1
|
Genin EC, Abou-Ali M, Paquis-Flucklinger V. Mitochondria, a Key Target in Amyotrophic Lateral Sclerosis Pathogenesis. Genes (Basel) 2023; 14:1981. [PMID: 38002924 PMCID: PMC10671245 DOI: 10.3390/genes14111981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
Mitochondrial dysfunction occurs in numerous neurodegenerative diseases, particularly amyotrophic lateral sclerosis (ALS), where it contributes to motor neuron (MN) death. Of all the factors involved in ALS, mitochondria have been considered as a major player, as secondary mitochondrial dysfunction has been found in various models and patients. Abnormal mitochondrial morphology, defects in mitochondrial dynamics, altered activities of respiratory chain enzymes and increased production of reactive oxygen species have been described. Moreover, the identification of CHCHD10 variants in ALS patients was the first genetic evidence that a mitochondrial defect may be a primary cause of MN damage and directly links mitochondrial dysfunction to the pathogenesis of ALS. In this review, we focus on the role of mitochondria in ALS and highlight the pathogenic variants of ALS genes associated with impaired mitochondrial functions. The multiple pathways demonstrated in ALS pathogenesis suggest that all converge to a common endpoint leading to MN loss. This may explain the disappointing results obtained with treatments targeting a single pathological process. Fighting against mitochondrial dysfunction appears to be a promising avenue for developing combined therapies in the future.
Collapse
Affiliation(s)
- Emmanuelle C. Genin
- Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d’Azur, Inserm U1081, CNRS UMR7284, Centre Hospitalier Universitaire (CHU) de Nice, 06200 Nice, France; (M.A.-A.); (V.P.-F.)
| | | | | |
Collapse
|
2
|
Cannariato M, Miceli M, Deriu MA. In silico investigation of Alsin RLD conformational dynamics and phosphoinositides binding mechanism. PLoS One 2022; 17:e0270955. [PMID: 35849605 PMCID: PMC9292110 DOI: 10.1371/journal.pone.0270955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022] Open
Abstract
Alsin is a protein known for its major role in neuronal homeostasis and whose mutation is associated with early-onset neurodegenerative diseases. It has been shown that its relocalization from the cytoplasm to the cell membrane is crucial to induce early endosomes maturation. In particular, evidences suggest that the N-terminal regulator of chromosome condensation 1 like domain (RLD) is necessary for membrane association thanks to its affinity to phosphoinositides, membrane lipids involved in the regulation of several signaling processes. Interestingly, this domain showed affinity towards phosphatidylinositol 3-phosphate [PI(3)P], which is highly expressed in endosomes membrane. However, Alsin structure has not been experimentally resolved yet and molecular mechanisms associated with its biological functions are mostly unknown. In this work, Alsin RLD has been investigated through computational molecular modeling techniques to analyze its conformational dynamics and obtain a representative 3D model of this domain. Moreover, a putative phosphoinositide binding site has been proposed and PI(3)P interaction mechanism studied. Results highlight the substantial conformational stability of Alsin RLD secondary structure and suggest the role of one highly flexible region in the phosphoinositides selectivity of this domain.
Collapse
Affiliation(s)
- Marco Cannariato
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marcello Miceli
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Agostino Deriu
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
- * E-mail:
| |
Collapse
|
3
|
Cannariato M, Miceli M, Cavaglià M, Deriu MA. Prediction of Protein–Protein Interactions Between Alsin DH/PH and Rac1 and Resulting Protein Dynamics. Front Mol Neurosci 2022; 14:772122. [PMID: 35126051 PMCID: PMC8811474 DOI: 10.3389/fnmol.2021.772122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Alsin is a protein of 1,657 amino acids known for its crucial role in vesicular trafficking in neurons thanks to its ability to interact with two guanosine triphosphatases, Rac1 and Rab5. Evidence suggests that Rac1 can bind Alsin central region, composed by a Dbl Homology (DH) domain followed by a Pleckstrin Homology (PH) domain, leading to Alsin relocalization. However, Alsin three-dimensional structure and its relationship with known biological functions of this protein are still unknown. In this work, a homology model of the Alsin DH/PH domain was developed and studied through molecular dynamics both in the presence and in the absence of its binding partner, Rac1. Due to different conformations of DH domain, the presence of Rac1 seems to stabilize an open state of the protein, while the absence of its binding partner results in closed conformations. Furthermore, Rac1 interaction was able to reduce the fluctuations in the second conserved region of DH motif, which may be involved in the formation of a homodimer. Moreover, the dynamics of DH/PH was described through a Markov State Model to study the pathways linking the open and closed states. In conclusion, this work provided an all-atom model for the DH/PH domain of Alsin protein; moreover, molecular dynamics investigations suggested underlying molecular mechanisms in the signal transduction between Rac1 and Alsin, providing the basis for a deeper understanding of the whole structure–function relationship for Alsin protein.
Collapse
|
4
|
Miceli M, Exertier C, Cavaglià M, Gugole E, Boccardo M, Casaluci RR, Ceccarelli N, De Maio A, Vallone B, Deriu MA. ALS2-Related Motor Neuron Diseases: From Symptoms to Molecules. BIOLOGY 2022; 11:77. [PMID: 35053075 PMCID: PMC8773251 DOI: 10.3390/biology11010077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 11/27/2022]
Abstract
Infantile-onset Ascending Hereditary Spastic Paralysis, Juvenile Primary Lateral Sclerosis and Juvenile Amyotrophic Lateral Sclerosis are all motor neuron diseases related to mutations on the ALS2 gene, encoding for a 1657 amino acids protein named Alsin. This ~185 kDa multi-domain protein is ubiquitously expressed in various human tissues, mostly in the brain and the spinal cord. Several investigations have indicated how mutations within Alsin's structured domains may be responsible for the alteration of Alsin's native oligomerization state or Alsin's propensity to interact with protein partners. In this review paper, we propose a description of differences and similarities characterizing the above-mentioned ALS2-related rare neurodegenerative disorders, pointing attention to the effects of ALS2 mutation from molecule to organ and at the system level. Known cases were collected through a literature review and rationalized to deeply elucidate the neurodegenerative clinical outcomes as consequences of ALS2 mutations.
Collapse
Affiliation(s)
- Marcello Miceli
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy; (M.M.); (M.C.); (M.B.); (R.R.C.); (N.C.); (A.D.M.)
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy; (C.E.); (E.G.); (B.V.)
| | - Marco Cavaglià
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy; (M.M.); (M.C.); (M.B.); (R.R.C.); (N.C.); (A.D.M.)
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy; (C.E.); (E.G.); (B.V.)
| | - Marta Boccardo
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy; (M.M.); (M.C.); (M.B.); (R.R.C.); (N.C.); (A.D.M.)
| | - Rossana Rita Casaluci
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy; (M.M.); (M.C.); (M.B.); (R.R.C.); (N.C.); (A.D.M.)
| | - Noemi Ceccarelli
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy; (M.M.); (M.C.); (M.B.); (R.R.C.); (N.C.); (A.D.M.)
| | - Alessandra De Maio
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy; (M.M.); (M.C.); (M.B.); (R.R.C.); (N.C.); (A.D.M.)
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy; (C.E.); (E.G.); (B.V.)
| | - Marco A. Deriu
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy; (M.M.); (M.C.); (M.B.); (R.R.C.); (N.C.); (A.D.M.)
| |
Collapse
|
5
|
Rossi Sebastiano M, Ermondi G, Hadano S, Caron G. AI-based protein structure databases have the potential to accelerate rare diseases research: AlphaFoldDB and the case of IAHSP/Alsin. Drug Discov Today 2021; 27:1652-1660. [PMID: 34958957 DOI: 10.1016/j.drudis.2021.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022]
Abstract
Artificial intelligence (AI)-based protein structure databases are expected to have an impact on drug discovery. Here, we show how AlphaFold could support rare diseases research programs. We focus on Alsin, a protein responsible for rare motor neuron diseases, such as infantile-onset ascending hereditary spastic paralysis (IAHSP) and juvenile primary lateral sclerosis (JPLS), and involved in some cases of amyotrophic lateral sclerosis (ALS). First, we compared the AlphaFoldDB human Alsin model with homology models of alsin domains. We then evaluated the flexibility profile of Alsin and of experimentally characterized mutants present in patients with IAHSP. Next, we compared preliminary models of dimeric/tetrameric Alsin responsible for its physiological action with hypothetical models reported in the literature. Finally, we suggest the best animal model for drug candidates testing. Overall, we computationally show that drug discovery efforts toward Alsin-involving diseases should be pursued.
Collapse
Affiliation(s)
- Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Shinji Hadano
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, University of Torino, Quarello 15, 10135 Torino, Italy.
| |
Collapse
|
6
|
Shimakura K, Sato K, Mitsui S, Ono S, Otomo A, Hadano S. The N-terminal intrinsically disordered region mediates intracellular localization and self-oligomerization of ALS2. Biochem Biophys Res Commun 2021; 569:106-111. [PMID: 34243065 DOI: 10.1016/j.bbrc.2021.06.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/31/2022]
Abstract
ALS2, a product of the causative gene for familial amyotrophic lateral sclerosis (ALS) type 2, plays a pivotal role in the regulation of endosome dynamics by activating small GTPase Rab5 via its intrinsic guanine nucleotide-exchange factor activity. Previously, we have reported that the N-terminal region of ALS2 has crucial roles in its endosomal localization and self-oligomerization, both of which are indispensable for the cellular function of ALS2. The N-terminus of ALS2 contains the regulator of chromosome condensation 1-like domain (RLD), which is predicted to form a seven-bladed β-propeller structure. Interestingly, the RLD is interrupted by the intrinsically disordered region (IDR), within which there are several amino acid residues which undergo phosphorylation. In this study, we sought to investigate as to whether and how the IDR as well as phosphorylation at either Ser483, Ser492 or Thr510 affect the intracellular localization and self-oligomerization of ALS2. All phospho- and dephospho-mimetic ALS2 mutants that were transiently expressed in HeLa cells were diffusely distributed throughout the cytosol with a partial localization to early endosomes. When expressed under Rac1-activating conditions, these mutants were localized to membrane ruffles as well as enlarged endosomes. Further, gel-filtration analysis revealed that these mutants primarily existed as a tetramer in cells. However, all these phenotypes were indistinguishable from those of wild-type ALS2. On the other hand, IDR-deleted ALS2 mutant was exclusively present in perinuclear aggregates colocalizing with the autophagy-related protein SQSTM1. Moreover, IDR-deleted ALS2 mutant formed an abnormally high molecular weight complex compared to wild-type ALS2. These results indicate that the IDR of ALS2 plays a crucial role not only in the regulation of intracellular localization but also in the self-oligomerization of ALS2 in cells, whereas phosphorylation of certain residues within the IDR exerts limited effects on such phenotypes.
Collapse
Affiliation(s)
- Kento Shimakura
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kai Sato
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Shun Mitsui
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Suzuka Ono
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Asako Otomo
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan; The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Shinji Hadano
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan; The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, 259-1193, Japan; Research Center for Brain and Nervous Diseases, Tokai University Graduate School of Medicine, Isehara, Kanagawa, 259-1193, Japan.
| |
Collapse
|
7
|
Sprute R, Jergas H, Ölmez A, Alawbathani S, Karasoy H, Dafsari HS, Becker K, Daimagüler HS, Nürnberg P, Muntoni F, Topaloglu H, Uyanik G, Cirak S. Genotype-phenotype correlation in seven motor neuron disease families with novel ALS2 mutations. Am J Med Genet A 2020; 185:344-354. [PMID: 33155358 DOI: 10.1002/ajmg.a.61951] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/25/2020] [Accepted: 10/19/2020] [Indexed: 11/05/2022]
Abstract
Autosomal-recessive mutations in the Alsin Rho guanine nucleotide exchange factor (ALS2) gene may cause specific subtypes of childhood-onset progressive neurodegenerative motor neuron diseases (MND). These diseases can manifest with a clinical continuum from infantile ascending hereditary spastic paraplegia (IAHSP) to juvenile-onset forms with or without lower motor neuron involvement, the juvenile primary lateral sclerosis (JPLS) and the juvenile amyotrophic lateral sclerosis (JALS). We report 11 patients from seven unrelated Turkish and Yemeni families with clinical signs of IAHSP or JPLS. We performed haplotype analysis or next-generation panel sequencing followed by Sanger Sequencing to unravel the genetic disease cause. We described their clinical phenotype and analyzed the pathogenicity of the detected variants with bioinformatics tools. We further reviewed all previously reported cases with ALS2-related MND. We identified five novel homozygous pathogenic variants in ALS2 at various positions: c.275_276delAT (p.Tyr92CysfsTer11), c.1044C>G (p.Tyr348Ter), c.1718C>A (p.Ala573Glu), c.3161T>C (p.Leu1054Pro), and c.1471+1G>A (NM_020919.3, NP_065970.2). In our cohort, disease onset was in infancy or early childhood with rapid onset of motor neuron signs. Muscle weakness, spasticity, severe dysarthria, dysphagia, and facial weakness were common features in the first decade of life. Frameshift and nonsense mutations clustered in the N-terminal Alsin domains are most prevalent. We enriched the mutational spectrum of ALS2-related disorders with five novel pathogenic variants. Our study indicates a high detection rate of ALS2 mutations in patients with a clinically well-characterized early onset MND. Intrafamilial and even interfamilial diversity in patients with identical pathogenic variants suggest yet unknown modifiers for phenotypic expression.
Collapse
Affiliation(s)
- Rosanne Sprute
- Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, Cologne, Germany
| | - Hannah Jergas
- Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Department of Neurology, University of Cologne, Cologne, Germany
| | - Akgün Ölmez
- Department of Pediatric Neurology, Hacettepe University, Ankara, Turkey
| | - Salem Alawbathani
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Hatice Karasoy
- Department of Neurology, Ege University School of Medicine, Izmir, Turkey
| | - Hormos Salimi Dafsari
- Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, Cologne, Germany
| | - Kerstin Becker
- Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, Cologne, Germany
| | - Hülya-Sevcan Daimagüler
- Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, National Institute for Health Research Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Haluk Topaloglu
- Department of Pediatric Neurology, Hacettepe University, Ankara, Turkey
| | - Gökhan Uyanik
- Medical School, Sigmund Freud Private University, Vienna, Austria.,Center for Medical Genetics, Hanusch Hospital, Vienna, Austria
| | - Sebahattin Cirak
- Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, Cologne, Germany
| |
Collapse
|
8
|
Sato K, Otomo A, Ueda MT, Hiratsuka Y, Suzuki-Utsunomiya K, Sugiyama J, Murakoshi S, Mitsui S, Ono S, Nakagawa S, Shang HF, Hadano S. Altered oligomeric states in pathogenic ALS2 variants associated with juvenile motor neuron diseases cause loss of ALS2-mediated endosomal function. J Biol Chem 2018; 293:17135-17153. [PMID: 30224357 DOI: 10.1074/jbc.ra118.003849] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/13/2018] [Indexed: 02/05/2023] Open
Abstract
Familial amyotrophic lateral sclerosis type 2 (ALS2) is a juvenile autosomal recessive motor neuron disease caused by the mutations in the ALS2 gene. The ALS2 gene product, ALS2/alsin, forms a homophilic oligomer and acts as a guanine nucleotide-exchange factor (GEF) for the small GTPase Rab5. This oligomerization is crucial for both Rab5 activation and ALS2-mediated endosome fusion and maturation in cells. Recently, we have shown that pathogenic missense ALS2 mutants retaining the Rab5 GEF activity fail to properly localize to endosomes via Rac1-stimulated macropinocytosis. However, the molecular mechanisms underlying dysregulated distribution of ALS2 variants remain poorly understood. Therefore, we sought to clarify the relationship between intracellular localization and oligomeric states of pathogenic ALS2 variants. Upon Rac family small GTPase 1 (Rac1) activation, all mutants tested moved from the cytosol to membrane ruffles but not to macropinosomes and/or endosomes. Furthermore, most WT ALS2 complexes were tetramers. Importantly, the sizes of an ALS2 complex carrying missense mutations in the N terminus of the regulator of chromosome condensation 1-like domain (RLD) or in-frame deletion in the pleckstrin homology domain were shifted toward higher molecular weight, whereas the C-terminal vacuolar protein sorting 9 (VPS9) domain missense mutant existed as a smaller dimeric or trimeric smaller form. Furthermore, in silico mutagenesis analyses using the RLD protein structure in conjunction with a cycloheximide chase assay in vitro disclosed that these missense mutations led to a decrease in protein stability. Collectively, disorganized higher structures of ALS2 variants might explain their impaired endosomal localization and the stability, leading to loss of the ALS2 function.
Collapse
Affiliation(s)
- Kai Sato
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Asako Otomo
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.,The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan.,Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
| | | | - Yui Hiratsuka
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Kyoko Suzuki-Utsunomiya
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Junya Sugiyama
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Shuji Murakoshi
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Shun Mitsui
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Suzuka Ono
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - So Nakagawa
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.,The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan.,Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
| | - Hui-Fang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China, and
| | - Shinji Hadano
- From the Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan, .,The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan.,Research Center for Brain and Nervous Diseases, Tokai University Graduate School of Medicine, Isehara, Kanagawa 259-1193, Japan
| |
Collapse
|
9
|
McCooke JK, Appels R, Barrero RA, Ding A, Ozimek-Kulik JE, Bellgard MI, Morahan G, Phillips JK. A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8. BMC Genomics 2012; 13:393. [PMID: 22899815 PMCID: PMC3441220 DOI: 10.1186/1471-2164-13-393] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 08/06/2012] [Indexed: 01/03/2023] Open
Abstract
Background Nephronophthisis (NPHP) as a cause of cystic kidney disease is the most common genetic cause of progressive renal failure in children and young adults. NPHP is characterized by abnormal and/or loss of function of proteins associated with primary cilia. Previously, we characterized an autosomal recessive phenotype of cystic kidney disease in the Lewis Polycystic Kidney (LPK) rat. Results In this study, quantitative trait locus analysis was used to define a ~1.6Mbp region on rat chromosome 10q25 harbouring the lpk mutation. Targeted genome capture and next-generation sequencing of this region identified a non-synonymous mutation R650C in the NIMA (never in mitosis gene a)- related kinase 8 ( Nek8) gene. This is a novel Nek8 mutation that occurs within the regulator of chromosome condensation 1 (RCC1)-like region of the protein. Specifically, the R650C substitution is located within a G[QRC]LG repeat motif of the predicted seven bladed beta-propeller structure of the RCC1 domain. The rat Nek8 gene is located in a region syntenic to portions of human chromosome 17 and mouse 11. Scanning electron microscopy confirmed abnormally long cilia on LPK kidney epithelial cells, and fluorescence immunohistochemistry for Nek8 protein revealed altered cilia localisation. Conclusions When assessed relative to other Nek8 NPHP mutations, our results indicate the whole propeller structure of the RCC1 domain is important, as the different mutations cause comparable phenotypes. This study establishes the LPK rat as a novel model system for NPHP and further consolidates the link between cystic kidney disease and cilia proteins.
Collapse
Affiliation(s)
- John K McCooke
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Wywial E, Singh SM. Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana. BMC PLANT BIOLOGY 2010; 10:157. [PMID: 20678208 PMCID: PMC3017826 DOI: 10.1186/1471-2229-10-157] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 08/02/2010] [Indexed: 05/02/2023]
Abstract
BACKGROUND FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)P). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded beta-sheets, and a C-terminal alpha-helix, which houses eight conserved Zn2+ ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated. RESULTS We carried out an extensive examination of all Arabidopsis FYVE domains, including their identification, classification, molecular modeling and biophysical characterization using computational approaches. Our classification of fifteen Arabidopsis FYVE proteins at the outset reveals unique domain architectures for FYVE containing proteins, which are not paralleled in other organisms. Detailed sequence analysis and biophysical characterization of the structural models are used to predict membrane interaction mechanisms previously described for other FYVE domains and their subtle variations as well as novel mechanisms that seem to be specific to plants. CONCLUSIONS Our study contributes to the understanding of the molecular basis of FYVE-based membrane targeting in plants on a genomic scale. The results show that FYVE domain containing proteins in plants have evolved to incorporate significant differences from those in other organisms implying that they play a unique role in plant signaling pathways and/or play similar/parallel roles in signaling to other organisms but use different protein players/signaling mechanisms.
Collapse
Affiliation(s)
- Ewa Wywial
- Department of Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Shaneen M Singh
- Department of Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| |
Collapse
|