Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes.

Calcium binding proteins (CBPs) function in response to changes in intracellular calcium (Ca ²⁺ ) levels by modulating intracellular signaling pathways. Calcium sensors, including Nucleobindins (Nucb1/2) undergo Ca ²⁺ -binding induced conformational changes and bind to target proteins. Nucleobindins possess additional uncharacterized domains including partly characterized EF-hands. We study the molecular evolution of Nucleobindins in eukaryotes emphasizing on the N-terminal DNA binding domain (DBD) that emerged as a result of domain insertion event in Nucb1/2 domain-scaffold in an ancestor to the opisthokonts. Our results from in silico analyses and functional assays revealed that DBD of Nucb1 binds to canonical E-box sequences and triggers cell epithelial-mesenchymal transition (EMT). Thus, post gene duplication, Nucb1 has emerged as unconventional Ca ²⁺ -binding transcriptional regulators that can induce EMT. Highlights: Nucleobindins emerged from prokaryotic EF-hand containing protein. The DNA-binding domain was gained in these in opisthokonts. Gene duplication in ancestor of euteleostomes, lead to emergence of Nucb1/2. Nucb1 emerged as a canonical E-box binding protein promoting EMT

Mitofusin mediate fusion of outer mitochondrial membranes (OMM). Recent studies have explained the role of GTPase domain for Mfn1 dimerization and outer mitochondrial membrane (OMM) fusion. Coiled-coiled domains [namely, coiled-coil/Middle domains (CC1MD) and coiled-coil-2 GTPase effector domain (CC2/GED)] form helical bundles that mediate open-to-close conformations of Mfn1 upon GTP binding and have been previously reported to be important for OMM tethering and OMM fusion. To further decipher the significance of helical structure of MD, we functionally characterized the heptad repeat regions of MD. Consistent with previous studies, we show that MD consists of two heptad repeats (HR1, namely HR1a and HR1b) and both of these are crucial for Mfn1 mediated OMM fusion.