{"title":"基因表达和调控网络为固氮和丛枝菌根共生的相似性提供了新的见解。","authors":"Zefeng Wu, Yali Sun, Jun Yang, Zigang Liu, Yining Niu, Xiaowei Zhang","doi":"10.1093/pcp/pcaf082","DOIUrl":null,"url":null,"abstract":"<p><p>Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbuscular mycorrhizal symbiosis (AMS). A growing number of symbiosis-regulated genes have been characterized through either genetic analysis or phylogenomic profiling. However, the underlying similarities and specificities of the transcription regulatory machinery in AMS and NFS remain largely unclarified. Here, we systematically profiled the gene expression changes in three legume species, namely Medicago truncatula, Glycine max, and Lotus japonicus, during AMS and NFS. Additionally, we investigated gene expression changes in three non-legume plants, Solanum lycopersicum, Zea mays, and Oryza sativa, during AMS. We identified thousands of genes that were activated by AMS or NFS in their respective host plants. Through comparative genomics analysis, we systematically explored the conservation and specificity of genes responsive to AMS or NFS. Employing M. truncatula and G. max as illustrative cases, we harnessed the XGboost machine-learning model to construct co-expression-based gene regulatory networks (GRNs) for AMS and NFS within these two species. Through this approach, we successfully illuminated the similarities and unique features of the two symbiotic types at the GRN level. Further, utilizing known symbiosis genes as queries, we pinpointed a multitude of genes that are intimately associated with AMS and NFS. Overall, via in-depth gene expression profiling and regulatory network analysis, our results indicate that, while NFS in legumes has regulatory circuits similar to those of AMS, there exist certain symbiosis type-specific molecular components.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1330-1345"},"PeriodicalIF":4.0000,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Gene expression and regulatory networks provide new insights into the similarity between nitrogen fixing and arbuscular mycorrhizal symbioses.\",\"authors\":\"Zefeng Wu, Yali Sun, Jun Yang, Zigang Liu, Yining Niu, Xiaowei Zhang\",\"doi\":\"10.1093/pcp/pcaf082\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbuscular mycorrhizal symbiosis (AMS). A growing number of symbiosis-regulated genes have been characterized through either genetic analysis or phylogenomic profiling. However, the underlying similarities and specificities of the transcription regulatory machinery in AMS and NFS remain largely unclarified. Here, we systematically profiled the gene expression changes in three legume species, namely Medicago truncatula, Glycine max, and Lotus japonicus, during AMS and NFS. Additionally, we investigated gene expression changes in three non-legume plants, Solanum lycopersicum, Zea mays, and Oryza sativa, during AMS. We identified thousands of genes that were activated by AMS or NFS in their respective host plants. Through comparative genomics analysis, we systematically explored the conservation and specificity of genes responsive to AMS or NFS. Employing M. truncatula and G. max as illustrative cases, we harnessed the XGboost machine-learning model to construct co-expression-based gene regulatory networks (GRNs) for AMS and NFS within these two species. Through this approach, we successfully illuminated the similarities and unique features of the two symbiotic types at the GRN level. Further, utilizing known symbiosis genes as queries, we pinpointed a multitude of genes that are intimately associated with AMS and NFS. Overall, via in-depth gene expression profiling and regulatory network analysis, our results indicate that, while NFS in legumes has regulatory circuits similar to those of AMS, there exist certain symbiosis type-specific molecular components.</p>\",\"PeriodicalId\":20575,\"journal\":{\"name\":\"Plant and Cell Physiology\",\"volume\":\" \",\"pages\":\"1330-1345\"},\"PeriodicalIF\":4.0000,\"publicationDate\":\"2025-09-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plant and Cell Physiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/pcp/pcaf082\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CELL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant and Cell Physiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/pcp/pcaf082","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CELL BIOLOGY","Score":null,"Total":0}
Gene expression and regulatory networks provide new insights into the similarity between nitrogen fixing and arbuscular mycorrhizal symbioses.
Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbuscular mycorrhizal symbiosis (AMS). A growing number of symbiosis-regulated genes have been characterized through either genetic analysis or phylogenomic profiling. However, the underlying similarities and specificities of the transcription regulatory machinery in AMS and NFS remain largely unclarified. Here, we systematically profiled the gene expression changes in three legume species, namely Medicago truncatula, Glycine max, and Lotus japonicus, during AMS and NFS. Additionally, we investigated gene expression changes in three non-legume plants, Solanum lycopersicum, Zea mays, and Oryza sativa, during AMS. We identified thousands of genes that were activated by AMS or NFS in their respective host plants. Through comparative genomics analysis, we systematically explored the conservation and specificity of genes responsive to AMS or NFS. Employing M. truncatula and G. max as illustrative cases, we harnessed the XGboost machine-learning model to construct co-expression-based gene regulatory networks (GRNs) for AMS and NFS within these two species. Through this approach, we successfully illuminated the similarities and unique features of the two symbiotic types at the GRN level. Further, utilizing known symbiosis genes as queries, we pinpointed a multitude of genes that are intimately associated with AMS and NFS. Overall, via in-depth gene expression profiling and regulatory network analysis, our results indicate that, while NFS in legumes has regulatory circuits similar to those of AMS, there exist certain symbiosis type-specific molecular components.
期刊介绍:
Plant & Cell Physiology (PCP) was established in 1959 and is the official journal of the Japanese Society of Plant Physiologists (JSPP). The title reflects the journal''s original interest and scope to encompass research not just at the whole-organism level but also at the cellular and subcellular levels.
Amongst the broad range of topics covered by this international journal, readers will find the very best original research on plant physiology, biochemistry, cell biology, molecular genetics, epigenetics, biotechnology, bioinformatics and –omics; as well as how plants respond to and interact with their environment (abiotic and biotic factors), and the biology of photosynthetic microorganisms.