Recent gene duplications dominate evolutionary dynamics of adaptor protein complex subunits in embryophytes

Abstract

Adaptor protein complexes and the related complexes COPI and TSET function in packaging vesicles for transport among endomembrane compartments in eukaryotic cells. Differences in the complement of these complexes in lineages such as yeast and mammals as well as apicomplexan and kinetoplastid parasites via loss or duplication of subunits appears to reflect specialization in their respective trafficking systems. The model plant Arabidopsis thaliana possesses multiple paralogues for adaptor protein complex subunits, raising questions as to the timing and extent of these duplications in embryophytes (land plants). However, adaptor protein complex evolution in embryophytes is unexplored. Therefore, we analyzed genomes of diverse embryophytes and closely related green algae using extensive homology searches and phylogenetic analysis of 35 complex subunit proteins. The results reveal numerous paralogues, the vast majority of which, approximately 97%, arose from recent duplication events. This suggests that specialization of these protein complexes may occur frequently but independently in embryophytes.

An ancestral genomic sequence that serves as a nucleation site for de novo gene birth

“…The evolutionary formation of the BCRP3 sequence and gene presents a sharp contrast to the creation of the gene linc-UR-UB, the regulatory long non-coding RNA gene found in the human genome and believed to be involved in immune system regulation and formed by a simple transcriptional read through process [15]. This reiterates the wealth of mechanisms that life forms have used to create new genes [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]. Lastly, the mechanism of initiation of DNA synthesis, the DNA template for FAM247 synthesis, or if there is a template involved is a "black box".…”

“…Protein genes are created by varied processes that include gene duplication [1][2][3][4][5], retrogenes [6] and de novo formation [6][7][8][9][10][11][12]. With respect to the latter, Knowles and McLysaght [8] first reported that several human protein-coding genes arose by a de novo mechanism, and Wu et al [9] identified 60 protein-coding genes that are also born by a de novo process.…”

PAM: diverse roles in neuroendocrine cells, cardiomyocytes, and green algae

“…In prokaryotes, this process is used to secrete proteins; the luminal compartments present in eukaryotes allow secretion of folded proteins. Strikingly, many of the proteins known to play essential roles in membrane trafficking and organelle identity are highly conserved [24,25]. The last eukaryotic common ancestor (LECA), a hypothetical organism living about a billion years ago, is thought to have included a nuclear envelope, ER, Golgi stacks, lysosomes, and a single motile cilium [17,26].…”

“…The last eukaryotic common ancestor (LECA), a hypothetical organism living about a billion years ago, is thought to have included a nuclear envelope, ER, Golgi stacks, lysosomes, and a single motile cilium [17,26]. Maintenance of these structures required the extensive use of targeted vesicular trafficking to control multiple biosynthetic, endocytic, and intra-organellar trafficking pathways [17][18][19][20][21]24,27]. At least nine distinct vesicle coat protein complexes, including COPI, COPII, the clathrin/adaptor protein (AP) complexes, retromer and ESCRT are thought to have been present in LECA.…”

An ancestral genomic sequence that serves as a nucleation site for de novo gene birth

“…Protein genes are created by varied processes that include gene duplication [ 1 – 5 ], retrogenes [ 6 ] and de novo formation [ 6 – 12 ]. With respect to the latter, Knowles and McLysaght [ 8 ] first reported that several human protein-coding genes arose by a de novo mechanism, and Wu et al [ 9 ] identified 60 protein-coding genes that are also born by a de novo process.…”