title: NKD Transcription Factors Are Central Regulators of Maize Endosperm Development.
abstract: NAKED ENDOSPERM1 (NKD1) and NKD2 are duplicate INDETERMINATE DOMAIN (IDD) transcription factors important for maize (Zea mays) endosperm development. RNA-seq analysis of the nkd1 nkd2 mutant endosperm revealed that NKD1 and NKD2 influence 6.4% of the transcriptome in developing aleurone and 6.7% in starchy endosperm. Processes regulated by NKD1 and NKD2 include gene expression, epigenetic functions, cell growth and division, hormone pathways, and resource reserve deposition. The NKD1 and NKD2 proteins bind a consensus DNA sequence of TTGTCGT with slightly different properties. This motif was enriched in the promoters of gene transcripts differentially expressed (DE) in mutant endosperm. DE genes with a NKD binding motif in the 5' promoter region were considered as likely direct targets of NKD1 and NKD2 regulation, and these putative direct target genes were notably enriched for storage proteins. Transcription assays demonstrate that NKD1 and NKD2 can directly regulate gene transcription, including activation of opaque2 and viviparous1 promoters. NKD2 functions as a negative regulator of nkd1 transcription, consistent with previously reported feedback regulation. NKD1 and NKD2 can homo- and heterodimerize through their ID domains. These analyses implicate NKD1 and NKD2 as central regulators of gene expression in developing maize endosperm.
authors.affiliation: Plant Biology Program, Iowa State University, Ames, Iowa 50011.|Genetics, Development, and Cell Biology Department, Iowa State University, Ames, Iowa 50011.
authors.forename: Bryan C
authors.identifier: 0000-0001-8847-0653
authors.initials: BC
authors.lastname: Gontarek
authors.affiliation: Genetics, Development, and Cell Biology Department, Iowa State University, Ames, Iowa 50011.
authors.forename: Anjanasree K
authors.identifier: 0000-0002-3551-308X
authors.initials: AK
authors.lastname: Neelakandan
authors.affiliation: Genetics, Development, and Cell Biology Department, Iowa State University, Ames, Iowa 50011.
authors.forename: Hao
authors.identifier: 0000-0003-0535-5348
authors.initials: H
authors.lastname: Wu
authors.affiliation: Plant Biology Program, Iowa State University, Ames, Iowa 50011 becraft@iastate.edu.|Genetics, Development, and Cell Biology Department, Iowa State University, Ames, Iowa 50011.|Agronomy Department, Iowa State University, Ames, Iowa 50011.
authors.forename: Philip W
authors.identifier: 0000-0002-3299-2126
authors.initials: PW
authors.lastname: Becraft
mesh_terms: D056625:Endosperm / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D003313:Zea mays / Q000235:genetics / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors