TRPV4 mbecich

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Author Information

Michael Becich

Basic Information

  • ID: TRPV4_mbecich
  • Name: TRPV4 (Transient receptor potential cation channel subfamily V member 4)
  • Organism: Homo sapiens (Human)
  • Description: My motivation for including this gene comes from its potential implications in magnetogenetics, a progressive, non-invasive form of cellular activation using magnetic fields. I pursued this project in BioE44, and now I would love to see it synthesized in our team project. This isoform is found in humans, but I codon-optimized it for E. coli. Although the lack of membrane-bound organelle may render it useless (along with its long length), I was still intrigued by its potential power of magnetic induction. TRPV4 is a non-selective calcium permeant cation channel involved in osmotic sensitivity and mechanosensitivity. Activation by exposure to hypotonicity within the physiological range exhibits an outward rectification (PubMed:18826956, PubMed:18695040). Also activated by heat, low pH, citrate and phorbol esters (PubMed:18826956, PubMed:18695040). Increase of intracellular Ca2+ potentiates currents. Channel activity seems to be regulated by a calmodulin-dependent mechanism with a negative feedback mechanism (PubMed:12724311, PubMed:18826956). Promotes cell-cell junction formation in skin keratinocytes and plays an important role in the formation and/or maintenance of functional intercellular barriers (By similarity). Acts as a regulator of intracellular Ca2+ in synoviocytes (PubMed:19759329). Plays an obligatory role as a molecular component in the nonselective cation channel activation induced by 4-alpha-phorbol 12,13-didecanoate and hypotonic stimulation in synoviocytes and also regulates production of IL-8 (PubMed:19759329). Together with PKD2, forms mechano- and thermosensitive channels in cilium (PubMed:18695040). Negatively regulates expression of PPARGC1A, UCP1, oxidative metabolism and respiration in adipocytes (By similarity). Regulates expression of chemokines and cytokines related to proinflammatory pathway in adipocytes (By similarity). Together with AQP5, controls regulatory volume decrease in salivary epithelial cells (By similarity).[1] The TRPV4 gene provides instructions for making a protein that acts as a calcium channel. This channel, which transports positively charged atoms of calcium (calcium ions) across cell membranes, is found in many types of cells and tissues. Studies suggest that the TRPV4 channel plays a role in a number of different functions in the body. These include the development of bones and cartilage, the tough but flexible tissue that makes up much of the skeleton during early development. It is also be involved in maintaining the body's water balance (osmoregulation) and in certain types of sensation, particularly the sensation of pain. The TRPV4 channel may also play a role in the self-destruction of cells (apoptosis). It likely has additional functions that have not been identified.[2]
  • DNA Length: 2658 base pairs (Note: this gene is over 2000bp long so synthesis/expression may experience issues.)
  • DNA sequence (codon-optimized for E. coli, start codon to stop codon):ATG GCA GAC TCC TCG GAG GGA CCT CGC GCT GGA CCC GGA GAA GTC GCG GAG TTG CCA GGG GAT GAG TCC GGA ACC CCA GGA GGG GAG GCG TTT CCG TTA TCA AGC TTA GCG AAT CTT TTT GAA GGA GAA GAC GGG TCG TTA AGC CCT TCA CCG GCC GAC GCA TCT CGT CCC GCC GGG CCA GGT GAC GGG CGC CCA AAC TTG CGC ATG AAA TTC CAG GGG GCC TTC CGC AAA GGC GTA CCC AAC CCT ATC GAT CTT CTT GAA AGT ACA TTA TAC GAG TCT TCG GTA GTC CCC GGT CCG AAA AAG GCG CCG ATG GAC AGC TTA TTT GAT TAT GGA ACT TAT CGC CAT CAC TCC TCA GAT AAT AAG CGC TGG CGT AAG AAG ATT ATC GAA AAA CAG CCC CAA TCA CCG AAA GCC CCT GCA CCC CAG CCG CCT CCT ATC CTT AAA GTA TTT AAC CGT CCT ATT TTA TTT GAC ATC GTC TCA CGT GGG TCC ACA GCG GAC TTG GAC GGC CTT CTT CCA TTC CTT CTG ACC CAC AAG AAA CGT CTT ACG GAC GAA GAA TTT CGT GAG CCA TCC ACG GGA AAG ACC TGC CTG CCA AAA GCC TTA CTG AAC TTA TCT AAC GGA CGC AAT GAC ACC ATC CCG GTC CTT TTA GAT ATT GCC GAA CGT ACC GGG AAC ATG CGT GAA TTC ATT AAT AGC CCA TTC CGC GAC ATT TAC TAC CGT GGC CAA ACC GCG TTG CAT ATT GCG ATC GAA CGT CGT TGT AAA CAC TAC GTT GAA CTG CTG GTG GCT CAA GGA GCG GAC GTC CAT GCG CAG GCC CGT GGT CGC TTT TTT CAG CCC AAA GAC GAG GGA GGA TAC TTC TAC TTT GGA GAG TTA CCG CTG TCT TTG GCA GCC TGC ACG AAC CAA CCC CAT ATT GTA AAT TAT TTG ACG GAG AAC CCT CAT AAG AAA GCC GAC ATG CGC CGC CAG GAC AGC CGC GGA AAT ACC GTA TTG CAC GCT TTA GTA GCT ATT GCT GAC AAC ACT CGC GAG AAC ACA AAG TTT GTG ACA AAA ATG TAT GAT CTT CTT TTA CTT AAA TGT GCA CGC CTT TTT CCG GAT TCT AAT CTG GAA GCA GTT TTG AAT AAC GAC GGC TTA TCT CCA TTA ATG ATG GCG GCT AAG ACC GGA AAA ATT GGA ATC TTT CAG CAT ATT ATC CGT CGC GAA GTG ACA GAC GAG GAT ACT CGT CAC CTG TCG CGT AAG TTT AAA GAT TGG GCA TAC GGA CCA GTA TAT TCT TCT CTT TAC GAT TTA TCA TCC CTT GAC ACC TGC GGA GAA GAA GCG AGC GTG TTG GAA ATT TTG GTC TAC AAT TCT AAG ATC GAG AAT CGT CAC GAA ATG CTG GCG GTA GAA CCA ATT AAC GAA TTG CTG CGT GAC AAG TGG CGT AAG TTC GGT GCT GTC TCT TTT TAT ATT AAC GTT GTC TCT TAT CTT TGT GCC ATG GTC ATT TTT ACG CTT ACT GCG TAC TAT CAG CCA CTT GAG GGG ACA CCC CCG TAT CCA TAC CGT ACC ACC GTA GAC TAC CTG CGT TTG GCT GGA GAA GTT ATC ACG TTG TTC ACG GGG GTC CTT TTC TTC TTC ACT AAC ATT AAG GAC CTT TTT ATG AAA AAG TGC CCT GGT GTT AAT AGC TTG TTT ATT GAT GGA AGC TTT CAG TTG TTA TAT TTC ATT TAC TCC GTA TTG GTT ATT GTG TCA GCC GCG CTT TAC CTG GCC GGA ATT GAG GCC TAT TTG GCT GTA ATG GTC TTC GCC TTG GTG CTG GGG TGG ATG AAT GCC CTG TAC TTT ACA CGT GGC TTG AAG CTG ACG GGT ACG TAT TCT ATC ATG ATC CAG AAG ATT TTA TTC AAG GAT CTT TTT CGT TTT TTA TTA GTC TAT CTG TTG TTT ATG ATC GGC TAT GCC AGC GCG CTT GTA TCA CTG CTT AAT CCG TGC GCC AAC ATG AAA GTG TGC AAC GAG GAC CAA ACG AAC TGC ACT GTA CCC ACG TAC CCA AGC TGC CGT GAC TCT GAA ACG TTT AGT ACC TTC CTG CTT GAC CTG TTT AAA CTT ACT ATC GGC ATG GGC GAT TTA GAA ATG TTG AGC TCG ACG AAG TAC CCG GTG GTG TTC ATC ATC CTG TTG GTA ACT TAC ATT ATC TTA ACT TTT GTC TTG CTG TTG AAC ATG TTA ATC GCC TTA ATG GGA GAG ACC GTT GGA CAA GTG TCT AAG GAA AGT AAG CAC ATC TGG AAA CTT CAG TGG GCA ACT ACA ATT TTG GAC ATT GAA CGT AGT TTC CCG GTG TTT CTG CGT AAG GCT TTT CGC TCG GGA GAG ATG GTG ACA GTA GGC AAA TCA AGT GAT GGG ACG CCC GAC CGT CGC TGG TGT TTT CGT GTC GAT GAG GTG AAC TGG TCT CAC TGG AAC CAA AAT CTT GGC ATT ATC AAC GAG GAC CCT GGT AAA AAC GAA ACG TAC CAG TAT TAC GGA TTT AGT CAT ACT GTA GGT CGC CTT CGT CGC GAT CGC TGG TCG TCT GTA GTC CCC CGT GTA GTG GAA TTG AAT AAA AAC AGC AAT CCC GAT GAA GTT GTG GTT CCG CTG GAC AGC ATG GGA AAT CCT CGT TGT GAT GGC CAC CAA CAG GGT TAT CCT CGT AAA TGG CGC ACA GAC GAT GCA CCT TTA TAA
  • Amino Acid length: 886 amino acids.
  • Amino Acid sequence:

MADSSEGPRAGPGEVAELPGDESGTPGGEAFPLSSLANLFEGEDGSLSPSPADASRPAGP GDGRPNLRMKFQGAFRKGVPNPIDLLESTLYESSVVPGPKKAPMDSLFDYGTYRHHSSDN KRWRKKIIEKQPQSPKAPAPQPPPILKVFNRPILFDIVSRGSTADLDGLLPFLLTHKKRL TDEEFREPSTGKTCLPKALLNLSNGRNDTIPVLLDIAERTGNMREFINSPFRDIYYRGQT ALHIAIERRCKHYVELLVAQGADVHAQARGRFFQPKDEGGYFYFGELPLSLAACTNQPHI VNYLTENPHKKADMRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLLKCARLFPDS NLEAVLNNDGLSPLMMAAKTGKIGIFQHIIRREVTDEDTRHLSRKFKDWAYGPVYSSLYD LSSLDTCGEEASVLEILVYNSKIENRHEMLAVEPINELLRDKWRKFGAVSFYINVVSYLC AMVIFTLTAYYQPLEGTPPYPYRTTVDYLRLAGEVITLFTGVLFFFTNIKDLFMKKCPGV NSLFIDGSFQLLYFIYSVLVIVSAALYLAGIEAYLAVMVFALVLGWMNALYFTRGLKLTG TYSIMIQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCANMKVCNEDQTNCTVPTYPSC RDSETFSTFLLDLFKLTIGMGDLEMLSSTKYPVVFIILLVTYIILTFVLLLNMLIALMGE TVGQVSKESKHIWKLQWATTILDIERSFPVFLRKAFRSGEMVTVGKSSDGTPDRRWCFRV DEVNWSHWNQNLGIINEDPGKNETYQYYGFSHTVGRLRRDRWSSVVPRVVELNKNSNPDE VVVPLDSMGNPRCDGHQQGYPRKWRTDDAPL*

Function and Homologs

  • Product: Transient receptor potential cation channel subfamily V member 4
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Name, Max score/Query Cover/E-Value/Ident, [link Accession]
  • Human
    • OTRPC4 [Homo sapiens], 1804/100%/0.0/99%, AAG16127.1
    • vanilloid receptor-related osmotically activated channel [Homo sapiens], 1803/100%/0.0/99%, AAG28029.1
    • vanilloid receptor like channel-2 [Homo sapiens], 1803/100%/0.0/99%, BAB69040.1
  • Non-human:
    • PREDICTED: transient receptor potential cation channel subfamily V member 4 isoform X1 Pan paniscus, 1796/100%/0.0/99%/XP_008956168.1
    • PREDICTED: transient receptor potential cation channel subfamily V member 4 isoform X1 Gorilla gorilla gorilla, 1790/100%/0.0/99%/XP_018894818.1
  • E. coli:
    • Chain A, From Darpins To Loopdarpins: Novel Loopdarpin Design Allows The Selection Of Low Picomolar Binders In A Single Round Of Ribosome Display, 55.5/93.2/10%/6e-07/40%, 4K5C_A
  • Equivalent E. coli functional protein: No E. coli equivalent because mechanism depends on membrane-bound organelle. Closest E. coli result shown in BLAST results above: Chain A, From Darpins To Loopdarpins.

Expression

  • Expression Level: low
  • Expression Level Hypothesis: Despite encoding calcium channels, this protein does not serve a clear/critical function within the cell; instead by hijacking this gene and overexpressing in alternative systems, its interesting magnetic properties become apparent.

think the gene is expressed at this level? (one or two sentences)

  • Expression Level References and Description: Researchers have found low expression levels in humans.[3]
  • Expression Time: early
  • Expression Level Hypothesis: TRPV4 is commonly expressed in epithelium and lining the spinal cord in humans (likely because of calcium channels contributing to neuronal activity). Since it may play a developmental role in the central nervous system, we would expect early expression to occur.
  • Expression Time References and Description: Same OMIM expression data as above.

Gene Context

  • Other Components: TRPV3 Transient receptor potential channels (TRP channels) are a group of ion channels located mostly on the plasma membrane of numerous animal cell types. As its name implies, TRPV4 is member 4 of a family of subunits, each encoding nonselective cation channels that interact across membranes.
  • Possible Dependencies: VR-OAC This vanilloid receptor-related osmotically activated channel protein may activate simultaneously with TRPV4, which also displays osmotic activation.
  • Process: Non-selective calcium permeant cation channel influx
    • Inputs: Extracellular Ca2+
    • Outputs: Intracellular Ca2+

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file
  • http://www.uniprot.org/uniprot/Q9HBA0
  • https://ghr.nlm.nih.gov/gene/TRPV4
  • http://omim.org/entry/605427
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