The heterochronic LIN-14 protein is a BEN domain transcription factor

Abstract

Heterochrony is a foundational concept in animal development and evolution, first introduced by Ernst Haeckel in 1875 and later popularized by Stephen J. Gould1Gould S.J. Ontogeny and Phylogeny. Harvard University Press, Cambridge, MA1977Google Scholar. A molecular understanding of heterochrony was first established by genetic mutant analysis in the nematode C. elegans, revealing a genetic pathway that controls the proper timing of cellular patterning events executed during distinct postembryonic juvenile and adult stages2Ambros V. Horvitz H.R. Heterochronic mutants of the nematode Caenorhabditis elegans.Science. 1984; 226: 409-416Crossref PubMed Scopus (585) Google Scholar. This genetic pathway is composed of a complex temporal cascade of multiple regulatory factors, including the first-ever discovered miRNA, lin-4, and its target gene, lin-14, which encodes a nuclear, DNA-binding protein2Ambros V. Horvitz H.R. Heterochronic mutants of the nematode Caenorhabditis elegans.Science. 1984; 226: 409-416Crossref PubMed Scopus (585) Google Scholar,3Ruvkun G. Giusto J. The Caenorhabditis elegans heterochronic gene lin-14 encodes a nuclear protein that forms a temporal developmental switch.Nature. 1989; 338: 313-319Crossref PubMed Scopus (162) Google Scholar,4Hristova M. Birse D. Hong Y. Ambros V. The Caenorhabditis elegans heterochronic regulator LIN-14 is a novel transcription factor that controls the developmental timing of transcription from the insulin/insulin-like growth factor gene ins-33 by direct DNA binding.Mol. Cell Biol. 2005; 25: 11059-11072Crossref PubMed Scopus (42) Google Scholar. While all core members of the pathway have homologs based on primary sequences in other organisms, homologs for LIN-14 have never been identified by sequence homology. We report that the AlphaFold-predicted structure of the LIN-14 DNA binding domain is homologous to the BEN domain, found in a family of DNA binding proteins previously thought to have no nematode homologs5Dai Q. Ren A. Westholm J.O. Serganov A.A. Patel D.J. Lai E.C. The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors.Genes Dev. 2013; 27: 602-614Crossref PubMed Scopus (57) Google Scholar. We confirmed this prediction through targeted mutations of predicted DNA-contacting residues, which disrupt in vitro DNA binding and in vivo function. Our findings shed new light on potential mechanisms of LIN-14 function and suggest that BEN domain-containing proteins may have a conserved role in developmental timing.

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