Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM Domains
<i>Armillaria</i> sp. 541, a genus of root-infecting fungi, forms a symbiosis with traditional Chinese medicine <i>Gastrodia elata</i> (Orchid) and <i>Polyporus umbellatus</i> via extensive networks of durable rhizomorphs. It is not clear the hallmarks of comparat...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-07-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/8/1914 |
| _version_ | 1797583785367175168 |
|---|---|
| author | Bing Li Liu Liu Dawei Zhang Shunxing Guo |
| author_facet | Bing Li Liu Liu Dawei Zhang Shunxing Guo |
| author_sort | Bing Li |
| collection | DOAJ |
| description | <i>Armillaria</i> sp. 541, a genus of root-infecting fungi, forms a symbiosis with traditional Chinese medicine <i>Gastrodia elata</i> (Orchid) and <i>Polyporus umbellatus</i> via extensive networks of durable rhizomorphs. It is not clear the hallmarks of comparative transcriptome between the rhizomorphs and hyphae of <i>Armillaria</i> sp. 541. In the present study, transcriptomic analysis of <i>Armillaria</i> sp. 541 identified 475 differentially expressed genes (DEGs) between <i>Armillaria</i> rhizomorphs (AR) and hyphae (AH). Of them, 285 genes were upregulated and 190 were downregulated. Bioinformatics analyses and tests demonstrated DEGs involved in oxidoreductase activity and peptidoglycan binding were significantly enriched in this process when rhizomorph formed from hyphae. We accordingly obtained 14 gene-encoding proteins containing the LysM domain, and further consensus pattern and phylogenetic analysis indicated that their amino acid sequences were conserved and their biological functions may be peptidoglycan binding for recognition between the fungus and host. Among these genes, one, named <i>Armillaria LysM domain recognition gene</i> (<i>aLDRG</i>), was expressed significantly when rhizomorphs were differentiated from hyphae. It was located in the cortical cells of the rhizomorph by in situ hybridization. Furthermore, biolayer interferometry (BLI) assay demonstrated that aLDRG can bind specifically to chitin oligosaccharide of the fungal cell wall, including <i>N</i>,<i>N</i>′,<i>N</i>″-Triacetylchitotriose (CO3) and <i>N</i>,<i>N</i>′,<i>N</i>″,<i>N</i>′″,<i>N</i>″″-Pentaacetylchitopentaose (CO5). Therefore, we deduced that <i>Armillaria</i> sp. 541 expressed higher levels of LysM protein aLDRG for better binding of oligosaccharide after rhizomorphs were generated. This study provides functional genes for further studies on the interaction between <i>Armillaria</i> sp. 541 and its host. |
| first_indexed | 2024-03-10T23:43:56Z |
| format | Article |
| id | doaj.art-ba5282d77c8a41baaa95934642f3c6a9 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T23:43:56Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-ba5282d77c8a41baaa95934642f3c6a92023-11-19T02:15:57ZengMDPI AGMicroorganisms2076-26072023-07-01118191410.3390/microorganisms11081914Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM DomainsBing Li0Liu Liu1Dawei Zhang2Shunxing Guo3Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China<i>Armillaria</i> sp. 541, a genus of root-infecting fungi, forms a symbiosis with traditional Chinese medicine <i>Gastrodia elata</i> (Orchid) and <i>Polyporus umbellatus</i> via extensive networks of durable rhizomorphs. It is not clear the hallmarks of comparative transcriptome between the rhizomorphs and hyphae of <i>Armillaria</i> sp. 541. In the present study, transcriptomic analysis of <i>Armillaria</i> sp. 541 identified 475 differentially expressed genes (DEGs) between <i>Armillaria</i> rhizomorphs (AR) and hyphae (AH). Of them, 285 genes were upregulated and 190 were downregulated. Bioinformatics analyses and tests demonstrated DEGs involved in oxidoreductase activity and peptidoglycan binding were significantly enriched in this process when rhizomorph formed from hyphae. We accordingly obtained 14 gene-encoding proteins containing the LysM domain, and further consensus pattern and phylogenetic analysis indicated that their amino acid sequences were conserved and their biological functions may be peptidoglycan binding for recognition between the fungus and host. Among these genes, one, named <i>Armillaria LysM domain recognition gene</i> (<i>aLDRG</i>), was expressed significantly when rhizomorphs were differentiated from hyphae. It was located in the cortical cells of the rhizomorph by in situ hybridization. Furthermore, biolayer interferometry (BLI) assay demonstrated that aLDRG can bind specifically to chitin oligosaccharide of the fungal cell wall, including <i>N</i>,<i>N</i>′,<i>N</i>″-Triacetylchitotriose (CO3) and <i>N</i>,<i>N</i>′,<i>N</i>″,<i>N</i>′″,<i>N</i>″″-Pentaacetylchitopentaose (CO5). Therefore, we deduced that <i>Armillaria</i> sp. 541 expressed higher levels of LysM protein aLDRG for better binding of oligosaccharide after rhizomorphs were generated. This study provides functional genes for further studies on the interaction between <i>Armillaria</i> sp. 541 and its host.https://www.mdpi.com/2076-2607/11/8/1914<i>Armillaria</i> sp.rhizomorphLysM domain<i>aLDRG</i>chitinoligosaccharide |
| spellingShingle | Bing Li Liu Liu Dawei Zhang Shunxing Guo Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM Domains Microorganisms <i>Armillaria</i> sp. rhizomorph LysM domain <i>aLDRG</i> chitinoligosaccharide |
| title | Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM Domains |
| title_full | Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM Domains |
| title_fullStr | Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM Domains |
| title_full_unstemmed | Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM Domains |
| title_short | Hallmarks of Comparative Transcriptome between Rhizomorphs and Hyphae of <i>Armillaria</i> sp. 541 Participating in Fungal Symbiosis with Emphasis on LysM Domains |
| title_sort | hallmarks of comparative transcriptome between rhizomorphs and hyphae of i armillaria i sp 541 participating in fungal symbiosis with emphasis on lysm domains |
| topic | <i>Armillaria</i> sp. rhizomorph LysM domain <i>aLDRG</i> chitinoligosaccharide |
| url | https://www.mdpi.com/2076-2607/11/8/1914 |
| work_keys_str_mv | AT bingli hallmarksofcomparativetranscriptomebetweenrhizomorphsandhyphaeofiarmillariaisp541participatinginfungalsymbiosiswithemphasisonlysmdomains AT liuliu hallmarksofcomparativetranscriptomebetweenrhizomorphsandhyphaeofiarmillariaisp541participatinginfungalsymbiosiswithemphasisonlysmdomains AT daweizhang hallmarksofcomparativetranscriptomebetweenrhizomorphsandhyphaeofiarmillariaisp541participatinginfungalsymbiosiswithemphasisonlysmdomains AT shunxingguo hallmarksofcomparativetranscriptomebetweenrhizomorphsandhyphaeofiarmillariaisp541participatinginfungalsymbiosiswithemphasisonlysmdomains |