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Penny GM, Dutcher SK. Gene dosage of independent dynein arm motor preassembly factors influences cilia assembly in Chlamydomonas reinhardtii. PLoS Genet 2024; 20:e1011038. [PMID: 38498551 PMCID: PMC11020789 DOI: 10.1371/journal.pgen.1011038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 04/16/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Motile cilia assembly utilizes over 800 structural and cytoplasmic proteins. Variants in approximately 58 genes cause primary ciliary dyskinesia (PCD) in humans, including the dynein arm (pre)assembly factor (DNAAF) gene DNAAF4. In humans, outer dynein arms (ODAs) and inner dynein arms (IDAs) fail to assemble motile cilia when DNAAF4 function is disrupted. In Chlamydomonas reinhardtii, a ciliated unicellular alga, the DNAAF4 ortholog is called PF23. The pf23-1 mutant assembles short cilia and lacks IDAs, but partially retains ODAs. The cilia of a new null allele (pf23-4) completely lack ODAs and IDAs and are even shorter than cilia from pf23-1. In addition, PF23 plays a role in the cytoplasmic modification of IC138, a protein of the two-headed IDA (I1/f). As most PCD variants in humans are recessive, we sought to test if heterozygosity at two genes affects ciliary function using a second-site non-complementation (SSNC) screening approach. We asked if phenotypes were observed in diploids with pairwise heterozygous combinations of 21 well-characterized ciliary mutant Chlamydomonas strains. Vegetative cultures of single and double heterozygous diploid cells did not show SSNC for motility phenotypes. When protein synthesis is inhibited, wild-type Chlamydomonas cells utilize the pool of cytoplasmic proteins to assemble half-length cilia. In this sensitized assay, 8 double heterozygous diploids with pf23 and other DNAAF mutations show SSNC; they assemble shorter cilia than wild-type. In contrast, double heterozygosity of the other 203 strains showed no effect on ciliary assembly. Immunoblots of diploids heterozygous for pf23 and wdr92 or oda8 show that PF23 is reduced by half in these strains, and that PF23 dosage affects phenotype severity. Reductions in PF23 and another DNAAF in diploids affect the ability to assemble ODAs and IDAs and impedes ciliary assembly. Thus, dosage of multiple DNAAFs is an important factor in cilia assembly and regeneration.
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Affiliation(s)
- Gervette M. Penny
- Department of Genetics, Washington University in Saint Louis, Saint Louis,Missouri, United States of America
| | - Susan K. Dutcher
- Department of Genetics, Washington University in Saint Louis, Saint Louis,Missouri, United States of America
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Xu Z, Xu H, Chen X, Huang X, Tian J, Zhao J, Liu B, Shi F, Wu J, Pu J. CCDC103 as a Prognostic Biomarker Correlated with Tumor Progression and Immune Infiltration in Glioma. Onco Targets Ther 2023; 16:819-837. [PMID: 37873495 PMCID: PMC10590567 DOI: 10.2147/ott.s429958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023] Open
Abstract
Background The Coiled-coil domain-containing proteins (CCDCs) are expressed in many cancers, but the role of Coiled-coil domain-containing protein 103 (CCDC103) in cancers remains unclear. Further investigations are necessary to ascertain its diagnostic significance and understand its biological function in cancers. This study aims to elucidate the biological functionalities of CCDC103 in glioma and evaluate the correlation between CCDC103 expression with glioma progression. Methods Clinical data on glioma patients were acquired from The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), and the Gene Expression Omnibus (GEO). The evaluation encompassed the examination of correlations between CCDC103 expression, pathological characteristics, and clinical outcomes. Furthermore, the analysis included the assessment of the correlations between CCDC103 expression and immune cell infiltration as well as glioma progression. Results Gliomas have higher levels of CCDC103 expression than the para-carcinoma tissues. Poorer prognosis, unfavorable histological characteristics, the absence of IDH gene mutations, and the absence of chromosome 1p and 19q deletions were all associated with higher expression of CCDC103 in gliomas. In addition to patient age, tumor grade, the absence of IDH mutations, and the absence of chromosome 1p and 19q deletions, univariate and multivariate Cox analyses showed that CCDC103 expression was independently prognostic of overall survival, disease-free survival, and progression-free survival in patients with glioma. Furthermore, tumor infiltration of B cells, neutrophils, macrophages, and dendritic cells were all linked with elevated expression of CCDC103. High CCDC103 expression was linked to immune response-related signaling pathways and cell proliferation, according to gene set enrichment analysis (GSEA). Notably, the knockdown of CCDC103 in glioma cell lines resulted in a significant reduction in cell proliferation and migration. Conclusion The correlation between CCDC103 expression and both glioma progression and immune cell infiltration implies that CCDC103 expression holds promise as a valuable prognostic biomarker for glioma.
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Affiliation(s)
- Zhixing Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
- Department of Neurosurgery, The Pu’er People’s Hospital, Pu’er, 665000, People’s Republic of China
| | - Haitao Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Xi Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Xiaobing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Jintao Tian
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Jinxi Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Bohu Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
| | - Fengcai Shi
- Department of Neurosurgery, The Pu’er People’s Hospital, Pu’er, 665000, People’s Republic of China
| | - Jin Wu
- Department of Neurosurgery, The Pu’er People’s Hospital, Pu’er, 665000, People’s Republic of China
| | - Jun Pu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650223, People’s Republic of China
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Braschi B, Omran H, Witman GB, Pazour GJ, Pfister KK, Bruford EA, King SM. Consensus nomenclature for dyneins and associated assembly factors. J Cell Biol 2022; 221:e202109014. [PMID: 35006274 PMCID: PMC8754002 DOI: 10.1083/jcb.202109014] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/10/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Dyneins are highly complex, multicomponent, microtubule-based molecular motors. These enzymes are responsible for numerous motile behaviors in cytoplasm, mediate retrograde intraflagellar transport (IFT), and power ciliary and flagellar motility. Variants in multiple genes encoding dyneins, outer dynein arm (ODA) docking complex subunits, and cytoplasmic factors involved in axonemal dynein preassembly (DNAAFs) are associated with human ciliopathies and are of clinical interest. Therefore, clear communication within this field is particularly important. Standardizing gene nomenclature, and basing it on orthology where possible, facilitates discussion and genetic comparison across species. Here, we discuss how the human gene nomenclature for dyneins, ODA docking complex subunits, and DNAAFs has been updated to be more functionally informative and consistent with that of the unicellular green alga Chlamydomonas reinhardtii, a key model organism for studying dyneins and ciliary function. We also detail additional nomenclature updates for vertebrate-specific genes that encode dynein chains and other proteins involved in dynein complex assembly.
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Affiliation(s)
- Bryony Braschi
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - George B. Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Worcester, MA
| | - K. Kevin Pfister
- Cell Biology Department, School of Medicine University of Virginia, Charlottesville, VA
| | - Elspeth A. Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, Cambridgeshire, UK
| | - Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT
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Qiu T, Roy S. Ciliary dynein arms: Cytoplasmic preassembly, intraflagellar transport, and axonemal docking. J Cell Physiol 2022; 237:2644-2653. [DOI: 10.1002/jcp.30689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/04/2022] [Accepted: 01/14/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Tao Qiu
- Institute of Molecular and Cell Biology, Proteos Singapore Singapore
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos Singapore Singapore
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Department of Pediatrics, Yong Loo Ling School of Medicine National University of Singapore Singapore Singapore
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Falkenberg LG, Beckman SA, Ravisankar P, Dohn TE, Waxman JS. Ccdc103 promotes myeloid cell proliferation and migration independent of motile cilia. Dis Model Mech 2021; 14:dmm048439. [PMID: 34028558 PMCID: PMC8214733 DOI: 10.1242/dmm.048439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
The pathology of primary ciliary dyskinesia (PCD) is predominantly attributed to impairment of motile cilia. However, PCD patients also have perplexing functional defects in myeloid cells, which lack motile cilia. Here, we show that coiled-coil domain-containing protein 103 (CCDC103), one of the genes that, when mutated, is known to cause PCD, is required for the proliferation and directed migration of myeloid cells. CCDC103 is expressed in human myeloid cells, where it colocalizes with cytoplasmic microtubules. Zebrafish ccdc103/schmalhans (smh) mutants have macrophages and neutrophils with reduced proliferation, abnormally rounded cell morphology and an inability to migrate efficiently to the site of sterile wounds, all of which are consistent with a loss of cytoplasmic microtubule stability. Furthermore, we demonstrate that direct interactions between CCDC103 and sperm associated antigen 6 (SPAG6), which also promotes microtubule stability, are abrogated by CCDC103 mutations from PCD patients, and that spag6 zebrafish mutants recapitulate the myeloid defects observed in smh mutants. In summary, we have illuminated a mechanism, independent of motile cilia, to explain functional defects in myeloid cells from PCD patients. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Lauren G. Falkenberg
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati OH 45267, USA
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sarah A. Beckman
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Padmapriyadarshini Ravisankar
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tracy E. Dohn
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati OH 45267, USA
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joshua S. Waxman
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Rodríguez CF, Llorca O. RPAP3 C-Terminal Domain: A Conserved Domain for the Assembly of R2TP Co-Chaperone Complexes. Cells 2020; 9:cells9051139. [PMID: 32384603 PMCID: PMC7290369 DOI: 10.3390/cells9051139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/28/2020] [Accepted: 05/02/2020] [Indexed: 11/25/2022] Open
Abstract
The Rvb1-Rvb2-Tah1-Pih1 (R2TP) complex is a co-chaperone complex that works together with HSP90 in the activation and assembly of several macromolecular complexes, including RNA polymerase II (Pol II) and complexes of the phosphatidylinositol-3-kinase-like family of kinases (PIKKs), such as mTORC1 and ATR/ATRIP. R2TP is made of four subunits: RuvB-like protein 1 (RUVBL1) and RuvB-like 2 (RUVBL2) AAA-type ATPases, RNA polymerase II-associated protein 3 (RPAP3), and the Protein interacting with Hsp90 1 (PIH1) domain-containing protein 1 (PIH1D1). R2TP associates with other proteins as part of a complex co-chaperone machinery involved in the assembly and maturation of a growing list of macromolecular complexes. Recent progress in the structural characterization of R2TP has revealed an alpha-helical domain at the C-terminus of RPAP3 that is essential to bring the RUVBL1 and RUVBL2 ATPases to R2TP. The RPAP3 C-terminal domain interacts directly with RUVBL2 and it is also known as RUVBL2-binding domain (RBD). Several human proteins contain a region homologous to the RPAP3 C-terminal domain, and some are capable of assembling R2TP-like complexes, which could have specialized functions. Only the RUVBL1-RUVBL2 ATPase complex and a protein containing an RPAP3 C-terminal-like domain are found in all R2TP and R2TP-like complexes. Therefore, the RPAP3 C-terminal domain is one of few components essential for the formation of all R2TP and R2TP-like co-chaperone complexes.
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Affiliation(s)
| | - Oscar Llorca
- Correspondence: ; Tel.: +34-91-732-8000 (ext. 3000/3033)
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