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miR827 orchestrates the regulation of SPX-MFS1 and SPX-MFS5 with the assistance of lncRNA767 to enhance phosphate starvation tolerance and maize development miR827 在 lncRNA767 的协助下协调 SPX-MFS1 和 SPX-MFS5 的调控,以增强磷酸盐饥饿耐受性和玉米的生长发育
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-16 DOI: 10.1111/pbi.14469
Lei Chen, Juan He, Xufeng Wang, Shiru Zhang, Jinkang Pan, Jianxiang Peng, Beixin Mo, Lin Liu
MicroRNA827 (miR827) is functionally conserved among different plant species and displays species-specific characteristics, but the mechanisms by which miR827 regulates phosphate (Pi) starvation tolerance and maize development remain elusive. We found that miR827 selectively targets the Pi transporter genes SPX-MFS1 and SPX-MFS5. miR827 overexpression improved the Pi starvation tolerance, plant architecture and grain yield and quality, whereas miR827 suppression yielded a contrasting phenotype. In addition, we identified a specific long noncoding RNA (lncRNA767) that serves as a direct target and a facilitator of miR827 and can stabilize the SPX-MFS1 and SPX-MFS5 transcripts, leading to their translation inhibition. The orchestrated regulation of SPX-MFS1 and SPX-MFS5 modulates PHR1; 1 and PHR1; 2, which are critical transcription factors in Pi signalling, and thereby affects the expression of downstream Pi starvation-induced genes. Together, these findings demonstrate that miR827, assisted by lncRNA767, enhances SPX-MFS1 and SPX-MFS5 suppression and thus exerts a significant impact on Pi homeostasis and several essential agronomic traits of maize.
microRNA827(miR827)在不同植物物种间具有功能保守性,并显示出物种特异性,但miR827调控磷酸盐(Pi)饥饿耐受性和玉米生长发育的机制仍不清楚。我们发现,miR827 选择性地靶向 Pi 转运体基因 SPX-MFS1 和 SPX-MFS5。miR827 的过表达提高了玉米的 Pi 饥饿耐受性、植株结构和谷物产量与品质,而 miR827 的抑制则产生了相反的表型。此外,我们还发现了一种特异的长非编码 RNA(lncRNA767),它是 miR827 的直接靶标和促进因子,能稳定 SPX-MFS1 和 SPX-MFS5 转录本,从而抑制它们的翻译。SPX-MFS1和SPX-MFS5的协调调控调节了π信号转导中的关键转录因子PHR1; 1和PHR1; 2,从而影响了下游π饥饿诱导基因的表达。这些发现共同表明,miR827 在 lncRNA767 的辅助下增强了对 SPX-MFS1 和 SPX-MFS5 的抑制,从而对玉米的π稳态和几个重要农艺性状产生了重大影响。
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引用次数: 0
Natural variations in the Cis-elements of GhRPRS1 contributing to petal colour diversity in cotton GhRPRS1顺式元素的自然变化导致棉花花瓣颜色的多样性
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-16 DOI: 10.1111/pbi.14468
Wei Hu, Yanli Chen, Zhenzhen Xu, Linqiang Liu, Da Yan, Miaoyang Liu, Qingdi Yan, Yihao Zhang, Lan Yang, Chenxu Gao, Renju Liu, Wenqiang Qin, Pengfei Miao, Meng Ma, Peng Wang, Babai Gao, Fuguang Li, Zhaoen Yang
The cotton genus comprises both diploid and allotetraploid species, and the diversity in petal colour within this genus offers valuable targets for studying orthologous gene function differentiation and evolution. However, the genetic basis for this diversity in petal colour remains largely unknown. The red petal colour primarily comes from C, G, K, and D genome species, and it is likely that the common ancestor of cotton had red petals. Here, by employing a clone mapping strategy, we mapped the red petal trait to a specific region on chromosome A07 in upland cotton. Genomic comparisons and phylogenetic analyses revealed that the red petal phenotype introgressed from G. bickii. Transcriptome analysis indicated that GhRPRS1, which encodes a glutathione S-transferase, was the causative gene for the red petal colour. Knocking out GhRPRS1 resulted in white petals and the absence of red spots, while overexpression of both genotypes of GhRPRS1 led to red petals. Further analysis suggested that GhRPRS1 played a role in transporting pelargonidin-3-O-glucoside and cyanidin-3-O-glucoside. Promoter activity analysis indicated that variations in the promoter, but not in the gene body of GhRPRS1, have led to different petal colours within the genus. Our findings provide new insights into orthologous gene evolution as well as new strategies for modifying promoters in cotton breeding.
棉花属包括二倍体和异源四倍体物种,该属花瓣颜色的多样性为研究正交基因功能分化和进化提供了宝贵的目标。然而,花瓣颜色多样性的遗传基础在很大程度上仍然未知。红色花瓣主要来自 C、G、K 和 D 基因组物种,棉花的共同祖先很可能具有红色花瓣。在此,我们采用克隆作图策略,将红色花瓣性状绘制到陆地棉 A07 染色体上的一个特定区域。基因组比较和系统进化分析表明,红色花瓣表型是从 G. bickii 传入的。转录组分析表明,编码谷胱甘肽 S-转移酶的 GhRPRS1 是红色花瓣的致病基因。敲除 GhRPRS1 会导致花瓣变白且没有红色斑点,而过表达两种基因型的 GhRPRS1 则会导致花瓣变红。进一步的分析表明,GhRPRS1 在运输鹅掌楸素-3-O-葡萄糖苷和青花素-3-O-葡萄糖苷中发挥作用。启动子活性分析表明,启动子(而非 GhRPRS1 基因体)的变异导致了花瓣属中花瓣颜色的不同。我们的研究结果为同源基因的进化提供了新的视角,也为棉花育种中修改启动子提供了新的策略。
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引用次数: 0
Metabolic engineering of vitamin D3 in Solanaceae plants 茄科植物维生素 D3 的代谢工程
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-16 DOI: 10.1111/pbi.14459
Marianna Boccia, Kerstin Ploβ, Maritta Kunert, Radhika Keshan, Mustafa Hatam, Veit Grabe, Sarah E. O'Connor, Prashant D. Sonawane
<p>Vitamin D is a lipid-soluble sterol that plays an essential role in human health. Deficiency of this vitamin increases the risk of osteoporosis, hypertension, autoimmune diseases, infectious disease, diabetes and cancer. Vitamin D exists in two major forms: vitamin D<sub>3</sub> (cholecalciferol), mainly found in animal food source, and vitamin D<sub>2</sub> (ergocalciferol), typically present in sundried and ultraviolet-B (UV-B) exposed fungi and yeast (Jäpelt <i>et al</i>., <span>2013</span>). Vitamin D<sub>3</sub> is produced in human skin upon sunlight exposure, where pro-vitamin D<sub>3</sub> (7-dehydrocholesterol; 7-DHC) is converted to vitamin D<sub>3</sub> by UV-B light (290–315 nm). Unfortunately, vitamin D<sub>3</sub> deficiency is common in both children and adults worldwide. Endogenous synthesis of vitamin D<sub>3</sub> in human skin is inhibited by several factors such as melanin presence, sunlight intensity, pollution and geographic location. Therefore, dietary sources are essential for maintaining consistent vitamin D<sub>3</sub> levels. Unfortunately, few dietary sources and supplements naturally contain vitamin D<sub>3</sub> and most of these are animal-based foods (e.g. meat and eggs), which raises concerns about vitamin D<sub>3</sub> levels among those populations that consume low amounts of animal products (Black <i>et al</i>., <span>2017</span>).</p><p>Plants harbour an enormous reservoir of diverse steroidal molecules and, in principle, could be a source of vitamin D<sub>3</sub>. However, although vitamin D<sub>3</sub> has been identified in some plants and algae, the levels are much lower compared to animal-based sources. The precursor of vitamin D<sub>3</sub>, 7-DHC, is also the immediate precursor for cholesterol biosynthesis in plants (Figure 1a) (Sonawane <i>et al</i>., <span>2017</span>). Since most plants produce cholesterol in very low amounts, 7-DHC levels are low as well. Notably, <i>Solanaceae</i> family members (e.g. tomato and <i>Nicotiana benthamiana</i>) accumulate naturally high levels of cholesterol. In tomato and other <i>Solanum</i> food crops such as potato and eggplant, cholesterol serves as a starting precursor for biosynthesis of defensive steroidal glycoalkaloids (SGAs) (Sonawane <i>et al</i>., <span>2017</span>). Using the recently elucidated cholesterol pathway in plants along with gene editing strategies, it is now possible to engineer high levels of 7-DHC and therefore, vitamin D<sub>3</sub> in plants. Here, we report metabolic engineering approaches to enhance vitamin D<sub>3</sub> production in tomato (<i>Solanum lycopersicum</i>) and <i>N. benthamiana</i> plants.</p><figure><picture><source media="(min-width: 1650px)" srcset="/cms/asset/85d61b05-6977-4ef7-89be-4819803e5579/pbi14459-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/85d61b05-6977-4ef7-89be-4819803e5579/pbi14459-fig-0001-m.jpg" loading="lazy" src="/cms/asset/a7f4769b-85b3-4d88
我们进一步分析了过表达 BmNVD 的同源 7-dr2ko 突变株系(BmNVDOx + 7-dr2ko)的类固醇代谢物特征变化(图 1F;图 S4c,d,f,g)。虽然与 WT 相比,在 BmNVDOx + 7-dr2ko 转基因品系的叶片中观察到高水平的 7-DHC,但我们仍然注意到胆固醇在这些品系中显著积累(图 S4c,f),这表明参与铜绿素类固醇生物合成的 7-DR1 具有补偿活性。对 BmNVDOx + 7-dr2ko 基因型的叶片和绿色果实进行紫外线-B 处理后,维生素 D3 水平分别比 7-dr2ko 突变体单独产生的水平高出约 3 倍和 5 倍(叶片中为 18 ± 2.1 Vs 5.1 ± 1.2 μg/g DW,绿色果实中为 0.76 ± 0.14 Vs 0.15 ± 0.01 μg/g DW)(图 1C;图 S4e、h)。与之前观察到的 7-dr2ko 突变株系一样,处理 BmNVDOx + 7-dr2ko 植物的红色果实也没有产生任何可量化的维生素 D3。番茄废料(如叶片)中产生的维生素 D3 水平为植物提取的维生素 D3 补充剂提供了一个很有前景的来源,而且很容易达到建议的维生素 D3 每日摄入量(主要根据年龄在 10 至 20 μg 之间)。总之,我们的研究结果有助于探索维生素 D3 生物强化的创新方法,通过一个可持续的、以植物为基础的、具有成本效益的平台,解决全球维生素 D3 缺乏的问题,并提高维生素 D3 的可及性。
{"title":"Metabolic engineering of vitamin D3 in Solanaceae plants","authors":"Marianna Boccia, Kerstin Ploβ, Maritta Kunert, Radhika Keshan, Mustafa Hatam, Veit Grabe, Sarah E. O'Connor, Prashant D. Sonawane","doi":"10.1111/pbi.14459","DOIUrl":"https://doi.org/10.1111/pbi.14459","url":null,"abstract":"&lt;p&gt;Vitamin D is a lipid-soluble sterol that plays an essential role in human health. Deficiency of this vitamin increases the risk of osteoporosis, hypertension, autoimmune diseases, infectious disease, diabetes and cancer. Vitamin D exists in two major forms: vitamin D&lt;sub&gt;3&lt;/sub&gt; (cholecalciferol), mainly found in animal food source, and vitamin D&lt;sub&gt;2&lt;/sub&gt; (ergocalciferol), typically present in sundried and ultraviolet-B (UV-B) exposed fungi and yeast (Jäpelt &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2013&lt;/span&gt;). Vitamin D&lt;sub&gt;3&lt;/sub&gt; is produced in human skin upon sunlight exposure, where pro-vitamin D&lt;sub&gt;3&lt;/sub&gt; (7-dehydrocholesterol; 7-DHC) is converted to vitamin D&lt;sub&gt;3&lt;/sub&gt; by UV-B light (290–315 nm). Unfortunately, vitamin D&lt;sub&gt;3&lt;/sub&gt; deficiency is common in both children and adults worldwide. Endogenous synthesis of vitamin D&lt;sub&gt;3&lt;/sub&gt; in human skin is inhibited by several factors such as melanin presence, sunlight intensity, pollution and geographic location. Therefore, dietary sources are essential for maintaining consistent vitamin D&lt;sub&gt;3&lt;/sub&gt; levels. Unfortunately, few dietary sources and supplements naturally contain vitamin D&lt;sub&gt;3&lt;/sub&gt; and most of these are animal-based foods (e.g. meat and eggs), which raises concerns about vitamin D&lt;sub&gt;3&lt;/sub&gt; levels among those populations that consume low amounts of animal products (Black &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;).&lt;/p&gt;\u0000&lt;p&gt;Plants harbour an enormous reservoir of diverse steroidal molecules and, in principle, could be a source of vitamin D&lt;sub&gt;3&lt;/sub&gt;. However, although vitamin D&lt;sub&gt;3&lt;/sub&gt; has been identified in some plants and algae, the levels are much lower compared to animal-based sources. The precursor of vitamin D&lt;sub&gt;3&lt;/sub&gt;, 7-DHC, is also the immediate precursor for cholesterol biosynthesis in plants (Figure 1a) (Sonawane &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;). Since most plants produce cholesterol in very low amounts, 7-DHC levels are low as well. Notably, &lt;i&gt;Solanaceae&lt;/i&gt; family members (e.g. tomato and &lt;i&gt;Nicotiana benthamiana&lt;/i&gt;) accumulate naturally high levels of cholesterol. In tomato and other &lt;i&gt;Solanum&lt;/i&gt; food crops such as potato and eggplant, cholesterol serves as a starting precursor for biosynthesis of defensive steroidal glycoalkaloids (SGAs) (Sonawane &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;). Using the recently elucidated cholesterol pathway in plants along with gene editing strategies, it is now possible to engineer high levels of 7-DHC and therefore, vitamin D&lt;sub&gt;3&lt;/sub&gt; in plants. Here, we report metabolic engineering approaches to enhance vitamin D&lt;sub&gt;3&lt;/sub&gt; production in tomato (&lt;i&gt;Solanum lycopersicum&lt;/i&gt;) and &lt;i&gt;N. benthamiana&lt;/i&gt; plants.&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/85d61b05-6977-4ef7-89be-4819803e5579/pbi14459-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/85d61b05-6977-4ef7-89be-4819803e5579/pbi14459-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/a7f4769b-85b3-4d88","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"115 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234058","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 gain‐of‐function mutation at the C‐terminus of FT‐D1 promotes heading by interacting with 14‐3‐3A and FDL6 in wheat 小麦中 FT-D1 C 端的功能增益突变通过与 14-3-3A 和 FDL6 相互作用而促进头状花序的形成
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-14 DOI: 10.1111/pbi.14474
Yuting Li, Hongchun Xiong, Huijun Guo, Yongdun Xie, Linshu Zhao, Jiayu Gu, Huiyuan Li, Shirong Zhao, Yuping Ding, Chunyun Zhou, Zhengwu Fang, Luxiang Liu
SummaryVernalization and photoperiod pathways converging at FT1 control the transition to flowering in wheat. Here, we identified a gain‐of‐function mutation in FT‐D1 that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray‐induced eh1 wheat mutant. Knockout of the wild‐type and overexpression of the mutated FT‐D1 indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT‐D1eh1 exon 3 led to gain‐of‐function interactions with 14‐3‐3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering‐related transcriptomic programme. This mutation did not affect FT‐D1eh1 interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT‐D1 translocation to the shoot apical meristem. Furthermore, the ‘Segment B’ external loop is essential for FT‐D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, ELF5, was identified as the FT‐D1 regulatory target. This study illustrates FT‐D1 function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines.
摘要在 FT1 处汇聚的冬化和光周期途径控制着小麦向开花的过渡。在这里,我们发现了 FT-D1 的功能增益突变,该突变导致伽马射线诱导的 eh1 小麦突变体的打顶日期(HD)提前、株高和穗长缩短。敲除野生型和过表达突变的 FT-D1 表明,两个等位基因都具有影响 HD 和株高的功能。蛋白质相互作用测定表明,FT-D1eh1 外显子 3 的框架移位突变导致了与 14-3-3A 和 FDL6 的功能增益相互作用,从而使花粉激活复合物(FAC)得以形成,进而激活了与开花相关的转录组程序。这种突变并不影响 FT-D1eh1 与 TaNaKR5 或 TaFTIP7 的相互作用,这两种物质都可能通过介导 FT-D1 向嫩枝顶端分生组织的转位来调节 HD。此外,"B 段 "外环是 FT-D1 与 FDL6 相互作用的必要条件,而残基 Y85 则是与 TaNaKR5 和 TaFTIP7 相互作用的必要条件。最后,开花调控中枢基因 ELF5 被确定为 FT-D1 的调控靶标。这项研究说明了 FT-D1 在决定小麦 HD 与一系列相互作用伙伴中的功能,并为调整小麦精英品系的 HD 提供了遗传资源。
{"title":"A gain‐of‐function mutation at the C‐terminus of FT‐D1 promotes heading by interacting with 14‐3‐3A and FDL6 in wheat","authors":"Yuting Li, Hongchun Xiong, Huijun Guo, Yongdun Xie, Linshu Zhao, Jiayu Gu, Huiyuan Li, Shirong Zhao, Yuping Ding, Chunyun Zhou, Zhengwu Fang, Luxiang Liu","doi":"10.1111/pbi.14474","DOIUrl":"https://doi.org/10.1111/pbi.14474","url":null,"abstract":"SummaryVernalization and photoperiod pathways converging at <jats:italic>FT1</jats:italic> control the transition to flowering in wheat. Here, we identified a gain‐of‐function mutation in <jats:italic>FT‐D1</jats:italic> that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray‐induced <jats:italic>eh1</jats:italic> wheat mutant. Knockout of the wild‐type and overexpression of the mutated <jats:italic>FT‐D1</jats:italic> indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT‐D1<jats:sup><jats:italic>eh1</jats:italic></jats:sup> exon 3 led to gain‐of‐function interactions with 14‐3‐3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering‐related transcriptomic programme. This mutation did not affect <jats:italic>FT‐D1</jats:italic><jats:sup><jats:italic>eh1</jats:italic></jats:sup> interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT‐D1 translocation to the shoot apical meristem. Furthermore, the ‘Segment B’ external loop is essential for FT‐D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, <jats:italic>ELF5</jats:italic>, was identified as the <jats:italic>FT‐D1</jats:italic> regulatory target. This study illustrates <jats:italic>FT‐D1</jats:italic> function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"7 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233345","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 natural variation contributes to sugar accumulation in fruit during tomato domestication 番茄驯化过程中的自然变异有助于果实中的糖分积累
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-13 DOI: 10.1111/pbi.14471
Zhiqiang Wang, Yarong Zhao, Minmin Zheng, Shuojun Yu, Yang Gao, Guangtao Zhu, Jian-Kang Zhu, Kai Hua, Zhen Wang
<p>Tomato is the most widely consumed fruit and vegetable crop in the world, serving as an important source of micronutrients in human diet (Zhu <i>et al</i>., <span>2018</span>). The impact of sugar on the taste of tomato fruits is generally estimated by determining their total soluble solids (TSS) accumulation (Kader, <span>2008</span>), therefore, the determination of TSS is responsible for the fruit quality of tomato designed for fresh market. However, domestication has resulted in a decline in fruit taste from wild ancestors to modern tomato cultivars (Tieman <i>et al</i>., <span>2017</span>). To understand the genetic basis causing this decline, we measured the TSS contents in fruits from a population consisting of 46 wild <i>Solanum pimpinellifolium</i> (SP), 94 semi-domesticated <i>S. lycopersicum</i> var. <i>cerasiforme</i> (SLC) and 148 fully domesticated <i>S. lycopersicum</i> var. <i>lycopersicum</i> (SLL) with large natural variations (Figure S1a; Data set S1). We conducted a genome-wide association study (GWAS) for the TSS using this tomato population with a total of 7 632 172 common SNPs (Zhu <i>et al</i>., <span>2018</span>). The <i>P</i>-value of 1.31 × 10<sup>−7</sup> was set as the significance threshold after Bonferroni-adjusted correction. Two significant associations with TSS levels were identified on chromosomes 8 and 9 (Figure 1a). An extracellular invertase encoding gene <i>Lin5</i> (Solyc09g010080) was found from 11 018 to 6892 bp upstream of the leading SNP (SNP<sub>t</sub>, <i>P</i> = 1.10 × 10<sup>−7</sup>) on chromosome 9 (Figure 1b; Data set S2). The Lin5 facilitates the cleavage of sucrose in apoplast, impacting sugar supply from source organs to fruits in tomato. The variation for <i>Brix9-2-5</i> of <i>Lin5</i> resulted in the conversion of asparagine to glutamic acid at position 348 in <i>S. lycopersicum</i>, which was considered to be a major reason for the decrease in enzyme activity and fruit sink strength compared to the green-fruited <i>S. pennellii</i> (Fridman <i>et al</i>., <span>2004</span>). Sequence analysis revealed the variation of <i>Brix9-2-5</i> was not involved in the red-fruited tomato population, while another significant variation SNP2458 residing in <i>Lin5</i> coding region (2458 bp relative to the start codon) was in strong linkage disequilibrium (<i>r</i><sup><i>2</i></sup> = 0.89) with SNP<sub>t</sub>, thus closely associating with TSS levels (Figure 1b; Data set S3). Based on the reference genome, we found that the SNP2458 variation causes a conversion of adenine (A) to guanine (G), resulting in the substitution of asparagine (N) with aspartic acid (D) at position 366 of Lin5 (Figure 1b). All accessions were subsequently classified into two haplotype groups according to the SNP2458 variation. Accessions with alternative <i>Lin5</i><sup><i>2458G</i></sup> belong to haplotype 1 (Hap1) group, whereas genotypes with reference <i>Lin5</i><sup><i>2458A</i></sup> are representatives of Hap2 gr
由聚合酶 II(CaMV 35S 增强子-CmYLCV)和 III(拟南芥 U6-26)启动子组成的复合启动子用于启动 pegRNA 转录,而与 SpCas9(R221K/N394K/H840A)缺口酶融合的莫隆尼鼠白血病病毒反转录酶(M-MLV RT)的表达则由两个串联重复的 CaMV 35S(2× 35S)启动子驱动(Yourik 等人,2019 年)。由 2× 35S 启动子驱动的 rbcsE9 终止子上游的表达盒 SlPMS1dn-amiR-SlMSH2 被特别添加到 tPE4max 编辑器中,以抑制 DNA 错配修复途径。针对 SNP2458 变异设计了两个 pegRNA,分别产生野生番茄 TS-21 中的 D366N 替换和栽培番茄 Ailsa Craig(AC)中的 N366D 替换(图 1f)。在再生的 TS-21 植株中,tPE4max 的编辑效率为 12.7%,显著高于 tPE2max 的 7.4%;而在再生的稳定 AC 植株中,tPE4max 的编辑效率高达 20.3%,与 tPE2max 的 20.7%相近(图 1g、h)。桑格测序表明,在基因编辑品系中,所有六个潜在的脱靶位点都不包含突变(表 S1)。遗传性分析表明,同源编辑株系的所有后代都保持了 SNP2458 上的编辑碱基,而杂合编辑植株的后代在该位点上发生了遗传分离(图 1h),这表明两个主编辑器可以在番茄基因组中实现可遗传的精确碱基替换,但编辑效率还可以进一步提高。番茄果重与含糖量之间的负相关被认为可能与 Lin5 基因的多态性有关(Tieman 等,2017 年)。因此,我们测量了同源编辑番茄品系果实的鲜重和TSS水平。结果显示,与野生型植株相比,编辑的 TS-21 株系果实中的 TSS 水平降低,而编辑的 AC 株系果实中的 TSS 水平升高,但果实生物量与野生型植株相当(图 1-k),这证明在番茄驯化过程中,Lin5 基因中的 SNP2458 可能是造成果实糖分积累的原因,而不是果实大小。总之,我们的研究结果表明,在番茄驯化过程中,Lin5编码区的自然变异导致了栽培番茄TSS含量的下降。野生 Lin5 变异为番茄果实品质的改良提供了宝贵的天然资源和遗传标记。我们成功地克服了在番茄中使用基因编辑技术的障碍,这无疑将有助于野生番茄的快速驯化。
{"title":"A natural variation contributes to sugar accumulation in fruit during tomato domestication","authors":"Zhiqiang Wang, Yarong Zhao, Minmin Zheng, Shuojun Yu, Yang Gao, Guangtao Zhu, Jian-Kang Zhu, Kai Hua, Zhen Wang","doi":"10.1111/pbi.14471","DOIUrl":"https://doi.org/10.1111/pbi.14471","url":null,"abstract":"&lt;p&gt;Tomato is the most widely consumed fruit and vegetable crop in the world, serving as an important source of micronutrients in human diet (Zhu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;). The impact of sugar on the taste of tomato fruits is generally estimated by determining their total soluble solids (TSS) accumulation (Kader, &lt;span&gt;2008&lt;/span&gt;), therefore, the determination of TSS is responsible for the fruit quality of tomato designed for fresh market. However, domestication has resulted in a decline in fruit taste from wild ancestors to modern tomato cultivars (Tieman &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;). To understand the genetic basis causing this decline, we measured the TSS contents in fruits from a population consisting of 46 wild &lt;i&gt;Solanum pimpinellifolium&lt;/i&gt; (SP), 94 semi-domesticated &lt;i&gt;S. lycopersicum&lt;/i&gt; var. &lt;i&gt;cerasiforme&lt;/i&gt; (SLC) and 148 fully domesticated &lt;i&gt;S. lycopersicum&lt;/i&gt; var. &lt;i&gt;lycopersicum&lt;/i&gt; (SLL) with large natural variations (Figure S1a; Data set S1). We conducted a genome-wide association study (GWAS) for the TSS using this tomato population with a total of 7 632 172 common SNPs (Zhu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;). The &lt;i&gt;P&lt;/i&gt;-value of 1.31 × 10&lt;sup&gt;−7&lt;/sup&gt; was set as the significance threshold after Bonferroni-adjusted correction. Two significant associations with TSS levels were identified on chromosomes 8 and 9 (Figure 1a). An extracellular invertase encoding gene &lt;i&gt;Lin5&lt;/i&gt; (Solyc09g010080) was found from 11 018 to 6892 bp upstream of the leading SNP (SNP&lt;sub&gt;t&lt;/sub&gt;, &lt;i&gt;P&lt;/i&gt; = 1.10 × 10&lt;sup&gt;−7&lt;/sup&gt;) on chromosome 9 (Figure 1b; Data set S2). The Lin5 facilitates the cleavage of sucrose in apoplast, impacting sugar supply from source organs to fruits in tomato. The variation for &lt;i&gt;Brix9-2-5&lt;/i&gt; of &lt;i&gt;Lin5&lt;/i&gt; resulted in the conversion of asparagine to glutamic acid at position 348 in &lt;i&gt;S. lycopersicum&lt;/i&gt;, which was considered to be a major reason for the decrease in enzyme activity and fruit sink strength compared to the green-fruited &lt;i&gt;S. pennellii&lt;/i&gt; (Fridman &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2004&lt;/span&gt;). Sequence analysis revealed the variation of &lt;i&gt;Brix9-2-5&lt;/i&gt; was not involved in the red-fruited tomato population, while another significant variation SNP2458 residing in &lt;i&gt;Lin5&lt;/i&gt; coding region (2458 bp relative to the start codon) was in strong linkage disequilibrium (&lt;i&gt;r&lt;/i&gt;&lt;sup&gt;&lt;i&gt;2&lt;/i&gt;&lt;/sup&gt; = 0.89) with SNP&lt;sub&gt;t&lt;/sub&gt;, thus closely associating with TSS levels (Figure 1b; Data set S3). Based on the reference genome, we found that the SNP2458 variation causes a conversion of adenine (A) to guanine (G), resulting in the substitution of asparagine (N) with aspartic acid (D) at position 366 of Lin5 (Figure 1b). All accessions were subsequently classified into two haplotype groups according to the SNP2458 variation. Accessions with alternative &lt;i&gt;Lin5&lt;/i&gt;&lt;sup&gt;&lt;i&gt;2458G&lt;/i&gt;&lt;/sup&gt; belong to haplotype 1 (Hap1) group, whereas genotypes with reference &lt;i&gt;Lin5&lt;/i&gt;&lt;sup&gt;&lt;i&gt;2458A&lt;/i&gt;&lt;/sup&gt; are representatives of Hap2 gr","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"27 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198028","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
Editing of OsPsaL gene improves both yield and antiviral immunity in rice 编辑 OsPsaL 基因可提高水稻产量和抗病毒免疫力
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-13 DOI: 10.1111/pbi.14473
Ruifang Zhang, Hehong Zhang, Lulu Li, Yanjun Li, Kaili Xie, Jianping Chen, Zongtao Sun
<p>Rice (<i>Oryza sativa</i>) is a staple food supply for over half of the global population. Various phytopathogens including viruses pose a significant threat to rice yield and quality. Southern rice black-streaked dwarf virus (SRBSDV), belonged to the genus <i>Fijivirus</i>, family <i>Reoviridae</i>, has become a major virus species leading to substantial crop losses in Asian nations (Zhang <i>et al</i>., <span>2023</span>). Traditional breeding and commercial rice varieties face challenges in achieving viral resistance due to the absence of natural resistance. Therefore, it is crucial to utilize biotechnology methods to create and cultivate resistant germplasm for the prevention and control of viral diseases.</p><p>Oxygenic photosynthesis is the primary process that converts sunlight into chemical energy in higher plants. The light reaction of photosynthesis is driven by photosystems I and II (PSI and PSII). PSI is a membrane protein complex that enables sunlight-driven transmembrane electron transfer as a component of the photosynthetic machinery (Malavath <i>et al</i>., <span>2018</span>; Varotto <i>et al</i>., <span>2000</span>). As a component of PSI, PsaL is crucial for the formation of PSI trimers, a process likely reliant on the binding of calcium ions to the PsaL subunit. However, the involvement of PsaL in plant growth and immunity remains unclear.</p><p>Clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) technology have been effectively utilized to create new cultivars from wild species via de novo domestication (Bai <i>et al</i>., <span>2023</span>). In this study, we demonstrate the successful application of CRISPR/Cas9 in rice to create the transgenic lines with superior agronomic traits and resistance to SRBSDV. We firstly found that the expression level of <i>OsPsaL</i> gene was significantly down-regulated following SRBSDV infection (Figure 1a). Then, we generated two independent <i>ospsal-ko</i> mutants (<i>ospsal-1</i> and <i>ospsal-2</i>) via the CRISPR/Cas9 system in the <i>Nipponbare</i> (NIP) background (Figure 1b,c). Subsequently, we used chlorophyll fluorescence to assess the photosynthetic traits of transgenic plants. In contrast to the wild type, the electron transport rate (ETR) and net photosynthetic efficiency (pN) notably increased, while Y(NO), an indicator of unregulated heat dissipation and fluorescence, decreased as light intensity rose in <i>ospsal-ko</i> (Figure 1d–f), indicating that photosynthesis has been enhanced in the mutant. We further constructed overexpressing <i>OsPsaL</i>-transgenic rice named <i>OsPsaL-ox</i> (<i>OsPsaL-3#</i> and <i>OsPsaL-4#</i>) (Figure S1a,b). <i>OsPsaL-ox</i> plants displayed a decreased electron transport rate and net photosynthetic efficiency but exhibited no variance in Y (NO) compared to wild type (Figure S1c–e). Statistical analysis revealed that <i>ospsal-ko</i> has a higher number of tillers, panicles, and grains per plant, b
与野生型植株相比,OsPsaL-ox 植株表现出更严重的矮化,病毒的 RNA 和蛋白质水平积累更高(图 S1l-n)。这些结果表明,OsPsaL 在水稻抵抗 SRBSDV 的过程中起负作用。为了探索ospsal-ko的广谱抗病性,我们给转基因植株接种了不同类型的水稻病毒(水稻条纹病毒,RSV),结果发现ospsal-ko也表现出对RSV的抗性,而OsPsaL-ox对RSV表现出更高的敏感性(图1p-r和图S1o-q)。我们进一步对 ZH11 和 OsPsaL-ox 感染 SRBSDV 的反应进行了转录组测序,研究了在 OsPsaL-3#-V 与 OsPsaL-3#-H 的比较中具有特异表达,但在 ZH11-V 与 ZH11-H 的比较中未发现的差异表达基因,结果发现了 2178 个基因(图 S1r)。与 ZH11 相比,这些基因在 SRBSDV 感染的 OsPsaL-3# 植株中大多受到抑制。GO 分析表明,这些下调基因高度富集于光合作用中(图 S1s)。这些发现表明 OsPsaL-ox 水稻的光合作用受到 SRBSDV 的严重影响。此外,对转录组的全面分析表明,与 ZH11 相比,OsPsaL-3# 中与茉莉酸(JA)相关的几个基因显著下调(图 S1t)。JA 通常被认为是重要的抗病毒途径(Li 等人,2021 年;Zhang 等人,2023 年)。进一步的 RT-qPCR 检测表明,与野生型植株相比,JA 相关基因(OsLOX2、OsAOC、OsAOS2 和 OsJMT1)的表达在 ospsal-ko 中被显著激活,而在 OsPsaL-ox 中则被抑制(图 1s;图 S1u-x)。JA 含量测定显示,与野生型植株相比,ospsal-ko 中的 JA 浓度明显较高,而 OsPsaL-ox 中则较低(图 1t;图 S1y)。JA敏感性分析表明,与对照组相比,ospsal-ko的根长明显缩短,而OsPsaL-ox的根长更长(图1u,v;图S1z,a2),表明OsPsaL在JA通路中的负调控作用。综上所述,我们发现了一个新的易感因子 OsPsaL,并证明敲除 OsPsaL 基因可提高水稻产量和抗病毒免疫力。因此,本研究为今后提高水稻产量和抗病毒免疫力的研究提供了宝贵的遗传资源。
{"title":"Editing of OsPsaL gene improves both yield and antiviral immunity in rice","authors":"Ruifang Zhang, Hehong Zhang, Lulu Li, Yanjun Li, Kaili Xie, Jianping Chen, Zongtao Sun","doi":"10.1111/pbi.14473","DOIUrl":"https://doi.org/10.1111/pbi.14473","url":null,"abstract":"&lt;p&gt;Rice (&lt;i&gt;Oryza sativa&lt;/i&gt;) is a staple food supply for over half of the global population. Various phytopathogens including viruses pose a significant threat to rice yield and quality. Southern rice black-streaked dwarf virus (SRBSDV), belonged to the genus &lt;i&gt;Fijivirus&lt;/i&gt;, family &lt;i&gt;Reoviridae&lt;/i&gt;, has become a major virus species leading to substantial crop losses in Asian nations (Zhang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;). Traditional breeding and commercial rice varieties face challenges in achieving viral resistance due to the absence of natural resistance. Therefore, it is crucial to utilize biotechnology methods to create and cultivate resistant germplasm for the prevention and control of viral diseases.&lt;/p&gt;\u0000&lt;p&gt;Oxygenic photosynthesis is the primary process that converts sunlight into chemical energy in higher plants. The light reaction of photosynthesis is driven by photosystems I and II (PSI and PSII). PSI is a membrane protein complex that enables sunlight-driven transmembrane electron transfer as a component of the photosynthetic machinery (Malavath &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;; Varotto &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2000&lt;/span&gt;). As a component of PSI, PsaL is crucial for the formation of PSI trimers, a process likely reliant on the binding of calcium ions to the PsaL subunit. However, the involvement of PsaL in plant growth and immunity remains unclear.&lt;/p&gt;\u0000&lt;p&gt;Clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) technology have been effectively utilized to create new cultivars from wild species via de novo domestication (Bai &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;). In this study, we demonstrate the successful application of CRISPR/Cas9 in rice to create the transgenic lines with superior agronomic traits and resistance to SRBSDV. We firstly found that the expression level of &lt;i&gt;OsPsaL&lt;/i&gt; gene was significantly down-regulated following SRBSDV infection (Figure 1a). Then, we generated two independent &lt;i&gt;ospsal-ko&lt;/i&gt; mutants (&lt;i&gt;ospsal-1&lt;/i&gt; and &lt;i&gt;ospsal-2&lt;/i&gt;) via the CRISPR/Cas9 system in the &lt;i&gt;Nipponbare&lt;/i&gt; (NIP) background (Figure 1b,c). Subsequently, we used chlorophyll fluorescence to assess the photosynthetic traits of transgenic plants. In contrast to the wild type, the electron transport rate (ETR) and net photosynthetic efficiency (pN) notably increased, while Y(NO), an indicator of unregulated heat dissipation and fluorescence, decreased as light intensity rose in &lt;i&gt;ospsal-ko&lt;/i&gt; (Figure 1d–f), indicating that photosynthesis has been enhanced in the mutant. We further constructed overexpressing &lt;i&gt;OsPsaL&lt;/i&gt;-transgenic rice named &lt;i&gt;OsPsaL-ox&lt;/i&gt; (&lt;i&gt;OsPsaL-3#&lt;/i&gt; and &lt;i&gt;OsPsaL-4#&lt;/i&gt;) (Figure S1a,b). &lt;i&gt;OsPsaL-ox&lt;/i&gt; plants displayed a decreased electron transport rate and net photosynthetic efficiency but exhibited no variance in Y (NO) compared to wild type (Figure S1c–e). Statistical analysis revealed that &lt;i&gt;ospsal-ko&lt;/i&gt; has a higher number of tillers, panicles, and grains per plant, b","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"44 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198219","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
High-yield, plant-based production of an antimicrobial peptide with potent activity in a mouse model 在小鼠模型中以植物为基础高产生产具有强效活性的抗菌肽
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-12 DOI: 10.1111/pbi.14460
Shahid Chaudhary, Zahir Ali, Aarón Pantoja-Angles, Sherin Abdelrahman, Cynthia Olivia Baldelamar Juárez, Gundra Sivakrishna Rao, Pei-Ying Hong, Charlotte Hauser, Magdy Mahfouz
Plants offer a promising chassis for the large-scale, cost-effective production of diverse therapeutics, including antimicrobial peptides (AMPs). However, key advances will reduce production costs, including simplifying the downstream processing and purification steps. Here, using Nicotiana benthamiana plants, we present an improved modular design that enables AMPs to be secreted via the endomembrane system and sequestered in an extracellular compartment, the apoplast. Additionally, we translationally fused an AMP to a mutated small ubiquitin-like modifier sequence, thereby enhancing peptide yield and solubilizing the peptide with minimal aggregation and reduced occurrence of necrotic lesions in the plant. This strategy resulted in substantial peptide accumulation, reaching around 2.9 mg AMP per 20 g fresh weight of leaf tissue. Furthermore, the purified AMP demonstrated low collateral toxicity in primary human skin cells, killed pathogenic bacteria by permeabilizing the membrane and exhibited anti-infective efficacy in a preclinical mouse (Mus musculus) model system, reducing bacterial loads by up to three orders of magnitude. A base-case techno-economic analysis demonstrated the economic advantages and scalability of our plant-based platform. We envision that our work can establish plants as efficient bioreactors for producing preclinical-grade AMPs at a commercial scale, with the potential for clinical applications.
植物为大规模、经济高效地生产包括抗菌肽(AMPs)在内的各种治疗药物提供了一个前景广阔的底盘。然而,关键的进步将降低生产成本,包括简化下游处理和纯化步骤。在这里,我们利用烟草植物提出了一种改进的模块化设计,它能使 AMPs 通过内膜系统分泌,并被封存在细胞外区室--凋亡体中。此外,我们还将 AMP 与突变的小泛素样修饰序列进行了翻译融合,从而提高了多肽的产量,并使多肽在溶解过程中的聚集最小化,减少了植物坏死病变的发生。这一策略使多肽大量积累,达到每 20 克叶片组织鲜重约 2.9 毫克 AMP。此外,纯化的 AMP 在人类原生皮肤细胞中显示出较低的附带毒性,通过渗透膜杀死致病细菌,并在临床前小鼠(麝香猫)模型系统中显示出抗感染功效,可将细菌数量减少三个数量级。基础技术经济分析表明了我们基于植物的平台的经济优势和可扩展性。我们设想,我们的工作可以将植物建成高效的生物反应器,以商业规模生产临床前级 AMPs,并有可能应用于临床。
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引用次数: 0
Comparative evaluation of gene copy number estimation techniques in genetically modified crops: insights from Southern blotting, qPCR, dPCR and NGS 转基因作物基因拷贝数估算技术的比较评估:Southern 印迹、qPCR、dPCR 和 NGS 的启示
IF 13.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-12 DOI: 10.1111/pbi.14466
Wenting Xu, Jingang Liang, Fan Wang, Litao Yang
<p>Gene copy number is crucial for understanding genomic architecture and its implications in plant and animal genetics (Alonge <i>et al</i>., <span>2020</span>; Castagnone-Sereno <i>et al</i>., <span>2019</span>). In agriculture, variations in gene copy number (CNVs) are vital as they affect yield, stress resistance and metabolic capabilities (Yuan <i>et al</i>., <span>2021</span>). Transgenesis, involving the introduction of foreign DNA into plant genomes, has revolutionized agriculture by creating genetically modified (GM) plants with desirable traits. Assessing gene copy numbers in GMOs ensures stability and expression of introduced traits and is crucial for regulatory compliance and biosafety assessments (Liang <i>et al</i>., <span>2022</span>). Evaluating gene copy numbers in transgenic plants is technically challenging due to variability in transgene integration events (Faure, <span>2021</span>). Various techniques like Southern blotting (SB), quantitative real-time PCR (qPCR), digital PCR (dPCR) and paired-end whole-genome sequencing (PE-WGS) have been reported for gene copy number determination (Cusenza <i>et al</i>., <span>2021</span>). However, no systematic comparison of these four methods has been reported, especially concerning PE-WGS.</p><p>Here, we performed a comparative benchmarking of gene copy number assessment techniques, including SB, qPCR, dPCR and PE-WGS, employing 4 GM crop events (FG72 soybean, 12-5 maize, G6H1 and G281 rice) as examples (Figure 1a; Data S1).</p><figure><picture><source media="(min-width: 1650px)" srcset="/cms/asset/800ca9d8-87ce-48cd-b7cf-1f99deca6de1/pbi14466-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/800ca9d8-87ce-48cd-b7cf-1f99deca6de1/pbi14466-fig-0001-m.jpg" loading="lazy" src="/cms/asset/dec6a469-300e-43d3-a4bf-08ed5e20ab2a/pbi14466-fig-0001-m.png" title="Details are in the caption following the image"/></picture><figcaption><div><strong>Figure 1<span style="font-weight:normal"></span></strong><div>Open in figure viewer<i aria-hidden="true"></i><span>PowerPoint</span></div></div><div>(a) The workflow of the benchmarking study of gene copy number estimation, the diagrams of exogenous gene cassettes of the tested GM events (FG72, G281, G6H1 and 12-5), and the position of hybrid probes in Southern blotting analysis. (b) Southern blotting analysis of four events with various restriction enzymes. GM, GM event; M, DNA marker; P, positive control; WT, the corresponding recipient line of GM event. (c) The constructed standard curves of qPCR assays employing corresponding plasmid calibrators of exogenous and endogenous genes. (d) Summarizes the copy numbers of transgenes determined from Southern blotting, qPCR, ddPCR and PE-WGS analysis. (e) Advantages and disadvantages of the four methods in transgene copy number evaluation. dPCR, digital PCR; GM, genetically modified; PCR, polymerase chain reaction; PE-WGS, paired-end whole-genome sequencing;
基因拷贝数对于了解基因组结构及其对动植物遗传学的影响至关重要(Alonge 等人,2020 年;Castagnone-Sereno 等人,2019 年)。在农业领域,基因拷贝数(CNV)的变化至关重要,因为它们会影响产量、抗逆性和代谢能力(Yuan 等人,2021 年)。转基因涉及将外来 DNA 导入植物基因组,通过创造具有理想性状的转基因植物,使农业发生了革命性变化。评估转基因生物的基因拷贝数可确保所引入性状的稳定性和表达,对于监管合规和生物安全评估至关重要(Liang 等人,2022 年)。由于转基因整合事件的变异性,评估转基因植物的基因拷贝数在技术上具有挑战性(Faure,2021 年)。据报道,有多种技术可用于基因拷贝数测定,如 Southern 印迹(SB)、定量实时 PCR(qPCR)、数字 PCR(dPCR)和成对全基因组测序(PE-WGS)(Cusenza 等,2021 年)。在此,我们以 4 个转基因作物事件(FG72 大豆、12-5 玉米、G6H1 和 G281 水稻)为例,对基因拷贝数评估技术(包括 SB、qPCR、dPCR 和 PE-WGS)进行了比较基准测试(图 1a;数据 S1)。图 1在图形浏览器中打开PowerPoint(a)基因拷贝数估算基准研究的工作流程、被测转基因事件(FG72、G281、G6H1 和 12-5)的外源基因盒图以及 Southern 印迹分析中杂交探针的位置。(b) 用各种限制性酶对四个基因事件进行 Southern 印迹分析。GM,GM 事件;M,DNA 标记;P,阳性对照;WT,GM 事件的相应受体系。(c) 利用外源基因和内源基因的相应质粒校准物构建的 qPCR 检测标准曲线。(d) 通过 Southern 印迹、qPCR、ddPCR 和 PE-WGS 分析确定的转基因拷贝数。(dPCR, digital PCR; GM, genetically modified; PCR, polymerase chain reaction; PE-WGS, paired-end whole-genome sequencing; qPCR, quantitative PCR.在 SB 分析中,我们使用了多种限制性内切酶进行基因组 DNA 消化。在 G6H1 事件中,BamHI、SacI、KpnI 和 StuI 发现了 cry1Ab/vip3H 和 G6epsps 的一个拷贝。G281 事件显示了一个 hLF 拷贝,但 G6epsps 拷贝数不确定(一个或两个)。FG72 显示了 2mepsps 和 hppdPfW336 不一致的条带模式,表明拷贝数为一个或两个。用 KpnI 和 XbaI 分析的玉米 12-5 表明 G10epsps 和 cry1Ab/cry2Aj 只有一个拷贝(图 1b,表 S1)。所有检测方法都经过了高效和精确的验证(图 1c,表 S2)。实时定量 PCR 结果显示,G6H1 的 G6epsps 和 cry1Ab/vip3H 的值分别为 0.98 和 0.96;G281 的 G6epsps 和 hLF 的值分别为 1.68 和 1.54;FG72 的 2mepsps 和 hppdPfW336 的值分别为 1.72 和 1.67;玉米 12-5 的 G10epsps 和 cry1Ab/cry2Aj 的值分别为 0.81 和 0.83(表 S3)。这些数值表明 G6H1 和 12-5 有一个 T-DNA 片段整合,而 G281 和 FG72 有两个片段整合。结果显示,G6H1 的 G6epsps 和 cry1Ab/vip3H 的拷贝数分别为 0.94 和 0.97。G281 的 G6epsps 和 hLF 分别为 1.85 和 1.93。FG72 的 2mepsps 和 hppdPfW336 分别为 1.69 和 1.68。12-5 的 G10epsps 和 cry1Ab/cry2A 分别为 0.57 和 0.59(表 S4)。在 PE-WGS 分析中,G6H1、G281、FG72 和 12-5 的测序深度分别为 28.81、28.91、48.70 和 23.94(表 S5)。目标基因的读数被用来计算拷贝数:G6H1 有 1.08 个 G6epsps 拷贝和 0.83 个 cry1Ab/vip3H 拷贝;G281 有 2.01 个 G6epsps 拷贝和 1.91 个 hLF 拷贝;FG72 有 1.80 个 2mepsps 拷贝和 2.00 个 hppdPfW336 拷贝;12-5 有 0.我们对四种转基因事件的系统测量表明,所有四种技术在不同程度上都适用于这一目的。所有方法都能准确量化单拷贝基因,但在多拷贝基因方面出现了差异(图 1d)。图 1e 总结了每种方法在各方面的优势和局限性。Southern 印迹法往往会因串联重复等复杂排列而低估多拷贝基因,也会因消化不完全和交叉杂交而高估多拷贝基因。
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引用次数: 0
Towards chloroplastic nanofactories: formation of proteinaceous scaffolds for metabolic engineering. 迈向叶绿体纳米工厂:形成用于代谢工程的蛋白质支架。
IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-06 DOI: 10.1111/pbi.14462
Matthew E Dwyer, John E Froehlich, Daniel A Raba, Melissa Borrusch, Linda Danhof, Naveen Sharma, Eric J Young, Federica Brandizzi, Christoph Benning, Cheryl A Kerfeld
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引用次数: 0
eIF2Bβ confers resistance to Turnip mosaic virus by recruiting ALKBH9B to modify viral RNA methylation eIF2Bβ 通过招募 ALKBH9B 来改变病毒 RNA 的甲基化,从而产生对芜菁花叶病毒的抗性。
IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-04 DOI: 10.1111/pbi.14442
Tongyun Sha, Zhangping Li, Shirui Xu, Tongbing Su, Jannat Shopan, Xingming Jin, Yueying Deng, Xiaolong Lyu, Zhongyuan Hu, Mingfang Zhang, Jinghua Yang

Eukaryotic translation initiation factors (eIFs) are the primary targets for overcoming RNA virus resistance in plants. In a previous study, we mapped a BjeIF2Bβ from Brassica juncea representing a new class of plant virus resistance genes associated with resistance to Turnip mosaic virus (TuMV). However, the mechanism underlying eIF2Bβ-mediated virus resistance remains unclear. In this study, we discovered that the natural variation of BjeIF2Bβ in the allopolyploid B. juncea was inherited from one of its ancestors, B. rapa. By editing of eIF2Bβ, we were able to confer resistance to TuMV in B. juncea and in its sister species of B. napus. Additionally, we identified an N6-methyladenosine (m6A) demethylation factor, BjALKBH9B, for interaction with BjeIF2Bβ, where BjALKBH9B co-localized with both BjeIF2Bβ and TuMV. Furthermore, BjeIF2Bβ recruits BjALKBH9B to modify the m6A status of TuMV viral coat protein RNA, which lacks the ALKB homologue in its genomic RNA, thereby affecting viral infection. Our findings have applications for improving virus resistance in the Brassicaceae family through natural variation or genome editing of the eIF2Bβ. Moreover, we uncovered a non-canonical translational control of viral mRNA in the host plant.

真核翻译起始因子(eIF)是克服植物 RNA 病毒抗性的主要靶标。在之前的一项研究中,我们绘制了来自甘蓝的 BjeIF2Bβ,它代表了一类新的植物病毒抗性基因,与对芜菁花叶病毒(TuMV)的抗性有关。然而,eIF2Bβ介导病毒抗性的机制仍不清楚。在这项研究中,我们发现全多倍体君子兰(B. juncea)中 BjeIF2Bβ 的自然变异是由其祖先之一 B. rapa 遗传而来的。通过编辑 eIF2Bβ,我们能够赋予君子兰及其姊妹种油菜对 TuMV 的抗性。此外,我们还发现了一种 N6-甲基腺苷(m6A)去甲基化因子 BjALKBH9B 与 BjeIF2Bβ 相互作用,其中 BjALKBH9B 与 BjeIF2Bβ 和 TuMV 共定位。此外,BjeIF2Bβ招募BjALKBH9B来改变TuMV病毒衣壳蛋白RNA的m6A状态,而TuMV的基因组RNA中缺乏ALKB同源物,从而影响病毒感染。我们的发现可用于通过自然变异或基因组编辑 eIF2Bβ 来提高十字花科植物的抗病毒能力。此外,我们还发现了病毒 mRNA 在宿主植物中的非规范翻译控制。
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引用次数: 0
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Plant Biotechnology Journal
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