In Silico Analysis of Pax6 Interacting Proteins Indicates Missing Molecular Links in Development of Brain and Associated Disease
The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.
[1] Callaerts P, Halder G, and Gehring WJ. PAX-6 in development and
evolution. Annu. Rev. Neurosci. 20: 483-532. 1997.
[2] Chi N, Epstein JA. Getting Your Pax Straight: Pax proteins in
development disease. Trands Genet 18: 41-47. 2002.
[3] Tomarev SI. Pax-6, eyes absent, and Prox 1 in eye development. Int J
Dev Biol 41: 835-842. 1997.
[4] Halder G, Callaerts P, Gehring W. Induction of ectopic eyes by targeted
expression of the eyeless gene in Drosophila. Science 267: 1788-1792.
1995.
[5] Chow RL, Altmann CR, Lang AR. Pax6 induces ectopic eyes in a
vertebrate. Development 126: 4213-4222.1999.
[6] Duncan MK, Kozmik Z, Cveklova K. Overexpression of PAX6(5a) in
lens fiber cells results in cataract and upregulation of (alpha)5(beta)1
integrin expression. J Cell Sci 113: 3173-3185. 2000.
[7] Cvekl A, Piatigorsky J. Lens development and crystallin gene
expression: many roles for Pax-6. BioEssays 18: 621-630. 1996.
[8] Van Raamsdonk CD, Tilghman SM. Dosage requirement and allelic
expression of PAX6 during lens placode formation. Development 127:
5439-5448. 2000.
[9] Ashery-Padan R, Marquardt T, Zhou X. Pax6 activity in the lens
primordium is required for lens formation and for correct placement of a
single retina in the eye. Genes Dev 14: 2701-2711. 2000.
[10] Larsson LI, St-Onge L, Hougaard. Pax 4 and 6 regulate gastrointestinal
endocrine cell development. Mech. Dev 79: 153-159. 1998.
[11] St-Onge L, Sosa-Pineda B, Chowdhury K. Pax6 is required for
differentiation of glucagon-producing ╬▒-cells in mouse pancreas. Nature
387: 406-409. 1997.
[12] Sander M, Neubuser A, Kalamaras J. Genetic analysis reveals that
PAX6 is required for normal transcription of pancreatic hormone genes
and islet development. Genes Dev 11: 1662-1673. 1997.
[13] Muzio L, Mallamaci A. Emx1, Emx2 and Pax6 in Specification,
Regionalization and Arealization of the Cerebral Cortex. Cereb Cortex
13: 641-647. 2003.
[14] Kimura J, Suda Y, Kurokawa D Emx2 and Pax6 Function in
Cooperation with Otx2 and Otx1 to Develop Caudal Forebrain
Primordium That Includes Future Archipallium. Development 25: 5097-
5108. 2005.
[15] Yun K, Poter S, Rubenstein LR Gsh2 and Pax6 play complementary
roles in dorsoventral patterning of the mammalian telencephalon.
Development 128: 193-205. 2001.
[16] van Heyningen V, Williamson KA Pax6 in sensory development. Hum.
Mol. Genet 11: 1161-1167. 2000.
[17] Kimura J, Suda Y, Kurokawa D. Emx2 and Pax6 Function in
Cooperation with Otx2 and Otx1 to Develop Caudal Primordium That
Includes Future Archipallium. J. Neurosci 25: 5097-5108. 2005.
[18] Lengler J, Bittner T, Munster D. Agonistic and Antagonistic Action of
AP2, Msx2, Pax6, Prox1 and Six3 in the Regulation of Sox2 Expression.
Ophthalmic Res 37: 301-309. 2005.
[19] Plosk JE, Shamsher MK, Radu A. Paired-Type Homeodomain
Transcription Factors Are Imported into the Nucleus by Karyopherin 13.
MCB 24: 4824-4834. 2004.
[20] Hussain MA, Habener JF. Glucagon Gene Transcription Activation
Mediated by Synergistic Interactions of pax-6 and cdx-2 with the p300
Co-activator. JBC 41: 28950-28957. 1999.
[21] Planque N, Leconte L, Coquelle FM. Interaction of Maf Transcription
Factors with Pax-6 Results in Synergistic Activation of the Glucagon
Promoter. JBC 276: 35751-35760. 2001.
[22] Yang Y, Stopka T, Golestaneh N. Regulation of aA-crystallin via Pax6,
c-Maf, CREB and a broad domain of lens-specific chromatin. EMBO
25: 2107-2118. 2006.
[23] Cvekl A., Kashanchi F, Brady JN. Pax-6 Interactions with TATA-Box-
Binding Protein and Retinoblastoma Protein. Ophthalmol Vis Sci. 40:
1343-1350. 1999.
[24] Leconte L, Lecoin L, Martin P. Pax6 Interacts with cVax and Tbx5 to
Establish the Dorsoventral Boundary of the Developing Eye. JBC 279:
47272-47277. 2004.
[25] Kamachi Y, Uchikawa M, Tanouchi A. Pax6 and SOX2 form a co-
DNA-binding partner complex that regulates initiation of lens
development. Genes & Dev15: 1272-1286. 2001.
[26] Cooper ST, Hanson IM. A screen for proteins that interact with PAX6:
C-terminal mutations disrupt interaction with HOMER3, DNCL1 and
TRIM11. BMC Genetics 1471-2156/6/43. 2005.
[27] Sivak JM, West-Mays JA, Yee A. Transcription Factors Pax6 and AP-
2╬▒ Interact To Coordinate Corneal Epithelial Repair by Controlling
Expression of Matrix Metalloproteinase Gelatinase B. MCB 24: 245-
257. 2004.
[28] Planque N, Leconte L, Coquelle FM, Martin P, Saule S. Specific Pax-
6/Microphthalmia Transcription Factor Interactions Involve Their DNAbinding
Domains and Inhibit Transcriptional Properties of Both
Proteins. JBC 276: 29330-29337. 2001.
[29] Mikkola I, Bruun JA, Holm T, Johanseni T. Superactivation of Pax6-
mediated Transactivation from Paired Domain-binding Sites by DNAindependent
Recruitment of Different Homeodomain Proteins. JBC 276:
4109-4118. 2000.
[30] PIP: Potential Interactions of Proteins.
http://bmm.cancerresearchuk.org/~pip/.
[31] Jonsson PF, Cavanna T, Zicha D. Cluster analysis of networks
generated through homology: automatic identification of important
protein communities involved in cancer metastasis. BMC Bioinformatics
1471-2105-7-2. 2006.
[32] STRING: http://string.embl.de/newstring_cgi/show_network_section.pl
[33] Sommer L, Ma Q, Anderson DJ. Neurogenins, a novel family of
atonal-related bHLH transcription factors, are putative mammalian
neuronal determination genes that reveal progenitor cell heterogeneity in
the developing CNS and PNS. Molec. Cell. Neurosci. 8: 221-241.1996.
[34] Scardigli R, Schuurmans C, Gradwohl G. Crossregulation between
neurogenin2 and pathways specifying neuronal identity in the spinal
cord. Neuron 31: 203-217.2001.
[35] Lee Sy., Lee YD. et al.. Neural induction with neurogenin1 increases the
therapeutic effects of mesenchymal stem cells in the ischemic brain.
Stem Cells. ;26(9):2217-28. 2008.
[36] Wallis DE, Roessler E, Hehr U, Nanni L Mutations in the
homeodomain of the human SIX3 gene cause holoprosencephaly. Nature
Genet 22: 196-198.1999.
[37] Katsuoka F, Motohashi H, Tamagawa Y. Small Maf compound
mutants display central nervous system neuronal degeneration, aberrant
transcription, and Bach protein mislocalization coincident with
myoclonus and abnormal startle response. Molec Cell Biol 23: 1163-
1174.2003.
[38] Millet S, Campbell K, Epstein DJ. A role for Gbx2 in repression of
Otx2 and positioning the mid/hindbrain organizer. Nature 401: 161-
164.1999.
[39] Brunelli S, Faiella A, Capra V. Germline mutation in the homeobox
gene EMX2 in patients with severe schizencephaly. Nature Genet 12:
94-96.1996.
[40] Marigo V, Roberts DJ, Lee SMK. Cloning, expression, and
chromosomal location of SHH and IHH: two human homologues of the
Drosophila segment polarity gene hedgehog. Genomics 28: 44-51.1995.
[41] Echelard Y, Epstein DJ, St-Jacques B. Sonic hedgehog, a member of a
family of putative signaling molecules, is implicated in the regulation of
CNS polarity. Cell 75: 1417-1430.1993.
[42] Riddle RD, Johnson RL, Laufer E.Sonic hedgehog mediates the
polarizing activity of the ZPA. Cell 75: 1401-1416 1993.
[43] Johnson RL, Laufer E, Riddle , Ectopic expression of Sonic hedgehog
alters dorsal-ventral patterning of somites. Cell 79: 1165-1173.1994.
[44] Heussler HS, Suri M, Young ID. Extreme variability of expression of a
Sonic hedgehog mutation: attention difficulties and holoprosencephaly.
Arch Dis Child 86: 293-296.2002.
[45] Lee J E, Hollenberg SM, Snider L. Conversion of Xenopus ectoderm
into neurons by NeuroD, a basic helix-loop-helix protein. Science 268:
836-844.1995.
[46] Liu M, Pleasure SJ, Collins AE. Loss of BETA2/NeuroD leads to
malformation of the dentate gyrus and epilepsy. Proc Nat. Acad Sci
97: 865-870.2000.
[47] Meyers E N, Lewandoski M, Martin GR An Fgf8 mutant allelic series
generated by Cre- and Flp-mediated recombination. Nat. Genet. 18: 136-
141.1998.
[48] Xiao B, Tu JC, Petralia RS. Homer regulates the association of group 1
metabotropic glutamate receptors with multivalent complexes of homerrelated,
synaptic proteins. Neuron. 21:707-716.1998.
[1] Callaerts P, Halder G, and Gehring WJ. PAX-6 in development and
evolution. Annu. Rev. Neurosci. 20: 483-532. 1997.
[2] Chi N, Epstein JA. Getting Your Pax Straight: Pax proteins in
development disease. Trands Genet 18: 41-47. 2002.
[3] Tomarev SI. Pax-6, eyes absent, and Prox 1 in eye development. Int J
Dev Biol 41: 835-842. 1997.
[4] Halder G, Callaerts P, Gehring W. Induction of ectopic eyes by targeted
expression of the eyeless gene in Drosophila. Science 267: 1788-1792.
1995.
[5] Chow RL, Altmann CR, Lang AR. Pax6 induces ectopic eyes in a
vertebrate. Development 126: 4213-4222.1999.
[6] Duncan MK, Kozmik Z, Cveklova K. Overexpression of PAX6(5a) in
lens fiber cells results in cataract and upregulation of (alpha)5(beta)1
integrin expression. J Cell Sci 113: 3173-3185. 2000.
[7] Cvekl A, Piatigorsky J. Lens development and crystallin gene
expression: many roles for Pax-6. BioEssays 18: 621-630. 1996.
[8] Van Raamsdonk CD, Tilghman SM. Dosage requirement and allelic
expression of PAX6 during lens placode formation. Development 127:
5439-5448. 2000.
[9] Ashery-Padan R, Marquardt T, Zhou X. Pax6 activity in the lens
primordium is required for lens formation and for correct placement of a
single retina in the eye. Genes Dev 14: 2701-2711. 2000.
[10] Larsson LI, St-Onge L, Hougaard. Pax 4 and 6 regulate gastrointestinal
endocrine cell development. Mech. Dev 79: 153-159. 1998.
[11] St-Onge L, Sosa-Pineda B, Chowdhury K. Pax6 is required for
differentiation of glucagon-producing ╬▒-cells in mouse pancreas. Nature
387: 406-409. 1997.
[12] Sander M, Neubuser A, Kalamaras J. Genetic analysis reveals that
PAX6 is required for normal transcription of pancreatic hormone genes
and islet development. Genes Dev 11: 1662-1673. 1997.
[13] Muzio L, Mallamaci A. Emx1, Emx2 and Pax6 in Specification,
Regionalization and Arealization of the Cerebral Cortex. Cereb Cortex
13: 641-647. 2003.
[14] Kimura J, Suda Y, Kurokawa D Emx2 and Pax6 Function in
Cooperation with Otx2 and Otx1 to Develop Caudal Forebrain
Primordium That Includes Future Archipallium. Development 25: 5097-
5108. 2005.
[15] Yun K, Poter S, Rubenstein LR Gsh2 and Pax6 play complementary
roles in dorsoventral patterning of the mammalian telencephalon.
Development 128: 193-205. 2001.
[16] van Heyningen V, Williamson KA Pax6 in sensory development. Hum.
Mol. Genet 11: 1161-1167. 2000.
[17] Kimura J, Suda Y, Kurokawa D. Emx2 and Pax6 Function in
Cooperation with Otx2 and Otx1 to Develop Caudal Primordium That
Includes Future Archipallium. J. Neurosci 25: 5097-5108. 2005.
[18] Lengler J, Bittner T, Munster D. Agonistic and Antagonistic Action of
AP2, Msx2, Pax6, Prox1 and Six3 in the Regulation of Sox2 Expression.
Ophthalmic Res 37: 301-309. 2005.
[19] Plosk JE, Shamsher MK, Radu A. Paired-Type Homeodomain
Transcription Factors Are Imported into the Nucleus by Karyopherin 13.
MCB 24: 4824-4834. 2004.
[20] Hussain MA, Habener JF. Glucagon Gene Transcription Activation
Mediated by Synergistic Interactions of pax-6 and cdx-2 with the p300
Co-activator. JBC 41: 28950-28957. 1999.
[21] Planque N, Leconte L, Coquelle FM. Interaction of Maf Transcription
Factors with Pax-6 Results in Synergistic Activation of the Glucagon
Promoter. JBC 276: 35751-35760. 2001.
[22] Yang Y, Stopka T, Golestaneh N. Regulation of aA-crystallin via Pax6,
c-Maf, CREB and a broad domain of lens-specific chromatin. EMBO
25: 2107-2118. 2006.
[23] Cvekl A., Kashanchi F, Brady JN. Pax-6 Interactions with TATA-Box-
Binding Protein and Retinoblastoma Protein. Ophthalmol Vis Sci. 40:
1343-1350. 1999.
[24] Leconte L, Lecoin L, Martin P. Pax6 Interacts with cVax and Tbx5 to
Establish the Dorsoventral Boundary of the Developing Eye. JBC 279:
47272-47277. 2004.
[25] Kamachi Y, Uchikawa M, Tanouchi A. Pax6 and SOX2 form a co-
DNA-binding partner complex that regulates initiation of lens
development. Genes & Dev15: 1272-1286. 2001.
[26] Cooper ST, Hanson IM. A screen for proteins that interact with PAX6:
C-terminal mutations disrupt interaction with HOMER3, DNCL1 and
TRIM11. BMC Genetics 1471-2156/6/43. 2005.
[27] Sivak JM, West-Mays JA, Yee A. Transcription Factors Pax6 and AP-
2╬▒ Interact To Coordinate Corneal Epithelial Repair by Controlling
Expression of Matrix Metalloproteinase Gelatinase B. MCB 24: 245-
257. 2004.
[28] Planque N, Leconte L, Coquelle FM, Martin P, Saule S. Specific Pax-
6/Microphthalmia Transcription Factor Interactions Involve Their DNAbinding
Domains and Inhibit Transcriptional Properties of Both
Proteins. JBC 276: 29330-29337. 2001.
[29] Mikkola I, Bruun JA, Holm T, Johanseni T. Superactivation of Pax6-
mediated Transactivation from Paired Domain-binding Sites by DNAindependent
Recruitment of Different Homeodomain Proteins. JBC 276:
4109-4118. 2000.
[30] PIP: Potential Interactions of Proteins.
http://bmm.cancerresearchuk.org/~pip/.
[31] Jonsson PF, Cavanna T, Zicha D. Cluster analysis of networks
generated through homology: automatic identification of important
protein communities involved in cancer metastasis. BMC Bioinformatics
1471-2105-7-2. 2006.
[32] STRING: http://string.embl.de/newstring_cgi/show_network_section.pl
[33] Sommer L, Ma Q, Anderson DJ. Neurogenins, a novel family of
atonal-related bHLH transcription factors, are putative mammalian
neuronal determination genes that reveal progenitor cell heterogeneity in
the developing CNS and PNS. Molec. Cell. Neurosci. 8: 221-241.1996.
[34] Scardigli R, Schuurmans C, Gradwohl G. Crossregulation between
neurogenin2 and pathways specifying neuronal identity in the spinal
cord. Neuron 31: 203-217.2001.
[35] Lee Sy., Lee YD. et al.. Neural induction with neurogenin1 increases the
therapeutic effects of mesenchymal stem cells in the ischemic brain.
Stem Cells. ;26(9):2217-28. 2008.
[36] Wallis DE, Roessler E, Hehr U, Nanni L Mutations in the
homeodomain of the human SIX3 gene cause holoprosencephaly. Nature
Genet 22: 196-198.1999.
[37] Katsuoka F, Motohashi H, Tamagawa Y. Small Maf compound
mutants display central nervous system neuronal degeneration, aberrant
transcription, and Bach protein mislocalization coincident with
myoclonus and abnormal startle response. Molec Cell Biol 23: 1163-
1174.2003.
[38] Millet S, Campbell K, Epstein DJ. A role for Gbx2 in repression of
Otx2 and positioning the mid/hindbrain organizer. Nature 401: 161-
164.1999.
[39] Brunelli S, Faiella A, Capra V. Germline mutation in the homeobox
gene EMX2 in patients with severe schizencephaly. Nature Genet 12:
94-96.1996.
[40] Marigo V, Roberts DJ, Lee SMK. Cloning, expression, and
chromosomal location of SHH and IHH: two human homologues of the
Drosophila segment polarity gene hedgehog. Genomics 28: 44-51.1995.
[41] Echelard Y, Epstein DJ, St-Jacques B. Sonic hedgehog, a member of a
family of putative signaling molecules, is implicated in the regulation of
CNS polarity. Cell 75: 1417-1430.1993.
[42] Riddle RD, Johnson RL, Laufer E.Sonic hedgehog mediates the
polarizing activity of the ZPA. Cell 75: 1401-1416 1993.
[43] Johnson RL, Laufer E, Riddle , Ectopic expression of Sonic hedgehog
alters dorsal-ventral patterning of somites. Cell 79: 1165-1173.1994.
[44] Heussler HS, Suri M, Young ID. Extreme variability of expression of a
Sonic hedgehog mutation: attention difficulties and holoprosencephaly.
Arch Dis Child 86: 293-296.2002.
[45] Lee J E, Hollenberg SM, Snider L. Conversion of Xenopus ectoderm
into neurons by NeuroD, a basic helix-loop-helix protein. Science 268:
836-844.1995.
[46] Liu M, Pleasure SJ, Collins AE. Loss of BETA2/NeuroD leads to
malformation of the dentate gyrus and epilepsy. Proc Nat. Acad Sci
97: 865-870.2000.
[47] Meyers E N, Lewandoski M, Martin GR An Fgf8 mutant allelic series
generated by Cre- and Flp-mediated recombination. Nat. Genet. 18: 136-
141.1998.
[48] Xiao B, Tu JC, Petralia RS. Homer regulates the association of group 1
metabotropic glutamate receptors with multivalent complexes of homerrelated,
synaptic proteins. Neuron. 21:707-716.1998.
@article{"International Journal of Biological, Life and Agricultural Sciences:51818", author = "Ratnakar Tripathi and Rajnikant Mishra", title = "In Silico Analysis of Pax6 Interacting Proteins Indicates Missing Molecular Links in Development of Brain and Associated Disease", abstract = "The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.
", keywords = "Interacting Proteins, Pax6, PIP, STRING", volume = "3", number = "12", pages = "555-7", }
