scholarly journals Paralogous gene modules derived from ancient hybridization drive vesicle traffic evolution in yeast

2021 ◽  
Author(s):  
Ramya Purkanti ◽  
Mukund Thattai
Keyword(s):  
Paralogous Gene ◽  
Endomembrane System ◽  
Vesicle Budding ◽  
Vesicle Traffic ◽  
Selective Pressures ◽  
Large Gene ◽  
Hybridization Event ◽  
Interspecies Hybridization ◽  
Gene Modules ◽  
Endocytic Pathways

AbstractModules of interacting proteins regulate vesicle budding and fusion in eukaryotes. Distinct paralogous copies of these modules act at distinct sub-cellular locations. The processes by which such large gene modules are duplicated and retained remain unclear. Here we show that interspecies hybridization is a potent source of paralogous gene modules. We study the dynamics of paralog doublets derived from the 100-million-year-old hybridization event that gave rise to the whole genome duplication clade of budding yeast. We show that paralog doublets encoding vesicle traffic proteins are convergently retained across species. Vesicle coats and adaptors involved in secretory and early-endocytic pathways are retained as doublets, while tethers and other machinery involved in intra-Golgi traffic and later endocytic steps are reduced to singletons. These patterns reveal common selective pressures that have sculpted traffic pathways in diverse yeast species. They suggest that hybridization may have played a pivotal role in the expansion of the endomembrane system.

scholarly journals Stacking the odds for Golgi cisternal maturation

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Somya Mani ◽  
Mukund Thattai
Keyword(s):  
Golgi Apparatus ◽  
Molecular Interactions ◽  
Secretory Pathway ◽  
Traffic Networks ◽  
Minimal Set ◽  
Vesicle Budding ◽  
Vesicle Traffic

What is the minimal set of cell-biological ingredients needed to generate a Golgi apparatus? The compositions of eukaryotic organelles arise through a process of molecular exchange via vesicle traffic. Here we statistically sample tens of thousands of homeostatic vesicle traffic networks generated by realistic molecular rules governing vesicle budding and fusion. Remarkably, the plurality of these networks contain chains of compartments that undergo creation, compositional maturation, and dissipation, coupled by molecular recycling along retrograde vesicles. This motif precisely matches the cisternal maturation model of the Golgi, which was developed to explain many observed aspects of the eukaryotic secretory pathway. In our analysis cisternal maturation is a robust consequence of vesicle traffic homeostasis, independent of the underlying details of molecular interactions or spatial stacking. This architecture may have been exapted rather than selected for its role in the secretion of large cargo.

scholarly journals Evolution of gene-rich germline restricted chromosomes in black-winged fungus gnats through introgression (Diptera: Sciaridae)

2021 ◽  
Author(s):  
Christina N. Hodson ◽  
Kamil S. Jaron ◽  
Susan Gerbi ◽  
Laura Ross
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Sequence Coverage ◽  
Large Gene ◽  
Hybridization Event ◽  
Fungus Gnats ◽  
Fungus Gnat ◽  
Over Time ◽  
Ancient Hybridization

AbstractGermline restricted DNA has evolved in diverse animal taxa, and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline restricted DNA has evolved, especially in flies, in which three diverse families, Chironomidae, Cecidomyiidae, and Sciaridae exhibit germline restricted chromosomes (GRCs). We conducted a genomic analysis of germline restricted chromosomes in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which carries two large germline restricted “L” chromosomes. We sequenced and assembled the genome of B. coprophila, and used differences in sequence coverage and k-mer frequency between somatic and germ tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene-rich, and have many genes with paralogs on other chromosomes in the genome. We also found that the GRC genes are extraordinarily divergent from their paralogs, and have sequence similarity to another Dipteran family (Cecidomyiidae) in phylogenetic analyses, suggesting that these chromosomes have arisen in Sciaridae through introgression from a related lineage. These results suggest that the GRCs may have evolved through an ancient hybridization event, raising questions about how this may have occurred, how these chromosomes became restricted to the germline after introgression, and why they were retained over time.

scholarly journals Large Gene Family Expansion and Variable Selective Pressures for Cathepsin B in Aphids

2007 ◽  
Vol 25 (1) ◽  
pp. 5-17 ◽  
Author(s):  
C. Rispe ◽  
M. Kutsukake ◽  
V. Doublet ◽  
S. Hudaverdian ◽  
F. Legeai ◽  
...  
Keyword(s):  
Gene Family ◽  
Cathepsin B ◽  
Large Gene Family ◽  
Gene Family Expansion ◽  
Selective Pressures ◽  
Large Gene ◽  
Family Expansion

scholarly journals HOPS Interacts with Apl5 at the Vacuole Membrane and Is Required for Consumption of AP-3 Transport Vesicles

2009 ◽  
Vol 20 (21) ◽  
pp. 4563-4574 ◽  
Author(s):  
Cortney G. Angers ◽  
Alexey J. Merz
Keyword(s):  
Fluorescence Microscopy ◽  
Protein Complexes ◽  
Adaptor Protein ◽  
Vesicle Budding ◽  
Vesicle Docking ◽  
Vacuole Membrane ◽  
Vesicle Traffic ◽  
Transport Vesicles ◽  
Evolutionarily Conserved ◽  
Curved Membranes

Adaptor protein complexes (APs) are evolutionarily conserved heterotetramers that couple cargo selection to the formation of highly curved membranes during vesicle budding. In Saccharomyces cerevisiae , AP-3 mediates vesicle traffic from the late Golgi to the vacuolar lysosome. The HOPS subunit Vps41 is one of the few proteins reported to have a specific role in AP-3 traffic, yet its function remains undefined. We now show that although the AP-3 δ subunit, Apl5, binds Vps41 directly, this interaction occurs preferentially within the context of the HOPS docking complex. Fluorescence microscopy indicates that Vps41 and other HOPS subunits do not detectably colocalize with AP-3 at the late Golgi or on post-Golgi (Sec7-negative) vesicles. Vps41 and HOPS do, however, transiently colocalize with AP-3 vesicles when these vesicles dock at the vacuole membrane. In cells with mutations in HOPS subunits or the vacuole SNARE Vam3, AP-3 shifts from the cytosol to a membrane fraction. Fluorescence microscopy suggests that this fraction consists of post-Golgi AP-3 vesicles that have failed to dock or fuse at the vacuole membrane. We propose that AP-3 remains associated with budded vesicles, interacts with Vps41 and HOPS upon vesicle docking at the vacuole, and finally dissociates during docking or fusion.

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