CTBP2 explained

C-terminal-binding protein 2 also known as CtBP2 is a protein that in humans is encoded by the CTBP2 gene.^{[1] [2] [3]}

Function

The CtBPs - CtBP1 and CtBP2 in mammals - are among the best characterized transcriptional corepressors.^[4] They typically turn their target genes off. They do this by binding to sequence-specific DNA-binding proteins that carry a short motif of the general form Proline-Isoleucine-Aspartate-Leucine-Serine (the PIDLS motif). They then recruit histone modifying enzymes, histone deacetylases, histone methylases and histone demethylases. These enzymes are thought to work together to remove activating and add repressive histone marks. For example, histone deacetylase 1 (HDAC1) and HDAC2 can remove the activating mark histone 3 acetyl lysine 9 (H3K9Ac), then the histone methylase G9a can add methyl groups, while the histone demethylase lysine specific demethylase 1 (LSD1) can remove the activating mark H3K4me.^[5]

The CtBPs bind to many different DNA-binding proteins and also bind to co-repressors that are themselves bound to DNA-binding proteins, such as Friend of GATA (Fog).^[6] CtBPs can also dimerize and multimerize to bridge larger transcriptional complexes. They appear to be primarily scaffold proteins that allow the assembly of gene repression complexes.

One interesting aspect of CtBPs is their ability to bind to NADH and to a lesser extent NAD⁺. It has been proposed that this will enable them to sense the metabolic status of the cell and to regulate genes in response to changes in the NADH/NAD⁺ ratio. Accordingly, CtBPs have been found to be important in fat biology, binding to key proteins such as PRDM16, NRIP, and FOG2.^[7]

The full functional roles of CtBP proteins in mammals have been difficult to evaluate because of partial redundancy between CtBP1 and CtBP2.^[8] Similarly, the early lethality of the CtBP2 knockout and of double knockout mice has precluded detailed analysis of the cellular effects of deleting these proteins. Important results have emerged from model organisms where there is only a single CtBP gene. In Drosophila CtBP is involved in development and in circadian rhythms.^[9] In the worm C. elegans CtBP is involved in life span.^[10] Both circadian rhythms and life span appear to be linked to metabolism supporting the role for CtBPs in metabolic sensing.

The mammalian CtBP2 gene produces alternative transcripts encoding two distinct proteins. In addition to the transcriptional repressor (corepressor) discussed above, there is a longer isoform that is a major component of specialized synapses known as synaptic ribbons. Both proteins contain a NAD⁺ binding domain similar to NAD⁺-dependent 2-hydroxyacid dehydrogenases. A portion of the 3'-untranslated region was used to map this gene to chromosome 21q21.3; however, it was noted that similar loci elsewhere in the genome are likely. Blast analysis shows that this gene is present on chromosome 10.

Alternative Promoter Usage

In the vertebrate retina, the CtBP2 gene is transcribed from alternative promoters during retinal development yielding the CTBP2 transcriptional coregulator as well as the larger ribbon synapse scaffolding protein RIBEYE. ^[11] The multi use functionality of the CtBP2 locus appears to be conserved between avian and primate retinae with production of the RIBEYE mRNA being developmentally delayed by an epigenetic silencing mechanism. ^[12] In the developing human retina, transcription of the RIBEYE mRNA isoform is epigenetically regulated by DNA methylation. DNA sequences comprising the proximal RIBEYE promoter are enriched for DNA methylation and delay transcription of this isoform, possibly by inhibiting binding of the Cone-rod homeobox (CRX) transcription factor. Global transcript analysis of human pluripotent stem cell (hPSC)-derived 3D retinal organoids demonstrates early and persistent expression of the CTPB2 isoform followed by delayed RIBEYE expression in the developing human eye. ^[13]

Interactions

CTBP2 has been shown to interact with:

• FHL3,^[14]
• KLF3,^[14]
• KLF8,^[15]
• Mdm2,^[16]
• NRIP1,^{[17] [18]}
• SOX6,^[19] and
• ZFPM2.^[20]

Further reading

• Schaeper U, Boyd JM, Verma S, Uhlmann E, Subramanian T, Chinnadurai G . Molecular cloning and characterization of a cellular phosphoprotein that interacts with a conserved C-terminal domain of adenovirus E1A involved in negative modulation of oncogenic transformation . Proc. Natl. Acad. Sci. U.S.A. . 92 . 23 . 10467–71 . November 1995 . 7479821 . 40632 . 10.1073/pnas.92.23.10467 . 1995PNAS...9210467S . free .
• Sewalt RG, Gunster MJ, van der Vlag J, Satijn DP, Otte AP . C-Terminal binding protein is a transcriptional repressor that interacts with a specific class of vertebrate Polycomb proteins . Mol. Cell. Biol. . 19 . 1 . 777–87 . January 1999 . 9858600 . 83934 . 10.1128/MCB.19.1.777.
• Furusawa T, Moribe H, Kondoh H, Higashi Y . Identification of CtBP1 and CtBP2 as corepressors of zinc finger-homeodomain factor deltaEF1 . Mol. Cell. Biol. . 19 . 12 . 8581–90 . December 1999 . 10567582 . 84984 . 10.1128/mcb.19.12.8581.
• Yu X, Baer R . Nuclear localization and cell cycle-specific expression of CtIP, a protein that associates with the BRCA1 tumor suppressor . J. Biol. Chem. . 275 . 24 . 18541–9 . June 2000 . 10764811 . 10.1074/jbc.M909494199 . free .
• Schmitz F, Königstorfer A, Südhof TC . RIBEYE, a component of synaptic ribbons: a protein's journey through evolution provides insight into synaptic ribbon function . Neuron . 28 . 3 . 857–72 . December 2000 . 11163272 . 10.1016/S0896-6273(00)00159-8 . 15695695 . free .
• Valenta T, Lukas J, Korinek V . HMG box transcription factor TCF-4's interaction with CtBP1 controls the expression of the Wnt target Axin2/Conductin in human embryonic kidney cells . Nucleic Acids Res. . 31 . 9 . 2369–80 . May 2003 . 12711682 . 154232 . 10.1093/nar/gkg346 .
• Brandenberger R, Wei H, Zhang S, Lei S, Murage J, Fisk GJ, Li Y, Xu C, Fang R, Guegler K, Rao MS, Mandalam R, Lebkowski J, Stanton LW . Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation . Nat. Biotechnol. . 22 . 6 . 707–16 . June 2004 . 15146197 . 10.1038/nbt971 . 27764390 .
• Alpatov R, Munguba GC, Caton P, Joo JH, Shi Y, Shi Y, Hunt ME, Sugrue SP . Nuclear speckle-associated protein Pnn/DRS binds to the transcriptional corepressor CtBP and relieves CtBP-mediated repression of the E-cadherin gene . Mol. Cell. Biol. . 24 . 23 . 10223–35 . December 2004 . 15542832 . 529029 . 10.1128/MCB.24.23.10223-10235.2004 .

Notes and References

1. Turner J, Crossley M . Cloning and characterization of mCtBP2, a co-repressor that associates with basic Krüppel-like factor and other mammalian transcriptional regulators . EMBO J. . 17 . 17 . 5129–40 . September 1998 . 9724649 . 1170841 . 10.1093/emboj/17.17.5129 .
2. Chinnadurai G . CtBP, an unconventional transcriptional corepressor in development and oncogenesis . Mol. Cell . 9 . 2 . 213–24 . February 2002 . 11864595 . 10.1016/S1097-2765(02)00443-4 . free .
3. Web site: Entrez Gene: CTBP2 C-terminal binding protein 2.
4. Turner J, Crossley M . The CtBP family: enigmatic and enzymatic transcriptional co-repressors . BioEssays . 23 . 8 . 683–90 . August 2001 . 11494316 . 10.1002/bies.1097 . 22273095 . free .
5. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y . Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 . Cell . 119 . 7 . 941–53 . December 2004 . 15620353 . 10.1016/j.cell.2004.12.012 . 10847230 . free .
6. Fox AH, Liew C, Holmes M, Kowalski K, Mackay J, Crossley M . Transcriptional cofactors of the FOG family interact with GATA proteins by means of multiple zinc fingers . EMBO J. . 18 . 10 . 2812–22 . May 1999 . 10329627 . 1171362 . 10.1093/emboj/18.10.2812 .
7. Jack BH, Pearson RC, Crossley M . C-terminal binding protein: A metabolic sensor implicated in regulating adipogenesis . Int. J. Biochem. Cell Biol. . 43 . 5 . 693–6 . May 2011 . 21281737 . 10.1016/j.biocel.2011.01.017 .
8. Hildebrand JD, Soriano P . Overlapping and unique roles for C-terminal binding protein 1 (CtBP1) and CtBP2 during mouse development . Mol. Cell. Biol. . 22 . 15 . 5296–307 . August 2002 . 12101226 . 133942 . 10.1128/mcb.22.15.5296-5307.2002.
9. Itoh TQ, Matsumoto A, Tanimura T . C-terminal binding protein (CtBP) activates the expression of E-box clock genes with CLOCK/CYCLE in Drosophila . PLOS ONE . 8 . 4 . e63113 . 2013 . 23646183 . 3640014 . 10.1371/journal.pone.0063113 . 2013PLoSO...863113I . free .
10. Chen S, Whetstine JR, Ghosh S, Hanover JA, Gali RR, Grosu P, Shi Y . The conserved NAD(H)-dependent corepressor CTBP-1 regulates Caenorhabditis elegans life span . Proc. Natl. Acad. Sci. U.S.A. . 106 . 5 . 1496–501 . February 2009 . 19164523 . 2635826 . 10.1073/pnas.0802674106 . 2009PNAS..106.1496C . free .
11. Schmitz F, Konigstorfer A, and Sudhof TC . RIBEYE, a component of synaptic ribbons: a protein's journey through evolution provides insight into synaptic ribbon function . Neuron . 3 . 857–872 . 2000. 28 . 11163272 . 10.1016/s0896-6273(00)00159-8. free .
12. Gage E, Agarwal D, Chenault C, Washington-Brown K, Szvetecz S, Jahan N, Wang Z, Jones M, Zack, Enke RA, Wahlin KJ . Temporal and isoform-specific expression of CTBP2 is evolutionarily conserved between the developing chick and human retina . Front. Mol. Neurosci. . January 2022. 14 . 773356 . 10.3389/fnmol.2021.773356. 35095414 . 8793361 . free .
13. Agarwal D, Kuhns R, Dimitriou C, Barlow E, Wahlin KJ, Enke RA . Bulk RNA sequencing analysis of developing human induced pluripotent stem cell-derived retinal organoids . Sci. Data . December 2022. 9 . 1 . 759 . 10.1038/s41597-022-01853-x. 36494376 . 9734101 . free .
14. Turner J, Nicholas H, Bishop D, Matthews JM, Crossley M . The LIM protein FHL3 binds basic Krüppel-like factor/Krüppel-like factor 3 and its co-repressor C-terminal-binding protein 2 . J. Biol. Chem. . 278 . 15 . 12786–95 . 2003 . 12556451 . 10.1074/jbc.M300587200 . free .
15. van Vliet J, Turner J, Crossley M . Human Krüppel-like factor 8: a CACCC-box binding protein that associates with CtBP and represses transcription . Nucleic Acids Res. . 28 . 9 . 1955–62 . 2000 . 10756197 . 103308 . 10.1093/nar/28.9.1955.
16. Mirnezami AH, Campbell SJ, Darley M, Primrose JN, Johnson PW, Blaydes JP . Hdm2 recruits a hypoxia-sensitive corepressor to negatively regulate p53-dependent transcription . Curr. Biol. . 13 . 14 . 1234–9 . 2003 . 12867035 . 10.1016/S0960-9822(03)00454-8. 2003CBio...13.1234M . 2451241 .
17. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M . Towards a proteome-scale map of the human protein-protein interaction network . Nature . 437 . 7062 . 1173–8 . 2005 . 16189514 . 10.1038/nature04209 . 2005Natur.437.1173R . 4427026 .
18. Castet A, Boulahtouf A, Versini G, Bonnet S, Augereau P, Vignon F, Khochbin S, Jalaguier S, Cavaillès V . Multiple domains of the Receptor-Interacting Protein 140 contribute to transcription inhibition . Nucleic Acids Res. . 32 . 6 . 1957–66 . 2004 . 15060175 . 390375 . 10.1093/nar/gkh524 .
19. Murakami A, Ishida S, Thurlow J, Revest JM, Dickson C . SOX6 binds CtBP2 to repress transcription from the Fgf-3 promoter . Nucleic Acids Res. . 29 . 16 . 3347–55 . 2001 . 11504872 . 55854 . 10.1093/nar/29.16.3347.
20. Holmes M, Turner J, Fox A, Chisholm O, Crossley M, Chong B . hFOG-2, a novel zinc finger protein, binds the co-repressor mCtBP2 and modulates GATA-mediated activation . J. Biol. Chem. . 274 . 33 . 23491–8 . 1999 . 10438528 . 10.1074/jbc.274.33.23491. free .