This study investigated the preventive and protective effects of Portulaca oleracea polysaccharides (PP) on Acute liver injury (ALI) in mice and its regulatory effects on intestinal microorganisms, and explored the underlying protective mechanisms. Initially, PP was administered, and then CCl4 was used to induce the mouse ALI model. Serum and liver markers were measured by ELISA. The fecal microbiota was analyzed by 16S rRNA sequencing. The results showed that PP significantly decreased the expression levels of ALT and AST in the serum of mice. The expression levels of MDA, TNF-α, and IL-6 in liver tissue were found to be reduced, while the levels of GSH and SOD increased. At the same time, PP increased the number of Bacteroides, reduced the number of Proteobacteria, activated the GAG degradation pathway, protected the integrity of the intestinal barrier, inhibited oxidative stress and reduced inflammation, thereby assisting the prevention and protection of ALI.
{"title":"Purslane (Portulaca oleracea L.) polysaccharide attenuates carbon tetrachloride-induced acute liver injury by modulating the gut microbiota in mice","authors":"Jiahui Li, Yuyang Chen, Shuang Zhang, Yuehan Zhao, Demeng Gao, Jiaying Xing, YuYan Cao, Guangyu Xu","doi":"10.1016/j.ygeno.2024.110983","DOIUrl":"10.1016/j.ygeno.2024.110983","url":null,"abstract":"<div><div>This study investigated the preventive and protective effects of <em>Portulaca oleracea</em> polysaccharides (PP) on Acute liver injury (ALI) in mice and its regulatory effects on intestinal microorganisms, and explored the underlying protective mechanisms. Initially, PP was administered, and then CCl4 was used to induce the mouse ALI model. Serum and liver markers were measured by ELISA. The fecal microbiota was analyzed by 16S rRNA sequencing. The results showed that PP significantly decreased the expression levels of ALT and AST in the serum of mice. The expression levels of MDA, TNF-α, and IL-6 in liver tissue were found to be reduced, while the levels of GSH and SOD increased. At the same time, PP increased the number of <em>Bacteroides</em>, reduced the number of <em>Proteobacteria</em>, activated the GAG degradation pathway, protected the integrity of the intestinal barrier, inhibited oxidative stress and reduced inflammation, thereby assisting the prevention and protection of ALI.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110983"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142902875","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 : 2025-01-01DOI: 10.1016/j.ygeno.2024.110977
Shuqiang Huang , Cuiyu Tan , Wanru Chen , Tongtong Zhang , Liying Xu , Zhihong Li , Miaoqi Chen , Xiaojun Yuan , Cairong Chen , Qiuxia Yan
Background
Abnormal programmed cell death (PCD) plays a central role in spermatogenic dysfunction. However, the molecular mechanisms and biomarkers of PCD in patients with nonobstructive azoospermia (NOA) remain unclear.
Methods
The genetic conditions of NOA patients were analysed using bulk transcriptomic, single-cell transcriptomic, single nucleotide polymorphism (SNP), and clinical data from multiple centres. A total of 675 machine learning methods were applied to construct models from 12 different PCDs and to screen for distinctive genes. A new PCDscore system was created to measure the degree of PCD in patients. Using the NOA mouse model, TUNEL, qRT–PCR, Western blotting, and immunohistochemistry (IHC) were utilized to validate the PCD status in NOA testes and the expression levels of hub PCD-related genes (PCDRGs). Mouse testicular samples were used for sequencing of the whole transcriptome. The sequencing results were used to evaluate the correlation between PCD scores and expression of hub genes.
Results
A PCDscore system was built using 12 characteristic PCDRGs chosen by machine learning. PCD scores correlated with gene interaction and immune activity changes. Leydig, Sertoli, and T cells were prominent in cell interactions with PCDscore changes. PCDscore in the NOA mouse testis was increased. Among the 12 PCDRGs, BCL2L14, GGA1, GPX4, PHKG2, and SLC39A8 were strongly linked to spermatogenesis. BCL2L14, GGA1, GPX4, and PHKG2 strongly correlated with PCD statuses. The changes in the expression of these genes may be due to the effects of SNPs, which may lead to the male reproductive system disorders.
Conclusions
Our study provides new insights into PCD-related mechanisms in NOA patients via multiomics and proposes reliable models for the diagnosis of NOA via the use of PCD biomarkers. A deeper understanding of these mechanisms may aid in the clinical diagnosis and treatment of NOA.
{"title":"Multiomics identification of programmed cell death-related characteristics for nonobstructive azoospermia based on a 675-combination machine learning computational framework","authors":"Shuqiang Huang , Cuiyu Tan , Wanru Chen , Tongtong Zhang , Liying Xu , Zhihong Li , Miaoqi Chen , Xiaojun Yuan , Cairong Chen , Qiuxia Yan","doi":"10.1016/j.ygeno.2024.110977","DOIUrl":"10.1016/j.ygeno.2024.110977","url":null,"abstract":"<div><h3>Background</h3><div>Abnormal programmed cell death (PCD) plays a central role in spermatogenic dysfunction. However, the molecular mechanisms and biomarkers of PCD in patients with nonobstructive azoospermia (NOA) remain unclear.</div></div><div><h3>Methods</h3><div>The genetic conditions of NOA patients were analysed using bulk transcriptomic, single-cell transcriptomic, single nucleotide polymorphism (SNP), and clinical data from multiple centres. A total of 675 machine learning methods were applied to construct models from 12 different PCDs and to screen for distinctive genes. A new PCDscore system was created to measure the degree of PCD in patients. Using the NOA mouse model, TUNEL, qRT–PCR, Western blotting, and immunohistochemistry (IHC) were utilized to validate the PCD status in NOA testes and the expression levels of hub PCD-related genes (PCDRGs). Mouse testicular samples were used for sequencing of the whole transcriptome. The sequencing results were used to evaluate the correlation between PCD scores and expression of hub genes.</div></div><div><h3>Results</h3><div>A PCDscore system was built using 12 characteristic PCDRGs chosen by machine learning. PCD scores correlated with gene interaction and immune activity changes. Leydig, Sertoli, and T cells were prominent in cell interactions with PCDscore changes. PCDscore in the NOA mouse testis was increased. Among the 12 PCDRGs, <em>BCL2L14</em>, <em>GGA1</em>, <em>GPX4</em>, <em>PHKG2</em>, and <em>SLC39A8</em> were strongly linked to spermatogenesis. <em>BCL2L14</em>, <em>GGA1</em>, <em>GPX4</em>, and <em>PHKG2</em> strongly correlated with PCD statuses. The changes in the expression of these genes may be due to the effects of SNPs, which may lead to the male reproductive system disorders.</div></div><div><h3>Conclusions</h3><div>Our study provides new insights into PCD-related mechanisms in NOA patients via multiomics and proposes reliable models for the diagnosis of NOA via the use of PCD biomarkers. A deeper understanding of these mechanisms may aid in the clinical diagnosis and treatment of NOA.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110977"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812830","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 : 2025-01-01DOI: 10.1016/j.ygeno.2024.110981
Jinlei Han , Yan Dai , Jialiang Zhou , Jingjing Tian , Qi Chen , Xiaobing Kou , Ghulam Raza , Baohong Zhang , Kai Wang
Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.
{"title":"Tissue-specific chromatin accessibility and transcriptional regulation in maize cold stress response","authors":"Jinlei Han , Yan Dai , Jialiang Zhou , Jingjing Tian , Qi Chen , Xiaobing Kou , Ghulam Raza , Baohong Zhang , Kai Wang","doi":"10.1016/j.ygeno.2024.110981","DOIUrl":"10.1016/j.ygeno.2024.110981","url":null,"abstract":"<div><div>Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110981"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863318","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 : 2025-01-01DOI: 10.1016/j.ygeno.2024.110966
Zhijian Yang , Xue Liu , Xiaohui Qin , Zhen Xiao , Qian Luo , Danni Pan , Hong Yang , Sufeng Liao , Xuanyang Chen
Cuscuta gronovii Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of C. gronovii. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the nad4 and ccmB genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of C. gronovii but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus Cuscuta.
{"title":"Unveiling the intricate structural variability induced by repeat-mediated recombination in the complete mitochondrial genome of Cuscuta gronovii Willd","authors":"Zhijian Yang , Xue Liu , Xiaohui Qin , Zhen Xiao , Qian Luo , Danni Pan , Hong Yang , Sufeng Liao , Xuanyang Chen","doi":"10.1016/j.ygeno.2024.110966","DOIUrl":"10.1016/j.ygeno.2024.110966","url":null,"abstract":"<div><div><em>Cuscuta gronovii</em> Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of <em>C. gronovii</em>. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the <em>nad</em>4 and <em>ccm</em>B genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of <em>C. gronovii</em> but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus <em>Cuscuta</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110966"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686648","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 : 2025-01-01DOI: 10.1016/j.ygeno.2024.110975
Ling Pan , Lirong Cai , Yang Lu , Junming Zhao , Xuebing Yan , Xiaoshan Wang
Paspalum vaginatum, valued for its salt tolerance, is a vital species in the turfgrass and agricultural industries. Despite its significance, there are still gaps in its genetic composition, particularly in the mitochondrial (mtDNA) and chloroplast (cpDNA) genomes. Our study aimed to fill these knowledge gaps by investigating the evolutionary relationships within the paspalum family and examining the functions of organelle-encoded genes as well as the critical role of reactive oxygen species (ROS) in organelle-nucleus communication. By genome sequencing, assembly, and annotation, we determined 504,515 bp of P. vaginatum mtDNA and 140,483 bp of its cpDNA. Comparative analyses with other Paspalum species and major crops highlight the intricate evolutionary dynamics and varying levels of genetic relatedness observed across different organelle genomes. The complex response of organelle gene expression to salt stress in this study will aid in understanding the molecular mechanisms and evolutionary trajectories of P. vaginatum organelle genomes.
覆盆子（Paspalum vaginatum）因其耐盐性而受到重视，是草坪和农业领域的重要物种。尽管其重要性不言而喻，但其基因组成，尤其是线粒体（mtDNA）和叶绿体（cpDNA）基因组仍然存在空白。我们的研究旨在通过调查覆盆子家族内部的进化关系、研究细胞器编码基因的功能以及活性氧（ROS）在细胞器-细胞核交流中的关键作用来填补这些知识空白。通过基因组测序、组装和注释，我们确定了 504,515 bp 的 P. vaginatum mtDNA 和 140,483 bp 的 cpDNA。与其他覆盆子物种和主要农作物的比较分析凸显了在不同细胞器基因组中观察到的错综复杂的进化动态和不同程度的遗传相关性。本研究中细胞器基因表达对盐胁迫的复杂反应将有助于了解海带细胞器基因组的分子机制和进化轨迹。
{"title":"Genomic insights into Paspalum vaginatum: Mitochondrial and chloroplast genome mapping, evolutionary insights, and organelle-nucleus communication","authors":"Ling Pan , Lirong Cai , Yang Lu , Junming Zhao , Xuebing Yan , Xiaoshan Wang","doi":"10.1016/j.ygeno.2024.110975","DOIUrl":"10.1016/j.ygeno.2024.110975","url":null,"abstract":"<div><div><em>Paspalum vaginatum</em>, valued for its salt tolerance, is a vital species in the turfgrass and agricultural industries. Despite its significance, there are still gaps in its genetic composition, particularly in the mitochondrial (mtDNA) and chloroplast (cpDNA) genomes. Our study aimed to fill these knowledge gaps by investigating the evolutionary relationships within the paspalum family and examining the functions of organelle-encoded genes as well as the critical role of reactive oxygen species (ROS) in organelle-nucleus communication. By genome sequencing, assembly, and annotation, we determined 504,515 bp of <em>P. vaginatum</em> mtDNA and 140,483 bp of its cpDNA. Comparative analyses with other Paspalum species and major crops highlight the intricate evolutionary dynamics and varying levels of genetic relatedness observed across different organelle genomes. The complex response of organelle gene expression to salt stress in this study will aid in understanding the molecular mechanisms and evolutionary trajectories of <em>P. vaginatum</em> organelle genomes.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110975"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822137","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 : 2025-01-01DOI: 10.1016/j.ygeno.2024.110969
Jing Ding , Jun Xu , Hongkun Wu , Mei Li , Yihan Xiao , Jie Fu , Xiangyu Zhu , Na Wu , Qiang Sun , Yaran Liu
Bronchopulmonary dysplasia (BPD), a chronic lung disease in preterm infants, is associated with inflammation and high oxygen exposure. However, the effects of antenatal inflammation and postnatal extended hyperoxia on the metabolome and microbiome remain unclear. In this study, pregnant rats received lipopolysaccharide or saline injections on gestational day 20 and were exposed to either 21 % or 80 % oxygen for 4 weeks post-birth. Analysis revealed an increase in Firmicutes, Proteobacteria, and Actinobacteria, with a decrease in Bacteroidetes in BPD rats. Metabolomic analysis identified 78 altered metabolites, primarily lipids, enriched in pathways including arginine biosynthesis, sphingolipid metabolism, and primary bile acid biosynthesis in BPD rats. Integration analysis revealed strong correlations between intestinal microbiota and metabolites in BPD rats. These findings underscored the impact of antenatal inflammation and prolonged postnatal hyperoxia on gut microbiota and serum metabolome, suggesting their role in BPD pathogenesis.
{"title":"The cross-talk between the metabolome and microbiome in a double-hit neonatal rat model of bronchopulmonary dysplasia","authors":"Jing Ding , Jun Xu , Hongkun Wu , Mei Li , Yihan Xiao , Jie Fu , Xiangyu Zhu , Na Wu , Qiang Sun , Yaran Liu","doi":"10.1016/j.ygeno.2024.110969","DOIUrl":"10.1016/j.ygeno.2024.110969","url":null,"abstract":"<div><div>Bronchopulmonary dysplasia (BPD), a chronic lung disease in preterm infants, is associated with inflammation and high oxygen exposure. However, the effects of antenatal inflammation and postnatal extended hyperoxia on the metabolome and microbiome remain unclear. In this study, pregnant rats received lipopolysaccharide or saline injections on gestational day 20 and were exposed to either 21 % or 80 % oxygen for 4 weeks post-birth. Analysis revealed an increase in <em>Firmicutes</em>, <em>Proteobacteria</em>, and <em>Actinobacteria</em>, with a decrease in <em>Bacteroidetes</em> in BPD rats. Metabolomic analysis identified 78 altered metabolites, primarily lipids, enriched in pathways including arginine biosynthesis, sphingolipid metabolism, and primary bile acid biosynthesis in BPD rats. Integration analysis revealed strong correlations between intestinal microbiota and metabolites in BPD rats. These findings underscored the impact of antenatal inflammation and prolonged postnatal hyperoxia on gut microbiota and serum metabolome, suggesting their role in BPD pathogenesis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110969"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142767960","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 : 2025-01-01DOI: 10.1016/j.ygeno.2024.110965
Rita Calisto , Ofélia Godinho , Damien P. Devos , Olga M. Lage
The biotechnological potential of Planctomycetota only recently started to be unveiled. 129 reference genomes and 5194 available genomes (4988 metagenome-assembled genomes (MAGs)) were analysed regarding the presence of Biosynthetic Gene Clusters (BGCs). By antiSMASH, 987 BGCs in the reference genomes and 22,841 BGCs in all the available genomes were detected. The classes Ca Uabimicrobiia, Ca Brocadiia and Planctomycetia had the higher number of BGC per genome, while Phycisphaerae had the lowest number. The most prevalent BGCs found in Planctomycetota reference genomes were terpenes, NRPS, type III PKS, type I PKS. As much as 88 % of the predicted regions had no similarity with known clusters in MIBiG database. This study strengthens the uniqueness of Planctomycetota for the isolation of new compounds and provide an overview of BGCs taxonomic distribution and of the type of predicted product. This outline allows the acceleration and focus of the research on drug discovery in Planctomycetota.
{"title":"“Genome-based in silico assessment of biosynthetic gene clusters in Planctomycetota: Evidences of its wide divergent nature”","authors":"Rita Calisto , Ofélia Godinho , Damien P. Devos , Olga M. Lage","doi":"10.1016/j.ygeno.2024.110965","DOIUrl":"10.1016/j.ygeno.2024.110965","url":null,"abstract":"<div><div>The biotechnological potential of <em>Planctomycetota</em> only recently started to be unveiled. 129 reference genomes and 5194 available genomes (4988 metagenome-assembled genomes (MAGs)) were analysed regarding the presence of Biosynthetic Gene Clusters (BGCs). By antiSMASH, 987 BGCs in the reference genomes and 22,841 BGCs in all the available genomes were detected. The classes <em>Ca Uabimicrobiia</em>, <em>Ca Brocadiia</em> and <em>Planctomycetia</em> had the higher number of BGC per genome, while <em>Phycisphaerae</em> had the lowest number. The most prevalent BGCs found in <em>Planctomycetota</em> reference genomes were terpenes, NRPS, type III PKS, type I PKS. As much as 88 % of the predicted regions had no similarity with known clusters in MIBiG database. This study strengthens the uniqueness of <em>Planctomycetota</em> for the isolation of new compounds and provide an overview of BGCs taxonomic distribution and of the type of predicted product. This outline allows the acceleration and focus of the research on drug discovery in <em>Planctomycetota</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110965"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692857","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}
The gradual rise of CO2 is one of the global climate changes, Cd stress is also a major abiotic stress factor that affects rice (Oryza sativa L.). The rice seedlings were treated under two CO2 concentrations and two CdCl2 concentrations for 7 days (treatments names: 400 ± 20 μmol mol−1 CO2 and 0 μmol L−1 CdCl2 concentrations, AC; 400 ± 20 μmol mol−1 CO2 and 150 μmol L−1 CdCl2 concentrations, Cd; 800 ± 20 μmol mol−1 CO2 and 0 μmol L−1 CdCl2 concentrations, EC; 800 ± 20 μmol mol−1 CO2 and 150 μmol L−1 CdCl2 concentrations, EC + Cd). The lncRNAs informations were analyzed and excavated using high-throughput sequencing, target genes annotation, and qRT-PCR analysis techniques so as to reveal the regulatory mechanism of lncRNAs in rice roots under high CO2 concentrations and/or Cd stress. The results show that: (1) 326 (AC vs Cd), 331 (AC vs EC), 343 (AC vs EC + Cd), 112 (Cd vs EC + Cd) DE-lncRNAs were identified. (2) MAPK signaling pathway-plant (relevant genes Os04g0534166, Os05g0399800 regulated by MSTRG.18576.11, MSTRG.20864.1) and diterpenoid biosynthesis (relevant genes Os12g0491800, Os02g0570400 regulated by MSTRG.8965.1, MSTRG.11509.1) were annotated in AC vs Cd; Under EC relative to AC, DE-lncRNAs were annotated significantly to the flavonoid biosynthesis (relevant genes Os10g0196100, Os10g0320100, Os11g0116300, Os03g0819600 regulated by MSTRG.4612.1, MSTRG.4668.1, MSTRG.6051.1, MSTRG.16669.1); Under composite treatments, relative to AC, DE-lncRNAs were mainly annotated in the plant hormone signal transduction pathway (relevant genes Os03g0180800, Os03g0180900, Os03g0181100 regulated by MSTRG.13776.1). Under combined treatment, elevated CO2 alleviates Cd stress damage by regulating phenylpropanoid biosynthesis through DE-lncRNAs (relevant genes Os09g0419200 regulated by MSTRG. 29,573.1).
CO2的逐渐升高是全球气候变化之一，Cd胁迫也是影响水稻（Oryza sativa L.）的主要非生物胁迫因子。水稻幼苗在2种CO2和2种CdCl2浓度下处理7 d(处理名称：400 ± 20 μmol mol-1 CO2和0 μmol L-1 CdCl2浓度，AC；400 ± 20 μmol mol-1 CO2和150 μmol L-1 CdCl2浓度，Cd；800 ± 20 μmol mol-1 CO2和0 μmol L-1 CdCl2浓度，EC；800 ± 20 μmol mol-1 CO2和150 μmol L-1 CdCl2浓度，EC + Cd)。利用高通量测序、靶基因注释和qRT-PCR分析技术对lncRNAs信息进行分析和挖掘，揭示高浓度CO2和/或Cd胁迫下水稻根系中lncRNAs的调控机制。结果表明：(1)共鉴定出326个（AC vs Cd）、331个（AC vs EC）、343个（AC vs EC + Cd）、112个（Cd vs EC + Cd） de - lncrna。(2)在AC vs Cd中标注了MAPK信号通路-植物（MSTRG.18576.11、MSTRG.20864.1调控的相关基因Os04g0534166、Os05g0399800）和二萜类生物合成（MSTRG.8965.1、MSTRG.11509.1调控的相关基因Os12g0491800、Os02g0570400）；在EC相对于AC的条件下，DE-lncRNAs在类黄酮生物合成中有显著的注释（相关基因Os10g0196100、Os10g0320100、Os11g0116300、Os03g0819600由MSTRG.4612.1、MSTRG.4668.1、MSTRG.6051.1、MSTRG.16669.1调控）；在复合处理下，相对于AC， de - lncrna主要在植物激素信号转导通路（MSTRG.13776.1调控的相关基因Os03g0180800、Os03g0180900、Os03g0181100）上有注释。联合处理下，CO2升高通过MSTRG调控的DE-lncRNAs（相关基因Os09g0419200）调控苯丙类生物合成，缓解Cd胁迫损伤。29573。1)。
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Pub Date : 2024-11-01DOI: 10.1016/j.ygeno.2024.110963
Christopher J. Giacoletto , Ronald Benjamin , Jerome I. Rotter , Martin R. Schiller
Many pathological conditions are a result of intragenic epistasis; however, there are ambiguities in current epistasis models. Herein, the new Mutation Interaction Spectrum model defines a discrete outcome, named a Mutation Interaction, for each double point mutation in a gene and its component single mutations. The model is a universal genetic model of all types of mutation interactions and their functional outcomes and is derived from digital logic, commonly used in electrical engineering. Mutation interactions are normally classified as positive and negative epistasis. The model logics unifies common genetic relationships into one model, normalizing biological nomenclature, and disambiguates them with the 16 possible logic-based interactions. The model was tested by assaying transcriptional activity induced by HIV-1 Tat protein, for a random sampling of 3429 double mutations and all 1615 single mutations. All possible types of logic were observed for the Tat mutation interactions.
许多病理状况都是基因内表观作用的结果；然而，目前的表观作用模型存在模糊之处。在这里，新的突变相互作用谱模型为基因中的每一个双点突变及其单点突变成分定义了一个离散的结果，命名为突变相互作用。该模型是所有类型突变相互作用及其功能结果的通用遗传模型，源自电子工程中常用的数字逻辑。突变相互作用通常分为正表性和负表性。该逻辑模型将常见的遗传关系统一到一个模型中，使生物术语规范化，并用 16 种可能的基于逻辑的相互作用来消除它们的歧义。该模型通过检测 HIV-1 Tat 蛋白诱导的转录活性进行了测试，随机抽取了 3429 个双突变和全部 1615 个单突变。在 Tat 突变相互作用中观察到了所有可能的逻辑类型。
{"title":"A fundamental and theoretical framework for mutation interactions and epistasis","authors":"Christopher J. Giacoletto , Ronald Benjamin , Jerome I. Rotter , Martin R. Schiller","doi":"10.1016/j.ygeno.2024.110963","DOIUrl":"10.1016/j.ygeno.2024.110963","url":null,"abstract":"<div><div>Many pathological conditions are a result of intragenic epistasis; however, there are ambiguities in current epistasis models. Herein, the new <strong>Mutation Interaction Spectrum</strong> model defines a discrete outcome, named a <strong>Mutation Interaction</strong>, for each double point mutation in a gene and its component single mutations. The model is a universal genetic model of all types of mutation interactions and their functional outcomes and is derived from digital logic, commonly used in electrical engineering. Mutation interactions are normally classified as positive and negative epistasis. The model logics unifies common genetic relationships into one model, normalizing biological nomenclature, and disambiguates them with the 16 possible logic-based interactions. The model was tested by assaying transcriptional activity induced by HIV-1 Tat protein, for a random sampling of 3429 double mutations and all 1615 single mutations. All possible types of logic were observed for the Tat mutation interactions.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110963"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675605","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 : 2024-11-01DOI: 10.1016/j.ygeno.2024.110964
Shuyao Wei , Feifei Ma , Shanshan Feng , Xiaoqin Ha
The liver plays an important role in glucose regulation, and their dysfunction is closely associated with the development of type 2 diabetes mellitus (T2DM), and insulin resistance (IR) in hepatocyte mediate the pathogenesis of diabetes mellitus. In T2DM rats and their correlated control, we investigated various genes expression at transcriptional and translational level by utilizing transcriptomic using RNA sequencing (RNA-seq) and proteomics using isobaric tags for relative and absolute quantification (iTRAQ) to disclose potential candidates for Type 2 diabetes diagnosis and therapy. We found the lecithin retinol acyltransferase (Lrat) gene regulate hepatocyte IR in T2DM. Furthermore, BRL-3A cells, rat liver cells, worked as the IR model in vitro study. Hence, Lrat gene was overexpressed in BRL-3A cells to explore the role of Lrat gene in IR by measuring the cellular glucose consumption, TCHO, and LDL-C levels. Finally, we found that Lrat gene can improve the level of glycolipid metabolism in BRL-3A cells and reduce the degree of IR in BRL-3A cells. Therefore, further exploration of Lrat gene related molecular mechanism is meaningful.
{"title":"Integrating transcriptomics and proteomics to understand the molecular mechanisms underlying the pathogenesis of type 2 diabetes mellitus","authors":"Shuyao Wei , Feifei Ma , Shanshan Feng , Xiaoqin Ha","doi":"10.1016/j.ygeno.2024.110964","DOIUrl":"10.1016/j.ygeno.2024.110964","url":null,"abstract":"<div><div>The liver plays an important role in glucose regulation, and their dysfunction is closely associated with the development of type 2 diabetes mellitus (T2DM), and insulin resistance (IR) in hepatocyte mediate the pathogenesis of diabetes mellitus. In T2DM rats and their correlated control, we investigated various genes expression at transcriptional and translational level by utilizing transcriptomic using RNA sequencing (RNA-seq) and proteomics using isobaric tags for relative and absolute quantification (iTRAQ) to disclose potential candidates for Type 2 diabetes diagnosis and therapy. We found the lecithin retinol acyltransferase (<em>Lrat</em>) gene regulate hepatocyte IR in T2DM. Furthermore, BRL-3A cells, rat liver cells, worked as the IR model in vitro study. Hence, <em>Lrat</em> gene was overexpressed in BRL-3A cells to explore the role of <em>Lrat</em> gene in IR by measuring the cellular glucose consumption, TCHO, and LDL-C levels. Finally, we found that <em>Lrat</em> gene can improve the level of glycolipid metabolism in BRL-3A cells and reduce the degree of IR in BRL-3A cells. Therefore, further exploration of <em>Lrat</em> gene related molecular mechanism is meaningful.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110964"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686676","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}
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