|Coordinate||109,020,954 bp (GRCm38)|
|Base Change||C ⇒ T (forward strand)|
|Gene Name||tubby bipartite transcription factor|
|Chromosomal Location||108,950,338-109,034,460 bp (+)|
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Tubby family of bipartite transcription factors. The encoded protein may play a role in obesity and sensorineural degradation. The crystal structure has been determined for a similar protein in mouse, and it functions as a membrane-bound transcription regulator that translocates to the nucleus in response to phosphoinositide hydrolysis. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants exhibit a late-developing obesity with hyperinsulinemia, retinal degeneration, and hearing loss associated with death of both outer and inner hair cells. [provided by MGI curators]
|Amino Acid Change||Arginine changed to Stop codon|
|Institutional Source||Beutler Lab|
|Gene Model||predicted gene model for protein(s): [ENSMUSP00000033341 †] [ENSMUSP00000113580 †] [ENSMUSP00000146894 †] † probably from a misspliced transcript|
AA Change: R60*
|Predicted Effect||probably null|
AA Change: R14*
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Meta Mutation Damage Score||0.9755|
|Is this an essential gene?||Non Essential (E-score: 0.000)|
|Candidate Explorer Status||CE: good candidate; human score: -0.5; ML prob: 0.454|
Linkage Analysis Data
|Alleles Listed at MGI|
|Mode of Inheritance||Autosomal Recessive|
|Local Stock||Live Mice, Sperm, gDNA|
|Last Updated||2019-09-04 9:46 PM by Bruce Beutler|
|Record Created||2015-01-08 11:57 PM by Jeff SoRelle|
The troy phenotype was identified in N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R1395, some of which showed increased body weights compared to wild-type controls (Figure 1).
|Nature of Mutation|
Whole exome HiSeq sequencing of the G1 grandsire identified 66 mutations. The increased body weight phenotype was linked to a mutation in Tub: a C to T transition at base pair 109,020,954 (v38) on chromosome 7, or base pair 10,075 in the GenBank genomic region NC_000073 encoding Tub. Linkage was found with a recessive model of inheritance (P = 1.826 x 10-5), wherein 8 variant homozygotes departed phenotypically from 14 homozygous reference mice and 16 heterozygous mice.
The mutation corresponds to residue 399 in the mRNA sequence NM_021885 within exon 3 of 12 total exons.
The mutated nucleotide is indicated in red and converts arginine (R) 60 of the Tub protein to a premature stop codon (R60*).
Tub encodes Tub, a member of the Tub family of proteins that also includes the tubby-like proteins (TULP) TULP1, TULP2, and TULP3 (Figure 3). The N-termini of the Tub family of proteins are variable, but resemble activation domains from known transcription factors (1). The N-terminus of Tub is able to activate GLUT4 reporter constructs, but the putative targets of Tub are unknown. The N-terminus directs the localization of Tub to the nucleus (2). Tub has four nuclear localization signal (NLS) consensus sequences: K39KKR, P56RSRRAR, P123RKEKKG, and K302RKK (where K is lysine, R is arginine, E is glutamic acid, G is glycine, A is alanine, P is proline, and S is serine) (1). In addition, the N-terminus of Tub has a motif similar to that in TULP3 which binds to the core subunits of the ciliary intraflagellar transport complex-A (IFT-A) (3). Five minimal phagocytic determinants (K/R(X)(1-2)KKK) at the N-terminus of Tub bind MerTK (4).
The C-terminal tubby domain (amino acids 257-499) of Tub is highly conserved between mouse and human as well as between the members of the Tub protein family (5;6). The C-terminus of mouse Tub (amino acids 243-505) has been crystallized (Figure 4; PDB:1I7E) (1). A central hydrophobic helix at the C-terminus traverses the interior of a closed 12-stranded ∼18 Å β-barrel (1). The β-barrel has an alternating up-down nearest-neighbor topology (1). There is a three-stranded β-sheet (designated as 9A, 9B, and 9C) between strands 9 and 10 of the barrel (1). Also, four helices (designated as H4, H6A, H6B, and H8) were in the corresponding loop regions between strands of the main barrel (1). A helix, helix H10, caps the top of the β-barrel and helix H12 traverses the inside of the barrel (1). The K302RKK putative NLS is at the base of β-strand 3 (1). The C-terminus binds to the plasma membrane through an association between the C-terminus and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) (2). β-strands 4, 5, and 6 and helix 6A form a pocket that associates with l-α-glycerophospho-d-myo-inositol 4,5-bisphosphate (GPMI-P2), an analog of the head group from PtdIns(4,5)P2 (2). Lys330 coordinates the interaction between the 4- and 5-phosphates, while Arg332 stabilizes the 4-phosphate. Arg363 coordinates with the inositol ring at the 3-position. Asn310 associates with the oxygen atoms at the 4- and 5-phosphoester positions (2). The 54 C-terminal amino acids of Tub interact with apoptotic cells during MerTK-dependent apoptosis (4).
In hypothalamic nuclei, the insulin receptor directly induces Tub tyrosine phosphorylation. Leptin-associated signaling (see the record for Potbelly and Business_class) also induces Tub phosphorylation through the kinase JAK2 (7). The phosphorylation of Tub is regulated by nutritional status: phosphorylation is decreased during fasting and increased after refeeding (7).
The troy mutation results in a premature stop codon at amino acid 60 near the N-terminus of Tub. Arg60 is within one of the putative NLS sequences in Tub. Expression and localization of Tubtroy has not been examined.
In the mouse, Tub is expressed in the central and peripheral nervous systems in differentiating neurons at embryonic day (E) 9.5 (8). At E13.5, Tub is expressed in most neuronal structures including the roof of the midbrain, the roof of the telencephalic vesicles and the striatum as well as in the olfactory neuronal structures, neural retina, and the spiral ganglion of the inner ear apparatus (8). In the adult mouse, Tub is highly expressed in the brain, eye, and testis; expression was not detect in the kidney, liver, lung, or spleen (1;5;6;8;9). Tub is moderately expressed in the large intestine, skeletal muscle, and heart and expressed at low levels in adipose, small intestine, lung, ovary, thymus, and liver (8;9). Within the brain, Tub is expressed primarily in the hippocampus, hypothalamus, and cortex; Tub is weakly expressed throughout the rest of the brain (5;8). Within the hypothalamus, Tub is highly expressed in the paraventricular, ventromedial, and arcuate nuclei (5;7).
Tub localizes to the plasma membrane, but translocates to the nucleus in neural cells upon activation of the G-protein, Gαq, as well as after insulin, leptin, and acetylcholine exposure (2;7). Gαq releases Tub from the plasma membrane by phospholipase C–β (PLC-β)–mediated hydrolysis of PtdIns(4,5)P2, and Tub subsequently translocates to the nucleus (2).
Tub has several putative functions (Figure 5). Tub is a downstream effector of G-protein coupled receptors (GPCRs) that signal through the Gq (Gαq and Gα11) subclass of Gα proteins (e.g., the serotonin receptor 5HT2c) (2). Receptor-mediated activation of Gαq releases Tub from the plasma membrane through the action of PLCβ. Once Tub translocates to the nucleus, the second messenger inositol 1,4,5-triphosphate (IP3) is released. The translocation of Tub to the nucleus upon 5HT2c activation points to a putative function as a transcription factor (1). Leptin- or insulin-induced Tub translocation to the nucleus results in altered expression of Pomc, Trh, Mch, and orexin mRNAs (7). Tub is proposed to bind double-stranded DNA through its C-terminus (10); however the transcriptional targets of Tub are unknown. Tub binds strongly with double-stranded DNA, but poorly with single-stranded DNA (1).
Tub has been identified as an adaptor protein downstream of the insulin receptor that links the insulin receptor to SH2-containing proteins such as Abl, lymphocyte-specific protein-tyrosine kinase (Lck; see the record for iconoclast), and PLCγ (see the record for queen) (11). Tub is a substrate of JAK2, a protein involved in leptin receptor signaling (see the record for Business_class). Tub has also been identified as a ligand for MerTK and mediates MerTK-dependent phagocytosis (4). Phagocytosis ligands mediate the selection of extracellular cargos and initiate engulfment. MerTK is a phagocytic receptor that functions in retinal homeostasis and prevention of autoimmunity (12;13). Tub induces MerTK autophosphorylation and subsequent activation. MerTK activation promotes non-muscle myosin II redistribution in retinal pigment epithelium (RPE) cells and colocalization with phagocytosed cargos (4). Tub forms heterodimers or heteroligmers with Tulp1 to synergistically facilitate RPE phagocytosis (14). Tub is also essential for MerTK-mediated microglial phagocytosis, indicating a putative function for Tub in CNS homeostasis and innate immune balance (15). Tub also functions in an endocytic pathway to regulate fat storage (16;17).
Tub regulates trafficking of select GPCRs in the neuronal and sensory cilia including rhodopsin (see the record for Bemr3) in the rod cell photoreceptor as well as melanin-concentrating hormone receptor 1 (MCHR1) and somatostatin receptor subtype 3 (SSTR3) in the brain. Olfactory cilia and the localization of olfactory GPCRs are not regulated by Tub (18). Tub is not necessary for ciliogenesis and/or maintenance or for general protein trafficking to the cilia (18). The association of Tub with membrane phosphoinositides is proposed to facilitate Tub-mediated trafficking of ciliary GPCRs [reviewed in (19)].
Tub mutant mouse models have been characterized including the tubby strain and a Tub knockout (Tub-/-) strain. The tubby strain has a spontaneous G to T transversion in the donor splice site of exon 11 in Tub, resulting in a frame-shift and coding of 25 aberrant amino acids at the C-terminus of Tub (5;20). Homozygous tubby mice and Tub-/- mice have late-onset weight gain starting at 8-12 weeks of age (at ~19 weeks of age the weight of Tub mutant mice is approximately double of wild-type mice). The tubby mice also have a gradual increase in their plasma insulin levels and food intake, but do not develop overt diabetes. The tubby mice have reduced energy expenditure (21;22). Triglyceride levels in the tubby mice were elevated approximately 1.5-fold compared to wild-type mice (23). In addition, the levels of high-density lipoprotein (HDL) cholesterol were mildly elevated in the male tubby mice compared to wild-type mice; female tubby mice did not exhibit a significant change in HDL levels (23). The tubby mice become infertile after becoming significantly obese; sperm cell motile function was normal in tubby (24). The tubby mice have a low respiratory exchange ratio (i.e., respiratory quotient) that is accompanied by altered metabolism in the liver (i.e., higher excretion of ketone bodies and accumulation of glycogen) and a failure to induce glucose-6-phosphate dehydrogenase, an enzyme in the pentose phosphate pathway that supplies NAPDH for de novo fatty acid synthesis and glutathione reduction (22). The tubby mice have altered expression of pro-opiomelanocortin and neuropeptide Y, factors involved in energy regulation and metabolism (25), and the thyroid hormone receptor, essential for growth and metabolism regulation, is a putative target of Tub-mediated transcription regulation (26). The tubby mice also exhibit progressive retinal and cochlear degeneration due to apoptosis of retinal (i.e., photoreceptor cells) and cochlear neurosensory cells (i.e., organ of Corti and ganglian cells in the basal end of the cochlea), respectively (24;27-30). At P17-21, there is extracellular accumulation of rhodopsin vesicles in the interphotoreceptor space surrounding the photoreceptor inner segments in the tubby retina (30). In addition, the light/dark compartmentalization of arrestin and transducin, two phototransduction proteins, was disrupted in the tubby mice (30). Tubby mice raised in darkness exhibited less photoreceptor loss than those raised in bright cyclic light, indicating that phototransduction regulates photoreceptor cell death in the tubby mice (30).
TUB is a candidate gene for influencing body weight in humans (31). In addition, mutations in TUB have been linked to body composition and eating behavior in middle-aged women (32). Homozygous mutations in TUB have been linked to retinal dystrophy, night blindness, decreased visual acuity, and early-onset obesity (33).
The link between the putative functions of Tub and the phenotypes exhibited by the tubby mice has not been determined; however a putative role of Tub (and the TULP proteins) in regulation of ciliary neurosensory functions by regulating the localization of ciliary proteins has been proposed (34). The high expression of Tub in the hypothalamus indicates that Tub may function in neuroendocrine control of satiety and metabolism. The obesity phenotype of the troy mice mimics that observed in the tubby mice indicates a loss of function of Tub. Other Tub-associated phenotypes (e.g., retinal degeneration, hearing loss, and elevated insulin levels) have not been examined in troy.
1) 94°C 2:00
The following sequence of 477 nucleotides is amplified (chromosome 7, + strand):
1 gctgacagct agtcagaaga tgccaataac atgagtcctg acccagacag ggtgggctag
Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.
1. Boggon, T. J., Shan, W. S., Santagata, S., Myers, S. C., and Shapiro, L. (1999) Implication of Tubby Proteins as Transcription Factors by Structure-Based Functional Analysis. Science. 286, 2119-2125.
2. Santagata, S., Boggon, T. J., Baird, C. L., Gomez, C. A., Zhao, J., Shan, W. S., Myszka, D. G., and Shapiro, L. (2001) G-Protein Signaling through Tubby Proteins. Science. 292, 2041-2050.
3. Mukhopadhyay, S., Wen, X., Chih, B., Nelson, C. D., Lane, W. S., Scales, S. J., and Jackson, P. K. (2010) TULP3 Bridges the IFT-A Complex and Membrane Phosphoinositides to Promote Trafficking of G Protein-Coupled Receptors into Primary Cilia. Genes Dev. 24, 2180-2193.
4. Caberoy, N. B., Zhou, Y., and Li, W. (2010) Tubby and Tubby-Like Protein 1 are New MerTK Ligands for Phagocytosis. EMBO J. 29, 3898-3910.
5. Kleyn, P. W., Fan, W., Kovats, S. G., Lee, J. J., Pulido, J. C., Wu, Y., Berkemeier, L. R., Misumi, D. J., Holmgren, L., Charlat, O., Woolf, E. A., Tayber, O., Brody, T., Shu, P., Hawkins, F., Kennedy, B., Baldini, L., Ebeling, C., Alperin, G. D., Deeds, J., Lakey, N. D., Culpepper, J., Chen, H., Glucksmann-Kuis, M. A., Carlson, G. A., Duyk, G. M., and Moore, K. J. (1996) Identification and Characterization of the Mouse Obesity Gene Tubby: A Member of a Novel Gene Family. Cell. 85, 281-290.
6. North, M. A., Naggert, J. K., Yan, Y., Noben-Trauth, K., and Nishina, P. M. (1997) Molecular Characterization of TUB, TULP1, and TULP2, Members of the Novel Tubby Gene Family and their Possible Relation to Ocular Diseases. Proc Natl Acad Sci U S A. 94, 3128-3133.
7. Prada, P. O., Quaresma, P. G., Caricilli, A. M., Santos, A. C., Guadagnini, D., Morari, J., Weissmann, L., Ropelle, E. R., Carvalheira, J. B., Velloso, L. A., and Saad, M. J. (2013) Tub has a Key Role in Insulin and Leptin Signaling and Action in Vivo in Hypothalamic Nuclei. Diabetes. 62, 137-148.
8. Sahly, I., Gogat, K., Kobetz, A., Marchant, D., Menasche, M., Castel, M., Revah, F., Dufier, J., Guerre-Millo, M., and Abitbol, M. M. (1998) Prominent Neuronal-Specific Tub Gene Expression in Cellular Targets of Tubby Mice Mutation. Hum Mol Genet. 7, 1437-1447.
9. Noben-Trauth, K., Naggert, J. K., North, M. A., and Nishina, P. M. (1996) A Candidate Gene for the Mouse Mutation Tubby. Nature. 380, 534-538.
10. Ikeda, A., Nishina, P. M., and Naggert, J. K. (2002) The Tubby-Like Proteins, a Family with Roles in Neuronal Development and Function. J Cell Sci. 115, 9-14.
11. Kapeller, R., Moriarty, A., Strauss, A., Stubdal, H., Theriault, K., Siebert, E., Chickering, T., Morgenstern, J. P., Tartaglia, L. A., and Lillie, J. (1999) Tyrosine Phosphorylation of Tub and its Association with Src Homology 2 Domain-Containing Proteins Implicate Tub in Intracellular Signaling by Insulin. J Biol Chem. 274, 24980-24986.
12. D'Cruz, P. M., Yasumura, D., Weir, J., Matthes, M. T., Abderrahim, H., LaVail, M. M., and Vollrath, D. (2000) Mutation of the Receptor Tyrosine Kinase Gene Mertk in the Retinal Dystrophic RCS Rat. Hum Mol Genet. 9, 645-651.
13. Seitz, H. M., Camenisch, T. D., Lemke, G., Earp, H. S., and Matsushima, G. K. (2007) Macrophages and Dendritic Cells use Different Axl/Mertk/Tyro3 Receptors in Clearance of Apoptotic Cells. J Immunol. 178, 5635-5642.
14. Caberoy, N. B., Alvarado, G., and Li, W. (2012) Tubby Regulates Microglial Phagocytosis through MerTK. J Neuroimmunol. 252, 40-48.
15. Caberoy, N. B. (2014) Synergistic Interaction of Tubby and Tubby-Like Protein 1 (Tulp1). Adv Exp Med Biol. 801, 503-509.
16. Mukhopadhyay, A., Pan, X., Lambright, D. G., and Tissenbaum, H. A. (2007) An Endocytic Pathway as a Target of Tubby for Regulation of Fat Storage. EMBO Rep. 8, 931-938.
17. Ashrafi, K., Chang, F. Y., Watts, J. L., Fraser, A. G., Kamath, R. S., Ahringer, J., and Ruvkun, G. (2003) Genome-Wide RNAi Analysis of Caenorhabditis Elegans Fat Regulatory Genes. Nature. 421, 268-272.
18. Sun, X., Haley, J., Bulgakov, O. V., Cai, X., McGinnis, J., and Li, T. (2012) Tubby is Required for Trafficking G Protein-Coupled Receptors to Neuronal Cilia. Cilia. 1, 21-2530-1-21.
19. Mukhopadhyay, S., and Jackson, P. K. (2013) Cilia, Tubby Mice, and Obesity. Cilia. 2, 1-2530-2-1. eCollection 2013.
20. Coleman, D. L., and Eicher, E. M. (1990) Fat (Fat) and Tubby (Tub): Two Autosomal Recessive Mutations Causing Obesity Syndromes in the Mouse. J Hered. 81, 424-427.
21. Stubdal, H., Lynch, C. A., Moriarty, A., Fang, Q., Chickering, T., Deeds, J. D., Fairchild-Huntress, V., Charlat, O., Dunmore, J. H., Kleyn, P., Huszar, D., and Kapeller, R. (2000) Targeted Deletion of the Tub Mouse Obesity Gene Reveals that Tubby is a Loss-of-Function Mutation. Mol Cell Biol. 20, 878-882.
22. Ohlemiller, K. K., Hughes, R. M., Mosinger-Ogilvie, J., Speck, J. D., Grosof, D. H., and Silverman, M. S. (1995) Cochlear and Retinal Degeneration in the Tubby Mouse. Neuroreport. 6, 845-849.
23. Ohlemiller, K. K., Hughes, R. M., Lett, J. M., Ogilvie, J. M., Speck, J. D., Wright, J. S., and Faddis, B. T. (1997) Progression of Cochlear and Retinal Degeneration in the Tubby (rd5) Mouse. Audiol Neurootol. 2, 175-185.
24. Ohlemiller, K. K., Mosinger Ogilvie, J., Lett, J. M., Hughes, R. M., LaRegina, M. C., and Olson, L. M. (1998) The Murine Tub (rd5) Mutation is Not Associated with a Primary Axonemal Defect. Cell Tissue Res. 291, 489-495.
25. Kong, L., Li, F., Soleman, C. E., Li, S., Elias, R. V., Zhou, X., Lewis, D. A., McGinnis, J. F., and Cao, W. (2006) Bright Cyclic Light Accelerates Photoreceptor Cell Degeneration in Tubby Mice. Neurobiol Dis. 21, 468-477.
26. Nishina, P. M., Lowe, S., Wang, J., and Paigen, B. (1994) Characterization of Plasma Lipids in Genetically Obese Mice: The Mutants Obese, Diabetes, Fat, Tubby, and Lethal Yellow. Metabolism. 43, 549-553.
27. Wang, Y., Seburn, K., Bechtel, L., Lee, B. Y., Szatkiewicz, J. P., Nishina, P. M., and Naggert, J. K. (2006) Defective Carbohydrate Metabolism in Mice Homozygous for the Tubby Mutation. Physiol Genomics. 27, 131-140.
28. Guan, X. M., Yu, H., and Van der Ploeg, L. H. (1998) Evidence of Altered Hypothalamic Pro-Opiomelanocortin/ Neuropeptide Y mRNA Expression in Tubby Mice. Brain Res Mol Brain Res. 59, 273-279.
29. Koritschoner, N. P., Alvarez-Dolado, M., Kurz, S. M., Heikenwalder, M. F., Hacker, C., Vogel, F., Munoz, A., and Zenke, M. (2001) Thyroid Hormone Regulates the Obesity Gene Tub. EMBO Rep. 2, 499-504.
30. Coyle, C. A., Strand, S. C., and Good, D. J. (2008) Reduced Activity without Hyperphagia Contributes to Obesity in Tubby Mutant Mice. Physiol Behav. 95, 168-175.
31. Shiri-Sverdlov, R., Custers, A., van Vliet-Ostaptchouk, J. V., van Gorp, P. J., Lindsey, P. J., van Tilburg, J. H., Zhernakova, S., Feskens, E. J., van der, A. D. L., Dolle, M. E., van Haeften, T. W., Koeleman, B. P., Hofker, M. H., and Wijmenga, C. (2006) Identification of TUB as a Novel Candidate Gene Influencing Body Weight in Humans. Diabetes. 55, 385-389.
32. van Vliet-Ostaptchouk, J. V., Onland-Moret, N. C., Shiri-Sverdlov, R., van Gorp, P. J., Custers, A., Peeters, P. H., Wijmenga, C., Hofker, M. H., and van der Schouw, Y. T. (2008) Polymorphisms of the TUB Gene are Associated with Body Composition and Eating Behavior in Middle-Aged Women. PLoS One. 3, e1405.
33. Borman, A. D., Pearce, L. R., Mackay, D. S., Nagel-Wolfrum, K., Davidson, A. E., Henderson, R., Garg, S., Waseem, N. H., Webster, A. R., Plagnol, V., Wolfrum, U., Farooqi, I. S., and Moore, A. T. (2014) A Homozygous Mutation in the TUB Gene Associated with Retinal Dystrophy and Obesity. Hum Mutat. 35, 289-293.
|Science Writers||Anne Murray|
|Authors||Jeff SoRelle, Zhe Chen|