s invasivity and adaptability. The <i>auxin response factor</i> (<i>ARF</i>) gene family was significantly expanded in <i>R. japonica</i>, and these genes were highly expressed in rhizomes. We also investigated the collaboration and differentiation of the duplicated genes resulting from auto- and allo-polyploidization at the genomic variation, gene family evolution, and gene expression levels in <i>R. japonica</i>. Transcriptomic analysis of stem internodes and apices at different developmental stages revealed that the octuplication and significant expansion of the SAUR19 and SAUR63 subfamilies due to tandem replication in SubA, and the high expression of these genes in stems, likely contribute to the rapid growth of <i>R. japonica</i>. Our study provides important clues into adaptive evolution and polyploidy dominant traits in invasive plants, and will also provide important guidance for the breeding of polyploid crops.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481429","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
Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70027
Damilola A. Raiyemo, Jacob S. Montgomery, Luan Cutti, Fatemeh Abdollahi, Victor Llaca, Kevin Fengler, Alexander J. Lopez, Sarah Morran, Christopher A. Saski, David R. Nelson, Eric L. Patterson, Todd A. Gaines, Patrick J. Tranel

Amaranthus palmeri (Palmer amaranth), Amaranthus retroflexus (redroot pigweed), and Amaranthus hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as “pigweeds,” these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. The development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweeds. By combining the haplotype-resolved assembly of A. palmeri with existing restriction site-associated DNA sequencing data, we identified an approximately 2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed that two genes, RESTORER OF FERTILITY 1 (RF1) and TLC DOMAIN-CONTAINING PROTEIN (TLC), within the male-specific region were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in A. palmeri. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target-site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in A. palmeri, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in A. palmeri and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.

{"title":"Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region","authors":"Damilola A. Raiyemo,&nbsp;Jacob S. Montgomery,&nbsp;Luan Cutti,&nbsp;Fatemeh Abdollahi,&nbsp;Victor Llaca,&nbsp;Kevin Fengler,&nbsp;Alexander J. Lopez,&nbsp;Sarah Morran,&nbsp;Christopher A. Saski,&nbsp;David R. Nelson,&nbsp;Eric L. Patterson,&nbsp;Todd A. Gaines,&nbsp;Patrick J. Tranel","doi":"10.1111/tpj.70027","DOIUrl":"https://doi.org/10.1111/tpj.70027","url":null,"abstract":"<p><i>Amaranthus palmeri</i> (Palmer amaranth), <i>Amaranthus retroflexus</i> (redroot pigweed), and <i>Amaranthus hybridus</i> (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as “pigweeds,” these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. The development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweeds. By combining the haplotype-resolved assembly of <i>A. palmeri</i> with existing restriction site-associated DNA sequencing data, we identified an approximately 2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed that two genes, <i>RESTORER OF FERTILITY 1</i> (<i>RF1</i>) and <i>TLC DOMAIN-CONTAINING PROTEIN</i> (<i>TLC</i>), within the male-specific region were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in <i>A. palmeri</i>. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target-site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in <i>A. palmeri</i>, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in <i>A. palmeri</i> and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481577","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
Ubiquitin-mediated degradation of the inhibitor FvMYB1 and the activator FvBBX20 by FvCSN5 balances anthocyanin biosynthesis in strawberry fruit
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70021
Yuxin Nie, Yingying Lei, Hongbo Jiao, Zhuo Zhang, Jinxiang Yao, He Li, Hongyan Dai, Zhihong Zhang, Junxiang Zhang

Plant CSN5 is widely recognized as the subunit of the COP9 signalosome and CSN5 is mainly involved in plant growth and development, and tolerance to biotic and abiotic stresses. However, the molecular mechanism of CSN5 regulating anthocyanin biosynthesis in plants is still largely unknown. Here, we identified FvCSN5 from the woodland strawberry yeast two-hybrid library using the anthocyanin pathway inhibitor MYB1 as bait. We demonstrated the interaction of FvCSN5 and FvMYB1 by H2Y, Pull-down, LCI, and BiFC assays. FvCSN5 was expressed in all test tissues and localized in the nucleus and cytosol with self-activation activity. Stable overexpression of FvCSN5 in woodland strawberries reduced anthocyanin accumulation in fruits. The protein level of FvMYB1 greatly decreased in overexpressing FvCSN5 plants compared with wild-type plants. Protein degradation assay and MG-132 treatment (a proteasome inhibitor blocking 26S proteasome activity) revealed FvCSN5 degraded FvMYB1 through the ubiquitination pathway. In addition, FvCSN5 also interacted with the anthocyanin activator FvBBX20 and FvBBX20 could be degraded by FvCSN5. Moreover, transient expression analysis showed the expression of anthocyanin biosynthetic genes FvCHS and FvF3H was greatly increased and decreased when FvCSN5 was co-expressed with FvMYB1 and FvBBX20, respectively. These results indicate that FvMYB1-FvCSN5-FvBBX20 is a novel ternary complex that regulates anthocyanin biosynthesis by the ubiquitination pathway.

{"title":"Ubiquitin-mediated degradation of the inhibitor FvMYB1 and the activator FvBBX20 by FvCSN5 balances anthocyanin biosynthesis in strawberry fruit","authors":"Yuxin Nie,&nbsp;Yingying Lei,&nbsp;Hongbo Jiao,&nbsp;Zhuo Zhang,&nbsp;Jinxiang Yao,&nbsp;He Li,&nbsp;Hongyan Dai,&nbsp;Zhihong Zhang,&nbsp;Junxiang Zhang","doi":"10.1111/tpj.70021","DOIUrl":"https://doi.org/10.1111/tpj.70021","url":null,"abstract":"<div>\u0000 \u0000 <p>Plant CSN5 is widely recognized as the subunit of the COP9 signalosome and CSN5 is mainly involved in plant growth and development, and tolerance to biotic and abiotic stresses. However, the molecular mechanism of CSN5 regulating anthocyanin biosynthesis in plants is still largely unknown. Here, we identified FvCSN5 from the woodland strawberry yeast two-hybrid library using the anthocyanin pathway inhibitor MYB1 as bait. We demonstrated the interaction of FvCSN5 and FvMYB1 by H2Y, Pull-down, LCI, and BiFC assays. FvCSN5 was expressed in all test tissues and localized in the nucleus and cytosol with self-activation activity. Stable overexpression of <i>FvCSN5</i> in woodland strawberries reduced anthocyanin accumulation in fruits. The protein level of FvMYB1 greatly decreased in overexpressing <i>FvCSN5</i> plants compared with wild-type plants. Protein degradation assay and MG-132 treatment (a proteasome inhibitor blocking 26S proteasome activity) revealed FvCSN5 degraded FvMYB1 through the ubiquitination pathway. In addition, FvCSN5 also interacted with the anthocyanin activator FvBBX20 and FvBBX20 could be degraded by FvCSN5. Moreover, transient expression analysis showed the expression of anthocyanin biosynthetic genes <i>FvCHS</i> and <i>FvF3H</i> was greatly increased and decreased when FvCSN5 was co-expressed with FvMYB1 and FvBBX20, respectively. These results indicate that FvMYB1-FvCSN5-FvBBX20 is a novel ternary complex that regulates anthocyanin biosynthesis by the ubiquitination pathway.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481430","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
Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70012
Gabriele Usai, Tommaso Giordani, Alberto Vangelisti, Marco Castellacci, Samuel Simoni, Emanuele Bosi, Lucia Natali, Flavia Mascagni, Andrea Cavallini

In this study, we produced a haplotype-phased genome sequence of the fig tree (Ficus carica L.), a non-Rosaceae fruit tree model species, providing a systematic overview of the organization of a heterozygous diploid genome and, for the first time in a fruit tree, evidence of allelic expression direction-shifting among haplotypes. The genome was used for whole genome analysis of heterozygosis, allelic cytosine methylation, and expression profiles in peel and pulp fruit tissues. The two pseudo-haplotypes spanned approximately 355 and 346 Mbp, respectively, and 97% of the sequences were associated with 13 chromosome pairs of the fig tree. Overall, the methylation profile in peel and pulp tissues showed no variations between the homologous chromosomes. However, we detected differential DNA methylation within defined heterozygous allelic gene regions, particularly in upstream regions. Among 6768 heterozygous coding sequences identified, 4024 exhibited allele-specific expression, with approximately 18% specific to the peel and 14% to the pulp. Specifically, 2715 genes were consistent, with one allele always more expressed than the other in both peel and pulp. On the contrary, 22 allele-specific expressed genes switched allele expression among the fig fruit peel and pulp tissues, indicating evidence of overdominance and suggesting that the genome can express one of the two alleles higher or lower depending on developmental or environmental triggers. Notably, these genes were associated with key biological processes, including fruit maturation regulation, seed maturation, and stress response, highlighting their potential role in the plant's developmental and adaptive functions in view of gene editing-based breeding.

{"title":"Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit","authors":"Gabriele Usai,&nbsp;Tommaso Giordani,&nbsp;Alberto Vangelisti,&nbsp;Marco Castellacci,&nbsp;Samuel Simoni,&nbsp;Emanuele Bosi,&nbsp;Lucia Natali,&nbsp;Flavia Mascagni,&nbsp;Andrea Cavallini","doi":"10.1111/tpj.70012","DOIUrl":"https://doi.org/10.1111/tpj.70012","url":null,"abstract":"<p>In this study, we produced a haplotype-phased genome sequence of the fig tree (<i>Ficus carica</i> L.), a non-Rosaceae fruit tree model species, providing a systematic overview of the organization of a heterozygous diploid genome and, for the first time in a fruit tree, evidence of allelic expression direction-shifting among haplotypes. The genome was used for whole genome analysis of heterozygosis, allelic cytosine methylation, and expression profiles in peel and pulp fruit tissues. The two pseudo-haplotypes spanned approximately 355 and 346 Mbp, respectively, and 97% of the sequences were associated with 13 chromosome pairs of the fig tree. Overall, the methylation profile in peel and pulp tissues showed no variations between the homologous chromosomes. However, we detected differential DNA methylation within defined heterozygous allelic gene regions, particularly in upstream regions. Among 6768 heterozygous coding sequences identified, 4024 exhibited allele-specific expression, with approximately 18% specific to the peel and 14% to the pulp. Specifically, 2715 genes were consistent, with one allele always more expressed than the other in both peel and pulp. On the contrary, 22 allele-specific expressed genes switched allele expression among the fig fruit peel and pulp tissues, indicating evidence of overdominance and suggesting that the genome can express one of the two alleles higher or lower depending on developmental or environmental triggers. Notably, these genes were associated with key biological processes, including fruit maturation regulation, seed maturation, and stress response, highlighting their potential role in the plant's developmental and adaptive functions in view of gene editing-based breeding.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481569","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
Growth and survival strategies of oilseed rape (Brassica napus L.) leaves under potassium deficiency stress: trade-offs in potassium ion distribution between vacuoles and chloroplasts
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70009
Hehe Gu, Ziyao He, Zhifeng Lu, Shipeng Liao, Yangyang Zhang, Xiaokun Li, Rihuan Cong, Tao Ren, Jianwei Lu

Potassium (K) is a prevalent limiting factor in terrestrial ecosystems, with approximately one-eighth of the world's soils undergoing K+ deficiency stress. Upon encountering K+ deficiency stress, leaf area (LA) declines before the net photosynthetic rate (An). The sequential alterations fundamentally represent the adaptive trade-off between survival and growth in plants subjected to K+ deficiency stress. This trade-off is hypothesized to be linked to the differences in the subcellular distribution of limited K+ resources. Thus, the K+ distribution and apparent concentration in subcellular compartments, along with the LA and An characteristics of rapeseed leaves at various developmental stages and K+ supply conditions were quantified to elucidate the mechanisms by which subcellular K+ regulates leaf growth and survival. The results revealed that during the early stages of K+ deficiency, leaves actively downregulate growth to sustain normal physiological functions. This is primarily accomplished by lowering the K+ distribution and apparent concentration in vacuoles, restricting LA expansion, and enhancing K+ distribution to chloroplasts to ensure An. Prolonged K+ deficiency decreased the apparent K+ concentration in chloroplasts below the critical threshold (37.8 mm), disrupting chloroplast structure and function, impairing An, and ultimately threatening the survival of rapeseed. Hence, sustaining an adequate concentration of K+ within chloroplasts is crucial for preserving leaf photosynthetic efficiency and ensuring survival under K+ deficiency stress. In conclusion, under K+ deficiency stress, leaves regulate LA and An by trade-offs in the K+ distribution between vacuoles and chloroplasts to coordinate growth and survival.

{"title":"Growth and survival strategies of oilseed rape (Brassica napus L.) leaves under potassium deficiency stress: trade-offs in potassium ion distribution between vacuoles and chloroplasts","authors":"Hehe Gu,&nbsp;Ziyao He,&nbsp;Zhifeng Lu,&nbsp;Shipeng Liao,&nbsp;Yangyang Zhang,&nbsp;Xiaokun Li,&nbsp;Rihuan Cong,&nbsp;Tao Ren,&nbsp;Jianwei Lu","doi":"10.1111/tpj.70009","DOIUrl":"https://doi.org/10.1111/tpj.70009","url":null,"abstract":"<div>\u0000 \u0000 <p>Potassium (K) is a prevalent limiting factor in terrestrial ecosystems, with approximately one-eighth of the world's soils undergoing K<sup>+</sup> deficiency stress. Upon encountering K<sup>+</sup> deficiency stress, leaf area (LA) declines before the net photosynthetic rate (<i>A</i><sub>n</sub>). The sequential alterations fundamentally represent the adaptive trade-off between survival and growth in plants subjected to K<sup>+</sup> deficiency stress. This trade-off is hypothesized to be linked to the differences in the subcellular distribution of limited K<sup>+</sup> resources. Thus, the K<sup>+</sup> distribution and apparent concentration in subcellular compartments, along with the LA and <i>A</i><sub>n</sub> characteristics of rapeseed leaves at various developmental stages and K<sup>+</sup> supply conditions were quantified to elucidate the mechanisms by which subcellular K<sup>+</sup> regulates leaf growth and survival. The results revealed that during the early stages of K<sup>+</sup> deficiency, leaves actively downregulate growth to sustain normal physiological functions. This is primarily accomplished by lowering the K<sup>+</sup> distribution and apparent concentration in vacuoles, restricting LA expansion, and enhancing K<sup>+</sup> distribution to chloroplasts to ensure <i>A</i><sub>n</sub>. Prolonged K<sup>+</sup> deficiency decreased the apparent K<sup>+</sup> concentration in chloroplasts below the critical threshold (37.8 m<span>m</span>), disrupting chloroplast structure and function, impairing <i>A</i><sub>n</sub>, and ultimately threatening the survival of rapeseed. Hence, sustaining an adequate concentration of K<sup>+</sup> within chloroplasts is crucial for preserving leaf photosynthetic efficiency and ensuring survival under K<sup>+</sup> deficiency stress. In conclusion, under K<sup>+</sup> deficiency stress, leaves regulate LA and <i>A</i><sub>n</sub> by trade-offs in the K<sup>+</sup> distribution between vacuoles and chloroplasts to coordinate growth and survival.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481364","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
Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70011
Angela Ricono, Ella Ludwig, Anna L. Casto, Stevan Zorich, Joshua Sumner, Kevin Bird, Patrick P. Edger, Todd C. Mockler, Adrian D. Hegeman, Malia A. Gehan, Kathleen Greenham

Water availability is a major determinant of crop production, and rising temperatures from climate change are leading to more extreme droughts. To combat the effects of climate change on crop yields, we need to develop varieties that are more tolerant to water-limited conditions. We aimed to determine how diverse crop types (winter/spring oilseed, tuberous, and leafy) of the allopolyploid Brassica napus, a species that contains the economically important rapeseed oilseed crop, respond to prolonged water limitation. We exposed plants to an 80% reduction in water and assessed growth and color on a high-throughput phenotyping system over 4 weeks and ended the experiment with tissue collection for a time course transcriptomic study. We found an overall reduction in growth across cultivars but to varying degrees. Diel transcriptome analyses revealed significant accession-specific changes in time-of-day regulation of photosynthesis, carbohydrate metabolism, and sulfur metabolism. Interestingly, there was extensive variation in which homoeologs from the two parental subgenomes responded to water limitation across crop types that could be due to differences in regulatory regions in these allopolyploid lines. Follow-up experiments on select cultivars confirmed that plants maintained photosynthetic health during the prolonged water limitation while slowing growth. In two cultivars examined, we found significant time of day changes in levels of glucosinolates, sulfur- and nitrogen -rich specialized metabolites, consistent with the diel transcriptomic responses. These results suggest that these lines are adjusting their sulfur and nitrogen stores under water-limited conditions through distinct time of day regulation.

{"title":"Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus","authors":"Angela Ricono,&nbsp;Ella Ludwig,&nbsp;Anna L. Casto,&nbsp;Stevan Zorich,&nbsp;Joshua Sumner,&nbsp;Kevin Bird,&nbsp;Patrick P. Edger,&nbsp;Todd C. Mockler,&nbsp;Adrian D. Hegeman,&nbsp;Malia A. Gehan,&nbsp;Kathleen Greenham","doi":"10.1111/tpj.70011","DOIUrl":"https://doi.org/10.1111/tpj.70011","url":null,"abstract":"<p>Water availability is a major determinant of crop production, and rising temperatures from climate change are leading to more extreme droughts. To combat the effects of climate change on crop yields, we need to develop varieties that are more tolerant to water-limited conditions. We aimed to determine how diverse crop types (winter/spring oilseed, tuberous, and leafy) of the allopolyploid <i>Brassica napus</i>, a species that contains the economically important rapeseed oilseed crop, respond to prolonged water limitation. We exposed plants to an 80% reduction in water and assessed growth and color on a high-throughput phenotyping system over 4 weeks and ended the experiment with tissue collection for a time course transcriptomic study. We found an overall reduction in growth across cultivars but to varying degrees. Diel transcriptome analyses revealed significant accession-specific changes in time-of-day regulation of photosynthesis, carbohydrate metabolism, and sulfur metabolism. Interestingly, there was extensive variation in which homoeologs from the two parental subgenomes responded to water limitation across crop types that could be due to differences in regulatory regions in these allopolyploid lines. Follow-up experiments on select cultivars confirmed that plants maintained photosynthetic health during the prolonged water limitation while slowing growth. In two cultivars examined, we found significant time of day changes in levels of glucosinolates, sulfur- and nitrogen -rich specialized metabolites, consistent with the diel transcriptomic responses. These results suggest that these lines are adjusting their sulfur and nitrogen stores under water-limited conditions through distinct time of day regulation.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481570","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 thylakoid lumen Deg1 protease affects non-photochemical quenching via the levels of violaxanthin de-epoxidase and PsbS
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.17263
Elinor Aviv-Sharon, Laure D. Sultan, Leah Naveh, Meital Kupervaser, Ziv Reich, Dana Charuvi, Zach Adam

Non-photochemical quenching (NPQ), the dissipation of excess light energy as heat, has been long recognized as a major protective mechanism that minimizes the potential for oxidative damage to photosystem II (PSII) reaction centers. Two major positive contributors to NPQ are the carotenoid zeaxanthin, generated from violaxanthin by the enzyme violaxanthin de-epoxidase (VDE or NPQ1), and the thylakoid protein PsbS (NPQ4). The involvement of the lumenal Deg proteases in the repair of PSII from photoinhibition prompted us to further explore their possible role in other responses of Arabidopsis thaliana to high light. Here we show that upon exposure to high light, the single deg1 and the triple deg158 mutants display different levels and kinetics of NPQ, compared with the deg58 mutant and WT that behave alike. In response to high light, the two genotypes lacking Deg1 overaccumulate NPQ1 and NPQ4. After temporal inhibition of protein translation in vivo, the level of these two proteins in deg1 is higher than in WT. Together, the results suggest that Deg1 represents a new level of regulation of the NPQ process through adjusting the quantity of NPQ1 and NPQ4 proteins, probably through their proteolysis.

非光化学淬灭(NPQ)是指将多余的光能以热能的形式耗散,长期以来一直被认为是一种主要的保护机制,可将光系统 II(PSII)反应中心可能受到的氧化损伤降至最低。类胡萝卜素玉米黄质(由玉米黄质脱氧化酶(VDE 或 NPQ1)从玉米黄质生成)和类木质蛋白 PsbS(NPQ4)是 NPQ 的两大积极贡献者。腔内 Deg 蛋白酶参与修复 PSII 的光抑制作用,促使我们进一步探索它们在拟南芥对强光的其他反应中可能发挥的作用。在这里,我们发现在暴露于强光下时,单deg1和三deg158突变体与deg58突变体和WT相比,表现出不同的NPQ水平和动力学。在强光下,缺乏 Deg1 的两个基因型会过度积累 NPQ1 和 NPQ4。在体内暂时抑制蛋白质翻译后,deg1 中这两种蛋白质的水平高于 WT。这些结果表明,Deg1 可能通过蛋白水解作用,调节 NPQ1 和 NPQ4 蛋白的数量,从而代表了 NPQ 过程的一个新的调节水平。
{"title":"The thylakoid lumen Deg1 protease affects non-photochemical quenching via the levels of violaxanthin de-epoxidase and PsbS","authors":"Elinor Aviv-Sharon,&nbsp;Laure D. Sultan,&nbsp;Leah Naveh,&nbsp;Meital Kupervaser,&nbsp;Ziv Reich,&nbsp;Dana Charuvi,&nbsp;Zach Adam","doi":"10.1111/tpj.17263","DOIUrl":"https://doi.org/10.1111/tpj.17263","url":null,"abstract":"<p>Non-photochemical quenching (NPQ), the dissipation of excess light energy as heat, has been long recognized as a major protective mechanism that minimizes the potential for oxidative damage to photosystem II (PSII) reaction centers. Two major positive contributors to NPQ are the carotenoid zeaxanthin, generated from violaxanthin by the enzyme violaxanthin de-epoxidase (VDE or NPQ1), and the thylakoid protein PsbS (NPQ4). The involvement of the lumenal Deg proteases in the repair of PSII from photoinhibition prompted us to further explore their possible role in other responses of <i>Arabidopsis thaliana</i> to high light. Here we show that upon exposure to high light, the single <i>deg1</i> and the triple <i>deg158</i> mutants display different levels and kinetics of NPQ, compared with the <i>deg58</i> mutant and WT that behave alike. In response to high light, the two genotypes lacking Deg1 overaccumulate NPQ1 and NPQ4. After temporal inhibition of protein translation in vivo, the level of these two proteins in <i>deg1</i> is higher than in WT. Together, the results suggest that Deg1 represents a new level of regulation of the NPQ process through adjusting the quantity of NPQ1 and NPQ4 proteins, probably through their proteolysis.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.17263","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143475644","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
Flavodiiron proteins in Physcomitrium patens: navigating the edge between photoprotection and efficiency
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-24 DOI: 10.1111/tpj.70052
Eleonora Traverso, Claudia Beraldo, Marco Armellin, Alessandro Alboresi, Tomas Morosinotto

Sunlight is the primary energy source for photosynthetic organisms, driving electron transport that supports the synthesis of ATP and NADPH. In dynamic environmental conditions, photosynthetic electron transport requires continuous modulation to prevent over-reduction and safeguard against potential damage. Flavodiiron proteins (FLV) contribute to photoprotection by accepting electrons downstream of Photosystem I, reducing oxygen to water. FLV were shown to have a seminal role in response to abrupt changes in illumination intensity in various photosynthetic organisms, such as cyanobacteria, green algae, mosses, and gymnosperms but were lost during evolution of angiosperms. In this work, Physcomitrium patens plants with strong FLV accumulation, up to 20 times higher than WT, were isolated. Overexpressor plants exhibited faster activation of electron transport but did not gain additional tolerance to light fluctuations, suggesting that the contribution to photoprotection from the FLV was already saturated in WT plants. On the contrary, strong protein overexpression caused a growth penalty under steady low or high light intensity suggesting that FLV overaccumulation can be detrimental, at least in some conditions, opening hypotheses to explain why these proteins were lost during the evolution of angiosperms.

{"title":"Flavodiiron proteins in Physcomitrium patens: navigating the edge between photoprotection and efficiency","authors":"Eleonora Traverso,&nbsp;Claudia Beraldo,&nbsp;Marco Armellin,&nbsp;Alessandro Alboresi,&nbsp;Tomas Morosinotto","doi":"10.1111/tpj.70052","DOIUrl":"https://doi.org/10.1111/tpj.70052","url":null,"abstract":"<p>Sunlight is the primary energy source for photosynthetic organisms, driving electron transport that supports the synthesis of ATP and NADPH. In dynamic environmental conditions, photosynthetic electron transport requires continuous modulation to prevent over-reduction and safeguard against potential damage. Flavodiiron proteins (FLV) contribute to photoprotection by accepting electrons downstream of Photosystem I, reducing oxygen to water. FLV were shown to have a seminal role in response to abrupt changes in illumination intensity in various photosynthetic organisms, such as cyanobacteria, green algae, mosses, and gymnosperms but were lost during evolution of angiosperms. In this work, <i>Physcomitrium patens</i> plants with strong FLV accumulation, up to 20 times higher than WT, were isolated. Overexpressor plants exhibited faster activation of electron transport but did not gain additional tolerance to light fluctuations, suggesting that the contribution to photoprotection from the FLV was already saturated in WT plants. On the contrary, strong protein overexpression caused a growth penalty under steady low or high light intensity suggesting that FLV overaccumulation can be detrimental, at least in some conditions, opening hypotheses to explain why these proteins were lost during the evolution of angiosperms.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481573","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
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The Plant Journal
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