Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

Int J Mol Sci. 2019 Nov 18;20(22):5796. doi: 10.3390/ijms20225796.

Abstract

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

Keywords: CCDs; Nicotiana tabacum; gene expression; genome-wide identification; hormones and abiotic stresses.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Carotenoids / metabolism
  • Chromosome Mapping
  • Conserved Sequence
  • Dioxygenases / chemistry
  • Dioxygenases / genetics*
  • Dioxygenases / metabolism*
  • Evolution, Molecular
  • Gene Expression Regulation, Plant
  • Multigene Family
  • Phylogeny
  • Plant Proteins / chemistry
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Promoter Regions, Genetic
  • Selection, Genetic
  • Sequence Analysis, DNA / methods*
  • Tobacco / enzymology*
  • Tobacco / genetics

Substances

  • Plant Proteins
  • Carotenoids
  • Dioxygenases