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Martinez D, Jiang E, Zhou Z. Overcoming genetic and cellular complexity to study the pathophysiology of X-linked intellectual disabilities. J Neurodev Disord 2024; 16:5. [PMID: 38424476 PMCID: PMC10902969 DOI: 10.1186/s11689-024-09517-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
X-linked genetic causes of intellectual disability (ID) account for a substantial proportion of cases and remain poorly understood, in part due to the heterogeneous expression of X-linked genes in females. This is because most genes on the X chromosome are subject to random X chromosome inactivation (XCI) during early embryonic development, which results in a mosaic pattern of gene expression for a given X-linked mutant allele. This mosaic expression produces substantial complexity, especially when attempting to study the already complicated neural circuits that underly behavior, thus impeding the understanding of disease-related pathophysiology and the development of therapeutics. Here, we review a few selected X-linked forms of ID that predominantly affect heterozygous females and the current obstacles for developing effective therapies for such disorders. We also propose a genetic strategy to overcome the complexity presented by mosaicism in heterozygous females and highlight specific tools for studying synaptic and circuit mechanisms, many of which could be shared across multiple forms of intellectual disability.
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Affiliation(s)
- Dayne Martinez
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Evan Jiang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Intellectual and Developmental Disabilities Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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Sakato-Antoku M, Patel-King RS, Balsbaugh JL, King SM. Methylation of ciliary dynein motors involves the essential cytosolic assembly factor DNAAF3/PF22. Proc Natl Acad Sci U S A 2024; 121:e2318522121. [PMID: 38261620 PMCID: PMC10835030 DOI: 10.1073/pnas.2318522121] [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: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Axonemal dynein motors drive ciliary motility and can consist of up to twenty distinct components with a combined mass of ~2 MDa. In mammals, failure of dyneins to assemble within the axonemal superstructure leads to primary ciliary dyskinesia. Syndromic phenotypes include infertility, rhinitis, severe bronchial conditions, and situs inversus. Nineteen specific cytosolic factors (Dynein Axonemal Assembly Factors; DNAAFs) are necessary for axonemal dynein assembly, although the detailed mechanisms involved remain very unclear. Here, we identify the essential assembly factor DNAAF3 as a structural ortholog of S-adenosylmethionine-dependent methyltransferases. We demonstrate that dynein heavy chains, especially those forming the ciliary outer arms, are methylated on key residues within various nucleotide-binding sites and on microtubule-binding domain helices directly involved in the transition to low binding affinity. These variable modifications, which are generally missing in a Chlamydomonas null mutant for the DNAAF3 ortholog PF22 (DAB1), likely impact on motor mechanochemistry fine-tuning the activities of individual dynein complexes.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
| | - Ramila S. Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT06269
| | - Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
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Sakato-Antoku M, Balsbaugh JL, King SM. N-Terminal Processing and Modification of Ciliary Dyneins. Cells 2023; 12:2492. [PMID: 37887336 PMCID: PMC10605206 DOI: 10.3390/cells12202492] [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: 09/15/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Axonemal dyneins are highly complex microtubule motors that power ciliary motility. These multi-subunit enzymes are assembled at dedicated sites within the cytoplasm. At least nineteen cytosolic factors are specifically needed to generate dynein holoenzymes and/or for their trafficking to the growing cilium. Many proteins are subject to N-terminal processing and acetylation, which can generate degrons subject to the AcN-end rule, alter N-terminal electrostatics, generate new binding interfaces, and affect subunit stoichiometry through targeted degradation. Here, we have used mass spectrometry of cilia samples and electrophoretically purified dynein heavy chains from Chlamydomonas to define their N-terminal processing; we also detail the N-terminal acetylase complexes present in this organism. We identify four classes of dynein heavy chain based on their processing pathways by two distinct acetylases, one of which is dependent on methionine aminopeptidase activity. In addition, we find that one component of both the outer dynein arm intermediate/light chain subcomplex and the docking complex is processed to yield an unmodified Pro residue, which may provide a setpoint to direct the cytosolic stoichiometry of other dynein complex subunits that contain N-terminal degrons. Thus, we identify and describe an additional level of processing and complexity in the pathways leading to axonemal dynein formation in cytoplasm.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA;
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269, USA;
| | - Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA;
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King SM. Inherently disordered regions of axonemal dynein assembly factors. Cytoskeleton (Hoboken) 2023:10.1002/cm.21789. [PMID: 37712517 PMCID: PMC10940205 DOI: 10.1002/cm.21789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
The dynein-driven beating of cilia is required to move individual cells and to generate fluid flow across surfaces and within cavities. These motor enzymes are highly complex and can contain upwards of 20 different protein components with a total mass approaching 2 MDa. The dynein heavy chains are enormous proteins consisting of ~4500 residues and ribosomes take approximately 15 min to synthesize one. Studies in a broad array of organisms ranging from the green alga Chlamydomonas to humans has identified 19 cytosolic factors (DNAAFs) that are needed to specifically build axonemal dyneins; defects in many of these proteins lead to primary ciliary dyskinesia in mammals which can result in infertility, severe bronchial problems, and situs inversus. How all these factors cooperate in a spatially and temporally regulated manner to promote dynein assembly in cytoplasm remains very uncertain. These DNAAFs contain a variety of well-folded domains many of which provide protein interaction surfaces. However, many also exhibit large regions that are predicted to be inherently disordered. Here I discuss the nature of these unstructured segments, their predicted propensity for driving protein phase separation, and their potential for adopting more defined conformations during the dynein assembly process.
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Affiliation(s)
- Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
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Keep RF, Jones HC, Hamilton MG, Drewes LR. A year in review: brain barriers and brain fluids research in 2022. Fluids Barriers CNS 2023; 20:30. [PMID: 37085841 PMCID: PMC10120509 DOI: 10.1186/s12987-023-00429-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Indexed: 04/23/2023] Open
Abstract
This aim of this editorial is to highlight progress made in brain barrier and brain fluid research in 2022. It covers studies on the blood-brain, blood-retina and blood-CSF barriers (choroid plexus and meninges), signaling within the neurovascular unit and elements of the brain fluid systems. It further discusses how brain barriers and brain fluid systems are impacted in CNS diseases, their role in disease progression and progress being made in treating such diseases.
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Affiliation(s)
- Richard F Keep
- Department of Neurosurgery, University of Michigan, R5018 BSRB 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA.
| | | | - Mark G Hamilton
- Department of Clinical Neurosciences, Division of Neurosurgery, University of Calgary, Alberta, Canada
| | - Lester R Drewes
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, MN, 55812, USA
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Olovnikov AM. Planetary Metronome as a Regulator of Lifespan and Aging Rate: The Metronomic Hypothesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1640-1650. [PMID: 36717453 DOI: 10.1134/s0006297922120197] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A metronomic mechanism for the duration control of ontogenetic cycle periods of an animal is proposed. The components of the proposed metronomic system include the ventricular system of the brain, planet Earth as a generator of metronomic signals, and temporal DNA (tDNA) as a substrate that is epigenetically marked to measure elapsed time of ontogenesis. The metronomic system generates repetitive signals in the form of hydrodynamic disturbances in the cerebrospinal fluid (CSF). The metronomic effect arises due to the superposition of two processes - the near-wall unidirectional flow of CSF and oscillations in the movement of the planet. Hydrodynamic impacts of the metronome are transformed into nerve impulses that initiate epigenetic modification of tDNA in neurons, changing the content of factors expressed by this DNA for innervated targets of the body. The duration of ontogenetic cycle periods, including duration of the adult life, depends on the rate of addition of epigenetic marks to tDNA. This rate depends mainly on the frequency of the metronomic signals used by each particular species. But epigenetic modifications can also be influenced by factors that modulate metabolism and the rate of chromatin modifications, such as a calorie-restricted diet.
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Affiliation(s)
- Alexey M Olovnikov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
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