Co-regulatory Network Analysis of the Main Secondary Metabolite (SM) Biosynthesis in Crocus Sativus L

Overview

Journal Sci Rep

Specialty Science

Date 2024 Jul 9

PMID 38982154

Authors

Mahsa Eshaghi

Sajad Rashidi-Monfared

Affiliations

Soon will be listed here.

Abstract

Saffron (Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the beneficial economic and medicinal properties of saffron, the regulatory mechanism of the correlation of TFs and genes related to the biosynthesis of the apocarotenoids pathway is less obvious. Realizing these regulatory hierarchies of gene expression networks related to secondary metabolites production events is the main challenge owing to the complex and extensive interactions between the genetic behaviors. Recently, high throughput expression data have been highly feasible for constructing co-regulation networks to reveal the regulated processes and identifying novel candidate hub genes in response to complex processes of the biosynthesis of secondary metabolites. Herein, we performed Weighted Gene Co-expression Network Analysis (WGCNA), a systems biology method, to identify 11 regulated modules and hub TFs related to secondary metabolites. Three specialized modules were found in the apocarotenoids pathway. Several hub TFs were identified in notable modules, including MADS, C2H2, ERF, bZIP, HD-ZIP, and zinc finger protein MYB and HB, which were potentially associated with apocarotenoid biosynthesis. Furthermore, the expression levels of six hub TFs and six co-regulated genes of apocarotenoids were validated with RT-qPCR. The results confirmed that hub TFs specially MADS, C2H2, and ERF had a high correlation (P < 0.05) and a positive effect on genes under their control in apocarotenoid biosynthesis (CCD2, GLT2, and ADH) among different C. sativus ecotypes in which the metabolite contents were assayed. Promoter analysis of the co-expressed genes of the modules involved in apocarotenoids biosynthesis pathway suggested that not only are the genes co-expressed, but also share common regulatory motifs specially related to hub TFs of each module and that they may describe their common regulation. The result can be used to engineer valuable secondary metabolites of C. sativus by manipulating the hub regulatory TFs.

References

Lopez-Jimenez A, Frusciante S, Niza E, Ahrazem O, Rubio-Moraga A, Diretto G . A New Glycosyltransferase Enzyme from Family 91, UGT91P3, Is Responsible for the Final Glucosylation Step of Crocins in Saffron ( L.). Int J Mol Sci. 2021; 22(16). PMC: 8396231. DOI: 10.3390/ijms22168815. View

Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R . The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2022; 51(D1):D638-D646. PMC: 9825434. DOI: 10.1093/nar/gkac1000. View

Mounet F, Moing A, Garcia V, Petit J, Maucourt M, Deborde C . Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development. Plant Physiol. 2009; 149(3):1505-28. PMC: 2649409. DOI: 10.1104/pp.108.133967. View

Tai Y, Liu C, Yu S, Yang H, Sun J, Guo C . Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis). BMC Genomics. 2018; 19(1):616. PMC: 6094456. DOI: 10.1186/s12864-018-4999-9. View

Kakeshpour T, Nayebi S, Rashidi Monfared S, Moieni A, Karimzadeh G . Identification and expression analyses of MYB and WRKY transcription factor genes in Papaver somniferum L. Physiol Mol Biol Plants. 2015; 21(4):465-78. PMC: 4646871. DOI: 10.1007/s12298-015-0325-z. View

Liu T, Yu S, Xu Z, Tan J, Wang B, Liu Y . Prospects and progress on crocin biosynthetic pathway and metabolic engineering. Comput Struct Biotechnol J. 2020; 18:3278-3286. PMC: 7653203. DOI: 10.1016/j.csbj.2020.10.019. View

Joshi-Saha A, Reddy K . Repeat length variation in the 5'UTR of myo-inositol monophosphatase gene is related to phytic acid content and contributes to drought tolerance in chickpea (Cicer arietinum L.). J Exp Bot. 2015; 66(19):5683-90. DOI: 10.1093/jxb/erv156. View

Dang Q, Sha H, Nie J, Wang Y, Yuan Y, Jia D . An apple (Malus domestica) AP2/ERF transcription factor modulates carotenoid accumulation. Hortic Res. 2021; 8(1):223. PMC: 8492665. DOI: 10.1038/s41438-021-00694-w. View

Khorasany A, Hosseinzadeh H . Therapeutic effects of saffron (Crocus sativus L.) in digestive disorders: a review. Iran J Basic Med Sci. 2016; 19(5):455-69. PMC: 4923465. View

10.

Husaini A, Jan K, Wani G . Saffron: A potential drug-supplement for severe acute respiratory syndrome coronavirus (COVID) management. Heliyon. 2021; 7(5):e07068. PMC: 8118646. DOI: 10.1016/j.heliyon.2021.e07068. View

11.

Yue J, Wang R, Ma X, Liu J, Lu X, Balaso Thakar S . Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in . Comput Struct Biotechnol J. 2020; 18:774-783. PMC: 7132054. DOI: 10.1016/j.csbj.2020.03.022. View

12.

Chin C, Chen S, Wu H, Ho C, Ko M, Lin C . cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014; 8 Suppl 4:S11. PMC: 4290687. DOI: 10.1186/1752-0509-8-S4-S11. View

13.

Smita S, Katiyar A, Chinnusamy V, Pandey D, Bansal K . Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice. Front Plant Sci. 2016; 6:1157. PMC: 4689866. DOI: 10.3389/fpls.2015.01157. View

14.

Demurtas O, de Brito Francisco R, Diretto G, Ferrante P, Frusciante S, Pietrella M . ABCC Transporters Mediate the Vacuolar Accumulation of Crocins in Saffron Stigmas. Plant Cell. 2019; 31(11):2789-2804. PMC: 6881118. DOI: 10.1105/tpc.19.00193. View

15.

Moschen S, Higgins J, Di Rienzo J, Heinz R, Paniego N, Fernandez P . Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower. BMC Bioinformatics. 2016; 17 Suppl 5:174. PMC: 4905614. DOI: 10.1186/s12859-016-1045-2. View

16.

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

17.

Sayadi V, Karimzadeh G, Rashidi Monfared S, Naghavi M . Identification and expression analysis of S-alk(en)yl-L-cysteine sulfoxide lyase isoform genes and determination of allicin contents in Allium species. PLoS One. 2020; 15(2):e0228747. PMC: 7039512. DOI: 10.1371/journal.pone.0228747. View

18.

Rohmer M, Knani M, SIMONIN P, Sutter B, Sahm H . Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate. Biochem J. 1993; 295 ( Pt 2):517-24. PMC: 1134910. DOI: 10.1042/bj2950517. View

19.

Qian X, Sun Y, Zhou G, Yuan Y, Li J, Huang H . Single-molecule real-time transcript sequencing identified flowering regulatory genes in Crocus sativus. BMC Genomics. 2019; 20(1):857. PMC: 6854690. DOI: 10.1186/s12864-019-6200-5. View

20.

Bouvier F, Suire C, Mutterer J, Camara B . Oxidative remodeling of chromoplast carotenoids: identification of the carotenoid dioxygenase CsCCD and CsZCD genes involved in Crocus secondary metabolite biogenesis. Plant Cell. 2003; 15(1):47-62. PMC: 143450. DOI: 10.1105/tpc.006536. View