RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i>
While the biological role of naturally occurring nitric oxide (NO) in filamentous fungi has been uncovered, the underlying molecular regulatory networks remain unclear. In this study, we conducted an analysis of transcriptome profiles to investigate the initial stages of understanding these NO regul...
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| Format: | Article |
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MDPI AG
2023-10-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/9/10/985 |
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| author | Nan-Nan Yu Mayura Veerana Wirinthip Ketya Hu-Nan Sun Gyungsoon Park |
| author_facet | Nan-Nan Yu Mayura Veerana Wirinthip Ketya Hu-Nan Sun Gyungsoon Park |
| author_sort | Nan-Nan Yu |
| collection | DOAJ |
| description | While the biological role of naturally occurring nitric oxide (NO) in filamentous fungi has been uncovered, the underlying molecular regulatory networks remain unclear. In this study, we conducted an analysis of transcriptome profiles to investigate the initial stages of understanding these NO regulatory networks in <i>Neurospora crassa</i>, a well-established model filamentous fungus. Utilizing RNA sequencing, differential gene expression screening, and various functional analyses, our findings revealed that the removal of intracellular NO resulted in the differential transcription of 424 genes. Notably, the majority of these differentially expressed genes were functionally linked to processes associated with carbohydrate and amino acid metabolism. Furthermore, our analysis highlighted the prevalence of four specific protein domains (zinc finger C2H2, PLCYc, PLCXc, and SH3) in the encoded proteins of these differentially expressed genes. Through protein–protein interaction network analysis, we identified eight hub genes with substantial interaction connectivity, with <i>mss-4</i> and <i>gel-3</i> emerging as possibly major responsive genes during NO scavenging, particularly influencing vegetative growth. Additionally, our study unveiled that NO scavenging led to the inhibition of gene transcription related to a protein complex associated with ribosome biogenesis. Overall, our investigation suggests that endogenously produced NO in <i>N. crassa</i> likely governs the transcription of genes responsible for protein complexes involved in carbohydrate and amino acid metabolism, as well as ribosomal biogenesis, ultimately impacting the growth and development of hyphae. |
| first_indexed | 2024-03-10T21:07:55Z |
| format | Article |
| id | doaj.art-75d4104262444e97bba9afe7ce162e1a |
| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-10T21:07:55Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-75d4104262444e97bba9afe7ce162e1a2023-11-19T17:00:37ZengMDPI AGJournal of Fungi2309-608X2023-10-0191098510.3390/jof9100985RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i>Nan-Nan Yu0Mayura Veerana1Wirinthip Ketya2Hu-Nan Sun3Gyungsoon Park4Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of KoreaDepartment of Applied Radiation and Isotopes, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandPlasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of KoreaCollege of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, ChinaPlasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of KoreaWhile the biological role of naturally occurring nitric oxide (NO) in filamentous fungi has been uncovered, the underlying molecular regulatory networks remain unclear. In this study, we conducted an analysis of transcriptome profiles to investigate the initial stages of understanding these NO regulatory networks in <i>Neurospora crassa</i>, a well-established model filamentous fungus. Utilizing RNA sequencing, differential gene expression screening, and various functional analyses, our findings revealed that the removal of intracellular NO resulted in the differential transcription of 424 genes. Notably, the majority of these differentially expressed genes were functionally linked to processes associated with carbohydrate and amino acid metabolism. Furthermore, our analysis highlighted the prevalence of four specific protein domains (zinc finger C2H2, PLCYc, PLCXc, and SH3) in the encoded proteins of these differentially expressed genes. Through protein–protein interaction network analysis, we identified eight hub genes with substantial interaction connectivity, with <i>mss-4</i> and <i>gel-3</i> emerging as possibly major responsive genes during NO scavenging, particularly influencing vegetative growth. Additionally, our study unveiled that NO scavenging led to the inhibition of gene transcription related to a protein complex associated with ribosome biogenesis. Overall, our investigation suggests that endogenously produced NO in <i>N. crassa</i> likely governs the transcription of genes responsible for protein complexes involved in carbohydrate and amino acid metabolism, as well as ribosomal biogenesis, ultimately impacting the growth and development of hyphae.https://www.mdpi.com/2309-608X/9/10/985nitric oxidefilamentous fungiRNA sequencing<i>Neurospora crassa</i>vegetative growth |
| spellingShingle | Nan-Nan Yu Mayura Veerana Wirinthip Ketya Hu-Nan Sun Gyungsoon Park RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i> Journal of Fungi nitric oxide filamentous fungi RNA sequencing <i>Neurospora crassa</i> vegetative growth |
| title | RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i> |
| title_full | RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i> |
| title_fullStr | RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i> |
| title_full_unstemmed | RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i> |
| title_short | RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in <i>Neurospora crassa</i> |
| title_sort | rna seq based transcriptome analysis of nitric oxide scavenging response in i neurospora crassa i |
| topic | nitric oxide filamentous fungi RNA sequencing <i>Neurospora crassa</i> vegetative growth |
| url | https://www.mdpi.com/2309-608X/9/10/985 |
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