Vimentin

Last updated

VIM
Protein VIM PDB 1gk4.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases VIM , CTRCT30, HEL113, vimentin
External IDs OMIM: 193060; MGI: 98932; HomoloGene: 2538; GeneCards: VIM; OMA:VIM - orthologs
Orthologs
SpeciesHumanMouse
Entrez

7431

22352

Ensembl

ENSG00000026025

ENSMUSG00000026728

UniProt

P08670

P20152

RefSeq (mRNA)

NM_003380

NM_011701

RefSeq (protein)

NP_003371

NP_035831

Location (UCSC) Chr 10: 17.23 – 17.24 Mb Chr 2: 13.58 – 13.59 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse
Immunofluorescence staining pattern of vimentin antibodies. Produced by incubating vimentin primary antibodies and FITC labelled secondary antibodies with HEp-20-10 cells. VIMENTIN.jpg
Immunofluorescence staining pattern of vimentin antibodies. Produced by incubating vimentin primary antibodies and FITC labelled secondary antibodies with HEp-20-10 cells.

Vimentin is a structural protein that in humans is encoded by the VIM gene. Its name comes from the Latin vimentum which refers to an array of flexible rods. [5]

Immunofluorescence staining of HeLa Cells with antibody to reveal vimentin containing intermediate filaments in green and antibody to LAMP1 to reveal lysosomes in red. Nuclear DNA is seen in blue. Antibodies and image courtesy EnCor Biotechnology Inc. HeLa cells showin Lamp1 in red, vimentin in green and DNA in blue.jpg
Immunofluorescence staining of HeLa Cells with antibody to reveal vimentin containing intermediate filaments in green and antibody to LAMP1 to reveal lysosomes in red. Nuclear DNA is seen in blue. Antibodies and image courtesy EnCor Biotechnology Inc.

Vimentin is a type III intermediate filament (IF) protein that is expressed in mesenchymal cells. IF proteins are found in all animal cells [6] as well as bacteria. [7] Intermediate filaments, along with tubulin-based microtubules and actin-based microfilaments, comprises the cytoskeleton. All IF proteins are expressed in a highly developmentally-regulated fashion; vimentin is the major cytoskeletal component of mesenchymal cells. Because of this, vimentin is often used as a marker of mesenchymally-derived cells or cells undergoing an epithelial-to-mesenchymal transition (EMT) during both normal development and metastatic progression.

Structure

The assembly of the fibrous vimentin filament that forms the cytoskeleton follows a gradual sequence. The vimentin monomer has a central α-helical domain, capped on each end by non-helical amino (head) and carboxyl (tail) domains. [8] Two monomers are likely co-translationally expressed in a way that facilitates their interaction forming a coiled-coil dimer, which is the basic subunit of vimentin assembly. [9] A pair of coiled-coil dimers connect in an antiparallel fashion to form a tetramer. Eight tetramers join to form what is known as the unit-length filament (ULF), ULFs then stick to each other and elongate followed by compaction to form the fibrous proteins. [10]

The α-helical sequences contain a pattern of hydrophobic amino acids that contribute to forming a "hydrophobic seal" on the surface of the helix. [8] In addition, there is a periodic distribution of acidic and basic amino acids that seems to play an important role in stabilizing coiled-coil dimers. [8] The spacing of the charged residues is optimal for ionic salt bridges, which allows for the stabilization of the α-helix structure. While this type of stabilization is intuitive for intrachain interactions, rather than interchain interactions, scientists have proposed that perhaps the switch from intrachain salt bridges formed by acidic and basic residues to the interchain ionic associations contributes to the assembly of the filament. [8]

Function

Vimentin plays a significant role in supporting and anchoring the position of the organelles in the cytosol. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. [11]

The dynamic nature of vimentin is important when offering flexibility to the cell. Scientists found that vimentin provided cells with a resilience absent from the microtubule or actin filament networks, when under mechanical stress in vivo. Therefore, in general, it is accepted that vimentin is the cytoskeletal component responsible for maintaining cell integrity. (It was found that cells without vimentin are extremely delicate when disturbed with a micropuncture). [12] Transgenic mice that lack vimentin appeared normal and did not show functional differences. [13] It is possible that the microtubule network may have compensated for the absence of the intermediate network. This result supports an intimate interaction between microtubules and vimentin. Moreover, when microtubule depolymerizers were present, vimentin reorganization occurred, once again implying a relationship between the two systems. [12] On the other hand, wounded mice that lack the vimentin gene heal slower than their wild type counterparts. [14]

In essence, vimentin is responsible for maintaining cell shape, integrity of the cytoplasm, and stabilizing cytoskeletal interactions. Vimentin has been shown to eliminate toxic proteins in JUNQ and IPOD inclusion bodies in asymmetric division of mammalian cell lines. [15]

Also, vimentin is found to control the transport of low-density lipoprotein, LDL, -derived cholesterol from a lysosome to the site of esterification. [16] With the blocking of transport of LDL-derived cholesterol inside the cell, cells were found to store a much lower percentage of the lipoprotein than normal cells with vimentin. This dependence seems to be the first process of a biochemical function in any cell that depends on a cellular intermediate filament network. This type of dependence has ramifications on the adrenal cells, which rely on cholesteryl esters derived from LDL. [16]

Vimentin plays a role in aggresome formation, where it forms a cage surrounding a core of aggregated protein. [17]

In addition to its conventional intracellular localisation, vimentin can be found extracellularly. Vimentin can be expressed as a cell surface protein and have suggested roles in immune reactions. It can also be released in phosphorylated forms to the extracellular space by activated macrophages, astrocytes are also known to release vimentin. [18]

Clinical significance

It has been used as a sarcoma tumor marker to identify mesenchyme. [19] [20] Its specificity as a biomarker has been disputed by Jerad Gardner. [21] Vimentin is present in spindle cell squameous cell carcinoma. [22] [23]

Methylation of the vimentin gene has been established as a biomarker of colon cancer and this is being utilized in the development of fecal tests for colon cancer. Statistically significant levels of vimentin gene methylation have also been observed in certain upper gastrointestinal pathologies such as Barrett's esophagus, esophageal adenocarcinoma, and intestinal type gastric cancer. [24] High levels of DNA methylation in the promoter region have also been associated with markedly decreased survival in hormone positive breast cancers. [25] Downregulation of vimentin was identified in cystic variant of papillary thyroid carcinoma using a proteomic approach. [26] See also Anti-citrullinated protein antibody for its use in diagnosis of rheumatoid arthritis.

Vimentin was discovered to be an attachment factor for SARS-CoV-2 by Nader Rahimi and colleagues. [27]

Interactions

Vimentin has been shown to interact with:

The 3' UTR of Vimentin mRNA has been found to bind a 46kDa protein. [39]

Related Research Articles

<span class="mw-page-title-main">Cytoskeleton</span> Network of filamentous proteins that forms the internal framework of cells

The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is composed of similar proteins in the various organisms. It is composed of three main components: microfilaments, intermediate filaments, and microtubules, and these are all capable of rapid growth and or disassembly depending on the cell's requirements.

<span class="mw-page-title-main">Intermediate filament</span> Cytoskeletal structure

Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma.

<span class="mw-page-title-main">Tubulin</span> Superfamily of proteins that make up microtubules

Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton. It was discovered and named by Hideo Mōri in 1968. Microtubules function in many essential cellular processes, including mitosis. Tubulin-binding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation and therefore cell division.

<span class="mw-page-title-main">Desmin</span> Mammalian protein found in humans

Desmin is a protein that in humans is encoded by the DES gene. Desmin is a muscle-specific, type III intermediate filament that integrates the sarcolemma, Z disk, and nuclear membrane in sarcomeres and regulates sarcomere architecture.

<span class="mw-page-title-main">Peripherin</span> Protein-coding gene in the species Homo sapiens

Peripherin is a type III intermediate filament protein expressed mainly in neurons of the peripheral nervous system. It is also found in neurons of the central nervous system that have projections toward peripheral structures, such as spinal motor neurons. Its size, structure, and sequence/location of protein motifs is similar to other type III intermediate filament proteins such as desmin, vimentin and glial fibrillary acidic protein. Like these proteins, peripherin can self-assemble to form homopolymeric filamentous networks, but it can also heteropolymerize with neurofilaments in several neuronal types. This protein in humans is encoded by the PRPH gene. Peripherin is thought to play a role in neurite elongation during development and axonal regeneration after injury, but its exact function is unknown. It is also associated with some of the major neuropathologies that characterize amyotropic lateral sclerosis (ALS), but despite extensive research into how neurofilaments and peripherin contribute to ALS, their role in this disease is still unidentified.

<span class="mw-page-title-main">Glial fibrillary acidic protein</span> Type III intermediate filament protein

Glial fibrillary acidic protein (GFAP) is a protein that is encoded by the GFAP gene in humans. It is a type III intermediate filament (IF) protein that is expressed by numerous cell types of the central nervous system (CNS), including astrocytes and ependymal cells during development. GFAP has also been found to be expressed in glomeruli and peritubular fibroblasts taken from rat kidneys, Leydig cells of the testis in both hamsters and humans, human keratinocytes, human osteocytes and chondrocytes and stellate cells of the pancreas and liver in rats.

Neurofilaments (NF) are classed as type IV intermediate filaments found in the cytoplasm of neurons. They are protein polymers measuring 10 nm in diameter and many micrometers in length. Together with microtubules (~25 nm) and microfilaments (7 nm), they form the neuronal cytoskeleton. They are believed to function primarily to provide structural support for axons and to regulate axon diameter, which influences nerve conduction velocity. The proteins that form neurofilaments are members of the intermediate filament protein family, which is divided into six types based on their gene organization and protein structure. Types I and II are the keratins which are expressed in epithelia. Type III contains the proteins vimentin, desmin, peripherin and glial fibrillary acidic protein (GFAP). Type IV consists of the neurofilament proteins NF-L, NF-M, NF-H and α-internexin. Type V consists of the nuclear lamins, and type VI consists of the protein nestin. The type IV intermediate filament genes all share two unique introns not found in other intermediate filament gene sequences, suggesting a common evolutionary origin from one primitive type IV gene.

The epithelial–mesenchymal transition (EMT) is a process by which epithelial cells lose their cell polarity and cell–cell adhesion, and gain migratory and invasive properties to become mesenchymal stem cells; these are multipotent stromal cells that can differentiate into a variety of cell types. EMT is essential for numerous developmental processes including mesoderm formation and neural tube formation. EMT has also been shown to occur in wound healing, in organ fibrosis and in the initiation of metastasis in cancer progression.

<span class="mw-page-title-main">Plectin</span> Mammalian protein found in Homo sapiens

Plectin is a giant protein found in nearly all mammalian cells which acts as a link between the three main components of the cytoskeleton: actin microfilaments, microtubules and intermediate filaments. In addition, plectin links the cytoskeleton to junctions found in the plasma membrane that structurally connect different cells. By holding these different networks together, plectin plays an important role in maintaining the mechanical integrity and viscoelastic properties of tissues.

Crescentin is a protein which is a bacterial relative of the intermediate filaments found in eukaryotic cells. Just as tubulins and actins, the other major cytoskeletal proteins, have prokaryotic homologs in, respectively, the FtsZ and MreB proteins, intermediate filaments are linked to the crescentin protein. Some of its homologs are erroneously labelled Chromosome segregation protein ParA. This protein family is found in Caulobacter and Methylobacterium.

<span class="mw-page-title-main">Protein filament</span> Long chain of protein monomers

In biology, a protein filament is a long chain of protein monomers, such as those found in hair, muscle, or in flagella. Protein filaments form together to make the cytoskeleton of the cell. They are often bundled together to provide support, strength, and rigidity to the cell. When the filaments are packed up together, they are able to form three different cellular parts. The three major classes of protein filaments that make up the cytoskeleton include: actin filaments, microtubules and intermediate filaments.

<span class="mw-page-title-main">Nestin (protein)</span> Protein-coding gene in the species Homo sapiens

Nestin is a protein that in humans is encoded by the NES gene.

<span class="mw-page-title-main">Keratin 5</span>

Keratin 5, also known as KRT5, K5, or CK5, is a protein that is encoded in humans by the KRT5 gene. It dimerizes with keratin 14 and forms the intermediate filaments (IF) that make up the cytoskeleton of basal epithelial cells. This protein is involved in several diseases including epidermolysis bullosa simplex and breast and lung cancers.

<span class="mw-page-title-main">Synemin</span> Protein found in humans

Synemin, also known as desmuslin, is a protein that in humans is encoded by the SYNM gene. Synemin is an intermediate filament (IF) family member. IF proteins are cytoskeletal proteins that confer resistance to mechanical stress and are encoded by a dispersed multigene family. This protein has been found to form a linkage between desmin, which is a subunit of the IF network, and the extracellular matrix, and provides an important structural support in muscle.

<span class="mw-page-title-main">Transforming protein RhoA</span> Protein and coding gene in humans

Transforming protein RhoA, also known as Ras homolog family member A (RhoA), is a small GTPase protein in the Rho family of GTPases that in humans is encoded by the RHOA gene. While the effects of RhoA activity are not all well known, it is primarily associated with cytoskeleton regulation, mostly actin stress fibers formation and actomyosin contractility. It acts upon several effectors. Among them, ROCK1 and DIAPH1 are the best described. RhoA, and the other Rho GTPases, are part of a larger family of related proteins known as the Ras superfamily, a family of proteins involved in the regulation and timing of cell division. RhoA is one of the oldest Rho GTPases, with homologues present in the genomes since 1.5 billion years. As a consequence, RhoA is somehow involved in many cellular processes which emerged throughout evolution. RhoA specifically is regarded as a prominent regulatory factor in other functions such as the regulation of cytoskeletal dynamics, transcription, cell cycle progression and cell transformation.

<span class="mw-page-title-main">PRKCI</span> Protein-coding gene in the species Homo sapiens

Protein kinase C iota type is an enzyme that in humans is encoded by the PRKCI gene.

<span class="mw-page-title-main">ANLN</span> Mammalian protein found in Homo sapiens

Anillin is a conserved protein implicated in cytoskeletal dynamics during cellularization and cytokinesis. The ANLN gene in humans and the scraps gene in Drosophila encode Anillin. In 1989, anillin was first isolated in embryos of Drosophila melanogaster. It was identified as an F-actin binding protein. Six years later, the anillin gene was cloned from cDNA originating from a Drosophila ovary. Staining with anti-anillin antibody showed the anillin localizes to the nucleus during interphase and to the contractile ring during cytokinesis. These observations agree with further research that found anillin in high concentrations near the cleavage furrow coinciding with RhoA, a key regulator of contractile ring formation.

<span class="mw-page-title-main">Cadherin-1</span> Human protein-coding gene

Cadherin-1 or Epithelial cadherin(E-cadherin), is a protein that in humans is encoded by the CDH1 gene. Mutations are correlated with gastric, breast, colorectal, thyroid, and ovarian cancers. CDH1 has also been designated as CD324. It is a tumor suppressor gene.

<span class="mw-page-title-main">IFFO1</span> Protein-coding gene in the species Homo sapiens

Intermediate filament family orphan 1 is a protein that in humans is encoded by the IFFO1 gene. IFFO1 has uncharacterized function and a weight of 61.98 kDa. IFFO1 proteins play an important role in the cytoskeleton and the nuclear envelope of most eukaryotic cell types.

<span class="mw-page-title-main">CAMSAP2</span> Protein found in humans

Calmodulin-regulated spectrin-associated protein family member 2 (CAMSAP2) is a protein in humans that is encoded by the CAMSAP2 gene. CAMSAP2 possesses a microtubule-binding domain near the C-terminal region where "microtubule interactions" occur. On the C-terminal regions, protein to protein interactions are accelerated by three coiled-coil domains, which function as molecular spacers. CAMSAP2 acts as a microtubule minus-end anchor and binds microtubules through its CKK domain. CAMSAP2 is necessary for the proper organization and stabilization of interphase microtubules. The protein also plays a role in cell migration. CAMSAP2 stabilizes and attaches microtubule minus ends to the Golgi through the AKAP9 complex and myomegalin. CLASP1 proteins are responsible for microtubule stability which are not required for the Golgi tethering. When no centromeres are present, AKAP9 and CAMSAP-2 dependent pathways of the microtubule minus ends become a dominant force and must exist in order to observe the maintenance of microtubule density.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000026025 – Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000026728 – Ensembl, May 2017
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  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ↑ Franke WW, Schmid E, Osborn M, Weber K (October 1978). "Different intermediate-sized filaments distinguished by immunofluorescence microscopy". Proceedings of the National Academy of Sciences of the United States of America. 75 (10): 5034–5038. Bibcode:1978PNAS...75.5034F. doi: 10.1073/pnas.75.10.5034 . PMC   336257 . PMID   368806.
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  32. ↑ Matsuzawa K, Kosako H, Inagaki N, Shibata H, Mukai H, Ono Y, et al. (May 1997). "Domain-specific phosphorylation of vimentin and glial fibrillary acidic protein by PKN". Biochemical and Biophysical Research Communications. 234 (3): 621–625. doi:10.1006/bbrc.1997.6669. PMID   9175763.
  33. ↑ Ratnayake WS, Apostolatos AH, Ostrov DA, Acevedo-Duncan M (November 2017). "Two novel atypical PKC inhibitors; ACPD and DNDA effectively mitigate cell proliferation and epithelial to mesenchymal transition of metastatic melanoma while inducing apoptosis". International Journal of Oncology. 51 (5): 1370–1382. doi:10.3892/ijo.2017.4131. PMC   5642393 . PMID   29048609.
  34. ↑ Ratnayake WS, Apostolatos CA, Apostolatos AH, Schutte RJ, Huynh MA, Ostrov DA, et al. (2018). "Oncogenic PKC-ι activates Vimentin during epithelial-mesenchymal transition in melanoma; a study based on PKC-ι and PKC-ζ specific inhibitors". Cell Adhesion & Migration. 12 (5): 447–463. doi:10.1080/19336918.2018.1471323. PMC   6363030 . PMID   29781749.
  35. ↑ Herrmann H, Wiche G (January 1987). "Plectin and IFAP-300K are homologous proteins binding to microtubule-associated proteins 1 and 2 and to the 240-kilodalton subunit of spectrin". The Journal of Biological Chemistry. 262 (3): 1320–1325. doi: 10.1016/S0021-9258(19)75789-5 . PMID   3027087.
  36. 1 2 Brown MJ, Hallam JA, Liu Y, Yamada KM, Shaw S (July 2001). "Cutting edge: integration of human T lymphocyte cytoskeleton by the cytolinker plectin". Journal of Immunology. 167 (2): 641–645. doi: 10.4049/jimmunol.167.2.641 . PMID   11441066.
  37. ↑ Russell RL, Cao D, Zhang D, Handschumacher RE, Pizzorno G (April 2001). "Uridine phosphorylase association with vimentin. Intracellular distribution and localization". The Journal of Biological Chemistry. 276 (16): 13302–13307. doi: 10.1074/jbc.M008512200 . PMID   11278417.
  38. ↑ Tzivion G, Luo ZJ, Avruch J (September 2000). "Calyculin A-induced vimentin phosphorylation sequesters 14-3-3 and displaces other 14-3-3 partners in vivo". The Journal of Biological Chemistry. 275 (38): 29772–29778. doi: 10.1074/jbc.M001207200 . PMID   10887173.
  39. ↑ Zehner ZE, Shepherd RK, Gabryszuk J, Fu TF, Al-Ali M, Holmes WM (August 1997). "RNA-protein interactions within the 3 ' untranslated region of vimentin mRNA". Nucleic Acids Research. 25 (16): 3362–3370. doi:10.1093/nar/25.16.3362. PMC   146884 . PMID   9241253.

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