RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in Neurospora crassa

Abstract

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 Neurospora crassa, 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 mss-4 and gel-3 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 N. crassa 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.

Nitric Oxide in Fungi: Production and Function

“…However, it was also reported in N. crassa that high levels of intracellular NO are detected in conidiophores, and the transcription level of genes that are highly expressed during conidiation is reduced upon intracellular NO scavenging [95]. Endogenous NO in N. crassa seems to promote hyphal growth, which may be related to the elevated expression of mss-4 and gel-3, as demonstrated in recent studies [95,96]. Other evidence of NO regulation during light-induced development has been demonstrated in P. blakesleeanus [38].…”

“…Light-induced conidiation and carotenogenesis [44,48] Regulate mycelial development and conidia formation [95] Impacting the growth and development of hyphae (vegetative growth) [96] Phycomyces blakesleeanus Light-induced development of sporangiophores [38] Physarum polycephalum Sporulation [98] Pleurotus ostreatus Primordia formation [94] Puccinia striiformis f.sp. tritici Induce spore germination [99] Response to stresses…”

“…Increase in level of styrylpyrone polyphenols in fungal interspecific interaction [42] Neurospora crassa Cellulolytic enzyme production [107] Carbohydrate and amino acid metabolism [96] Preussia sp. BSL-10 Improve rice plant growth and related gene expression [60] Shiraia sp.…”

“…In N. crassa, intracellular NO is actively involved in cellulase production, and cAMP participates in this regulatory effect [107]. An N. crassa transcriptome analysis demonstrates that endogenous NO regulates carbohydrate and amino acid metabolism, including pentose and glucuronate interconversion as well as fructose, mannose, galactose, amino and nucleotide sugar, arginine, proline, and tyrosine metabolism [96]. Preussia sp.…”