scholarly journals Construction of Light-Responsive Gene Regulatory Network for Growth, Development and Secondary Metabolite Production in Cordyceps militaris

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 71
Author(s):  
Ammarin In-on ◽  
Roypim Thananusak ◽  
Marasri Ruengjitchatchawalya ◽  
Wanwipa Vongsangnak ◽  
Teeraphan Laomettachit
Keyword(s):  
Gene Regulatory Network ◽  
Secondary Metabolite ◽  
Regulatory Network ◽  
Cordyceps Militaris ◽  
Secondary Metabolite Production ◽  
Metabolite Production ◽  
A Genome ◽  
Gene Regulatory ◽  
Growth Development ◽  
Genome Scale

Cordyceps militaris is an edible fungus that produces many beneficial compounds, including cordycepin and carotenoid. In many fungi, growth, development and secondary metabolite production are controlled by crosstalk between light-signaling pathways and other regulatory cascades. However, little is known about the gene regulation upon light exposure in C. militaris. This study aims to construct a gene regulatory network (GRN) that responds to light in C. militaris. First, a genome-scale GRN was built based on transcription factor (TF)-target gene interactions predicted from the Regulatory Sequence Analysis Tools (RSAT). Then, a light-responsive GRN was extracted by integrating the transcriptomic data onto the genome-scale GRN. The light-responsive network contains 2689 genes and 6837 interactions. From the network, five TFs, Snf21 (CCM_04586), an AT-hook DNA-binding motif TF (CCM_08536), a homeobox TF (CCM_07504), a forkhead box protein L2 (CCM_02646) and a heat shock factor Hsf1 (CCM_05142), were identified as key regulators that co-regulate a large group of growth and developmental genes. The identified regulatory network and expression profiles from our analysis suggested how light may induce the growth and development of C. militaris into a sexual cycle. The light-mediated regulation also couples fungal development with cordycepin and carotenoid production. This study leads to an enhanced understanding of the light-responsive regulation of growth, development and secondary metabolite production in the fungi.

scholarly journals Sequence-Based Analysis of Secondary-Metabolite Biosynthesis in Marine Actinobacteria

2010 ◽  
Vol 76 (8) ◽  
pp. 2487-2499 ◽  
Author(s):  
Erin A. Gontang ◽  
Susana P. Gaud�ncio ◽  
William Fenical ◽  
Paul R. Jensen
Keyword(s):  
Secondary Metabolite ◽  
Phylogenetic Analyses ◽  
Rapid Identification ◽  
Secondary Metabolite Production ◽  
Type I ◽  
Marine Actinobacteria ◽  
Metabolite Production ◽  
A Genome ◽  
Secondary Metabolite Biosynthesis ◽  
Primer Sets

ABSTRACT A diverse collection of 60 marine-sediment-derived Actinobacteria representing 52 operational taxonomic units was screened by PCR for genes associated with secondary-metabolite biosynthesis. Three primer sets were employed to specifically target adenylation domains associated with nonribosomal peptide synthetases (NRPSs) and ketosynthase (KS) domains associated with type I modular, iterative, hybrid, and enediyne polyketide synthases (PKSs). In total, two-thirds of the strains yielded a sequence-verified PCR product for at least one of these biosynthetic types. Genes associated with enediyne biosynthesis were detected in only two genera, while 88% of the ketosynthase sequences shared greatest homology with modular PKSs. Positive strains included representatives of families not traditionally associated with secondary-metabolite production, including the Corynebacteriaceae, Gordoniaceae, Intrasporangiaceae, and Micrococcaceae. In four of five cases where phylogenetic analyses of KS sequences revealed close evolutionary relationships to genes associated with experimentally characterized biosynthetic pathways, secondary-metabolite production was accurately predicted. Sequence clustering patterns were used to provide an estimate of PKS pathway diversity and to assess the biosynthetic richness of individual strains. The detection of highly similar KS sequences in distantly related strains provided evidence of horizontal gene transfer, while control experiments designed to amplify KS sequences from Salinispora arenicola strain CNS-205, for which a genome sequence is available, led to the detection of 70% of the targeted PKS pathways. The results provide a bioinformatic assessment of secondary-metabolite biosynthetic potential that can be applied in the absence of fully assembled pathways or genome sequences. The rapid identification of strains that possess the greatest potential to produce new secondary metabolites along with those that produce known compounds can be used to improve the process of natural-product discovery by providing a method to prioritize strains for fermentation studies and chemical analysis.

scholarly journals Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

Cell Systems ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 143-158.e13 ◽  
Author(s):  
Eva Yus ◽  
Verónica Lloréns-Rico ◽  
Sira Martínez ◽  
Carolina Gallo ◽  
Hinnerk Eilers ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
A Genome ◽  
Gene Regulatory

scholarly journals Genome-scale Transcriptomic Insights Into the Gene-regulatory Network of Seed Abortion in Triploid Siraitia Grosvenorii

2021 ◽  
Author(s):  
Rongchang Wei ◽  
Dongping Tu ◽  
Xiyang Huang ◽  
Zuliang Luo ◽  
Xiaohua Huang ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Developmental Stages ◽  
Differentially Expressed ◽  
Seed Abortion ◽  
Submicroscopic Structure ◽  
Medicinal Value ◽  
Siraitia Grosvenorii ◽  
Gene Regulatory ◽  
Genome Scale

Abstract BackgroundSiraitia grosvenorii (Swingle) C. Jeffrey, also known as Luohanguo or monk fruit, is a famous traditional Chinese medicine ingredient with important medicinal value and broad development prospects. Diploid S. grosvenorii has too many seeds. Thus, studying the molecular mechanism of seed abortion in triploid S. grosvenorii, identifying the abortion-related genes, and regulating their expression will be a new direction to obtain seedless S. grosvenorii. Herein, we examined the submicroscopic structure of triploid S. grosvenorii seeds during abortion. ResultsBy measuring the content of endogenous hormones, we found that abscisic acid (ABA) and trans-zeatin (ZR) levels were significantly downregulated at days 15 and 20 after flowering. RNA-seq of triploid seeds at different developmental stages was performed to identify the key genes regulating abortion of triploid S. grosvenorii seeds. Multiple differentially expressed genes between adjacent stages were identified; seven genes were differentially expressed across all stages. Weight gene co-expression network analysis revealed that the enhancement of monoterpene and terpene metabolic processes might lead to seed abortion by reducing substrate flow to ABA and ZR.ConclusionsThese findings provide insights into the gene-regulatory network of seed abortion in triploid S. grosvenorii from different perspectives, thereby facilitating the innovation of the breeding technology of S. grosvenorii.

scholarly journals A genome-wide assessment of the ancestral neural crest gene regulatory network

2018 ◽  
Author(s):  
Dorit Hockman ◽  
Vanessa Chong-Morrison ◽  
Daria Gavriouchkina ◽  
Stephen Green ◽  
Chris T. Amemiya ◽  
...  
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Regulatory Elements ◽  
Ancestral State ◽  
Enhancer Activity ◽  
Mesenchymal Transition ◽  
A Genome ◽  
Gene Regulatory ◽  
Insight Into

AbstractThe neural crest is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional profiles and chromatin accessibility of neural crest cells in the basal sea lamprey, in order to gain insight into the ancestral state of the neural crest gene regulatory network (GRN) at the dawn of vertebrates. Transcriptome analyses reveal clusters of co-regulated genes during neural crest specification and migration that show high conservation across vertebrates for dynamic programmes like Wnt modulation during the epithelial to mesenchymal transition, but also reveal novel transcription factors and cell-adhesion molecules not previously implicated in neural crest migration. ATAC-seq analysis refines the location of known cis-regulatory elements at the Hox-α2 locus and uncovers novel cis-regulatory elements for Tfap2B and SoxE1. Moreover, cross-species deployment of lamprey elements in zebrafish reveals that the lamprey SoxE1 enhancer activity is deeply conserved, mediating homologous expression in jawed vertebrates. Together, our data provide new insight into the core elements of the GRN that are conserved to the base of the vertebrates, as well as expose elements that are unique to lampreys.

scholarly journals A genome-wide assessment of the ancestral neural crest gene regulatory network

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Dorit Hockman ◽  
Vanessa Chong-Morrison ◽  
Stephen A. Green ◽  
Daria Gavriouchkina ◽  
Ivan Candido-Ferreira ◽  
...  
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Regulatory Elements ◽  
Embryonic Cell ◽  
Ancestral State ◽  
Enhancer Activity ◽  
A Genome ◽  
Gene Regulatory ◽  
Insight Into

Abstract The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.

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