A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans

Abstract

Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue‐specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70–80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.

NEKL-4 regulates microtubule stability and mitochondrial health inC. elegansciliated neurons

“…NEKL-4(KD) did not impact ciliary glutamylation, yet ectopically localized to abnormallyglutamylated cilia and suppressed the ccpp-1Δ Dyf phenotype. Therefore, we examined the microtubule ultrastructure of nekl-4(KD) and ccpp-1Δ; nekl-4(KD) amphid channel cilia (Fig 2a In ccpp-1Δ; nekl-4(KD), we observed ectopic microtubule singlets in the doublet region and ectopic doublets in the singlet region of some cilia (Fig 2c-d), similar to mutants of Tubulin Code "readers'' MAPK mapk-15 and homodimeric kinesin-2 osm-3 (Xie et al, 2020;Dobbelaere et al, 2023). We also observed additional ciliary defects in nekl-4(KD), ccpp-1Δ; nekl-4(KD), and nekl-4(PESTΔ) mutants, including loss of radial symmetry and increased, irregular distances between the doublets and the ciliary membrane (Fig 2c).…”

Centriolar satellites are sites of translation of centrosomal and ciliary proteins

“…Both types of defect could be reproduced by tissue-specific RNAi and rescued by introduction of a GFP transgene, confirming specificity of the mutant phenotype and functionality of the GFP transgene. Neither phenotype is shared by PCP genes, but both are highly reminiscent of what is observed following perturbation of centriolar or ciliary components ( 27, 28 ). A closer examination of ciliary morphology in the chordotonal neurons responsible for mechanosensation in the animals’ legs by DIC and immunofluorescence microscopy as well as ultrastructural analysis revealed only minor defects (fig.…”

“…Conserved motifs within PCM1 were identified by Meme (https://meme-suite.org/meme/) and sequences aligned using MUSCLE within Jalview (https://www.jalview.org). The presence of centrosomes and cilia within fungi, Nematomorpha and Platyhelminthes was inferred from the conservation of core centriolar (STIL/Ana2, SASS6/Sas6, CENPJ/Sas4, CEP135/Bld10), centrosomal (CDK5RAP2/Cnn, CEP192/Spd2) and ciliary (transition zone, IFT and BBS components, inner and outer dynein arm components, dynein assembly factors, nexins, N-DRC, radial spoke and central apparatus components, ( 28 )) proteins, as well as literature reports ( 21, 58 ).…”

“…1B. Conservation of PCM1 as well as core centriolar (STIL/Ana2, SASS6/Sas6, CENPJ/Sas4, CEP135/Bld10), centrosomal (CDK5RAP2/Cnn, CEP192/Spd2) and ciliary proteins (transition zone, IFT and BBS components, inner and outer dynein arm components, dynein assembly factors, nexins, N-DRC, radial spoke and central apparatus components, ( 28 )) across opisthokonts, based on reciprocal BLAST analysis and hidden Markov model-based searches. Color code is green > 2/3 of genes in indicated category present, yellow > 1/3 of genes present, magenta < 1/3 present.…”

“…4B,C). IFT and BBS proteins do not contribute to cilium biogenesis in Drosophila sperm ( 28, 38 ) and were not detected.…”