LEC1-LIKE paralog transcription factor: how to survive extinction and fit in NF-Y protein complex

Gene. 2014 Jun 15;543(2):220-33. doi: 10.1016/j.gene.2014.04.019. Epub 2014 Apr 13.


Transcription factor function is crucial for eukaryotic systems. The presence of transcription factor families in genomes represents a significant technical challenge for functional studies. To understand their function, we must understand how they evolved and maintained by organisms. Based on genome scale searches for homologs of LEAFY COTYLEDON-LIKE (L1L; AtNF-YB6), NF-YB transcription factor, we report the discovery and annotation of a complete repertoire of thirteen novel genes that belong to the L1L paralogous gene family of Solanum lycopersicum. Gene duplication events within the species resulted in the expansion of the L1L family. Sequence and structure-based phylogenetic analyses revealed two distinct groups of L1Ls in tomato. Natural selection appears to have contributed to the asymmetric evolution of paralogs. Our results point to key differences among SlL1L paralogs in the presence of motifs, structural features, cysteine composition and expression patterns during plant and fruit development. Furthermore, differences in the binding domains of L1L members suggest that some of them evolved new binding specificities. These results reveal dramatic functional diversification of L1L paralogs for their maintenance in tomato genome. Our comprehensive insights on tomato L1L family should provide the basis for further functional and genetic experimentation.

Keywords: Cysteine variation; Development; Gene evolution; NF-YB/L1L; Paralog transcription factor family.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • CCAAT-Binding Factor / chemistry*
  • CCAAT-Binding Factor / classification
  • CCAAT-Binding Factor / genetics*
  • Evolution, Molecular
  • Genetic Variation
  • Genome, Plant
  • Lycopersicon esculentum / genetics*
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Phylogeny
  • Plant Proteins / chemistry*
  • Plant Proteins / classification
  • Plant Proteins / genetics*


  • CCAAT-Binding Factor
  • Plant Proteins