Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses

Gomez‐Cano, Fabio; Chu, Yi‐Hsuan; Cruz‐Gomez, Mariel; Abdullah, Hesham M.; Lee, Yun Sun; Schnell, Danny J.; Grotewold, Erich

doi:10.1111/tpj.15682

Title: Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses

Journal Article · Sat Jan 22 00:00:00 EST 2022 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.15682· OSTI ID:1865586

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Michigan State Univ., East Lansing, MI (United States)
Michigan State Univ., East Lansing, MI (United States); Al-Azhar Univ., Cairo (Egypt)

SUMMARY Camelina ( Camelina sativa ) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co‐expressed with lipid‐related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well‐known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA‐binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP‐seq). Enrichment analyses of targets supported the co‐expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1‐2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1‐2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co‐expression data and DNA‐binding assays permitted us to generate a high‐confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.

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Research Organization:: Michigan State Univ., East Lansing, MI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0018269; DE‐SC0018269

OSTI ID:: 1865586

Alternate ID(s):: OSTI ID: 1846077

Journal Information:: The Plant Journal, Vol. 110, Issue 2; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Phosphorylation of WRINKLED1 by KIN10 Results in Its Proteasomal Degradation, Providing a Link between Energy Homeostasis and Lipid Biosynthesis Zhai, Zhiyang; Liu, Hui; Shanklin, John The Plant Cell, Vol. 29, Issue 4 https://doi.org/10.1105/tpc.17.00019	journal	March 2017
FUSCA3 activates triacylglycerol accumulation in Arabidopsis seedlings and tobacco BY2 cells Zhang, Meng; Cao, Xia; Jia, Qingli The Plant Journal, Vol. 88, Issue 1 https://doi.org/10.1111/tpj.13233	journal	August 2016
AGAMOUS-Like15 Promotes Somatic Embryogenesis in Arabidopsis and Soybean in Part by the Control of Ethylene Biosynthesis and Response Zheng, Qiaolin; Zheng, Yumei; Perry, Sharyn E. Plant Physiology, Vol. 161, Issue 4 https://doi.org/10.1104/pp.113.216275	journal	March 2013
Global Identification of Targets of the Arabidopsis MADS Domain Protein AGAMOUS-Like15 Zheng, Yumei; Ren, Na; Wang, Huai The Plant Cell, Vol. 21, Issue 9 https://doi.org/10.1105/tpc.109.068890	journal	September 2009

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