Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans

In most animals and fungi, centromere identity and function depend on the Scm3/Holliday junction recognition protein (HJURP) chaperone, which deposits CENPA at centromeres. However, Scm3/HJURP orthologs appeared to be missing in insects, nematodes, many vertebrates, and other metazoans, suggesting radical chaperone replacement in these lineages. Here, we combine remote homology detection, AlphaFold-based structural modeling, and functional genetics in zebrafish and Caenorhabditis elegans to identify previously unknown Scm3/HJURP orthologs that localize to centromeres and whose loss causes catastrophic mitotic failure. We further show that Drosophila CAL1, long considered a functional analog, is instead a highly diverged Scm3/HJURP ortholog. Despite rapid primary-sequence divergence, predicted and known structures reveal a broadly conserved CENPA-H4–binding scm3 fold across fungi, vertebrates, nematodes, insects, and most metazoans. Our work demonstrates how rapid divergence can obscure the broad conservation of essential centromere machinery and provides a generalizable strategy for unmasking missing orthologs.