Rakesh K. Upadhyay , Jonathan Shao , Grace E. Roberts , Autar K. Mattoo
{"title":"水生浮萍(Spirodela polyrhiza L.)的比较基因组学和不寻常多胺氧化途径的证据","authors":"Rakesh K. Upadhyay , Jonathan Shao , Grace E. Roberts , Autar K. Mattoo","doi":"10.1016/j.cpb.2024.100359","DOIUrl":null,"url":null,"abstract":"<div><p>Polyamines (PA) cellular levels are maintained through a balance between synthesis and catabolism, achieved by two classes of enzymes polyamine oxidases (PAOs) and copper amine oxidases (CuAO). Here we investigated the occurrence, molecular evolution and role(s) of PAOs and CuAO gene families in aquatic duckweed and their comparison with other aquatic plants -sea eelgrass, bladderwort, and Lotus. We identified eight <em>bona fide</em> PAO genes (<em>SpPAO1–SpPAO8</em>) and one <em>SpCuAO1</em> in the greater duckweed genome from three genome assemblies. Interestingly, duckweed PAO genes increased their number through a tandem duplication event, while contrary to this CuAO genes were significantly lost to a single gene <em>SpCuAO1</em>. Phylogenetic analysis revealed that tandemly duplicated <em>SpPAO2–7</em> share close similarity to well-known terminal catabolism (TC) pathway PAO genes while <em>SpPAO1</em> and <em>SpPAO8</em> seem to segregate along with back conversion (BC) participating known PAO genes<em>,</em> suggesting that all tandem duplicated PAOs are involved in TC pathway which is contrary to known trend in land plants where CuAOs are mainly involved in TC pathway. Comparative transcript abundance studies indicated that all eight PAOs and one CuAO gene respond to multiple stresses and principal component analysis identifies <em>SpPAO4</em> as a highly active gene in response to multiple stresses. Results showed that oxidation of higher polyamines (SPD/SPM) through the TC pathway is diversified in duckweeds. Taken together this study reveals unique insights into the genomic losses and gains of polyamine metabolism possibly involved in achieving the structural and physiological adaptations required for aquatic lifestyle of duckweeds.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"39 ","pages":"Article 100359"},"PeriodicalIF":5.4000,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000410/pdfft?md5=157b38d3bb6644527023b07fb7511765&pid=1-s2.0-S2214662824000410-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Comparative genomics and evidence for an unusual polyamine oxidation pathway in aquatic duckweed (Spirodela polyrhiza L.)\",\"authors\":\"Rakesh K. Upadhyay , Jonathan Shao , Grace E. Roberts , Autar K. Mattoo\",\"doi\":\"10.1016/j.cpb.2024.100359\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Polyamines (PA) cellular levels are maintained through a balance between synthesis and catabolism, achieved by two classes of enzymes polyamine oxidases (PAOs) and copper amine oxidases (CuAO). Here we investigated the occurrence, molecular evolution and role(s) of PAOs and CuAO gene families in aquatic duckweed and their comparison with other aquatic plants -sea eelgrass, bladderwort, and Lotus. We identified eight <em>bona fide</em> PAO genes (<em>SpPAO1–SpPAO8</em>) and one <em>SpCuAO1</em> in the greater duckweed genome from three genome assemblies. Interestingly, duckweed PAO genes increased their number through a tandem duplication event, while contrary to this CuAO genes were significantly lost to a single gene <em>SpCuAO1</em>. Phylogenetic analysis revealed that tandemly duplicated <em>SpPAO2–7</em> share close similarity to well-known terminal catabolism (TC) pathway PAO genes while <em>SpPAO1</em> and <em>SpPAO8</em> seem to segregate along with back conversion (BC) participating known PAO genes<em>,</em> suggesting that all tandem duplicated PAOs are involved in TC pathway which is contrary to known trend in land plants where CuAOs are mainly involved in TC pathway. Comparative transcript abundance studies indicated that all eight PAOs and one CuAO gene respond to multiple stresses and principal component analysis identifies <em>SpPAO4</em> as a highly active gene in response to multiple stresses. Results showed that oxidation of higher polyamines (SPD/SPM) through the TC pathway is diversified in duckweeds. Taken together this study reveals unique insights into the genomic losses and gains of polyamine metabolism possibly involved in achieving the structural and physiological adaptations required for aquatic lifestyle of duckweeds.</p></div>\",\"PeriodicalId\":38090,\"journal\":{\"name\":\"Current Plant Biology\",\"volume\":\"39 \",\"pages\":\"Article 100359\"},\"PeriodicalIF\":5.4000,\"publicationDate\":\"2024-06-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2214662824000410/pdfft?md5=157b38d3bb6644527023b07fb7511765&pid=1-s2.0-S2214662824000410-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Current Plant Biology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2214662824000410\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current Plant Biology","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2214662824000410","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0
摘要
多胺(PA)的细胞水平是通过多胺氧化酶(PAOs)和铜胺氧化酶(CuAO)这两类酶的合成和分解代谢之间的平衡来维持的。在此,我们研究了水生浮萍中 PAOs 和 CuAO 基因家族的出现、分子进化和作用,并将其与其他水生植物(海鳗草、膀胱草和莲花)进行了比较。我们从三个基因组装配中发现了大浮萍基因组中八个真正的 PAO 基因(SpPAO1-SpPAO8)和一个 SpCuAO1。有趣的是,浮萍的 PAO 基因通过串联复制事件增加了其数量,而与此相反,CuAO 基因却显著减少,只剩下一个 SpCuAO1 基因。系统发育分析表明,串联重复的 SpPAO2-7 与众所周知的末端分解(TC)途径 PAO 基因具有近似性,而 SpPAO1 和 SpPAO8 似乎与参与反向转换(BC)的已知 PAO 基因一起分离,这表明所有串联重复的 PAO 都参与了 TC 途径,这与陆生植物中 CuAO 主要参与 TC 途径的已知趋势相反。转录本丰度比较研究表明,所有八个 PAO 和一个 CuAO 基因都对多种胁迫做出了反应,主成分分析确定 SpPAO4 是对多种胁迫做出反应的高活性基因。结果表明,通过 TC 途径氧化高级多胺(SPD/SPM)在浮萍中具有多样性。总之,这项研究揭示了多胺代谢基因组损益的独特见解,多胺代谢可能参与实现浮萍水生生活方式所需的结构和生理适应。
Comparative genomics and evidence for an unusual polyamine oxidation pathway in aquatic duckweed (Spirodela polyrhiza L.)
Polyamines (PA) cellular levels are maintained through a balance between synthesis and catabolism, achieved by two classes of enzymes polyamine oxidases (PAOs) and copper amine oxidases (CuAO). Here we investigated the occurrence, molecular evolution and role(s) of PAOs and CuAO gene families in aquatic duckweed and their comparison with other aquatic plants -sea eelgrass, bladderwort, and Lotus. We identified eight bona fide PAO genes (SpPAO1–SpPAO8) and one SpCuAO1 in the greater duckweed genome from three genome assemblies. Interestingly, duckweed PAO genes increased their number through a tandem duplication event, while contrary to this CuAO genes were significantly lost to a single gene SpCuAO1. Phylogenetic analysis revealed that tandemly duplicated SpPAO2–7 share close similarity to well-known terminal catabolism (TC) pathway PAO genes while SpPAO1 and SpPAO8 seem to segregate along with back conversion (BC) participating known PAO genes, suggesting that all tandem duplicated PAOs are involved in TC pathway which is contrary to known trend in land plants where CuAOs are mainly involved in TC pathway. Comparative transcript abundance studies indicated that all eight PAOs and one CuAO gene respond to multiple stresses and principal component analysis identifies SpPAO4 as a highly active gene in response to multiple stresses. Results showed that oxidation of higher polyamines (SPD/SPM) through the TC pathway is diversified in duckweeds. Taken together this study reveals unique insights into the genomic losses and gains of polyamine metabolism possibly involved in achieving the structural and physiological adaptations required for aquatic lifestyle of duckweeds.
期刊介绍:
Current Plant Biology aims to acknowledge and encourage interdisciplinary research in fundamental plant sciences with scope to address crop improvement, biodiversity, nutrition and human health. It publishes review articles, original research papers, method papers and short articles in plant research fields, such as systems biology, cell biology, genetics, epigenetics, mathematical modeling, signal transduction, plant-microbe interactions, synthetic biology, developmental biology, biochemistry, molecular biology, physiology, biotechnologies, bioinformatics and plant genomic resources.