Yi Zhang, Yibo Xian, Heng Yang, Xuangang Yang, Tianli Yu, Sai Liu, Minting Liang, Xianzhi Jiang, Shulin Deng
SummaryExploring the new elements to re‐design the expression cassette is crucial in synthetic biology. Viruses are one of the most important sources for exploring gene expression elements. In this study, we found that the DNA sequence of the SBG51 deltasatellite from the Sweet potato leaf curl virus (SPLCV) greatly enhanced the gene expression when flanked downstream of the terminator. The SBG51 sequence increased transient GFP gene expression in Nicotiana benthamiana leaves by up to ~6 times and ~10 times compared to the gene expression controlled by the UBQ10 promoter and 35S promoter alone, respectively. The increased GFP gene expression level contributed to the continuous accumulation of GFP protein and GFP fluorescence until 8 days post‐inoculation (dpi). The SBG51 sequence also enhanced the gene expression in the transgenic Arabidopsis plants and maintained the spatio‐temporal pattern of the FLOWERING LOCUS T (FT) and TOO MANY MOUTHS (TMM) promoters. We identified a 123 bp of AT‐rich sequence containing seven “ATAAA” or “TTAAA” elements from the SBG51 DNA, which had the gene expression enhancement effect. Furthermore, the artificial synthetic sequences containing tandem repeated “ATAAA” or “TTAAA” elements were sufficient to increase the gene expression but did not alter the polyadenylation of mRNA, similar to the function of matrix attachment regions (MAR). Additionally, the compact artificial synthetic sequence also had an effect on yeast when the expression cassette was integrated into the genome. We conclude that the geminivirus deltasatellite‐derived sequence and the “ATAAA”/“TTAAA” elements are powerful tools for enhancing gene expression.
在合成生物学中，探索新的元件来重新设计表达盒是至关重要的。病毒是探索基因表达元件的重要来源之一。在本研究中，我们发现来自甘薯卷曲叶病毒（SPLCV）的SBG51三角洲卫星的DNA序列位于终止子的下游时，极大地增强了基因的表达。与UBQ10启动子和35S启动子相比，SBG51序列在烟叶中的瞬时GFP基因表达量分别提高了约6倍和约10倍。GFP基因表达水平的增加有助于GFP蛋白和GFP荧光的持续积累，直到接种后8天（dpi）。SBG51序列还增强了转基因拟南芥植株的基因表达，维持了开花位点T （FT）和TOO MANY mouth （TMM）启动子的时空格局。我们从SBG51 DNA中鉴定出一个123 bp的富含AT的序列，该序列包含7个“ATAAA”或“TTAAA”元件，具有基因表达增强作用。此外，含有串联重复“ATAAA”或“TTAAA”元件的人工合成序列足以增加基因表达，但不会改变mRNA的聚腺苷化，类似于基质附着区（matrix attachment regions， MAR）的功能。此外，当表达盒整合到基因组中时，紧凑的人工合成序列对酵母也有影响。我们得出结论，三角卫星衍生的双病毒序列和“ATAAA”/“TTAAA”元件是增强基因表达的有力工具。
{"title":"A novel geminivirus‐derived 3′ flanking sequence of terminator mediates the gene expression enhancement","authors":"Yi Zhang, Yibo Xian, Heng Yang, Xuangang Yang, Tianli Yu, Sai Liu, Minting Liang, Xianzhi Jiang, Shulin Deng","doi":"10.1111/pbi.14561","DOIUrl":"https://doi.org/10.1111/pbi.14561","url":null,"abstract":"SummaryExploring the new elements to re‐design the expression cassette is crucial in synthetic biology. Viruses are one of the most important sources for exploring gene expression elements. In this study, we found that the DNA sequence of the SBG51 deltasatellite from the <jats:italic>Sweet potato leaf curl virus</jats:italic> (SPLCV) greatly enhanced the gene expression when flanked downstream of the terminator. The SBG51 sequence increased transient <jats:italic>GFP</jats:italic> gene expression in <jats:italic>Nicotiana benthamiana</jats:italic> leaves by up to ~6 times and ~10 times compared to the gene expression controlled by the UBQ10 promoter and 35S promoter alone, respectively. The increased <jats:italic>GFP</jats:italic> gene expression level contributed to the continuous accumulation of GFP protein and GFP fluorescence until 8 days post‐inoculation (dpi). The SBG51 sequence also enhanced the gene expression in the transgenic Arabidopsis plants and maintained the spatio‐temporal pattern of the <jats:italic>FLOWERING LOCUS T</jats:italic> (<jats:italic>FT</jats:italic>) and <jats:italic>TOO MANY MOUTHS</jats:italic> (<jats:italic>TMM</jats:italic>) promoters. We identified a 123 bp of AT‐rich sequence containing seven “ATAAA” or “TTAAA” elements from the SBG51 DNA, which had the gene expression enhancement effect. Furthermore, the artificial synthetic sequences containing tandem repeated “ATAAA” or “TTAAA” elements were sufficient to increase the gene expression but did not alter the polyadenylation of mRNA, similar to the function of matrix attachment regions (MAR). Additionally, the compact artificial synthetic sequence also had an effect on yeast when the expression cassette was integrated into the genome. We conclude that the geminivirus deltasatellite‐derived sequence and the “ATAAA”/“TTAAA” elements are powerful tools for enhancing gene expression.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"1 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886773","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}
SummaryCelery (Apium graveolens L.) is an important vegetable crop in the Apiaceae family. It comprises three botanical varieties: common celery with solid and succulent petioles, celeriac or root celery with enlarged and fleshy hypocotyls and smallage or leaf celery with slender, leafy and usually hollow petioles. Here we present a chromosome‐level genome assembly of a celeriac cultivar and a comprehensive genome variation map constructed through resequencing of 177 representative celery accessions. Phylogenetic analysis revealed that smallage from the Mediterranean region represented the most ancient type of cultivated celery. Following initial domestication in this region, artificial selection has primarily aimed at enlarging the hypocotyl, resulting in celeriac, and at solidifying the petiole, leading to common celery. Selective sweep analysis and genome‐wide association study identified several genes associated with hypocotyl expansion and revealed that the hollow/solid petiole trait directly correlated with the presence/absence of a NAC gene. Our study elucidates the complex breeding history of celery and provides valuable genomic resources and molecular insights for future celery improvement and conservation efforts.
{"title":"Genome of root celery and population genomic analysis reveal the complex breeding history of celery","authors":"Enhui Lai, Sumin Guo, Pan Wu, Minghao Qu, Xiaofen Yu, Chenlu Hao, Shan Li, Haixu Peng, Yating Yi, Miao Zhou, Guodong Fu, Xingnuo Li, Huan Liu, Yi Zheng, Xin Wang, Zhangjun Fei, Lei Gao","doi":"10.1111/pbi.14551","DOIUrl":"https://doi.org/10.1111/pbi.14551","url":null,"abstract":"SummaryCelery (<jats:italic>Apium graveolens</jats:italic> L.) is an important vegetable crop in the Apiaceae family. It comprises three botanical varieties: common celery with solid and succulent petioles, celeriac or root celery with enlarged and fleshy hypocotyls and smallage or leaf celery with slender, leafy and usually hollow petioles. Here we present a chromosome‐level genome assembly of a celeriac cultivar and a comprehensive genome variation map constructed through resequencing of 177 representative celery accessions. Phylogenetic analysis revealed that smallage from the Mediterranean region represented the most ancient type of cultivated celery. Following initial domestication in this region, artificial selection has primarily aimed at enlarging the hypocotyl, resulting in celeriac, and at solidifying the petiole, leading to common celery. Selective sweep analysis and genome‐wide association study identified several genes associated with hypocotyl expansion and revealed that the hollow/solid petiole trait directly correlated with the presence/absence of a NAC gene. Our study elucidates the complex breeding history of celery and provides valuable genomic resources and molecular insights for future celery improvement and conservation efforts.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"76 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142867095","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}
Beneficial microorganisms (BMs) promote plant growth and enhance stress resistance. This review summarizes how BMs induce growth promotion by improving nutrient uptake, producing growth-promoting hormones and stimulating root development. How BMs enhance disease resistance and help protect plants from abiotic stresses has also been explored. Growth-defense trade-offs are known to affect the ability of plants to survive under unfavourable conditions. This review discusses studies demonstrating that BMs regulate growth-defense trade-offs through microbe-associated molecular patterns and multiple pathways, including the leucine-rich repeat receptor-like kinase pathway, abscisic acid signalling pathway and specific transcriptional factor regulation. This multifaceted relationship underscores the significance of BMs in sustainable agriculture. Finally, the need for integration of artificial intelligence to revolutionize biofertilizer research has been highlighted. This review also elucidates the cutting-edge advancements and potential of plant-microbe synergistic microbial agents.
{"title":"Beneficial microorganisms: Regulating growth and defense for plant welfare","authors":"Yan Liu, Aiqin Shi, Yue Chen, Zhihui Xu, Yongxin Liu, Yanlai Yao, Yiming Wang, Baolei Jia","doi":"10.1111/pbi.14554","DOIUrl":"https://doi.org/10.1111/pbi.14554","url":null,"abstract":"Beneficial microorganisms (BMs) promote plant growth and enhance stress resistance. This review summarizes how BMs induce growth promotion by improving nutrient uptake, producing growth-promoting hormones and stimulating root development. How BMs enhance disease resistance and help protect plants from abiotic stresses has also been explored. Growth-defense trade-offs are known to affect the ability of plants to survive under unfavourable conditions. This review discusses studies demonstrating that BMs regulate growth-defense trade-offs through microbe-associated molecular patterns and multiple pathways, including the leucine-rich repeat receptor-like kinase pathway, abscisic acid signalling pathway and specific transcriptional factor regulation. This multifaceted relationship underscores the significance of BMs in sustainable agriculture. Finally, the need for integration of artificial intelligence to revolutionize biofertilizer research has been highlighted. This review also elucidates the cutting-edge advancements and potential of plant-microbe synergistic microbial agents.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"1 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857957","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}
Tomato fruit ripening is a complex developmental process that is important for fruit quality and shelf life. Many factors, including ethylene and several key transcription factors, have been shown to play important roles in the regulation of tomato fruit ripening. However, our understanding of the regulation of tomato fruit ripening is still limited. Here, we describe mut26, an EMS-induced tomato (Solanum lycopersicum) mutant that exhibits chlorophyll-deficient phenotypes in various organs, including fruits. Genetic mapping and functional analyses revealed that a single-nucleotide substitution and a corresponding Pro398–>Ser mis-sense mutation in SlChlH (GENOMES UNCOUPLED 5, GUN5), which encodes the H subunit of magnesium chelatase, are responsible for the defects in the mut26 strain. Transcript analyses towards the expression of many SlPhANGs revealed that mut26 is defective in plastid retrograde signalling during tomato fruit ripening initiation, namely the transition from mature green to breaker stage. mut26 exhibits delayed progression of fruit ripening characterized by reduced fruit ethylene emission, increased fruit firmness, reduced carotenoid content and delayed plastid conversion from chloroplast to chromoplast. Given that fruit ripening requires signalling from plastids to nucleus, these data support the hypothesis that GUN5-mediated plastid retrograde signalling promotes tomato fruit ripening. We further showed that the delayed fruit ripening of mut26 is not likely caused by reduced chlorophyll content. Taken together, we identified a new function of SlChlH in the promotion of tomato fruit ripening and ethylene biosynthesis, suggesting that GUN5-mediated plastid retrograde signalling plays a promotive role in tomato fruit ripening.
{"title":"Characterization of a tomato chlh mis-sense mutant reveals a new function of ChlH in fruit ripening","authors":"Dawei Xu, Li Lin, Xiaorui Liu, MeLongying Wangzha, Xiaoqing Pang, Liping Feng, Bingbing Wan, Guo-Zhang Wu, Jingquan Yu, Jean-David Rochaix, Bernhard Grimm, Ruohe Yin","doi":"10.1111/pbi.14548","DOIUrl":"https://doi.org/10.1111/pbi.14548","url":null,"abstract":"Tomato fruit ripening is a complex developmental process that is important for fruit quality and shelf life. Many factors, including ethylene and several key transcription factors, have been shown to play important roles in the regulation of tomato fruit ripening. However, our understanding of the regulation of tomato fruit ripening is still limited. Here, we describe <i>mut26</i>, an EMS-induced tomato (<i>Solanum lycopersicum</i>) mutant that exhibits chlorophyll-deficient phenotypes in various organs, including fruits. Genetic mapping and functional analyses revealed that a single-nucleotide substitution and a corresponding Pro398–>Ser mis-sense mutation in <i>SlChlH</i> (<i>GENOMES UNCOUPLED 5, GUN5</i>), which encodes the H subunit of magnesium chelatase, are responsible for the defects in the <i>mut26</i> strain. Transcript analyses towards the expression of many <i>SlPhANGs</i> revealed that <i>mut26</i> is defective in plastid retrograde signalling during tomato fruit ripening initiation, namely the transition from mature green to breaker stage. <i>mut26</i> exhibits delayed progression of fruit ripening characterized by reduced fruit ethylene emission, increased fruit firmness, reduced carotenoid content and delayed plastid conversion from chloroplast to chromoplast. Given that fruit ripening requires signalling from plastids to nucleus, these data support the hypothesis that GUN5-mediated plastid retrograde signalling promotes tomato fruit ripening. We further showed that the delayed fruit ripening of <i>mut26</i> is not likely caused by reduced chlorophyll content. Taken together, we identified a new function of SlChlH in the promotion of tomato fruit ripening and ethylene biosynthesis, suggesting that GUN5-mediated plastid retrograde signalling plays a promotive role in tomato fruit ripening.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"62 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849616","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}
Chen Wang, Shaowen Song, Jun Fu, Kai Wang, Xuan Chen, Bin Bo, Zhe Chen, Linan Zhang, Lin Zhang, Xiaohui Wang, Niwen Tang, Xiangrong Tian, Liangbi Chen, Sheng Luan, Yuanzhu Yang, Dandan Mao
Over-application of potassium (K) fertilizer in fields has a negative impact on the environment. Developing rice varieties with high KUE will reduce fertilizer for sustainable agriculture. However, the genetic basis of KUE in a more diverse and inclusive population remains largely unexplored. Here, we show that the transcription factor OsNAC25 enhances K+ uptake and confers high KUE under low K+ supply. Disruption of OsNAC25 by CRISPR/Cas9-mediated mutagenesis led to a considerable loss of K+ uptake capacity in rice roots, coupled with reduced K+ accumulation in rice and severe plant growth defects under low- K+ conditions. However, the overexpression of OsNAC25 enhanced K+ accumulation by regulating proper K+ uptake capacity in rice roots. Further analysis displayed that OsNAC25 can bind to the promoter of OsSLAH3 to repress its transcription in response to low- K+ stress. Nucleotide diversity analyses suggested that OsNAC25 may be selected during japonica populations' adaptation of low K+ tolerance. Natural variation of OsNAC25 might cause differential expression in different haplotype varieties, thus conferring low K+ tolerance in the Hap 1 and Hap 4 -carrying varieties, and the japonica allele OsNAC25 could enhance low K+ tolerance in indica variety, conferring great potential to improve indica low K+ tolerance and grain development. Taken together, we have identified a new NAC regulator involved in rice low K+ tolerance and grain development, and provide a potential target gene for improving low K+ tolerance and grain development in rice.
{"title":"The transcription factor OsNAC25 regulates potassium homeostasis in rice","authors":"Chen Wang, Shaowen Song, Jun Fu, Kai Wang, Xuan Chen, Bin Bo, Zhe Chen, Linan Zhang, Lin Zhang, Xiaohui Wang, Niwen Tang, Xiangrong Tian, Liangbi Chen, Sheng Luan, Yuanzhu Yang, Dandan Mao","doi":"10.1111/pbi.14550","DOIUrl":"https://doi.org/10.1111/pbi.14550","url":null,"abstract":"Over-application of potassium (K) fertilizer in fields has a negative impact on the environment. Developing rice varieties with high KUE will reduce fertilizer for sustainable agriculture. However, the genetic basis of KUE in a more diverse and inclusive population remains largely unexplored. Here, we show that the transcription factor OsNAC25 enhances K<sup>+</sup> uptake and confers high KUE under low K<sup>+</sup> supply. Disruption of <i>OsNAC25</i> by CRISPR/Cas9-mediated mutagenesis led to a considerable loss of K<sup>+</sup> uptake capacity in rice roots, coupled with reduced K<sup>+</sup> accumulation in rice and severe plant growth defects under low- K<sup>+</sup> conditions. However, the overexpression of <i>OsNAC25</i> enhanced K<sup>+</sup> accumulation by regulating proper K<sup>+</sup> uptake capacity in rice roots. Further analysis displayed that <i>OsNAC25</i> can bind to the promoter of <i>OsSLAH3</i> to repress its transcription in response to low- K<sup>+</sup> stress. Nucleotide diversity analyses suggested that OsNAC25 may be selected during japonica populations' adaptation of low K<sup>+</sup> tolerance. Natural variation of <i>OsNAC25</i> might cause differential expression in different haplotype varieties, thus conferring low K<sup>+</sup> tolerance in the Hap 1 and Hap 4 -carrying varieties, and the japonica allele <i>OsNAC25</i> could enhance low K<sup>+</sup> tolerance in <i>indica</i> variety, conferring great potential to improve <i>indica</i> low K<sup>+</sup> tolerance and grain development. Taken together, we have identified a new NAC regulator involved in rice low K<sup>+</sup> tolerance and grain development, and provide a potential target gene for improving low K<sup>+</sup> tolerance and grain development in rice.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"86 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142841816","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}
Wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) is one of the most important food crops in the world. CRISPR/Cas12i3, which belongs to the type V-I Cas system, has attracted extensive attention recently due to its smaller protein size and its less-restricted canonical ‘TTN’ protospacer adjacent motif (PAM). However, due to its relatively lower editing efficacy in plants and the hexaploidy complex nature of wheat, Cas12i3/Cas12i3-5M-mediated genome editing in wheat has not been documented yet. Here, we report the engineering of a robust Cas12i3-5M-mediated genome editing system in wheat through the fusion of T5 exonuclease (T5E) in combination with an optimised crRNA expression strategy (Opt). We first showed that fusion of T5E, rather than ExoI, to Cas12i3-5M increased the gene editing efficiencies by up to 1.34-fold and 3.87-fold, compared to Cas12i3-5M and Cas12i3 in HEK293T cells, respectively. However, its editing efficiency remains low in wheat. We then optimised the crRNA expression strategy and demonstrated that Opt-T5E-Cas12i3-5M could enhance the editing efficiency by 1.20- to 1.33-fold and 4.05- to 7.95-fold in wheat stable lines compared to Opt-Cas12i3-5M and Opt-Cas12i3, respectively, due to progressive 5′-end resection of the DNA strand at the cleavage site with increased deletion size. The Opt-T5E-Cas12i3-5M enabled an editing efficiency ranging from 60.71% to 90.00% across four endogenous target genes in stable lines of three elite Chinese wheat varieties. Together, the developed robust Opt-T5E-Cas12i3-5M system enriches wheat genome editing toolkits for either biological research or genetic improvement and may be extended to other important polyploidy crop species.
{"title":"Engineering a robust Cas12i3 variant-mediated wheat genome editing system","authors":"Wenxue Wang, Lei Yan, Jingying Li, Chen Zhang, Yubing He, Shaoya Li, Lanqin Xia","doi":"10.1111/pbi.14544","DOIUrl":"https://doi.org/10.1111/pbi.14544","url":null,"abstract":"Wheat (<i>Triticum aestivum</i> L., 2<i>n</i> = 6<i>x</i> = 42, AABBDD) is one of the most important food crops in the world. CRISPR/Cas12i3, which belongs to the type V-I Cas system, has attracted extensive attention recently due to its smaller protein size and its less-restricted canonical ‘TTN’ protospacer adjacent motif (PAM). However, due to its relatively lower editing efficacy in plants and the hexaploidy complex nature of wheat, Cas12i3/Cas12i3-5M-mediated genome editing in wheat has not been documented yet. Here, we report the engineering of a robust Cas12i3-5M-mediated genome editing system in wheat through the fusion of T5 exonuclease (T5E) in combination with an optimised crRNA expression strategy (Opt). We first showed that fusion of T5E, rather than ExoI, to Cas12i3-5M increased the gene editing efficiencies by up to 1.34-fold and 3.87-fold, compared to Cas12i3-5M and Cas12i3 in HEK293T cells, respectively. However, its editing efficiency remains low in wheat. We then optimised the crRNA expression strategy and demonstrated that Opt-T5E-Cas12i3-5M could enhance the editing efficiency by 1.20- to 1.33-fold and 4.05- to 7.95-fold in wheat stable lines compared to Opt-Cas12i3-5M and Opt-Cas12i3, respectively, due to progressive 5′-end resection of the DNA strand at the cleavage site with increased deletion size. The Opt-T5E-Cas12i3-5M enabled an editing efficiency ranging from 60.71% to 90.00% across four endogenous target genes in stable lines of three elite Chinese wheat varieties. Together, the developed robust Opt-T5E-Cas12i3-5M system enriches wheat genome editing toolkits for either biological research or genetic improvement and may be extended to other important polyploidy crop species.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"1216 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142841817","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}
Tiller is an important factor in determining rice yield. Currently, researches mainly focus on the outgrowth of low-order tiller (LOT), while the regulation mechanism of high-order tiller (HOT) outgrowth has remained unknown. In this study, we detected one OsNL1 mutant, nl1, exhibiting HOT numbers increase, and found that OsNL1 interacts with OsTOPLESS2, which was mediated by the core motif of nine amino acids VDCTLSLGT within the HAN domain of OsNL1. The topless2 mutant exhibits similar HOT number increase as in the nl1. Through ChIP-seq analysis, we revealed that OsNL1 recruits OsTOPLESS2 to conduct histone deacetylation in the promoters of OsMOC1 and OsMOC3 to regulate HOT outgrowth. Moreover, we showed that the HAN domain is essential for OsNL1 function as a repressor. In summary, our study reveals partial mechanism of HOT outgrowth in rice and deciphers the molecular biology function of the HAN domain. This will contribute to the comprehensive understanding of tiller outgrowth and the role of HAN-domain-containing genes.
分蘖是决定水稻产量的重要因素。目前，研究主要集中在低阶分蘖（LOT）的生长上，而高阶分蘖（HOT）生长的调控机制尚不清楚。本研究发现，OsNL1与OsTOPLESS2之间存在相互作用，这种相互作用是由OsNL1的HAN结构域中的9个氨基酸VDCTLSLGT核心基序介导的。toppless2 突变体表现出与 nl1 相似的 HOT 数量增加。通过ChIP-seq分析，我们发现OsNL1招募OsTOPLESS2在OsMOC1和OsMOC3的启动子中进行组蛋白去乙酰化，从而调控HOT的生长。此外，我们还发现，HAN结构域对于OsNL1作为抑制因子的功能至关重要。总之，我们的研究揭示了水稻 HOT 外生长的部分机制，并解读了 HAN 结构域的分子生物学功能。这将有助于全面了解分蘖的生长和含HAN结构域基因的作用。
{"title":"The OsNL1-OsTOPLESS2-OsMOC1/3 pathway regulates high-order tiller outgrowth in rice","authors":"Xin Liu, Feng Zhang, Ziqi Xun, Jiale Shao, Wenfan Luo, Xiaokang Jiang, Jiachang Wang, Jian Wang, Shuai Li, Qibing Lin, Yulong Ren, Huixian Zhao, Zhijun Cheng, Jianmin Wan","doi":"10.1111/pbi.14547","DOIUrl":"https://doi.org/10.1111/pbi.14547","url":null,"abstract":"Tiller is an important factor in determining rice yield. Currently, researches mainly focus on the outgrowth of low-order tiller (LOT), while the regulation mechanism of high-order tiller (HOT) outgrowth has remained unknown. In this study, we detected one <i>OsNL1</i> mutant, <i>nl1</i>, exhibiting HOT numbers increase, and found that OsNL1 interacts with OsTOPLESS2, which was mediated by the core motif of nine amino acids VDCTLSLGT within the HAN domain of OsNL1. The <i>topless2</i> mutant exhibits similar HOT number increase as in the <i>nl1</i>. Through ChIP-seq analysis, we revealed that OsNL1 recruits OsTOPLESS2 to conduct histone deacetylation in the promoters of <i>OsMOC1</i> and <i>OsMOC3</i> to regulate HOT outgrowth. Moreover, we showed that the HAN domain is essential for OsNL1 function as a repressor. In summary, our study reveals partial mechanism of HOT outgrowth in rice and deciphers the molecular biology function of the HAN domain. This will contribute to the comprehensive understanding of tiller outgrowth and the role of HAN-domain-containing genes.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"12 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825071","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}
Chang Luo, Jiayi Luo, Mingzheng Han, Zhenzhen Song, Yahui Sun, Yaqin Wang, Yafei Zhao, Conglin Huang, Junping Gao, Bo Hong, Chao Ma
<p>Flavonoids play critical roles in plant adaptation to environmental changes and are valuable medicinal resources (Chagas <i>et al</i>., <span>2022</span>). Flavonoids are predominantly found in glycosylated forms, which exhibit increased structural complexity, solubility and stability. However, the aglycone forms of flavonoids exhibit greater antioxidant capacity and bioavailability (Xie <i>et al</i>., <span>2022</span>). Enhancing the content of flavonoid aglycones in crops can improve their nutritional value and health benefits for humans.</p> <p>In plants, UDP-rhamnose serves as a key sugar donor in flavonoid glycosylation, synthesized from UDP-glucose via the enzyme rhamnose synthase (RHM). In Arabidopsis (<i>Arabidopsis thaliana</i>), mutations in the <i>RHM1</i> lead to significant reduction in rhamnosylated flavonols (Saffer and Irish, <span>2018</span>). However, as Arabidopsis lacks flavone synthase and flavones, the impacts of UDP-rhamnose on flavone aglycone or glycoside biosynthesis are unknown.</p> <p><i>Chrysanthemum indicum</i>, a notable medicinal plant, has been used in traditional Chinese medicine for over 2000 years (He <i>et al</i>., <span>2016</span>). The dried flowers of <i>C. indicum</i>, known as ‘Yejuhua’ in the <i>Pharmacopoeia of the People's Republic of China</i> (2020 edition), are recognized for their anti-inflammatory, antioxidant, antimicrobial, anticancer and immunomodulatory properties (Xie <i>et al</i>., <span>2012</span>). These pharmaceutical effects are largely attributed to the high flavone content, particularly compounds like apigenin, luteolin and their derivatives (Shao <i>et al</i>., <span>2020</span>). Previous studies have shown significant variations in morphology and metabolic composition among different eco-geographic populations (ecotypes) of <i>C. indicum</i> in China, influencing their medicinal and nutritional value (Fang <i>et al</i>., <span>2012</span>).</p> <p>To explore the natural variation of flavones in <i>C. indicum</i>, we collected ecotypes from various regions across China, and quantified the major bioactive flavone, apigenin, in the flowers using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS). A metabolite-based genome-wide association study (mGWAS) was performed on 72 ecotypes exhibiting distinct apigenin content (Figure 1a; Dataset S1). The association analysis showed that the natural variation in apigenin content across these ecotypes was governed by two loci located on chromosomes 2 and 9 (Figure 1b–c). Within the locus on chromosome 2, we identified a <i>TREHALOSE-6-PHOSPHATE SYNTHASE1</i> gene (<i>CiTPS1</i>, Cse_sc000461.1_g010.1) and <i>CiRHM1</i> (Cse_sc000461.1_g020.1) (Figure 1b; Table S1). Collinearity analysis indicated that the <i>TPS1-RHM1</i> gene cluster is conserved among dicotyledonous plants (Figure S1). RNA-seq of 18 ecotypes showed that the expression of <i>CiRHM1</i> was negatively correlated with apigenin content (Figure 1d, Tab
{"title":"Identification and knockout of rhamnose synthase CiRHM1 enhances accumulation of flavone aglycones in chrysanthemum flower","authors":"Chang Luo, Jiayi Luo, Mingzheng Han, Zhenzhen Song, Yahui Sun, Yaqin Wang, Yafei Zhao, Conglin Huang, Junping Gao, Bo Hong, Chao Ma","doi":"10.1111/pbi.14556","DOIUrl":"https://doi.org/10.1111/pbi.14556","url":null,"abstract":"<p>Flavonoids play critical roles in plant adaptation to environmental changes and are valuable medicinal resources (Chagas <i>et al</i>., <span>2022</span>). Flavonoids are predominantly found in glycosylated forms, which exhibit increased structural complexity, solubility and stability. However, the aglycone forms of flavonoids exhibit greater antioxidant capacity and bioavailability (Xie <i>et al</i>., <span>2022</span>). Enhancing the content of flavonoid aglycones in crops can improve their nutritional value and health benefits for humans.</p>\u0000<p>In plants, UDP-rhamnose serves as a key sugar donor in flavonoid glycosylation, synthesized from UDP-glucose via the enzyme rhamnose synthase (RHM). In Arabidopsis (<i>Arabidopsis thaliana</i>), mutations in the <i>RHM1</i> lead to significant reduction in rhamnosylated flavonols (Saffer and Irish, <span>2018</span>). However, as Arabidopsis lacks flavone synthase and flavones, the impacts of UDP-rhamnose on flavone aglycone or glycoside biosynthesis are unknown.</p>\u0000<p><i>Chrysanthemum indicum</i>, a notable medicinal plant, has been used in traditional Chinese medicine for over 2000 years (He <i>et al</i>., <span>2016</span>). The dried flowers of <i>C. indicum</i>, known as ‘Yejuhua’ in the <i>Pharmacopoeia of the People's Republic of China</i> (2020 edition), are recognized for their anti-inflammatory, antioxidant, antimicrobial, anticancer and immunomodulatory properties (Xie <i>et al</i>., <span>2012</span>). These pharmaceutical effects are largely attributed to the high flavone content, particularly compounds like apigenin, luteolin and their derivatives (Shao <i>et al</i>., <span>2020</span>). Previous studies have shown significant variations in morphology and metabolic composition among different eco-geographic populations (ecotypes) of <i>C. indicum</i> in China, influencing their medicinal and nutritional value (Fang <i>et al</i>., <span>2012</span>).</p>\u0000<p>To explore the natural variation of flavones in <i>C. indicum</i>, we collected ecotypes from various regions across China, and quantified the major bioactive flavone, apigenin, in the flowers using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS). A metabolite-based genome-wide association study (mGWAS) was performed on 72 ecotypes exhibiting distinct apigenin content (Figure 1a; Dataset S1). The association analysis showed that the natural variation in apigenin content across these ecotypes was governed by two loci located on chromosomes 2 and 9 (Figure 1b–c). Within the locus on chromosome 2, we identified a <i>TREHALOSE-6-PHOSPHATE SYNTHASE1</i> gene (<i>CiTPS1</i>, Cse_sc000461.1_g010.1) and <i>CiRHM1</i> (Cse_sc000461.1_g020.1) (Figure 1b; Table S1). Collinearity analysis indicated that the <i>TPS1-RHM1</i> gene cluster is conserved among dicotyledonous plants (Figure S1). RNA-seq of 18 ecotypes showed that the expression of <i>CiRHM1</i> was negatively correlated with apigenin content (Figure 1d, Tab","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"1 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825072","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}
Chicoric acid, a phenolic compound derived from plants, exhibits a range of pharmacological activities. Light significantly influences the chicoric acid biosynthesis in Taraxacum mongolicum; however, the transcriptional regulatory network governing this process remains unclear. A combined analysis of the metabolome and transcriptome revealed that blue light markedly enhances chicoric acid accumulation compared to red light. The blue light-sensitive transcription factor ELONGATED HYPOCOTYL5 (HY5) is closely associated with multiple core proteins, transcription factors and chicoric acid synthase genes involved in light signalling. Both in vivo and in vitro experiments demonstrated that TmHY5 directly regulates several chicoric acid biosynthetic genes, including TmPAL3, Tm4CL1 and TmHQT2. Additionally, TmHY5 promotes the accumulation of luteolin and anthocyanins by increasing the expression of TmCHS2 and TmANS2. The E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) forms a protein complex with TmHY5, significantly inhibiting chicoric acid biosynthesis. Blue light inhibits TmCOP1-TmHY5 complex protein formation while enhancing the expression levels of TmCOP1 through TmHY5. Furthermore, TmHY5 elevates the expression levels of TmbZIP1, which indirectly activates Tm4CL1 expression. In vivo, TmCOP1 directly inhibits the expression of the TmHY5-Tm4CL1 complex. Therefore, we speculate that TmCOP1-TmHY5-mediated blue light signalling effectively activates chicoric acid biosynthesis, providing a foundation for the application of blue light supplementation technology in industrial production.
{"title":"TmCOP1-TmHY5 module-mediated blue light signal promotes chicoric acid biosynthesis in Taraxacum mongolicum","authors":"Qun Liu, Zhiqing Wu, Xiwu Qi, Hailing Fang, Xu Yu, Li Li, Zequn Chen, Jie Wu, Yugang Gao, Guoyin Kai, Chengyuan Liang","doi":"10.1111/pbi.14542","DOIUrl":"https://doi.org/10.1111/pbi.14542","url":null,"abstract":"Chicoric acid, a phenolic compound derived from plants, exhibits a range of pharmacological activities. Light significantly influences the chicoric acid biosynthesis in <i>Taraxacum mongolicum</i>; however, the transcriptional regulatory network governing this process remains unclear. A combined analysis of the metabolome and transcriptome revealed that blue light markedly enhances chicoric acid accumulation compared to red light. The blue light-sensitive transcription factor ELONGATED HYPOCOTYL5 (HY5) is closely associated with multiple core proteins, transcription factors and chicoric acid synthase genes involved in light signalling. Both <i>in vivo</i> and <i>in vitro</i> experiments demonstrated that TmHY5 directly regulates several chicoric acid biosynthetic genes, including <i>TmPAL3</i>, <i>Tm4CL1</i> and <i>TmHQT2</i>. Additionally, TmHY5 promotes the accumulation of luteolin and anthocyanins by increasing the expression of <i>TmCHS2</i> and <i>TmANS2</i>. The E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) forms a protein complex with TmHY5, significantly inhibiting chicoric acid biosynthesis. Blue light inhibits TmCOP1-TmHY5 complex protein formation while enhancing the expression levels of <i>TmCOP1</i> through TmHY5. Furthermore, TmHY5 elevates the expression levels of <i>TmbZIP1</i>, which indirectly activates <i>Tm4CL1</i> expression. <i>In vivo</i>, TmCOP1 directly inhibits the expression of the TmHY5-Tm4CL1 complex. Therefore, we speculate that TmCOP1-TmHY5-mediated blue light signalling effectively activates chicoric acid biosynthesis, providing a foundation for the application of blue light supplementation technology in industrial production.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"12 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816161","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}
Ostrinia furnacalis (O. furnacalis) is a commonly occurring agricultural pest that can severely impact corn yield and quality. Therefore, establishing and implementing effective control methods against O. furnacalis are of great significance. Chemical insecticides remain the most effective means to mitigate the damage caused by O. furnacalis. With the increasing resistance of O. furnacalis to insecticides, it is imperative to identify and develop compounds with novel mechanisms of action and high safety. The chitinase OfChi-h, identified and characterized in O. furnacalis, has been recognized as a potential insecticide target. In this study, a series of azo-aminopyrimidine analogues were synthesized as OfChi-h inhibitors employing rational molecular optimization. Among them, compounds 9b, 10a and 10g exhibited Ki values of 23.2, 19.4, and 43.2 nM against OfChi-h, respectively. Molecular docking studies were carried out to explore the molecular basis for the high efficacy of these compounds and OfChi-h. In addition, the morphological changes of the cuticle in inhibitor-treated O. furnacalis larvae were assessed using scanning electron microscopy. Furthermore, the target compounds were assayed in leaf dipping and pot experiments, with compound 10a exhibiting greater insecticidal activity against Plutella xylostella (P. xylostella) and O. furnacalis than diflubenzuron and chlorbenzuron. At the same time, the toxicity of these compounds to natural enemies Trichogramma ostriniae and rats was negligible. The present study demonstrates that the azo-aminopyrimidine skeleton can be used as a novel, low-cost scaffold for developing insect chitinolytic enzyme inhibitors, with the potential to be utilized as new environmentally friendly insecticides.
{"title":"Rational design of azo-aminopyrimidine derivatives as the potent lepidoptera-exclusive chitinase inhibitors","authors":"Baokang Ding, Shujie Ma, Meiling Yang, Quanguo Zhang, Xiujia Hua, Jiahao Zhang, Shenmeng Bai, Lihui Zhang, Jingao Dong, Shengqiang Shen, Lili Dong","doi":"10.1111/pbi.14538","DOIUrl":"https://doi.org/10.1111/pbi.14538","url":null,"abstract":"<i>Ostrinia furnacalis</i> (<i>O. furnacalis</i>) is a commonly occurring agricultural pest that can severely impact corn yield and quality. Therefore, establishing and implementing effective control methods against <i>O. furnacalis</i> are of great significance. Chemical insecticides remain the most effective means to mitigate the damage caused by <i>O. furnacalis</i>. With the increasing resistance of <i>O. furnacalis</i> to insecticides, it is imperative to identify and develop compounds with novel mechanisms of action and high safety. The chitinase O<i>f</i>Chi-h, identified and characterized in <i>O. furnacalis</i>, has been recognized as a potential insecticide target. In this study, a series of azo-aminopyrimidine analogues were synthesized as O<i>f</i>Chi-h inhibitors employing rational molecular optimization. Among them, compounds <b>9b</b>, <b>10a</b> and <b>10g</b> exhibited <i>K</i><sub>i</sub> values of 23.2, 19.4, and 43.2 nM against O<i>f</i>Chi-h, respectively. Molecular docking studies were carried out to explore the molecular basis for the high efficacy of these compounds and O<i>f</i>Chi-h. In addition, the morphological changes of the cuticle in inhibitor-treated <i>O. furnacalis</i> larvae were assessed using scanning electron microscopy. Furthermore, the target compounds were assayed in leaf dipping and pot experiments, with compound <b>10a</b> exhibiting greater insecticidal activity against <i>Plutella xylostella</i> (<i>P. xylostella</i>) and <i>O. furnacalis</i> than diflubenzuron and chlorbenzuron. At the same time, the toxicity of these compounds to natural enemies <i>Trichogramma ostriniae</i> and rats was negligible. The present study demonstrates that the azo-aminopyrimidine skeleton can be used as a novel, low-cost scaffold for developing insect chitinolytic enzyme inhibitors, with the potential to be utilized as new environmentally friendly insecticides.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"9 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142810156","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}
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