Background: Two-line hybrid wheat technology system is one way to harness wheat heterosis both domestically and internationally. Seed vigor is a crucial parameter for assessing seed quality, as enhanced seed vigor can lead to yield increments of over 20% to a certain extent. MicroRNAs (miRNAs) were known to participate in the development and vigor of seed in plants, but its impact on seed vigor in two-line hybrid wheat remains poorly elucidated.
Results: The hybrid (BS1453/11GF5135) wheat exhibited superiority in seed vigor and anti-aging capacity, compared to its male parent (11GF5135, MP) and female parent (BS1453, FP). We identified four miRNAs associated with seed vigor, all of which are novel miRNAs. The majority of targets of miRNAs were related to ubiquitin ligases, kinases, sucrose synthases and hydrolases, involving in starch and sucrose metabolism, hydrolysis, catalysis, plant hormone signal transduction, and other pathways, which played crucial roles in seed development. Additionally, we also found miR531 was differentially expressed in both male parent and hybrid, and its target gene was a component of the E1 subunit of α-ketoate dehydrogenase complex, which interacted with dihydrolipoamide acetyltransferase (E2) and dihydrolipoyl dehydrogenase (E3). Finally, We established a presumptive interaction model to speculate the relationship of miR531 and seed vigor.
Conclusions: This study analyzed the seed vigor of two-line hybrid wheat, and screened seed vigor-related miRNAs. Meanwhile speculated the genetic relationship of hybrid and parents, in terms of miRNAs. Consequently, the present study provides new insights into the miRNA-mediated gene and protein interaction network that regulates seed vigor. These findings hold significance for enhancing the yield and quality of two-line hybrid wheat, facilitating its future applications.
{"title":"Uncovering seed vigor responsive miRNA in hybrid wheat and its parents by deep sequencing.","authors":"Jie-Ru Yue, Yong-Jie Liu, Shao-Hua Yuan, Hui Sun, Hong-Yao Lou, Yan-Mei Li, Hao-Yu Guo, Zi-Han Liu, Feng-Ting Zhang, Nuo Zhai, Sheng-Quan Zhang, Jian-Fang Bai, Li-Ping Zhang","doi":"10.1186/s12864-024-10878-y","DOIUrl":"10.1186/s12864-024-10878-y","url":null,"abstract":"<p><strong>Background: </strong>Two-line hybrid wheat technology system is one way to harness wheat heterosis both domestically and internationally. Seed vigor is a crucial parameter for assessing seed quality, as enhanced seed vigor can lead to yield increments of over 20% to a certain extent. MicroRNAs (miRNAs) were known to participate in the development and vigor of seed in plants, but its impact on seed vigor in two-line hybrid wheat remains poorly elucidated.</p><p><strong>Results: </strong>The hybrid (BS1453/11GF5135) wheat exhibited superiority in seed vigor and anti-aging capacity, compared to its male parent (11GF5135, MP) and female parent (BS1453, FP). We identified four miRNAs associated with seed vigor, all of which are novel miRNAs. The majority of targets of miRNAs were related to ubiquitin ligases, kinases, sucrose synthases and hydrolases, involving in starch and sucrose metabolism, hydrolysis, catalysis, plant hormone signal transduction, and other pathways, which played crucial roles in seed development. Additionally, we also found miR531 was differentially expressed in both male parent and hybrid, and its target gene was a component of the E1 subunit of α-ketoate dehydrogenase complex, which interacted with dihydrolipoamide acetyltransferase (E2) and dihydrolipoyl dehydrogenase (E3). Finally, We established a presumptive interaction model to speculate the relationship of miR531 and seed vigor.</p><p><strong>Conclusions: </strong>This study analyzed the seed vigor of two-line hybrid wheat, and screened seed vigor-related miRNAs. Meanwhile speculated the genetic relationship of hybrid and parents, in terms of miRNAs. Consequently, the present study provides new insights into the miRNA-mediated gene and protein interaction network that regulates seed vigor. These findings hold significance for enhancing the yield and quality of two-line hybrid wheat, facilitating its future applications.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-22DOI: 10.1186/s12864-024-10920-z
Alishia van Heerden, Nam Q Pham, Brenda D Wingfield, Michael J Wingfield, P Markus Wilken
Elsinoë species are phytopathogenic fungi that cause serious scab diseases on economically important plants. The disease symptoms arise from the effects of a group of phytotoxins known as elsinochromes, produced via a type-I polyketide synthase (PKS) biosynthetic pathway. The elsinochrome gene cluster was first annotated in Elsinoë fawcettii where the main type-I PKS gene was characterized as EfPKS1. A later study showed that this gene and the associated cluster had not been correctly annotated, and that EfPKS1 was actually the anchor gene of the melanin biosynthetic pathway. A new type-I PKS gene EfETB1 associated with elsinochrome production was also identified. The aim of this study was to identify all type-I PKS genes in the genomes of seven Elsinoë species with the goal of independently verifying the PKS containing clusters for both melanin and elsinochrome production. A total of six type-I PKS classes were identified, although there was variation between the species in the number and type of classes present. Genes similar to the E. fawcettii EfPKS1 and EfETB1 type-I PKS genes were associated with melanin and elsinochrome production respectively in all species. The complete melanin and elsinochrome PKS containing clusters were subsequently annotated in all the species with high levels of synteny across Elsinoë species. This study provides a genus-level overview of type-I PKS distribution in Elsinoë species, including an additional line of support for the annotation of the melanin and elsinochrome PKS containing clusters in these important plant pathogens.
Elsinoë 是一种植物病原真菌,会对具有重要经济价值的植物造成严重的疮痂病。病害症状是由一组称为elsinochromes的植物毒素引起的,这些毒素是通过 I 型多酮合成酶(PKS)生物合成途径产生的。Elsinochrome 基因簇首次在 Elsinoë fawcettii 中得到注释,其中主要的 I 型 PKS 基因被命名为 EfPKS1。后来的研究表明,该基因及相关基因簇的注释并不正确,EfPKS1实际上是黑色素生物合成途径的锚基因。此外,还发现了一个与烯丙基色素生成有关的新的 I 型 PKS 基因 EfETB1。本研究的目的是鉴定 7 个 Elsinoë 物种基因组中的所有 I 型 PKS 基因,以独立验证含有黑色素和硒铬生产的 PKS 基因簇。共鉴定出六种 I 型 PKS 类群,但不同物种之间存在类群数量和类型的差异。在所有物种中,与 E. fawcettii EfPKS1 和 EfETB1 I 型 PKS 基因相似的基因分别与黑色素和硒铬的产生有关。随后,对所有物种中含有黑色素和硒铬的完整 PKS 基因簇进行了注释,发现 Elsinoë 物种之间具有高度的同源性。本研究提供了 Elsinoë 物种中 I 型 PKS 的属级分布概况,包括对这些重要植物病原体中含黑色素和硒铬 PKS 簇的注释的额外支持。
{"title":"Six type-I PKS classes and highly conserved melanin and elsinochrome gene clusters found in diverse Elsinoë species.","authors":"Alishia van Heerden, Nam Q Pham, Brenda D Wingfield, Michael J Wingfield, P Markus Wilken","doi":"10.1186/s12864-024-10920-z","DOIUrl":"10.1186/s12864-024-10920-z","url":null,"abstract":"<p><p>Elsinoë species are phytopathogenic fungi that cause serious scab diseases on economically important plants. The disease symptoms arise from the effects of a group of phytotoxins known as elsinochromes, produced via a type-I polyketide synthase (PKS) biosynthetic pathway. The elsinochrome gene cluster was first annotated in Elsinoë fawcettii where the main type-I PKS gene was characterized as EfPKS1. A later study showed that this gene and the associated cluster had not been correctly annotated, and that EfPKS1 was actually the anchor gene of the melanin biosynthetic pathway. A new type-I PKS gene EfETB1 associated with elsinochrome production was also identified. The aim of this study was to identify all type-I PKS genes in the genomes of seven Elsinoë species with the goal of independently verifying the PKS containing clusters for both melanin and elsinochrome production. A total of six type-I PKS classes were identified, although there was variation between the species in the number and type of classes present. Genes similar to the E. fawcettii EfPKS1 and EfETB1 type-I PKS genes were associated with melanin and elsinochrome production respectively in all species. The complete melanin and elsinochrome PKS containing clusters were subsequently annotated in all the species with high levels of synteny across Elsinoë species. This study provides a genus-level overview of type-I PKS distribution in Elsinoë species, including an additional line of support for the annotation of the melanin and elsinochrome PKS containing clusters in these important plant pathogens.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-22DOI: 10.1186/s12864-024-10906-x
Kgaugelo E Lekota, Refilwe O Mabeo, Tsepo Ramatla, Deidre A B Van Wyk, Oriel Thekisoe, Lesego G Molale-Tom, Cornelius C Bezuidenhout
Klebsiella variicola is considered an emerging pathogen, which may colonize a variety of hosts, including environmental sources. Klebsiella variicola investigated in this study was obtained from an influent wastewater treatment plant in the North-West Province, South Africa. Whole genome sequencing was conducted to unravel the genetic diversity and antibiotic resistance patterns of K. variicola. Whole genome core SNP phylogeny was employed on publicly available 170 genomes. Furthermore, capsule types and antibiotic resistance genes, particularly beta-lactamase and carbapenems genes were investigated from the compared genomes. A 38 099 bp bacteriophage was uncovered alongside with K. variicola genome. Whole genome sequencing revealed that the extended beta-lactamase blaLEN (75.3%) of the beta-lactamase is dominant among compared K. variicola strains. The identified IncF plasmid AA035 confers resistance genes of metal and heat element subtypes, i.e., silver, copper, and tellurium. The capsule type KL107-D1 is a predominant capsule type present in 88.2% of the compared K. variicola genomes. The phage was determined to be integrase-deficient consisting of a fosB gene associated with fosfomycin resistance and clusters with the Wbeta genus Bacillus phage group. In silico analysis showed that the phage genome interacts with B. cereus as opposed to K. variicola strain T2. The phage has anti-repressor proteins involved in the lysis-lysogeny decision. This phage will enhance our understanding of its impact on bacterial dissemination and how it may affect disease development and antibiotic resistance mechanisms in wastewater treatment plants. This study highlights the need for ongoing genomic epidemiological surveillance of environmental K. variicola isolates.
变异克雷伯氏菌被认为是一种新出现的病原体,可在包括环境来源在内的多种宿主体内定植。本研究调查的变异克雷伯氏菌来自南非西北省的一家污水处理厂。为揭示变异克雷伯氏菌的遗传多样性和抗生素耐药性模式,对其进行了全基因组测序。在公开的 170 个基因组上采用了全基因组核心 SNP 系统进化。此外,还从比较的基因组中研究了胶囊类型和抗生素耐药基因,特别是β-内酰胺酶和碳青霉烯类基因。结果发现,在 K. variicola 基因组中还有一个 38 099 bp 的噬菌体。全基因组测序显示,在所比较的变种克雷伯菌株中,扩展β-内酰胺酶blaLEN(75.3%)是主要的β-内酰胺酶。鉴定出的 IncF 质粒 AA035 赋予了金属和热元素亚型(即银、铜和碲)的抗性基因。KL107-D1噬菌体是一种主要的噬菌体类型,在88.2%的变种K.基因组中存在。该噬菌体被确定为整合酶缺陷型,由一个与磷霉素抗性相关的 fosB 基因组成,并与 Wbeta 属芽孢杆菌噬菌体群聚集在一起。硅学分析表明,该噬菌体基因组与 B. cereus(蜡样芽孢杆菌)而非 K. variicola 菌株 T2 相互作用。该噬菌体具有参与裂解-溶解决定的抗抑制蛋白。这种噬菌体将使我们进一步了解它对细菌传播的影响,以及它可能如何影响污水处理厂的疾病发展和抗生素耐药性机制。这项研究强调了对环境 K. variicola 分离物进行持续基因组流行病学监测的必要性。
{"title":"Genomic insight on Klebsiella variicola isolated from wastewater treatment plant has uncovered a novel bacteriophage.","authors":"Kgaugelo E Lekota, Refilwe O Mabeo, Tsepo Ramatla, Deidre A B Van Wyk, Oriel Thekisoe, Lesego G Molale-Tom, Cornelius C Bezuidenhout","doi":"10.1186/s12864-024-10906-x","DOIUrl":"https://doi.org/10.1186/s12864-024-10906-x","url":null,"abstract":"<p><p>Klebsiella variicola is considered an emerging pathogen, which may colonize a variety of hosts, including environmental sources. Klebsiella variicola investigated in this study was obtained from an influent wastewater treatment plant in the North-West Province, South Africa. Whole genome sequencing was conducted to unravel the genetic diversity and antibiotic resistance patterns of K. variicola. Whole genome core SNP phylogeny was employed on publicly available 170 genomes. Furthermore, capsule types and antibiotic resistance genes, particularly beta-lactamase and carbapenems genes were investigated from the compared genomes. A 38 099 bp bacteriophage was uncovered alongside with K. variicola genome. Whole genome sequencing revealed that the extended beta-lactamase bla<sub>LEN</sub> (75.3%) of the beta-lactamase is dominant among compared K. variicola strains. The identified IncF plasmid AA035 confers resistance genes of metal and heat element subtypes, i.e., silver, copper, and tellurium. The capsule type KL107-D1 is a predominant capsule type present in 88.2% of the compared K. variicola genomes. The phage was determined to be integrase-deficient consisting of a fosB gene associated with fosfomycin resistance and clusters with the Wbeta genus Bacillus phage group. In silico analysis showed that the phage genome interacts with B. cereus as opposed to K. variicola strain T2. The phage has anti-repressor proteins involved in the lysis-lysogeny decision. This phage will enhance our understanding of its impact on bacterial dissemination and how it may affect disease development and antibiotic resistance mechanisms in wastewater treatment plants. This study highlights the need for ongoing genomic epidemiological surveillance of environmental K. variicola isolates.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-22DOI: 10.1186/s12864-024-10892-0
Dulguunnaran Naranbat, Lothar À Brassard, Nabil Lawandy, Anubhav Tripathi
Whole genome sequencing (WGS) has become a gold standard for diagnosing genomic variation. Peripheral blood is a common sample source for the extraction of nucleic acids for Next-Generation Sequencing (NGS) applications. Here, we present an integrated and fully automated device design that uses new concepts of fluid mechanics, heat-mass transfer, and thermodynamics of enzymatic reactions to extract nucleic acids from the blood and perform DNA library preparation from a pre-filled plate. We demonstrate that the presented device effectively extracts dsDNA with an average of 25.03 µg/mL and 25.91 µg/mL yield from citrate-stabilized human peripheral blood stored in Fresh (4 °C) and Frozen (-20 °C) conditions, respectively. Furthermore, our method automatically extracts nucleic acids and creates a high-quality sequence-ready DNA library from blood stabilized with citrate and EDTA for 8 samples simultaneously in a single run with a total operation time of ~ 7 h. Our results show the required coverage and depth of the genome, highlighting an essential application of this device in processing blood samples for genome sequencing.
全基因组测序(WGS)已成为诊断基因组变异的黄金标准。外周血是提取核酸用于下一代测序(NGS)的常见样本来源。在这里,我们介绍了一种集成式全自动设备设计,它利用流体力学、热质传递和酶反应热力学的新概念从血液中提取核酸,并从预填充板中进行 DNA 文库制备。我们证明,该装置能有效地从新鲜(4 °C)和冷冻(-20 °C)条件下储存的柠檬酸盐稳定人外周血中提取dsDNA,平均提取率分别为25.03 µg/mL和25.91 µg/mL。此外,我们的方法还能自动提取核酸,并在一次运行中同时从 8 个样本的柠檬酸盐和乙二胺四乙酸盐稳定的血液中创建高质量的可用于测序的 DNA 文库,总运行时间约为 7 小时。我们的结果显示了基因组所需的覆盖范围和深度,突出了该设备在处理用于基因组测序的血液样本中的重要应用。
{"title":"Peripheral blood to next-generation sequencing ready DNA library: a novel engineering design for automation.","authors":"Dulguunnaran Naranbat, Lothar À Brassard, Nabil Lawandy, Anubhav Tripathi","doi":"10.1186/s12864-024-10892-0","DOIUrl":"https://doi.org/10.1186/s12864-024-10892-0","url":null,"abstract":"<p><p>Whole genome sequencing (WGS) has become a gold standard for diagnosing genomic variation. Peripheral blood is a common sample source for the extraction of nucleic acids for Next-Generation Sequencing (NGS) applications. Here, we present an integrated and fully automated device design that uses new concepts of fluid mechanics, heat-mass transfer, and thermodynamics of enzymatic reactions to extract nucleic acids from the blood and perform DNA library preparation from a pre-filled plate. We demonstrate that the presented device effectively extracts dsDNA with an average of 25.03 µg/mL and 25.91 µg/mL yield from citrate-stabilized human peripheral blood stored in Fresh (4 °C) and Frozen (-20 °C) conditions, respectively. Furthermore, our method automatically extracts nucleic acids and creates a high-quality sequence-ready DNA library from blood stabilized with citrate and EDTA for 8 samples simultaneously in a single run with a total operation time of ~ 7 h. Our results show the required coverage and depth of the genome, highlighting an essential application of this device in processing blood samples for genome sequencing.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142516289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: The tea plant Camellia sinensis (L.) O. Kuntze is a perennial crop, invaded by diversity of insect pest species, and pink tea mite is one of the most devastating pests for sustainable tea production. However, molecular mechanism of defense responses against pink tea mites in tea is still unknown. In this study, metabolomics and transcriptome profiles of susceptible and resistant tea varieties were compared before and after pink tea mite infestation.
Results: Metabolomics analysis revealed that abundance levels of polyphenol-related compounds changed significantly before and after infestation. At the transcript level, nearly 8 GB of clean reads were obtained from each sequenced library, and a comparison of infested plants of resistant and susceptible tea varieties revealed 9402 genes with significant differential expression. An array of genes enriched in plant pathogen interaction and biosynthetic pathways of phenylpropanoids showed significant differential regulation in response to pink tea mite invasion. In particular, the functional network linkage of disease resistant proteins, phenylalanine ammonia lyase, flavanone -3-hydroxylase, hydroxycinnamoyl-CoA shikimate transferase, brassinosteroid-6-oxidase 1, and gibberellin 2 beta-dioxygenase induced dynamic defense signals to suppress prolonged pink tea mite attacks. Further integrated analyses identified a complex network of transcripts and metabolites interlinked with precursors of various flavonoids that are likely modulate resistance against to pink tea mite.
Conclusions: Our results characterized the profiles of insect induced metabolic and transcript reprogramming and identified a defense regulatory network that can potentially be used to fend off pink tea mites damage.
背景:茶树(Camellia sinensis (L.) O. Kuntze)是一种多年生作物,受到多种害虫的侵袭,粉红茶螨是对茶叶可持续生产最具破坏性的害虫之一。然而,茶叶中粉红茶螨防御反应的分子机制尚不清楚。本研究比较了粉红茶螨侵染前后易感茶树和抗性茶树的代谢组学和转录组图谱:结果:代谢组学分析表明,粉红茶螨侵染前后,茶多酚相关化合物的丰度水平发生了显著变化。在转录本水平上,从每个测序文库中获得了近 8 GB 的纯净读数,通过比较抗性茶树和易感茶树的侵染植株,发现了 9402 个具有显著差异表达的基因。富集在植物病原体相互作用和苯丙酮类化合物生物合成途径中的一系列基因在粉红茶螨入侵时出现了显著的差异调控。尤其是抗病蛋白、苯丙氨酸氨化酶、黄烷酮-3-羟化酶、羟基肉桂酰-CoA莽草酸转移酶、铜绿素-6-氧化酶1和赤霉素2β-二氧酶的功能网络联系诱导了动态防御信号,以抑制粉红茶螨的长期侵袭。进一步的综合分析发现了一个复杂的转录本和代谢物网络,这些转录本和代谢物与可能调节粉红茶螨抗性的各种黄酮类化合物的前体相互关联:我们的研究结果描述了昆虫诱导的代谢和转录本重构的特征,并确定了一个防御调控网络,该网络可用于抵御粉红茶螨的危害。
{"title":"Metabolite profiling and transcriptome analyses reveal defense regulatory network against pink tea mite invasion in tea plant.","authors":"Limin Chen, Zaifa Shu, Dayun Zhou, Huijuan Zhou, Jinchao Wang, Yaqi Feng, Shenghong Zheng, Weizhong He","doi":"10.1186/s12864-024-10877-z","DOIUrl":"10.1186/s12864-024-10877-z","url":null,"abstract":"<p><strong>Background: </strong>The tea plant Camellia sinensis (L.) O. Kuntze is a perennial crop, invaded by diversity of insect pest species, and pink tea mite is one of the most devastating pests for sustainable tea production. However, molecular mechanism of defense responses against pink tea mites in tea is still unknown. In this study, metabolomics and transcriptome profiles of susceptible and resistant tea varieties were compared before and after pink tea mite infestation.</p><p><strong>Results: </strong>Metabolomics analysis revealed that abundance levels of polyphenol-related compounds changed significantly before and after infestation. At the transcript level, nearly 8 GB of clean reads were obtained from each sequenced library, and a comparison of infested plants of resistant and susceptible tea varieties revealed 9402 genes with significant differential expression. An array of genes enriched in plant pathogen interaction and biosynthetic pathways of phenylpropanoids showed significant differential regulation in response to pink tea mite invasion. In particular, the functional network linkage of disease resistant proteins, phenylalanine ammonia lyase, flavanone -3-hydroxylase, hydroxycinnamoyl-CoA shikimate transferase, brassinosteroid-6-oxidase 1, and gibberellin 2 beta-dioxygenase induced dynamic defense signals to suppress prolonged pink tea mite attacks. Further integrated analyses identified a complex network of transcripts and metabolites interlinked with precursors of various flavonoids that are likely modulate resistance against to pink tea mite.</p><p><strong>Conclusions: </strong>Our results characterized the profiles of insect induced metabolic and transcript reprogramming and identified a defense regulatory network that can potentially be used to fend off pink tea mites damage.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-21DOI: 10.1186/s12864-024-10891-1
Kevin Debatisse, Théophile Niault, Sarah Peeters, Amandine Maire, Busra Toktas, Baptiste Darracq, Zeynep Baharoglu, David Bikard, Didier Mazel, Céline Loot
Background: Vibrio cholerae O1 El Tor, the etiological agent responsible for the last cholera pandemic, has become a well-established model organism for which some genetic tools are available. While CRISPRi technology has been applied to V. cholerae, improvements were necessary to upscale it and enable pooled screening by high-throughput sequencing in this bacterium.
Results: In this study, we present a genome-wide CRISPR-dCas9 screen specifically optimized for the N16961 El Tor model strain of V. cholerae. This approach is characterized by a tight control of dCas9 expression and activity, as well as a streamlined experimental setup. Our library allows the depletion of 3,674 (98.9%) annotated genes from the V. cholerae genome. To confirm its effectiveness, we screened for genes that are essential during exponential growth in rich medium and identified 369 genes for which guides were significantly depleted from the library (log2FC < -2). Remarkably, 82% of these genes had previously been described as hypothetical essential genes in V. cholerae or in a closely related bacterium, V. natriegens.
Conclusion: We thus validated the robustness and accuracy of our CRISPRi-based approach for assessing gene fitness in a given condition. Our findings highlight the efficacy of the developed CRISPRi platform as a powerful tool for high-throughput functional genomics studies of V. cholerae.
背景:霍乱弧菌 O1 El Tor 是导致上一次霍乱大流行的病原体,它已成为一种成熟的模式生物,有一些遗传工具可用。虽然CRISPRi技术已被应用于霍乱弧菌,但仍需加以改进以扩大其应用范围,并通过高通量测序对该细菌进行集中筛选:在本研究中,我们提出了一种全基因组 CRISPR-dCas9 筛选方法,该方法专门针对霍乱弧菌 N16961 El Tor 模式菌株进行了优化。这种方法的特点是严格控制 dCas9 的表达和活性,以及简化实验设置。我们的文库可以删除霍乱弧菌基因组中的 3,674 个(98.9%)注释基因。为了证实它的有效性,我们筛选了在富培养基中指数生长过程中必不可少的基因,并确定了 369 个基因,这些基因的向导在文库中被显著删除(log2FC < -2)。值得注意的是,这些基因中有 82% 以前曾被描述为霍乱弧菌或近缘细菌纳氏霍乱弧菌中的假定必需基因:因此,我们验证了基于 CRISPRi 的方法在特定条件下评估基因适应性的稳健性和准确性。我们的研究结果凸显了所开发的 CRISPRi 平台作为霍乱弧菌高通量功能基因组学研究的强大工具的功效。
{"title":"Fine-tuning of a CRISPRi screen in the seventh pandemic Vibrio cholerae.","authors":"Kevin Debatisse, Théophile Niault, Sarah Peeters, Amandine Maire, Busra Toktas, Baptiste Darracq, Zeynep Baharoglu, David Bikard, Didier Mazel, Céline Loot","doi":"10.1186/s12864-024-10891-1","DOIUrl":"10.1186/s12864-024-10891-1","url":null,"abstract":"<p><strong>Background: </strong>Vibrio cholerae O1 El Tor, the etiological agent responsible for the last cholera pandemic, has become a well-established model organism for which some genetic tools are available. While CRISPRi technology has been applied to V. cholerae, improvements were necessary to upscale it and enable pooled screening by high-throughput sequencing in this bacterium.</p><p><strong>Results: </strong>In this study, we present a genome-wide CRISPR-dCas9 screen specifically optimized for the N16961 El Tor model strain of V. cholerae. This approach is characterized by a tight control of dCas9 expression and activity, as well as a streamlined experimental setup. Our library allows the depletion of 3,674 (98.9%) annotated genes from the V. cholerae genome. To confirm its effectiveness, we screened for genes that are essential during exponential growth in rich medium and identified 369 genes for which guides were significantly depleted from the library (log2FC < -2). Remarkably, 82% of these genes had previously been described as hypothetical essential genes in V. cholerae or in a closely related bacterium, V. natriegens.</p><p><strong>Conclusion: </strong>We thus validated the robustness and accuracy of our CRISPRi-based approach for assessing gene fitness in a given condition. Our findings highlight the efficacy of the developed CRISPRi platform as a powerful tool for high-throughput functional genomics studies of V. cholerae.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11492475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-21DOI: 10.1186/s12864-024-10903-0
Chengcheng Li, Xuanxuan Zhang, Linlin Zhao, Shenghao Liu
Background: Hydrogen peroxide (H2O2), a novel water treatment agent, can be used for disinfection, water quality adjustment, and disease prevention, while excessive H2O2 can injure farm animals, even leading to death. Hydrogen peroxide is a recommended disinfectant and bactericide for treating gill diseases and vibriosis in the greenfin horse-faced filefish Thamnaconus septentrionalis. However, its cumulative effect, toxic molecular mechanism and relevant signal transduction/metabolic networks in marine fishes are largely unknown.
Results: We employed a multi-omics approach to investigate the detrimental effects of 50 mg/L H2O2 exposure (2 h/d) on filefish for 2 d, 4 d, and 6 d. Transcriptome sequencing showed that differentially expressed genes (DEGs) were mainly classified into functions such as signal transduction, nervous system, liver and bile acid metabolism, energy metabolism, cell adhesion and communication, inflammation and immune response. Metabolomic analysis found that the significantly changed metabolites (SCMs) were involved in phenylalanine metabolism, inflammatory mediator regulation, linoleic acid metabolism, and necroptosis. The main SCMs were cholic acid, carnitine C12:1, dimethylmalonic acid, glutamic acid, L-lactic acid, shikimic acid, 2-methylsuccinic acid, and others. Moreover, H2O2-induced oxidative stress also disturbs the balance of the gut microbiota, altering the microbial composition and affecting digestive processes.
Conclusions: Integrated multiomics analysis revealed that H2O2-induced detrimental impacts include mucosal damage, inflammatory and immune responses, altered energy metabolism, and gut microbiota disorders. These findings offer novel insights into the harmful effects and signal transduction/metabolic pathways triggered by H2O2 exposure in marine fishes.
{"title":"Multi-omics profiling reveals the molecular mechanisms of H<sub>2</sub>O<sub>2</sub>-induced detrimental effects on Thamnaconus septentrionalis.","authors":"Chengcheng Li, Xuanxuan Zhang, Linlin Zhao, Shenghao Liu","doi":"10.1186/s12864-024-10903-0","DOIUrl":"10.1186/s12864-024-10903-0","url":null,"abstract":"<p><strong>Background: </strong>Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), a novel water treatment agent, can be used for disinfection, water quality adjustment, and disease prevention, while excessive H<sub>2</sub>O<sub>2</sub> can injure farm animals, even leading to death. Hydrogen peroxide is a recommended disinfectant and bactericide for treating gill diseases and vibriosis in the greenfin horse-faced filefish Thamnaconus septentrionalis. However, its cumulative effect, toxic molecular mechanism and relevant signal transduction/metabolic networks in marine fishes are largely unknown.</p><p><strong>Results: </strong>We employed a multi-omics approach to investigate the detrimental effects of 50 mg/L H<sub>2</sub>O<sub>2</sub> exposure (2 h/d) on filefish for 2 d, 4 d, and 6 d. Transcriptome sequencing showed that differentially expressed genes (DEGs) were mainly classified into functions such as signal transduction, nervous system, liver and bile acid metabolism, energy metabolism, cell adhesion and communication, inflammation and immune response. Metabolomic analysis found that the significantly changed metabolites (SCMs) were involved in phenylalanine metabolism, inflammatory mediator regulation, linoleic acid metabolism, and necroptosis. The main SCMs were cholic acid, carnitine C12:1, dimethylmalonic acid, glutamic acid, L-lactic acid, shikimic acid, 2-methylsuccinic acid, and others. Moreover, H<sub>2</sub>O<sub>2</sub>-induced oxidative stress also disturbs the balance of the gut microbiota, altering the microbial composition and affecting digestive processes.</p><p><strong>Conclusions: </strong>Integrated multiomics analysis revealed that H<sub>2</sub>O<sub>2</sub>-induced detrimental impacts include mucosal damage, inflammatory and immune responses, altered energy metabolism, and gut microbiota disorders. These findings offer novel insights into the harmful effects and signal transduction/metabolic pathways triggered by H<sub>2</sub>O<sub>2</sub> exposure in marine fishes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11492787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-21DOI: 10.1186/s12864-024-10661-z
Pansee Gamaleldin, Mustafa Alseqely, Benjamin A Evans, Hoda Omar, Alaa Abouelfetouh
Klebsiella pneumoniae is a common pathogen capable of causing a wide range of infections. Antibiotic resistance complicates treatment of these infections significantly. We are comparing resistance levels and genotypes among two collections of K. pneumoniae clinical isolates from Alexandria Main University Hospital (AMUH). We used disc diffusion and Minimum Inhibitory Concentration (MIC) by microbroth dilution to assess resistance levels and performed whole genome sequencing (WGS) to describe multilocus sequence types (MLST) and resistance gene presence. Among a collection of 56 K. pneumoniae clinical isolates (19 from 2019 to 37 from 2021), multidrug resistance (MDR) was 33% and 10%, extended drug resistance (XDR) was 24% and 46% and pan-drug resistance (PDR) was 43% and 43%, respectively. We identified 15 MLST STs including two novel types (ST-6118 and ST-6119 ). ST-101 and ST-383 were common between the two collections; ST-101 was the most common genotype in 2019 (28.6%) and ST-147 was most common in 2021 (25%). Ampicillin/sulbactam, amikacin, cefepime, ceftriaxone and ertapenem MICs were significantly higher in 2021. Prevalence of aph(3') - Ia, aph(3')-VI, mphA was significantly higher in 2021. The increasing resistance levels and the persistence of some MDR/XDR genotypes is concerning. Understanding mechanisms of resistance will inform infection control and antimicrobial stewardship plans to prevent evolution and spread of XDR and PDR strains.
{"title":"Comparison of genotypic features between two groups of antibiotic resistant Klebsiella pneumoniae clinical isolates obtained before and after the COVID-19 pandemic from Egypt.","authors":"Pansee Gamaleldin, Mustafa Alseqely, Benjamin A Evans, Hoda Omar, Alaa Abouelfetouh","doi":"10.1186/s12864-024-10661-z","DOIUrl":"10.1186/s12864-024-10661-z","url":null,"abstract":"<p><p>Klebsiella pneumoniae is a common pathogen capable of causing a wide range of infections. Antibiotic resistance complicates treatment of these infections significantly. We are comparing resistance levels and genotypes among two collections of K. pneumoniae clinical isolates from Alexandria Main University Hospital (AMUH). We used disc diffusion and Minimum Inhibitory Concentration (MIC) by microbroth dilution to assess resistance levels and performed whole genome sequencing (WGS) to describe multilocus sequence types (MLST) and resistance gene presence. Among a collection of 56 K. pneumoniae clinical isolates (19 from 2019 to 37 from 2021), multidrug resistance (MDR) was 33% and 10%, extended drug resistance (XDR) was 24% and 46% and pan-drug resistance (PDR) was 43% and 43%, respectively. We identified 15 MLST STs including two novel types (ST-6118 and ST-6119 ). ST-101 and ST-383 were common between the two collections; ST-101 was the most common genotype in 2019 (28.6%) and ST-147 was most common in 2021 (25%). Ampicillin/sulbactam, amikacin, cefepime, ceftriaxone and ertapenem MICs were significantly higher in 2021. Prevalence of aph(3') - Ia, aph(3')-VI, mphA was significantly higher in 2021. The increasing resistance levels and the persistence of some MDR/XDR genotypes is concerning. Understanding mechanisms of resistance will inform infection control and antimicrobial stewardship plans to prevent evolution and spread of XDR and PDR strains.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11492754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-20DOI: 10.1186/s12864-024-10872-4
Ricardo Soares, Bruno M Fonseca, Benjamin W Nash, Catarina M Paquete, Ricardo O Louro
Background: Multiheme cytochromes c (MHC) provide prokaryotes with a broad metabolic versatility that contributes to their role in the biogeochemical cycling of the elements and in energy production in bioelectrochemical systems. However, MHC have only been isolated and studied in detail from a limited number of species. Among these, Desulfuromonadia spp. are particularly MHC-rich. To obtain a broad view of the diversity of MHC, we employed bioinformatic tools to study the cytochromome encoded in the genomes of the Desulfuromonadia class.
Results: We found that the distribution of the MHC families follows a different pattern between the two orders of the Desulfuromonadia class and that there is great diversity in the number of heme-binding motifs in MHC. However, the vast majority of MHC have up to 12 heme-binding motifs. MHC predicted to be extracellular are the least conserved and show high diversity, whereas inner membrane MHC are well conserved and show lower diversity. Although the most prevalent MHC have homologues already characterized, nearly half of the MHC families in the Desulforomonadia class have no known characterized homologues. AlphaFold2 was employed to predict their 3D structures. This provides an atlas of novel MHC, including examples with high beta-sheet content and nanowire MHC with unprecedented high numbers of putative heme cofactors per polypeptide.
Conclusions: This work illuminates for the first time the universe of experimentally uncharacterized cytochromes that are likely to contribute to the metabolic versatility and to the fitness of Desulfuromonadia in diverse environmental conditions and to drive biotechnological applications of these organisms.
{"title":"A survey of the Desulfuromonadia \"cytochromome\" provides a glimpse of the unexplored diversity of multiheme cytochromes in nature.","authors":"Ricardo Soares, Bruno M Fonseca, Benjamin W Nash, Catarina M Paquete, Ricardo O Louro","doi":"10.1186/s12864-024-10872-4","DOIUrl":"10.1186/s12864-024-10872-4","url":null,"abstract":"<p><strong>Background: </strong>Multiheme cytochromes c (MHC) provide prokaryotes with a broad metabolic versatility that contributes to their role in the biogeochemical cycling of the elements and in energy production in bioelectrochemical systems. However, MHC have only been isolated and studied in detail from a limited number of species. Among these, Desulfuromonadia spp. are particularly MHC-rich. To obtain a broad view of the diversity of MHC, we employed bioinformatic tools to study the cytochromome encoded in the genomes of the Desulfuromonadia class.</p><p><strong>Results: </strong>We found that the distribution of the MHC families follows a different pattern between the two orders of the Desulfuromonadia class and that there is great diversity in the number of heme-binding motifs in MHC. However, the vast majority of MHC have up to 12 heme-binding motifs. MHC predicted to be extracellular are the least conserved and show high diversity, whereas inner membrane MHC are well conserved and show lower diversity. Although the most prevalent MHC have homologues already characterized, nearly half of the MHC families in the Desulforomonadia class have no known characterized homologues. AlphaFold2 was employed to predict their 3D structures. This provides an atlas of novel MHC, including examples with high beta-sheet content and nanowire MHC with unprecedented high numbers of putative heme cofactors per polypeptide.</p><p><strong>Conclusions: </strong>This work illuminates for the first time the universe of experimentally uncharacterized cytochromes that are likely to contribute to the metabolic versatility and to the fitness of Desulfuromonadia in diverse environmental conditions and to drive biotechnological applications of these organisms.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11492766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}