Abstract
BCL-2 proteins correspond to a structurally, functionally, and phylogenetically heterogeneous group of regulators that play crucial roles in the life and death of animal cells. Some of these regulators also represent therapeutic targets in human diseases including cancer. In the omics era, there is great need for easy data retrieval and fast analysis of the molecular players involved in cell death. In this chapter, we present generic and specific computational resources (such as the reference database BCL2DB) as well as bioinformatics tools that can be used to investigate BCL-2 homologs and BH3-only proteins.
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References
Bhola PD, Letai A (2016) Mitochondria-judges and executioners of cell death sentences. Mol Cell 61(5):695–704. https://doi.org/10.1016/j.molcel.2016.02.019
Moldoveanu T, Follis AV, Kriwacki RW, Green DR (2014) Many players in BCL-2 family affairs. Trends Biochem Sci 39(3):101–111. https://doi.org/10.1016/j.tibs.2013.12.006
Delbridge AR, Strasser A (2015) The BCL-2 protein family, BH3-mimetics and cancer therapy. Cell Death Differ 22(7):1071–1080. https://doi.org/10.1038/cdd.2015.50
Garner TP, Lopez A, Reyna DE, Spitz AZ, Gavathiotis E (2017) Progress in targeting the BCL-2 family of proteins. Curr Opin Chem Biol 39:133–142. https://doi.org/10.1016/j.cbpa.2017.06.014
Schenk RL, Strasser A, Dewson G (2017) BCL-2: long and winding path from discovery to therapeutic target. Biochem Biophys Res Commun 482(3):459–469. https://doi.org/10.1016/j.bbrc.2016.10.100
Aouacheria A, Combet C, Tompa P, Hardwick JM (2015) Redefining the BH3 death domain as a ‘Short linear motif’. Trends Biochem Sci 40(12):736–748. https://doi.org/10.1016/j.tibs.2015.09.007
Aouacheria A, Rech de Laval V, Combet C, Hardwick JM (2013) Evolution of Bcl-2 homology motifs: homology versus homoplasy. Trends Cell Biol 23(3):103–111. https://doi.org/10.1016/j.tcb.2012.10.010
Zheng JH, Viacava Follis A, Kriwacki RW, Moldoveanu T (2016) Discoveries and controversies in BCL-2 protein-mediated apoptosis. FEBS J 283(14):2690–2700. https://doi.org/10.1111/febs.13527
Czabotar PE, Lessene G, Strasser A, Adams JM (2014) Control of apoptosis by the BCL-2 protein family: implications for physiology and therapy. Nat Rev Mol Cell Biol 15(1):49–63. https://doi.org/10.1038/nrm3722
Delbridge AR, Grabow S, Strasser A, Vaux DL (2016) Thirty years of BCL-2: translating cell death discoveries into novel cancer therapies. Nat Rev Cancer 16(2):99–109. https://doi.org/10.1038/nrc.2015.17
Tait SW, Green DR (2013) Mitochondrial regulation of cell death. Cold Spring Harb Perspect Biol 5(9). https://doi.org/10.1101/cshperspect.a008706
Uren RT, Iyer S, Kluck RM (2017) Pore formation by dimeric Bak and Bax: an unusual pore? Philos Trans R Soc Lond B Biol Sci 372(1726). https://doi.org/10.1098/rstb.2016.0218
Aouacheria A (2014) The BCL-2 database, Act 2: moving beyond dualism to diversity and pleiotropy. Cell Death Dis 5:e981. https://doi.org/10.1038/cddis.2013.511
Bae J, Leo CP, Hsu SY, Hsueh AJ (2000) MCL-1S, a splicing variant of the antiapoptotic BCL-2 family member MCL-1, encodes a proapoptotic protein possessing only the BH3 domain. J Biol Chem 275(33):25255–25261. https://doi.org/10.1074/jbc.M909826199
Boise LH, Gonzalez-Garcia M, Postema CE, Ding L, Lindsten T, Turka LA, Mao X, Nunez G, Thompson CB (1993) Bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death. Cell 74(4):597–608
Cheng EH, Kirsch DG, Clem RJ, Ravi R, Kastan MB, Bedi A, Ueno K, Hardwick JM (1997) Conversion of Bcl-2 to a Bax-like death effector by caspases. Science 278(5345):1966–1968
Kucharczak JF, Simmons MJ, Duckett CS, Gelinas C (2005) Constitutive proteasome-mediated turnover of Bfl-1/A1 and its processing in response to TNF receptor activation in FL5.12 pro-B cells convert it into a prodeath factor. Cell Death Differ 12(9):1225–1239. https://doi.org/10.1038/sj.cdd.4401684
Kiefer MC, Brauer MJ, Powers VC, Wu JJ, Umansky SR, Tomei LD, Barr PJ (1995) Modulation of apoptosis by the widely distributed Bcl-2 homologue Bak. Nature 374(6524):736–739. https://doi.org/10.1038/374736a0
Aouacheria A, Arnaud E, Venet S, Lalle P, Gouy M, Rigal D, Gillet G (2001) Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis. Oncogene 20(41):5846–5855. https://doi.org/10.1038/sj.onc.1204740
Inohara N, Gourley TS, Carrio R, Muniz M, Merino J, Garcia I, Koseki T, Hu Y, Chen S, Nunez G (1998) Diva, a Bcl-2 homologue that binds directly to Apaf-1 and induces BH3-independent cell death. J Biol Chem 273(49):32479–32486
Jensen SA, Calvert AE, Volpert G, Kouri FM, Hurley LA, Luciano JP, Wu Y, Chalastanis A, Futerman AH, Stegh AH (2014) Bcl2L13 is a ceramide synthase inhibitor in glioblastoma. Proc Natl Acad Sci U S A 111(15):5682–5687. https://doi.org/10.1073/pnas.1316700111
Kataoka T, Holler N, Micheau O, Martinon F, Tinel A, Hofmann K, Tschopp J (2001) Bcl-rambo, a novel Bcl-2 homologue that induces apoptosis via its unique C-terminal extension. J Biol Chem 276(22):19548–19554. https://doi.org/10.1074/jbc.M010520200
Ke N, Godzik A, Reed JC (2001) Bcl-B, a novel Bcl-2 family member that differentially binds and regulates Bax and Bak. J Biol Chem 276(16):12481–12484. https://doi.org/10.1074/jbc.C000871200
Lee R, Chen J, Matthews CP, McDougall JK, Neiman PE (2001) Characterization of NR13-related human cell death regulator, boo/diva, in normal and cancer tissues. Biochim Biophys Acta 1520(3):187–194
Song Q, Kuang Y, Dixit VM, Vincenz C (1999) Boo, a novel negative regulator of cell death, interacts with Apaf-1. EMBO J 18(1):167–178. https://doi.org/10.1093/emboj/18.1.167
Zhang H, Holzgreve W, De Geyter C (2001) Bcl2-L-10, a novel anti-apoptotic member of the Bcl-2 family, blocks apoptosis in the mitochondria death pathway but not in the death receptor pathway. Hum Mol Genet 10(21):2329–2339
Aouacheria A, Baghdiguian S, Lamb HM, Huska JD, Pineda FJ, Hardwick JM (2017) Connecting mitochondrial dynamics and life-or-death events via Bcl-2 family proteins. Neurochem Int. https://doi.org/10.1016/j.neuint.2017.04.009
Gross A (2006) BID as a double agent in cell life and death. Cell Cycle 5(6):582–584
Hardwick JM, Soane L (2013) Multiple functions of BCL-2 family proteins. Cold Spring Harb Perspect Biol 5(2). https://doi.org/10.1101/cshperspect.a008722
Kvansakul M, Hinds MG (2015) The Bcl-2 family: structures, interactions and targets for drug discovery. Apoptosis 20(2):136–150. https://doi.org/10.1007/s10495-014-1051-7
Petros AM, Olejniczak ET, Fesik SW (2004) Structural biology of the Bcl-2 family of proteins. Biochim Biophys Acta 1644(2–3):83–94. https://doi.org/10.1016/j.bbamcr.2003.08.012
Aouacheria A, Le Goff E, Godefroy N, Baghdiguian S (2016) Evolution of the BCL-2-regulated apoptotic pathway. In: Pontarotti P (ed) Evolutionary biology. Springer, Switzerland, pp 137–156. https://doi.org/10.1007/978-3-319-41324-2_9
Graham SC, Bahar MW, Cooray S, Chen RA, Whalen DM, Abrescia NG, Alderton D, Owens RJ, Stuart DI, Smith GL, Grimes JM (2008) Vaccinia virus proteins A52 and B14 share a Bcl-2-like fold but have evolved to inhibit NF-kappaB rather than apoptosis. PLoS Pathog 4(8):e1000128. https://doi.org/10.1371/journal.ppat.1000128
Muchmore SW, Sattler M, Liang H, Meadows RP, Harlan JE, Yoon HS, Nettesheim D, Chang BS, Thompson CB, Wong SL, Ng SL, Fesik SW (1996) X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death. Nature 381(6580):335–341. https://doi.org/10.1038/381335a0
Neidel S, Maluquer de Motes C, Mansur DS, Strnadova P, Smith GL, Graham SC (2015) Vaccinia virus protein A49 is an unexpected member of the B-cell lymphoma (Bcl)-2 protein family. J Biol Chem 290(10):5991–6002. https://doi.org/10.1074/jbc.M114.624650
Kvansakul M, Hinds MG (2014) The structural biology of BH3-only proteins. Methods Enzymol 544:49–74. https://doi.org/10.1016/B978-0-12-417158-9.00003-0
Aouacheria A, Brunet F, Gouy M (2005) Phylogenomics of life-or-death switches in multicellular animals: Bcl-2, BH3-only, and BNip families of apoptotic regulators. Mol Biol Evol 22(12):2395–2416. https://doi.org/10.1093/molbev/msi234
Bender CE, Fitzgerald P, Tait SW, Llambi F, McStay GP, Tupper DO, Pellettieri J, Sanchez Alvarado A, Salvesen GS, Green DR (2012) Mitochondrial pathway of apoptosis is ancestral in metazoans. Proc Natl Acad Sci U S A 109(13):4904–4909. https://doi.org/10.1073/pnas.1120680109
Lee EF, Clarke OB, Evangelista M, Feng Z, Speed TP, Tchoubrieva EB, Strasser A, Kalinna BH, Colman PM, Fairlie WD (2011) Discovery and molecular characterization of a Bcl-2-regulated cell death pathway in schistosomes. Proc Natl Acad Sci U S A 108(17):6999–7003. https://doi.org/10.1073/pnas.1100652108
Prudent J, Popgeorgiev N, Bonneau B, Thibaut J, Gadet R, Lopez J, Gonzalo P, Rimokh R, Manon S, Houart C, Herbomel P, Aouacheria A, Gillet G (2013) Bcl-wav and the mitochondrial calcium uniporter drive gastrula morphogenesis in zebrafish. Nat Commun 4:2330. https://doi.org/10.1038/ncomms3330
Aouacheria A, Banyai M, Rigal D, Schmidt CJ, Gillet G (2003) Characterization of vnr-13, the first alphaherpesvirus gene of the bcl-2 family. Virology 316(2):256–266
Rech de Laval V, Deleage G, Aouacheria A, Combet C (2014) BCL2DB: database of BCL-2 family members and BH3-only proteins. Database 2014. https://doi.org/10.1093/database/bau013
Galperin MY, Fernandez-Suarez XM, Rigden DJ (2017) The 24th annual nucleic acids research database issue: a look back and upcoming changes. Nucleic Acids Res 45(9):5627. https://doi.org/10.1093/nar/gkx021
Alavian KN, Li H, Collis L, Bonanni L, Zeng L, Sacchetti S, Lazrove E, Nabili P, Flaherty B, Graham M, Chen Y, Messerli SM, Mariggio MA, Rahner C, McNay E, Shore GC, Smith PJ, Hardwick JM, Jonas EA (2011) Bcl-xL regulates metabolic efficiency of neurons through interaction with the mitochondrial F1FO ATP synthase. Nat Cell Biol 13(10):1224–1233. https://doi.org/10.1038/ncb2330
Chen YB, Aon MA, Hsu YT, Soane L, Teng X, McCaffery JM, Cheng WC, Qi B, Li H, Alavian KN, Dayhoff-Brannigan M, Zou S, Pineda FJ, O'Rourke B, Ko YH, Pedersen PL, Kaczmarek LK, Jonas EA, Hardwick JM (2011) Bcl-xL regulates mitochondrial energetics by stabilizing the inner membrane potential. J Cell Biol 195(2):263–276. https://doi.org/10.1083/jcb.201108059
Rung J, Brazma A (2013) Reuse of public genome-wide gene expression data. Nat Rev Genet 14(2):89–99. https://doi.org/10.1038/nrg3394
Arntzen MO, Thiede B (2012) ApoptoProteomics, an integrated database for analysis of proteomics data obtained from apoptotic cells. Mol Cell Proteomics 11(2). https://doi.org/10.1074/mcp.M111.010447
Acknowledgment
This work was supported by CNRS and Montpellier University. We also acknowledge financial support from the Fondation ARC (AA) and Ligue Contre le Cancer ComitÕ du Gard (AA).
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Aouacheria, A., Navratil, V., Combet, C. (2019). Database and Bioinformatic Analysis of BCL-2 Family Proteins and BH3-Only Proteins. In: Gavathiotis, E. (eds) BCL-2 Family Proteins. Methods in Molecular Biology, vol 1877. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8861-7_2
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