Genomics, proteomics & bioinformatics最新文献_第2页

colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs. colorSV：从匹配的肿瘤-正常共组装图中调用的远程体细胞结构变异。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-09-17 DOI: 10.1093/gpbjnl/qzaf082

Megan K Le, Qian Qin, Heng Li

{"title":"colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs.","authors":"Megan K Le, Qian Qin, Heng Li","doi":"10.1093/gpbjnl/qzaf082","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf082","url":null,"abstract":"The accurate identification of somatic structural variants (SVs) is important for understanding the basis and evolution of cancerous tumor growth. Though long-read sequencing has facilitated the development of more accurate SV calling methods, existing somatic SV callers still struggle with achieving simultaneously high precision and high recall. In this work, we present colorSV (COassembly-based LOng-Range SV caller), a long-read-based method for calling long-range SVs by examining the local topology of joint assembly graphs from matched tumor-normal samples. colorSV is the first somatic SV calling method that uses a co-assembly approach, as well as the first SV caller that identifies variants by examining characteristics of the assembly graph itself. We demonstrate near-perfect precision and sensitivity for calling translocations on the COLO829 cell line, outperforming four existing somatic SV callers (Severus, Sniffles2, nanomonsv, and SAVANA) in both metrics. We also evaluated colorSV for calling translocations on the HCC1395 cell line, finding that our method achieved a good balance between sensitivity and precision (where the sensitivity was outperformed by Severus and SAVANA, and the precision was only outperformed by nanomonsv). Our work establishes a novel joint assembly-based strategy for characterizing long-range somatic variation, which could be further expanded or modified for the identification of SVs of different types and sizes. colorSV is available at https://github.com/mktle/colorSV.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Boosting the Power of Rare Variant Association Studies by Imputation Using Large-scale Sequencing Population. 利用大规模测序群体的代入提高罕见变异关联研究的能力。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-09-17 DOI: 10.1093/gpbjnl/qzaf084

Jinglan Dai, Yixin Zhang, Yuan Gao, Hongru Li, Sha Du, Hao Hong, Dongfang You, Zaiming Li, Ruyang Zhang, Yang Zhao, Zhonghua Liu, David C Christiani, Feng Chen, Sipeng Shen

{"title":"Boosting the Power of Rare Variant Association Studies by Imputation Using Large-scale Sequencing Population.","authors":"Jinglan Dai, Yixin Zhang, Yuan Gao, Hongru Li, Sha Du, Hao Hong, Dongfang You, Zaiming Li, Ruyang Zhang, Yang Zhao, Zhonghua Liu, David C Christiani, Feng Chen, Sipeng Shen","doi":"10.1093/gpbjnl/qzaf084","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf084","url":null,"abstract":"With the emergence of population-scale whole-genome sequencing (WGS), rare variants can be captured precisely. Studying rare variants explains part of the heritability of complex traits that is ignored by conventional genome-wide association studies (GWASs). However, how much the power of using imputed data can approximate or improve that of using WGS in rare variant association studies remains unclear. Using WGS (n = 150,119) as the ground truth, we first evaluated the consistency of rare variants in the single nucleotide polymorphism (SNP) array imputed from TOPMed or HRC+UK10K in the UK Biobank. Imputation quality (average R-square of the TOPMed-imputed data could reach 0.6 for even extremely rare variants with minor allele count ≤ 5. TOPMed-imputed data were closer to WGS for three ethnicities with the average Cramer's V > 0.75. Furthermore, association tests were performed on 45 traits. Under the same sample size, neither of the two imputed data outperformed WGS, but the results of TOPMed-imputed data were more consistent with WGS. When the sample size increased to n = 488,377, the number of identified rare variants in TOPMed-imputed data increased by 27.71% for quantitative traits and approximately 10-fold for binary traits. Finally, we meta-analyzed the association results of SNP array and WGS for lung cancer and epithelial ovarian cancer respectively. Compared to WGS-based results, more variants and genes could be identified. Our findings highlight that incorporating rare variants imputed from large-scale sequencing populations can boost the power of rare variant association tests when WGS has limited sample sizes.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives. 线粒体功能的单细胞组学评估：现状和未来展望。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-09-17 DOI: 10.1093/gpbjnl/qzaf081

Xu Zhang, Peng An, Zhengyang Zhang, Yanling Hao, Xiaoxian Guo, Yinhua Zhu, Zhenglong Gu, Yongting Luo, Junjie Luo

{"title":"Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives.","authors":"Xu Zhang, Peng An, Zhengyang Zhang, Yanling Hao, Xiaoxian Guo, Yinhua Zhu, Zhenglong Gu, Yongting Luo, Junjie Luo","doi":"10.1093/gpbjnl/qzaf081","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf081","url":null,"abstract":"In recent years, single-cell omics technologies have seen significant advancements, offering new insights into the study of mitochondria. These technologies are particularly suitable for investigating mitochondria due to their capacity to address intracellular and intercellular heterogeneity. In this review, we categorize the mitochondrial dysfunction and variability identified in both pathological and physiological contexts through single-cell omics assessments. We examine the cutting-edge single-cell omics technologies and track the evolution of studies on mitochondria, highlighting the transition from low-throughput to high-throughput capabilities and from single data types to the integration of multiple genomic and phenomic profiles. Furthermore, we emphasize the applications of single-cell mitochondrial assessment methods in exploring mechanisms, disease screening and prevention, and their potential impacts on lineage tracing, drug discovery, and genetic counseling. Insights gained from single-cell technologies may lead to the development of novel therapeutic strategies, offering promising avenues for addressing diseases associated with mitochondrial dysfunction. Lastly, we identify the limitations of current methodologies and propose areas of focus for future research.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic Insights into Hybridization and Speciation of Mitten Crabs in the Eriocheir Genus. 绒螯蟹属中绒螯蟹杂交和物种形成的基因组学见解。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-09-15 DOI: 10.1093/gpbjnl/qzaf079

Jun Wang, Xin Hou, Xiaowen Chen, Roland Nathan Mandal, Nusrat Hasan Kanika, Chunhong Yuan, Yongju Luo, Chenghui Wang

{"title":"Genomic Insights into Hybridization and Speciation of Mitten Crabs in the Eriocheir Genus.","authors":"Jun Wang, Xin Hou, Xiaowen Chen, Roland Nathan Mandal, Nusrat Hasan Kanika, Chunhong Yuan, Yongju Luo, Chenghui Wang","doi":"10.1093/gpbjnl/qzaf079","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf079","url":null,"abstract":"Hybridization is a prominent and influential phenomenon with significant implications for adaptive evolution, species distribution, and biodiversity. However, the intricacies of how hybridization influences genomic structure and facilitates adaptive evolution still elude our full understanding. Analyzing whole-genome data from seven populations within Eriocheir genus across diverse geographic regions, we have validated a complex hybridization history between Chinese and Japanese mitten crabs. This hybridization gave rise to two distinct ecological species: Hepu and Russian mitten crabs with unique genomic architectures and adaptations. Genes related to reproduction, development, and temperature adaptation exhibit divergent selection signals, potentially contributing to their phenotypic diversity and ecological niches. Meanwhile, genes associated with reproduction, namely Birc6, Bap31, and Poxn, displayed robust evidence of selective sweeps in Hepu mitten crab. Notably, the favored alleles for these genes originated from the parental lineages during the hybridization process. Furthermore, Hepu mitten crab is a homoploid hybrid species that originated from an ancient hybridization event, resolving its longstanding taxonomic controversy. Our study sheds light on the evolutionary history of mitten crabs and highlights the crucial role of hybridization in driving adaptation, range expansion, and diversification within the Eriochier genus.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

HiLand Resource: A Comprehensive Database of Highland Human Populations. 海岛资源：高原人口综合数据库。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-09-14 DOI: 10.1093/gpbjnl/qzaf083

Weijie Zhang, Xiaoning Chen, Yanling Sun, Yibo Wang, Bixia Tang, Yu Zhang, Kai Liu, Wenming Zhao, Bing Su, Yaoxi He

{"title":"HiLand Resource: A Comprehensive Database of Highland Human Populations.","authors":"Weijie Zhang, Xiaoning Chen, Yanling Sun, Yibo Wang, Bixia Tang, Yu Zhang, Kai Liu, Wenming Zhao, Bing Su, Yaoxi He","doi":"10.1093/gpbjnl/qzaf083","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf083","url":null,"abstract":"Over 80 million people worldwide live at high altitudes (> 2500 m), where numerous studies have documented the remarkable biological adaptations of highland populations to these extreme environments. However, current resources for accessing and analyzing highlander-specific data remain limited. To address this gap, we present the HiLand Resource (HLR), a comprehensive database that integrates phenomic, genomic, and genetic association data from 29,977 highlanders across three major high-altitude regions: the Qinghai-Xizang Plateau, the Andean Plateau, and the Ethiopian Plateau. HLR offers six key functions: (1) visualization of phenotypic pattern among Qinghai-Xizang highlanders across different altitudes, as well as comparison between highlanders and lowlanders, and between sexes; (2) an interactive interface to explore genomic diversity, population structure, ancestral composition, and signatures of natural selection of high-altitude populations; (3) access to a comprehensive catalog of genome-wide variants and genes identified in highlanders; (4) a genome browser built on a high-quality Tibetan genome assembly; (5) a curated collection of genotype-phenotype associations derived from genome-wide association studies (GWAS) in highland populations; and (6) an online, user-friendly tool for genotype imputation using a highland-specific reference panel. Collectively, HLR provides a novel and in-depth resource for understanding the biological features of high-altitude human populations. It holds significant potential for advancing research on human adaptation to hypoxic environments and improving medical studies focused on highland communities. The HLR database is freely available at: https://ngdc.cncb.ac.cn/hiland/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes. 真核生物转录组中CDS和UTR非规范RNA g -四重体结构的差异进化

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-09-14 DOI: 10.1093/gpbjnl/qzaf078

Eugene Yui-Ching Chow, Jieyu Zhao, Chun Kit Kwok, Ting-Fung Chan

{"title":"Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes.","authors":"Eugene Yui-Ching Chow, Jieyu Zhao, Chun Kit Kwok, Ting-Fung Chan","doi":"10.1093/gpbjnl/qzaf078","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf078","url":null,"abstract":"RNA G-quadruplexes (rG4s) are non-classical, four-stranded secondary RNA structures that play regulatory roles in various biological processes. Although canonical rG4s have been studied extensively, recent advancements have underscored the importance of non-canonical rG4s. In this study, we experimentally determined rG4 structures from multiple eukaryotic species. Bioinformatic analysis revealed that across 1 billion years of evolution, rG4s have comprised an integral feature of eukaryotic transcriptomes; additionally, non-canonical rG4s consistently were found to dominate the surveyed rG4omes. Over time, the overall size of the rG4ome has expanded progressively, accompanied by a notable compositional shift such that untranslated region (UTR) rG4s became favored over protein coding-sequence (CDS) rG4s. Additionally, we observed distinct evolutionary patterns for CDS and UTR rG4s, which involved differential evolutionary origins and canonicality drift patterns. Our findings suggest that new UTR rG4 sequences emerged rapidly during early mammalian evolution, whereas the more gradual increase in CDS rG4s is linked to changes in selective amino acid residue preferences. This plausible theory accounts for both the prevalence of UTR rG4s and the emergence of canonical motifs in mammalian models. Access to all of the rG4 structures identified in this study is available through the rG4-seq Database application at https://rg4s.science/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nuclei RNA Sequencing Data. 从单细胞/细胞核RNA测序数据定量测量基因表达的精确性和准确性。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-26 DOI: 10.1093/gpbjnl/qzaf077

Rujia Dai, Ming Zhang, Tianyao Chu, Richard Kopp, Chunling Zhang, Kefu Liu, Yue Wang, Xusheng Wang, Chao Chen, Chunyu Liu

{"title":"Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nuclei RNA Sequencing Data.","authors":"Rujia Dai, Ming Zhang, Tianyao Chu, Richard Kopp, Chunling Zhang, Kefu Liu, Yue Wang, Xusheng Wang, Chao Chen, Chunyu Liu","doi":"10.1093/gpbjnl/qzaf077","DOIUrl":"10.1093/gpbjnl/qzaf077","url":null,"abstract":"Single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) have become essential tools for profiling gene expression across different cell types in biomedical research. While factors like RNA integrity, cell count, and sequencing depth are known to influence data quality, quantitative benchmarks and actionable guidelines are lacking. This gap contributes to variability in study designs and inconsistencies in downstream analyses. In this study, we systematically evaluated quantitative precision and accuracy in expression measures across 23 sc/snRNA-seq datasets comprising 3,682,576 cells from 339 samples. Precision was assessed using technical replicates based on pseudo-bulks created from subsampling. Accuracy was evaluated using sample-matched scRNA-seq and pooled-cell RNA sequencing (RNA-seq) data of mononuclear phagocytes from four species. Our results show that precision and accuracy are generally low at the single-cell level, with reproducibility being strongly influenced by cell count and RNA quality. We established data-driven thresholds for optimizing study design, recommending at least 500 cells per cell type per individual to achieve reliable quantification. Furthermore, we showed that signal-to-noise ratio is a key metric for identifying reproducible differentially expressed genes. To support future research, we developed Variability In single-Cell gene Expressions (VICE), a tool that evaluates sc/snRNA-seq data quality and estimates the true positive rate of differential expression results based on sample size, observed noise levels, and expected effect size. These findings provide practical, evidence-based guidelines to enhance the reliability and reproducibility of sc/snRNA-seq studies.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in NSCLC. METTL1/ wdr4介导的SCLT1 mRNA m7G高甲基化促进非小细胞肺癌对吉非替尼的耐药。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-26 DOI: 10.1093/gpbjnl/qzaf076

Shaoxuan Zhou, Yueqin Wang, Jingyao Wei, Ke An, Yong Shi, Xuran Zhang, Han Wang, Luyao Feng, Lulu He, Yu Zhang, Tong Ren, Ouwen Li, Yun-Gui Yang, Xin Tian

{"title":"METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in NSCLC.","authors":"Shaoxuan Zhou, Yueqin Wang, Jingyao Wei, Ke An, Yong Shi, Xuran Zhang, Han Wang, Luyao Feng, Lulu He, Yu Zhang, Tong Ren, Ouwen Li, Yun-Gui Yang, Xin Tian","doi":"10.1093/gpbjnl/qzaf076","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf076","url":null,"abstract":"Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have produced durable complete responses, but the eventual development of acquired resistance presents a major challenge in the treatment of non-small cell lung cancer (NSCLC). N7-methylguanosine (m7G), a prevalent post-transcriptional modification within RNA, plays regulatory roles in RNA stability, expression dynamics, and functional diversity. Despite these insights, the contribution of m7G methylation to EGFR-TKIs resistance remains poorly characterized. Here, we demonstrate that internal m7G modifications of mRNA and their associated methyltransferase complex, methyltransferase-like 1 (METTL1)/WD repeat domain 4 (WDR4), are significantly elevated in NSCLC specimens, which correlates with therapeutic resistance. Functional assays confirmed that METTL1/WDR4 enhances gefitinib resistance in both cellular and animal models through internal RNA m7G methyltransferase activity in NSCLC. Mechanistically, m7G MeRIP-seq combined with RNA-seq identified sodium channel and clathrin linker 1 (SCLT1) as the m7G target of METTL1/WDR4. METTL1/WDR4 knockdown led to decreased methylation level and mRNA stability of the SCLT1 transcript. Importantly, overexpression of wild-type METTL1, but not its catalytically inactive mutant, restored mRNA stability. Furthermore, METTL1/WDR4-mediated m7G modification of SCLT1 regulates gefitinib resistance by activating the NF-κB signaling. Our findings reveal the crucial role of aberrant mRNA internal m7G modification in EGFR-TKIs resistance, suggesting that targeting the METTL1/WDR4-SCLT1-NF-κB axis holds a promising therapeutic potential for overcoming EGFR-TKIs resistance.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Duckweed Evolution: from Land back to Water. 浮萍的进化：从陆地回到水中。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-23 DOI: 10.1093/gpbjnl/qzaf074

Yang Fang, Xueping Tian, Yanling Jin, Anping Du, Yanqiang Ding, Zhihua Liao, Kaize He, Yonggui Zhao, Ling Guo, Yao Xiao, Yaliang Xu, Shuang Chen, Yuqing Che, Li Tan, Songhu Wang, Jiatang Li, Zhuolin Yi, Lanchai Chen, Leyi Zhao, Fangyuan Zhang, Guoyou Li, Jinmeng Li, Qinli Xiong, Yongmei Zhang, Qing Zhang, Xuan Hieu Cao, Hai Zhao

{"title":"Duckweed Evolution: from Land back to Water.","authors":"Yang Fang, Xueping Tian, Yanling Jin, Anping Du, Yanqiang Ding, Zhihua Liao, Kaize He, Yonggui Zhao, Ling Guo, Yao Xiao, Yaliang Xu, Shuang Chen, Yuqing Che, Li Tan, Songhu Wang, Jiatang Li, Zhuolin Yi, Lanchai Chen, Leyi Zhao, Fangyuan Zhang, Guoyou Li, Jinmeng Li, Qinli Xiong, Yongmei Zhang, Qing Zhang, Xuan Hieu Cao, Hai Zhao","doi":"10.1093/gpbjnl/qzaf074","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf074","url":null,"abstract":"Terrestialization is an important evolutionary process that plants experienced. However, little is known about how land plants acquired aquatic growth behaviors. Here we integrate multiproxy evidence to elucidate the evolution of the aquatic plant duckweed. Three genera of duckweed show chronologically gradual degeneration in root structure and stomatal function and decrease in lignocellulose content, accompanied by gradual contraction in the number of relevant genes and/or their transcriptional decline. The gene numbers in the main phytohormonal pathway are also gradually decreased. The co-action of genes involved in auxin and rhizoid development causes a gradual decrease in adventitious roots. The significant expansion of the flavonoid pathway is also related to the adaptation of duckweed to floating growth. This study reconstructs the evolution history of the duckweed habitat from land back to water, reversing that of early land plants.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crosstalk Between Lysine Lactylation and Acetylation Regulates Lactate Dehydrogenase in Streptococcus mutans. 变形链球菌乳酸脱氢酶与赖氨酸乙酰化的相互作用。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-22 DOI: 10.1093/gpbjnl/qzaf073

Qizhao Ma, Tao Hu, Yongwang Lin, Jing Li, Jun Huang, Qiong Zhang, Tao Gong, Xuedong Zhou, Lei Lei, Jing Zou, Yuqing Li

{"title":"Crosstalk Between Lysine Lactylation and Acetylation Regulates Lactate Dehydrogenase in Streptococcus mutans.","authors":"Qizhao Ma, Tao Hu, Yongwang Lin, Jing Li, Jun Huang, Qiong Zhang, Tao Gong, Xuedong Zhou, Lei Lei, Jing Zou, Yuqing Li","doi":"10.1093/gpbjnl/qzaf073","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf073","url":null,"abstract":"Post-translational modifications (PTMs) provide essential fine-tuning of protein functions in response to environmental changes. Among the PTMs, lysine acetylation (Kac) and the recently identified lysine lactylation (Kla) play crucial roles in metabolic regulation considering that lactate and acetyl-CoA (Ac-CoA) are generated from pyruvate as the outlet of glycolysis. However, their crosstalk and regulatory mechanisms remain largely unknown, particularly in prokaryotes. Herein, we investigated the intricate interrelation between Kla and Kac in the cariogenic bacterium Streptococcus mutans, a prolific producer of lactate. We conducted a comprehensive profiling of Kla and Kac, observing their wide distribution in glycolytic enzymes. Lactate dehydrogenase (LDH), the terminal enzyme of glycolysis, exhibited dynamic Kla and Kac shifts in line with glycolytic intermediates, where the ratio of Kla to Kac denotes the metabolic influx. Furthermore, ActA was pinpointed as a dual-function acyltransferase catalyzing the Kla and Kac of LDH, both negatively regulating its enzymatic activity. Importantly, the study identifies lysine 307 (K307) on LDH as a critical site, with its acylation significantly altering LDH activity, thereby lactate production and bacterial growth. Our insights into the metabolic regulation mediated by Kla and Kac contribute to the understanding of the metabolism-PTM-metabolism feedback loop, allowing bacteria to fine-tune their metabolism based on the availability of metabolic intermediates.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0