title: Identification, cloning and characterization of the tomato TCP transcription factor family.
abstract: BACKGROUND
  TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome.
  
  
  RESULTS
  We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato.
  
  
  CONCLUSIONS
  The comprehensive analysis we performed, like phylogenetic analysis, expression studies, identification of the upstream regulators and the dimerization specificity of the tomato TCP transcription factor family provides the basis for functional studies to reveal the role of this family in tomato development.
authors.forename: Violeta
authors.initials: V
authors.lastname: Parapunova
authors.forename: Marco
authors.initials: M
authors.lastname: Busscher
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Busscher-Lange
authors.forename: Michiel
authors.initials: M
authors.lastname: Lammers
authors.forename: Rumyana
authors.initials: R
authors.lastname: Karlova
authors.forename: Arnaud G
authors.initials: AG
authors.lastname: Bovy
authors.forename: Gerco C
authors.initials: GC
authors.lastname: Angenent
authors.affiliation: Plant Research International, P,O, Box 619, 6700 AP Wageningen, the Netherlands. ruud.demaagd@wur.nl.
authors.forename: Ruud A
authors.initials: RA
authors.lastname: de Maagd
mesh_terms: D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000378:metabolism; D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D005809:Genes, Regulator; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development; D008969:Molecular Sequence Data; D005810:Multigene Family; D009154:Mutation / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020798:Two-Hybrid System Techniques
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins; D014157:Transcription Factors