Biology:Vimentin

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Short description: Type III intermediate filament protein


A representation of the 3D structure of the protein myoglobin showing turquoise α-helices.
Generic protein structure example
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.[1]

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[2] as well as bacteria.[3] 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.[4] 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.[5] 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. [6]

The α-helical sequences contain a pattern of hydrophobic amino acids that contribute to forming a "hydrophobic seal" on the surface of the helix.[4] 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.[4] 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.[4]

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.[7]

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).[8] Transgenic mice that lack vimentin appeared normal and did not show functional differences.[9] 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.[8] On the other hand, wounded mice that lack the vimentin gene heal slower than their wild type counterparts.[10]

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.[11]

Also, vimentin is found to control the transport of low-density lipoprotein, LDL, -derived cholesterol from a lysosome to the site of esterification.[12] 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.[12]

Vimentin plays a role in aggresome formation, where it forms a cage surrounding a core of aggregated protein.[13]

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. [14]

Clinical significance

It has been used as a sarcoma tumor marker to identify mesenchyme.[15][16] Its specificity as a biomarker has been disputed by Jerad Gardner.[17]

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.[18] High levels of DNA methylation in the promoter region have also been associated with markedly decreased survival in hormone positive breast cancers.[19] Downregulation of vimentin was identified in cystic variant of papillary thyroid carcinoma using a proteomic approach.[20] 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.[21]

Interactions

Vimentin has been shown to interact with:

The 3' UTR of Vimentin mRNA has been found to bind a 46kDa protein.[33]

References

  1. ↑ "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. October 1978. doi:10.1073/pnas.75.10.5034. PMID 368806. Bibcode: 1978PNAS...75.5034F. 
  2. ↑ "Introducing intermediate filaments: from discovery to disease". The Journal of Clinical Investigation 119 (7): 1763–1771. July 2009. doi:10.1172/JCI38339. PMID 19587451. 
  3. ↑ "The bacterial cytoskeleton". Annual Review of Genetics 44: 365–392. 2010. doi:10.1146/annurev-genet-102108-134845. PMID 21047262. 
  4. ↑ 4.0 4.1 4.2 4.3 "Intermediate filaments: structure, dynamics, function, and disease". Annual Review of Biochemistry 63: 345–382. 1994. doi:10.1146/annurev.bi.63.070194.002021. PMID 7979242. 
  5. ↑ "Assembling an intermediate filament network by dynamic cotranslation". The Journal of Cell Biology 172 (5): 747–758. February 2006. doi:10.1083/jcb.200511033. PMID 16505169. 
  6. ↑ "Vimentin Diversity in Health and Disease". Cells 7 (10): 147. September 2018. doi:10.3390/cells7100147. PMID 30248895. 
  7. ↑ "The role of the vimentin intermediate filaments in rat 3Y1 cells elucidated by immunoelectron microscopy and computer-graphic reconstruction". Biology of the Cell 68 (2): 139–146. 1990. doi:10.1016/0248-4900(90)90299-I. PMID 2192768. 
  8. ↑ 8.0 8.1 "The function of intermediate filaments in cell shape and cytoskeletal integrity". The Journal of Cell Biology 134 (4): 971–983. August 1996. doi:10.1083/jcb.134.4.971. PMID 8769421. 
  9. ↑ "Mice lacking vimentin develop and reproduce without an obvious phenotype". Cell 79 (4): 679–694. November 1994. doi:10.1016/0092-8674(94)90553-3. PMID 7954832. 
  10. ↑ "Impaired wound healing in embryonic and adult mice lacking vimentin". Journal of Cell Science 113 (13): 2455–2462. July 2000. doi:10.1242/jcs.113.13.2455. PMID 10852824. 
  11. ↑ "Dynamic JUNQ inclusion bodies are asymmetrically inherited in mammalian cell lines through the asymmetric partitioning of vimentin". Proceedings of the National Academy of Sciences of the United States of America 111 (22): 8049–8054. June 2014. doi:10.1073/pnas.1324035111. PMID 24843142. Bibcode: 2014PNAS..111.8049O. 
  12. ↑ 12.0 12.1 "A functional role for vimentin intermediate filaments in the metabolism of lipoprotein-derived cholesterol in human SW-13 cells". The Journal of Biological Chemistry 267 (27): 19455–19463. September 1992. doi:10.1016/S0021-9258(18)41797-8. PMID 1527066. 
  13. ↑ "Aggresomes: a cellular response to misfolded proteins". The Journal of Cell Biology 143 (7): 1883–1898. December 1998. doi:10.1083/jcb.143.7.1883. PMID 9864362. 
  14. ↑ "Vimentin: Regulation and pathogenesis". Biochimie 197: 96–112. June 2022. doi:10.1016/j.biochi.2022.02.003. PMID 35151830. 
  15. ↑ "Vimentin: an evaluation of its role as a tumour marker". Histopathology 11 (1): 63–72. January 1987. doi:10.1111/j.1365-2559.1987.tb02609.x. PMID 2435649. 
  16. ↑ "Immunohistochemistry from the Washington Animal Disease Diagnostic laboratory (WADDL)of the College of Veterinary Medicine, Washington State University". http://www.vetmed.wsu.edu/depts_Waddl/ICS.aspx. 
  17. ↑ "How to Interpret Vimentin Immunostain". 23 September 2010. https://www.youtube.com/watch?v=UDnp14nnNC4. 
  18. ↑ "Aberrant vimentin methylation is characteristic of upper gastrointestinal pathologies". Cancer Epidemiology, Biomarkers & Prevention 21 (4): 594–600. April 2012. doi:10.1158/1055-9965.EPI-11-1060. PMID 22315367. 
  19. ↑ "Vimentin DNA methylation predicts survival in breast cancer". Breast Cancer Research and Treatment 137 (2): 383–396. January 2013. doi:10.1007/s10549-012-2353-5. PMID 23239149. 
  20. ↑ "Differential protein expression profiles of cyst fluid from papillary thyroid carcinoma and benign thyroid lesions". PLOS ONE 10 (5): e0126472. 2015. doi:10.1371/journal.pone.0126472. PMID 25978681. Bibcode: 2015PLoSO..1026472D. 
  21. ↑ "Extracellular vimentin is an attachment factor that facilitates SARS-CoV-2 entry into human endothelial cells". Proceedings of the National Academy of Sciences of the United States of America 119 (6). February 2022. doi:10.1073/pnas.2113874119. e2113874119. PMID 35078919. 
  22. ↑ "Two-hybrid analysis reveals fundamental differences in direct interactions between desmoplakin and cell type-specific intermediate filaments". The Journal of Biological Chemistry 272 (34): 21495–21503. August 1997. doi:10.1074/jbc.272.34.21495. PMID 9261168. 
  23. ↑ "Menin's interaction with glial fibrillary acidic protein and vimentin suggests a role for the intermediate filament network in regulating menin activity". Experimental Cell Research 278 (2): 175–183. August 2002. doi:10.1006/excr.2002.5575. PMID 12169273. 
  24. ↑ "Towards a proteome-scale map of the human protein-protein interaction network". Nature 437 (7062): 1173–1178. October 2005. doi:10.1038/nature04209. PMID 16189514. Bibcode: 2005Natur.437.1173R. 
  25. ↑ "A human protein-protein interaction network: a resource for annotating the proteome". Cell 122 (6): 957–968. September 2005. doi:10.1016/j.cell.2005.08.029. PMID 16169070. 
  26. ↑ "Domain-specific phosphorylation of vimentin and glial fibrillary acidic protein by PKN". Biochemical and Biophysical Research Communications 234 (3): 621–625. May 1997. doi:10.1006/bbrc.1997.6669. PMID 9175763. 
  27. ↑ "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. November 2017. doi:10.3892/ijo.2017.4131. PMID 29048609. 
  28. ↑ "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. 2018. doi:10.1080/19336918.2018.1471323. PMID 29781749. 
  29. ↑ "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. January 1987. doi:10.1016/S0021-9258(19)75789-5. PMID 3027087. 
  30. ↑ 30.0 30.1 "Cutting edge: integration of human T lymphocyte cytoskeleton by the cytolinker plectin". Journal of Immunology 167 (2): 641–645. July 2001. doi:10.4049/jimmunol.167.2.641. PMID 11441066. 
  31. ↑ "Uridine phosphorylase association with vimentin. Intracellular distribution and localization". The Journal of Biological Chemistry 276 (16): 13302–13307. April 2001. doi:10.1074/jbc.M008512200. PMID 11278417. 
  32. ↑ "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. September 2000. doi:10.1074/jbc.M001207200. PMID 10887173. 
  33. ↑ "RNA-protein interactions within the 3 ' untranslated region of vimentin mRNA". Nucleic Acids Research 25 (16): 3362–3370. August 1997. doi:10.1093/nar/25.16.3362. PMID 9241253. 

Further reading

External links



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