The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants

Abstract

Main conclusion We advanceUlva’s genetic tractability and highlight its value as a model organism by characterizing its APAF1_C/WD40 domain-encoding gene, which belongs to a family that bears homology to R genes. Abstract The multicellular chlorophyte alga Ulva mutabilis (Ulvophyceae, Ulvales) is native to coastal ecosystems worldwide and attracts both high socio-economic and scientific interest. To further understand the genetic mechanisms that guide its biology, we present a protocol, based on adapter ligation-mediated PCR, for retrieving flanking sequences in U. mutabilis vector-insertion mutants. In the created insertional library, we identified a null mutant with an insertion in an apoptotic protease activating factor 1 helical domain (APAF1_C)/WD40 repeat domain-encoding gene. Protein domain architecture analysis combined with phylogenetic analysis revealed that this gene is a member of a subfamily that arose early in the evolution of green plants (Viridiplantae) through the acquisition of a gene that also encoded N-terminal nucleotide-binding adaptor shared by APAF-1, certain R-gene products and CED-4 (NB-ARC) and winged helix-like (WH-like) DNA-binding domains. Although phenotypic analysis revealed no mutant phenotype, gene expression levels in control plants correlated to the presence of bacterial symbionts, which U. mutabilis requires for proper morphogenesis. In addition, our analysis led to the discovery of a putative Ulva nucleotide-binding site and leucine-rich repeat (NBS-LRR) Resistance protein (R-protein), and we discuss how the emergence of these R proteins in green plants may be linked to the evolution of the APAF1_C/WD40 protein subfamily.

Genome-Wide Identification, Evolution, and Expression Analysis of the WD40 Subfamily in Oryza Genus

“…WD40 proteins generally have additional structural domains to recruit other factors to form protein-protein complexes [20]. Therefore, the WD40 protein family participates in many plant development and physiological processes and regulates the assembly of multiple complexes in plant resistance and abiotic stress response [21][22][23]. For example, in wheat (Tritivum aestivum L.), TaWD40D encoding seven WD40 domains was identified, which was a positive regulator of plant responses to salt stress and osmotic stress.…”

Ulva: An emerging green seaweed model for systems biology

“…Image depicts the morphology of a slender individual. Numbers relate to the following references: 1: Føyn (1958), 2: Føyn (1959), 3: Føyn (1960), 4: Føyn (1961), 5: Løvlie (1964), 6: Bråten & Løvlie (1966), 7: Løvlie & Bråten (1968), 8: Løvlie (1969), 9: Fjeld (1970), 10: Fjeld (1971), 11: Nordby & Hoxmark (1972), 12: Bryhni (1974), 13: Nordby (1974), 14: Fjeld & Børresen (1975), 15: Bråten (1975), 16: Nilsen & Nordby (1975), 17: Løvlie (1978), 18: Stratmann et al (1996), 19: Wichard & Oertel (2010), 20: Spoerner et al (2012), 21: Oertel et al (2015), 22: Alsufyani et al (2017); Kessler et al (2017), 23: Kessler et al (2018), 24: De Clerck et al (2018), 25: Steinhagen et al (2018), 26: Alsufyani et al (2020), 27: Blomme et al (2021), 28: Kwantes & Wichard (2022), 29: Liu et al (2022), and 30: Dhiman et al (2022). [Color figure can be viewed at wileyonlinelibrary.com]…”

“…The "mutabilis" trait resulted in strains with a tubular "slender" or "long," a hollow spherical "bubble," a disorganized "lumpy," or a globular "globose" thallus phenotype that triggered studies on cell division and vegetative development (Bryhni, 1974;Føyn, 1959Føyn, , 1961. More recently, similar and new developmental mutants (e.g., callus, filamentous branched, forked, and serrated) were generated by insertional mutagenesis, and genes are being functionally characterized (Kwantes & Wichard, 2022;Oertel et al, 2015;Wichard, 2023). Such forwardgenetics methods have been employed to generate large mutant libraries in Chlamydomonas, but reaching a stage wherein every single gene is mutated is difficult (Li et al, 2016).…”