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CHARGED MULTIVESICULAR BODY PROTEIN 1A; CHMP1A

CHARGED MULTIVESICULAR BODY PROTEIN 1A; CHMP1A

Alternative titles; symbolsCHMP FAMILY, MEMBER 1ACHROMATIN-MODIFYING PROTEIN 1ACHMP1PROCOLLAGEN, TYPE III, N-ENDOPEPTIDASE; PCOLN3METALLOPROTEASE 1; PRSM1METALLO...

Alternative titles; symbols

  • CHMP FAMILY, MEMBER 1A
  • CHROMATIN-MODIFYING PROTEIN 1A
  • CHMP1
  • PROCOLLAGEN, TYPE III, N-ENDOPEPTIDASE; PCOLN3
  • METALLOPROTEASE 1; PRSM1
  • METALLOPROTEASE, 33-KD

HGNC Approved Gene Symbol: CHMP1A

Cytogenetic location: 16q24.3 Genomic coordinates (GRCh38): 16:89,644,434-89,657,707 (from NCBI)

▼ Description

CHMP1A belongs to the chromatin-modifying protein/charged multivesicular body protein (CHMP) family. These proteins are components of ESCRT-III (endosomal sorting complex required for transport III), a complex involved in degradation of surface receptor proteins and formation of endocytic multivesicular bodies (MVBs). Some CHMPs, including CHMP1A, have both nuclear and cytoplasmic/vesicular distributions, and CHMP1A is required for both MVB formation and regulation of cell cycle progression (Tsang et al., 2006).

▼ Cloning and Expression

Halila et al. (1989) isolated a cDNA for PCOLN3 from a human placenta cDNA library. By screening a human placenta cDNA library with polyclonal antibodies raised against human PCOLN3 and using 5-prime RACE and primer extension strategies on the isolated cDNAs, Scott et al. (1996) cloned PCOLN3, which they called PRSM1. PRSM1 belongs to the gluzincin subfamily of metallopeptidases. The zincin superfamily comprises metallopeptidases that contain an HEXXH zinc-binding consensus sequence, and gluzincins have glutamic acid as a third zinc ligand. The full-length sequence of PRSM1 encodes a deduced 318-amino acid protein with an HELGH pentapeptide fitting the consensus sequence characteristic of zincins, and a glutamic acid 25 residues C-terminal of the first histidine, fitting the pattern of gluzincins for a third zinc-binding ligand. PRSM1 contains 3 clusters of cysteine residues: 1 cluster of 4 residues and 1 cluster of 6 residues at the N terminus, and a cluster of 6 residues at the C terminus. However, the predicted sequence lacks potential glycosylation sites. Immunoblot analysis of placenta revealed an approximately 30-kD protein. Northern blot analysis of human fibroblast culture mRNA detected a transcript of approximately 2.5 kb. By Northern blot analysis, Nomura et al. (1994) found that PRSM1, which they designated KIAA0047, was expressed ubiquitously, with highest levels in lung and kidney and in HeLa and KG-1 cell lines.

By yeast 2-hybrid screening of a mouse embryo cDNA library using the mouse Polycomb group (PcG) protein Pcl1 (PHF1; 602881) as bait, followed by RT-PCR of human placenta RNA, Stauffer et al. (2001) cloned a variant of PRSM1 that they called CHMP1. CHMP1 uses an alternative reading frame distinct from that of PRSM1. The deduced 196-amino acid CHMP1 protein contains an N-terminal nuclear localization signal. CHMP1 is most closely related to CHMP1B (606486) and BC2 (CHMP2A; 610893), and more distantly related to S. cerevisiae proteins involved in vesicle trafficking. Western blot analysis of HEK293 human embryonic kidney cells showed a doublet of 32- and 35-kD CHMP1 proteins. Subcellular fractionation of HEK293 cells and several other human cell lines revealed that the 35-kD protein was exclusively nuclear, whereas the 32-kD protein was predominantly cytoplasmic, with a detectable level present in the nuclear fraction. Analysis of mouse whole tissue extracts showed that both Chmp1 proteins were widely expressed, with increased levels of the 35-kD form in heart, kidney, and liver.

Mochida et al. (2012) found that the subcellular localization of CHMP1A appears to vary depending on cell type. In mouse embryonic 3T3 cells, Chmp1a was excluded from the nucleus where Bmi1 (164831) was detected. In human HEK 293T cells, CHMP1A showed prominent cytoplasmic and some nuclear immunoreactivity. Primary cultures of cerebellar granule cells from mice showed predominantly cytoplasmic localization of Chmp1a along with a speckled nuclear pattern. Chmp1a and Bmi1 did not prominently colocalize within the nucleus. In the developing mouse cerebellum and cortex, variable expression of Chmp1a was seen in the cytoplasm and nucleus of dividing and postmitotic cells, including Purkinje, granule, and neuroepithelial cells. These findings, combined with other data (see MOLECULAR GENETICS and ANIMAL MODEL), suggested that CHMP1A is an essential central nervous system regulator of BMI1, which is a key regulator of stem cell self-renewal.

▼ Gene Function

By Western blot analysis of synchronized HEK293 cells, Stauffer et al. (2001) showed that the ratio of cytoplasmic to nuclear CHMP1 was largely invariant throughout interphase. In mitotic cells, nuclear CHMP1 localized to the chromosome scaffold fraction. Immunocytochemical analysis detected CHMP1 in a punctate arrangement on condensed chromosomes during telophase. The cytoplasmic CHMP1 form exhibited a perinuclear localization. Overexpression of CHMP1 altered the cell cycle, producing an increase in the number of cells in late S phase. Overexpression of CHMP1 also resulted in altered chromatin structure, with modified histones at the periphery of nuclear bodies, and nuclease-resistant condensed chromatin within. CHMP1 recruited the PcG protein BMI1 to these regions of condensed chromatin, and it cooperated with coexpressed Pcl in a Xenopus embryo PcG assay. Stauffer et al. (2001) concluded that CHMP1 plays a role in stable gene silencing within the nucleus.

Howard et al. (2001) found that the cytoplasmic form of CHMP1 localized in a punctate asymmetrical pattern centered over the microtubule organizing center and colocalized with an early endosomal marker. Differential extraction showed that cytoplasmic CHMP1 associated with membranes through ionic interactions. Yeast 2-hybrid screening and in vitro binding assays demonstrated that cytoplasmic CHMP1 interacted with SKD1 (VPS4B; 609983). Overexpression of CHMP1 dilated endosomal compartments and disrupted the normal distribution of several endosomal markers. Deletion of S. cerevisiae Chm1, the homolog of CHMP1, resulted in defective sorting of carboxypeptidases S and Y and production of abnormal, multilamellar prevacuolar compartments. Howard et al. (2001) concluded that CHMP1 is involved in vesicle trafficking.

Tsang et al. (2006) performed a systematic yeast 2-hybrid analysis of human ESCRT-III components, including CHMP1A. Like most CHMPs, CHMP1A interacted with VPS4A (609982). CHMP1A also interacted with the SUMO (see SUMO1; 601912)-conjugating enzyme UBE2I (601661) and appeared to be part of a network connecting CHMP1A, CHMP4B (610897), and CHMP5 (610900) with UBE2I, SUMO1, PIAS2 (603567), and HIPK2 (606868), all of which are involved in nuclear sumoylation processes.

Using yeast 2-hybrid screens, followed by coimmunoprecipitation and protein-binding assays, Bajorek et al. (2009) found that human IST1 (616434) interacted with several ESCRT proteins, including CHMP1A and CHMP1B, as well as with VPS4A and VPS4B. IST1 bound CHMP1 directly, and like IST1, CHMP1 has a C-terminal MIM element that bound VPS4 MIT domains. Depletion of either IST1 or CHMP1 in HeLa cells blocked VPS4 recruitment to the midbody during cytokinesis and blocked cell division. Time-lapse imaging revealed that IST1 depletion caused dividing cells to arrest during the abscission stage. Cells remained tethered together through their midbodies before eventually recoalescing into a single cell with multiple nuclei. Bajorek et al. (2009) concluded that IST1 is specifically required for the cytokinesis function of ESCRT and that IST1 and CHMP1 recruit VPS4 to the midbody for abscission.

▼ Gene Structure

Scott et al. (1996) found that the first exon of the PRSM1 gene is 72% GC rich, contains 34 CpG dinucleotides, and appears to lie within a CpG island.

▼ Mapping

By analysis of somatic cell hybrids, Halila et al. (1992) mapped the CHMP1 gene to the telomeric region of the long arm of chromosome 16. By the same method, Scott et al. (1996) mapped the CHMP1 gene to chromosome 16q24.3.

▼ Molecular Genetics

By linkage analysis followed by candidate gene sequencing in families with autosomal recessive pontocerebellar hypoplasia type 8 (PCH8; 614961), Mochida et al. (2012) identified 2 different homozygous mutations in the CHMP1A gene (164010.0001 and 164010.0002). The phenotype was characterized by severe psychomotor retardation, abnormal movements, hypotonia, spasticity, and variable visual defects. Brain MRI showed pontocerebellar hypoplasia with relative preservation of the cerebellar folia, decreased cerebral white matter, and a thin corpus callosum. Patient-derived cell lines showed severely impaired doubling times compared to control, suggesting a defect in cell proliferation. Quantitative PCR analysis of patient cells showed abnormally high expression of the BMI1 target INK4A (see CDKN2A, 600160) and decreased BMI1 binding to the INK4A promoter compared to control, suggesting derepression of this CDKN2A isoform. INK4A is a negative regulator of stem cell proliferation. Binding of BMI1 to the ARF promoter was unaffected. Mochida et al. (2012) noted the parallels in brain morphology between individuals with CHMP1A mutations and Bmi1-deficient mice, which show cerebellar hypoplasia. The findings suggested that CHMP1A serves as a link between cytoplasmic signals and BMI1-mediated chromatin modification that regulates proliferation of central nervous system progenitor cells.

▼ Animal Model

Mochida et al. (2012) found that morpholino-based knockdown of Chmp1a in zebrafish resulted in reduced cerebellar and forebrain volume compared to control that could be partially rescued by expression of wildtype Chmp1a. The phenotype of these zebrafish resembled that seen in those after Bmi1 knockdown, supporting a link between Chmp1a and Bmi1. In Chmp1a knockdown models, the internal granule and molecular layers were more severely affected than the Purkinje cells, which was consistent with the relatively preserved folia observed in humans with CHMP1A mutations.

▼ ALLELIC VARIANTS ( 2 Selected Examples):

.0001 PONTOCEREBELLAR HYPOPLASIA, TYPE 8
CHMP1A, GLN30TER

In affected members of 2 Puerto Rican families with pontocerebellar hypoplasia type 8 (PCH8; 614961), Mochida et al. (2012) identified a homozygous 88C-T transition in exon 3 of the CHMP1A gene, resulting in a gln30-to-ter (Q30X) substitution. The mutation was found by linkage analysis followed by candidate gene sequencing. Haplotype analysis indicated a founder effect. No CHMP1A protein was found in patient-derived cells. Patient-derived cell lines showed severely impaired doubling times compared to control, suggesting a defect in cell proliferation. There was also increased expression of INK4A (see CDKN2A; 600160), a negative regulator of stem cell proliferation.

.0002 PONTOCEREBELLAR HYPOPLASIA, TYPE 8
CHMP1A, IVS2AS, G-A, -13

In 3 members of a consanguineous family of Peruvian origin with PCH8 (614961), Mochida et al. (2012) identified a homozygous G-to-A transition in intron 2 of the CHMP1A gene, creating an aberrant splice acceptor site leading to an 11-bp insertion in the spliced mRNA product. The mutation was not seen in 281 normal control samples or in several large control databases. No normal CHMP1A mRNA transcript or protein was found in patient-derived cells. Patient-derived cell lines showed severely impaired doubling times compared to control, suggesting a defect in cell proliferation. There was also increased expression of INK4A (see CDKN2A, 600160), a negative regulator of stem cell proliferation.

Tags: 16q24.3