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Suraweera CD, Espinoza B, Hinds MG, Kvansakul M. Mastering Death: The Roles of Viral Bcl-2 in dsDNA Viruses. Viruses 2024; 16:879. [PMID: 38932171 PMCID: PMC11209288 DOI: 10.3390/v16060879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Proteins of the Bcl-2 family regulate cellular fate via multiple mechanisms including apoptosis, autophagy, senescence, metabolism, inflammation, redox homeostasis, and calcium flux. There are several regulated cell death (RCD) pathways, including apoptosis and autophagy, that use distinct molecular mechanisms to elicit the death response. However, the same proteins/genes may be deployed in multiple biochemical pathways. In apoptosis, Bcl-2 proteins control the integrity of the mitochondrial outer membrane (MOM) by regulating the formation of pores in the MOM and apoptotic cell death. A number of prosurvival genes populate the genomes of viruses including those of the pro-survival Bcl-2 family. Viral Bcl-2 proteins are sequence and structural homologs of their cellular counterparts and interact with cellular proteins in apoptotic and autophagic pathways, potentially allowing them to modulate these pathways and determine cellular fate.
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Affiliation(s)
- Chathura D. Suraweera
- Genome Sciences and Cancer Division, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia;
| | - Benjamin Espinoza
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, VIC 3086, Australia;
| | - Mark G. Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Marc Kvansakul
- Genome Sciences and Cancer Division, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia;
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2
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Sun H, Tian Y, Fu Y, Lei Y, Wang Y, Yan X, Wang J. Single-molecule scale quantification reveals interactions underlying protein-protein interface: from forces to non-covalent bonds. Phys Chem Chem Phys 2023; 25:31791-31803. [PMID: 37966041 DOI: 10.1039/d3cp04351g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Protein-protein interactions (PPIs) between the B-cell lymphoma 2 (Bcl-2) family are considered a major driving force in cell cycle regulation and signaling. However, how this interfacial noncovalent interaction is achieved molecularly remains poorly understood. Herein, anti-apoptotic protein (Bcl-2) and pro-apoptotic protein (BAX) were used as models and their PPIs were explored for the first time using atomic force microscopy-based single-molecule force spectroscopy (SMFS) and in silico approaches. In addition, we used advanced analytical models, including multiple kinetic models, thermodynamic models, Poisson distributions, and contact angle molecular recognition to fully reveal the complexity of the BAX/Bcl-2 interaction interfaces. We propose that the binding kinetics between BAX/Bcl-2 are mainly mediated by specific (hydrogen bonding) and non-specific forces (hydrophobic interactions and electrostatic interactions) and show that the complicated multivalent binding interaction induces stable BAX/Bcl-2 complexes. This study enriches our understanding of the molecular mechanisms by which BAX interacts with Bcl-2. It provides valuable insights into the physical factors that need to be considered when designing PPI inhibitors.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yichen Tian
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yongrong Lei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yani Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Xinrui Yan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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3
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Fareed MM, Dutta K, Dandekar T, Tarabonda H, Skorb EV, Shityakov S. In silico investigation of nonsynonymous single nucleotide polymorphisms in BCL2 apoptosis regulator gene to design novel protein-based drugs against cancer. J Cell Biochem 2022; 123:2044-2056. [PMID: 36146908 DOI: 10.1002/jcb.30330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/04/2022] [Accepted: 09/10/2022] [Indexed: 12/24/2022]
Abstract
BCL2 apoptosis regulator gene encodes Bcl-2 pro-survival protein, which plays an important role to evade apoptosis in various cancers. Moreover, single nucleotide polymorphisms (SNPs) in the BCL2 gene can be nonsynonymous (nsSNPs), which might affect the protein stability and probably its function. Therefore, we implement cutting-edge computational techniques based on the Spherical Polar Fourier and Monte-Carlo algorithms to investigate the impact of these SNPs on the B cell lymphoma-2 (Bcl-2) stability and therapeutic potential of protein-based molecules to inhibit this protein. As a result, we identified two nsSNPs (Q118R and R129C) to be deleterious and highly conserved, having a negative effect on protein stability. Additionally, molecular docking and molecular dynamics simulations confirmed the decreased binding affinity of mutated Bcl-2 variants to bind three-helix bundle protein inhibitor as these mutations occurred in the protein-protein binding site. Overall, this computational approach investigating nsSNPs provides a useful basis for designing novel molecules to inhibit Bcl-2 pro-survival pathway in malignant cells.
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Affiliation(s)
- Muhammad Mazhar Fareed
- Department of Computer Science, School of Science and Engineering, Università degli studi di Verona, Verona, Italy
| | - Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Midnapore, West Bengal, India
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Herman Tarabonda
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
| | - Ekaterina V Skorb
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
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4
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Sora V, Papaleo E. Structural Details of BH3 Motifs and BH3-Mediated Interactions: an Updated Perspective. Front Mol Biosci 2022; 9:864874. [PMID: 35685242 PMCID: PMC9171138 DOI: 10.3389/fmolb.2022.864874] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022] Open
Abstract
Apoptosis is a mechanism of programmed cell death crucial in organism development, maintenance of tissue homeostasis, and several pathogenic processes. The B cell lymphoma 2 (BCL2) protein family lies at the core of the apoptotic process, and the delicate balance between its pro- and anti-apoptotic members ultimately decides the cell fate. BCL2 proteins can bind with each other and several other biological partners through the BCL2 homology domain 3 (BH3), which has been also classified as a possible Short Linear Motif and whose distinctive features remain elusive even after decades of studies. Here, we aim to provide an updated overview of the structural features characterizing BH3s and BH3-mediated interactions (with a focus on human proteins), elaborating on the plasticity of BCL2 proteins and the motif properties. We also discussed the implication of these findings for the discovery of interactors of the BH3-binding groove of BCL2 proteins and the design of mimetics for therapeutic purposes.
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Affiliation(s)
- Valentina Sora
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Elena Papaleo, ,
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5
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Fores-Martos J, Cervera-Vidal R, Sierra-Roca J, Lozano-Asencio C, Fedele V, Cornelissen S, Edvarsen H, Tadeo-Cervera I, Eroles P, Lluch A, Tabares-Seisdedos R, Falcó A, Van't Veer LJ, Schmidt M, Quigley DA, Børresen-Dale AL, Kristensen VN, Balmain A, Climent J. Circadian PERformance in breast cancer: a germline and somatic genetic study of PER3 VNTR polymorphisms and gene co-expression. NPJ Breast Cancer 2021; 7:118. [PMID: 34508103 PMCID: PMC8433453 DOI: 10.1038/s41523-021-00329-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022] Open
Abstract
Polymorphisms in the PER3 gene have been associated with several human disease phenotypes, including sleep disorders and cancer. In particular, the long allele of a variable number of tandem repeat (VNTR) polymorphism has been previously linked to an increased risk of breast cancer. Here we carried out a combined germline and somatic genetic analysis of the role of the PER3VNRT polymorphism in breast cancer. The combined data from 8284 individuals showed a non-significant trend towards increased breast cancer risk in the 5-repeat allele homozygous carriers (OR = 1.17, 95% CI: 0.97–1.42). We observed allelic imbalance at the PER3 locus in matched blood and tumor DNA samples, showing a significant retention of the long variant (risk) allele in tumor samples, and a preferential loss of the short repetition allele (p = 0.0005). Gene co-expression analysis in healthy and tumoral breast tissue samples uncovered significant associations between PER3 expression levels with those from genes which belong to several cancer-associated pathways. Finally, relapse-free survival (RFS) analysis showed that low expression levels of PER3 were linked to a significant lower RSF in luminal A (p = 3 × 10−12) but not in the rest of breast cancer subtypes.
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Affiliation(s)
- Jaume Fores-Martos
- ESI International Chair at CEU-UCH, CEU Universities, Valencia, Spain.,Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain
| | | | | | - Carlos Lozano-Asencio
- INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Vita Fedele
- Digestive Molecular Clinical Oncology Research Unit, Section of Medical Oncology, Department of Medicine, University of Verona, Verona, Italy
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Hege Edvarsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Irene Tadeo-Cervera
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos. Facultad de Veterinaria, Universidad CEU Cardenal Herrera. CEU Universities, Valencia, Spain
| | - Pilar Eroles
- INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Ana Lluch
- INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Rafa Tabares-Seisdedos
- Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Medicine, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Antonio Falcó
- ESI International Chair at CEU-UCH, CEU Universities, Valencia, Spain.,Departamento de Matemáticas, Física y Ciencias Tecnológicas, Escuela Superior de Enseñanzas Técnicas, Universidad CEU Cardenal Herrera, CEU Universities, Valencia, Spain
| | - Laura J Van't Veer
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Marjanka Schmidt
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos. Facultad de Veterinaria, Universidad CEU Cardenal Herrera. CEU Universities, Valencia, Spain
| | - David A Quigley
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Departments of Urology and Epidemiology & Biostatistics, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Allan Balmain
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Joan Climent
- ESI International Chair at CEU-UCH, CEU Universities, Valencia, Spain. .,INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain. .,Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos. Facultad de Veterinaria, Universidad CEU Cardenal Herrera. CEU Universities, Valencia, Spain.
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6
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Diversity in the intrinsic apoptosis pathway of nematodes. Commun Biol 2020; 3:478. [PMID: 32859965 PMCID: PMC7456325 DOI: 10.1038/s42003-020-01208-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/03/2020] [Indexed: 11/08/2022] Open
Abstract
Early studies of the free-living nematode C. elegans informed us how BCL-2-regulated apoptosis in humans is regulated. However, subsequent studies showed C. elegans apoptosis has several unique features compared with human apoptosis. To date, there has been no detailed analysis of apoptosis regulators in nematodes other than C. elegans. Here, we discovered BCL-2 orthologues in 89 free-living and parasitic nematode taxa representing four evolutionary clades (I, III, IV and V). Unlike in C. elegans, 15 species possess multiple (two to five) BCL-2-like proteins, and some do not have any recognisable BCL-2 sequences. Functional studies provided no evidence that BAX/BAK proteins have evolved in nematodes, and structural studies of a BCL-2 protein from the basal clade I revealed it lacks a functionally important feature of the C. elegans orthologue. Clade I CED-4/APAF-1 proteins also possess WD40-repeat sequences associated with apoptosome assembly, not present in C. elegans, or other nematode taxa studied.
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7
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BCL-w: apoptotic and non-apoptotic role in health and disease. Cell Death Dis 2020; 11:260. [PMID: 32317622 PMCID: PMC7174325 DOI: 10.1038/s41419-020-2417-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/17/2022]
Abstract
The BCL-2 family of proteins integrates signals that trigger either cell survival or apoptosis. The balance between pro-survival and pro-apoptotic proteins is important for tissue development and homeostasis, while impaired apoptosis contributes to several pathologies and can be a barrier against effective treatment. BCL-w is an anti-apoptotic protein that shares a sequence similarity with BCL-XL, and exhibits a high conformational flexibility. BCL-w level is controlled by a number of signaling pathways, and the repertoire of transcriptional regulators largely depends on the cellular and developmental context. As only a few disease-relevant genetic alterations of BCL2L2 have been identified, increased levels of BCL-w might be a consequence of abnormal activation of signaling cascades involved in the regulation of BCL-w expression. In addition, BCL-w transcript is a target of a plethora of miRNAs. Besides its originally recognized pro-survival function during spermatogenesis, BCL-w has been envisaged in different types of normal and diseased cells as an anti-apoptotic protein. BCL-w contributes to survival of senescent and drug-resistant cells. Its non-apoptotic role in the promotion of cell migration and invasion has also been elucidated. Growing evidence indicates that a high BCL-w level can be therapeutically relevant in neurodegenerative disorders, neuron dysfunctions and after small intestinal resection, whereas BCL-w inhibition can be beneficial for cancer patients. Although several drugs and natural compounds can bi-directionally affect BCL-w level, agents that selectively target BCL-w are not yet available. This review discusses current knowledge on the role of BCL-w in health, non-cancerous diseases and cancer.
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8
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Kasthuriarachchi TDW, Wan Q, Lee J. Identification, expression profiling and functional characterization of interleukin 11a ortholog from redlip mullet Liza haematocheila: Insight into its roles in the inflammation and apoptosis regulation. FISH & SHELLFISH IMMUNOLOGY 2020; 99:44-51. [PMID: 32001356 DOI: 10.1016/j.fsi.2020.01.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/01/2020] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
Interleukin 11 (IL-11) is a secretory cytokine with pleotropic properties, including anti-inflammatory and anti-apoptotic functions. This study aimed to functionally characterize a teleostean IL-11a ortholog from redlip mullet (LhIL-11a) through bioinformatic analysis, transcriptional expression profiling and protein function assays. The deduced LhIL-11a protein sequence is 200 amino acids long, with a predicted molecular weight of 23.168 kDa. Multiple sequence alignment indicates that LhIL-11a has a typical four-bundle architecture of α-helixes as observed in other IL-11s. The identity-similarity matrix show a higher identity between LhIL-11a and other fish IL-11a sequences. Phylogenetic analysis demonstrated that LhIL-11a falls within a clade including other fish counterparts. In the tissue distribution analysis, the highest constitutive expression of LhIL-11a mRNA was observed in the mullet gastrointestinal tract and brain tissues. Following the challenges with LPS, poly I:C and Lactococcus garvie, the transcription levels of LhIL-11a were significantly upregulated in both PBCs and liver. In the biological functional assay, recombinant LhIL-11a protein showed strong activities of suppressing pro-inflammatory cytokines and apoptotic gene expression in mullet kidney cells and reducing LPS stimulated NO production in murine macrophage cells. Overall, the findings in this study provide the experimental clues to understanding the functional roles of fish IL-11a in inflammation and apoptosis regulation during host defense against invading microbial pathogens.
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Affiliation(s)
- T D W Kasthuriarachchi
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Qiang Wan
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea.
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9
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Beard HA, Hauser JR, Walko M, George RM, Wilson AJ, Bon RS. Photocatalytic proximity labelling of MCL-1 by a BH3 ligand. Commun Chem 2019; 2:133. [PMID: 33763603 PMCID: PMC7610391 DOI: 10.1038/s42004-019-0235-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ligand-directed protein labelling allows the introduction of diverse chemical functionalities onto proteins without the need for genetically encoded tags. Here we report a method for the rapid labelling of a protein using a ruthenium-bipyridyl (Ru(II)(bpy)3)-modified peptide designed to mimic an interacting BH3 ligand within a BCL-2 family protein-protein interactions. Using sub-stoichiometric quantities of (Ru(II)(bpy)3)-modified NOXA-B and irradiation with visible light for 1 min, the anti-apoptotic protein MCL-1 can be photolabelled with a variety of functional tags. In contrast with previous reports on Ru(II)(bpy)3-mediated photolabelling, tandem mass spectrometry experiments reveal that the labelling site is a cysteine residue of MCL-1. MCL-1 can be labelled selectively in mixtures with other proteins, including the structurally related BCL-2 member, BCL-xL. These results demonstrate that proximity-induced photolabelling is applicable to interfaces that mediate protein-protein interactions, and pave the way towards future use of ligand-directed proximity labelling for dynamic analysis of the interactome of BCL-2 family proteins.
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Affiliation(s)
- Hester A Beard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Jacob R Hauser
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Martin Walko
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Rachel M George
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Robin S Bon
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Leeds Institute of Cardiovascular and Metabolic Medicine, LIGHT laboratories, University of Leeds, Leeds LS2 9JT, UK
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10
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Than VT, Tran HTT, Ly DV, Dang HV, Nguyen MN, Truong AD. Bioinformatic identification and expression analysis of the chicken B cell lymphoma (BCL) gene. Genes Genomics 2019; 41:1195-1206. [PMID: 31313104 DOI: 10.1007/s13258-019-00849-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/03/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND B cell lymphoma (BCL) families play an important role in apoptosis as a growth factor, cell death programming, cytokine expression and immune-related genes expression. OBJECTIVES In this study, to investigate the roles of BCLs, we performed genome-wide identification, expression and functional analyses of the BCL family in chicken. METHODS Chicken BCLs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the BCLs genes in different chicken tissues were obtained from the genome-wide RNA-seq in the GEO, and Cluster and Java Treeview, respectively. RESULTS A total of 16 BCLs genes were identified from the chicken genome, which could be further classified into five distinct groups in the phylogenetic tree. On the other hand, the interaction among BCLs proteins and between BCLs proteins with NF-κB subunits are limited, indicating that the remaining the functions of BCLs protein could be investigated in chicken. Moreover, KEGG pathway analysis indicated that BCL gene family was involved in regulation of apoptotic and immune response. Finally, BCL gene family was differentially expressed in chicken tissues, pathogen infection and growth stages of early chicken early embryo. CONCLUSION This study provides significant insights into the potential functions of BCLs in chicken, including the regulation of apoptosis, cell death and expression of immune-related genes.
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Affiliation(s)
- Van Thai Than
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, 700000, Vietnam.
| | - Ha Thi Thanh Tran
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam
| | - Duc Viet Ly
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam
| | - Hoang Vu Dang
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam
| | - Minh Nam Nguyen
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Anh Duc Truong
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam.
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11
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The Structural Biology of Bcl-x L. Int J Mol Sci 2019; 20:ijms20092234. [PMID: 31067648 PMCID: PMC6540150 DOI: 10.3390/ijms20092234] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/12/2023] Open
Abstract
Interactions between the pro-survival and pro-apoptotic members of the Bcl-2 family of proteins dictate whether a cell lives or dies. Much of our knowledge of the molecular details of these interactions has come from biochemical and structural studies on the pro-survival protein Bcl-xL. The first high-resolution structure of any Bcl-2 family member was of Bcl-xL, which revealed the conserved topology amongst all family members. Subsequent structures of Bcl-xL complexes with pro-apoptotic ligands demonstrated the general features of all pro-survival:pro-apoptotic complexes. Structural studies involving Bcl-xL were also the basis for the discovery of the first small-molecule pro-survival protein inhibitors, leading ultimately to the development of a new class of drugs now successfully used for cancer treatment in the clinic. This article will review our current knowledge of the structural biology of Bcl-xL and how this has impacted our understanding of the molecular details of the intrinsic apoptotic pathway.
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12
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Vasquez-Montes V, Vargas-Uribe M, Pandey NK, Rodnin MV, Langen R, Ladokhin AS. Lipid-modulation of membrane insertion and refolding of the apoptotic inhibitor Bcl-xL. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:691-700. [PMID: 31004798 DOI: 10.1016/j.bbapap.2019.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Bcl-xL is a member of the Bcl-2 family of apoptotic regulators, responsible for inhibiting the permeabilization of the mitochondrial outer membrane, and a promising anti-cancer target. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (a) a soluble folded conformation, (b) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (c) refolded membrane-inserted conformations, for which no structural data are available. Previous studies established that in the cell Bcl-xL exists in a dynamic equilibrium between soluble and membranous states, however, no direct evidence exists in support of either anchored or inserted conformation of the membranous state in vivo. In this in vitro study, we employed a combination of fluorescence and EPR spectroscopy to characterize structural features of the bilayer-inserted conformation of Bcl-xL and the lipid modulation of its membrane insertion transition. Our results indicate that the core hydrophobic helix α6 inserts into the bilayer without adopting a transmembrane orientation. This insertion disrupts the packing of Bcl-xL and releases the regulatory N-terminal BH4 domain (α1) from the rest of the protein structure. Our data demonstrate that both insertion and refolding of Bcl-xL are modulated by lipid composition, which brings the apparent pKa of insertion to the threshold of physiological pH. We hypothesize that conformational rearrangements associated with the bilayer insertion of Bcl-xL result in its switching to a so-called non-canonical mode of apoptotic inhibition. Presented results suggest that the alteration in lipid composition before and during apoptosis can serve as an additional factor regulating the permeabilization of the mitochondrial outer membrane.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Nitin K Pandey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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13
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Ke FFS, Vanyai HK, Cowan AD, Delbridge ARD, Whitehead L, Grabow S, Czabotar PE, Voss AK, Strasser A. Embryogenesis and Adult Life in the Absence of Intrinsic Apoptosis Effectors BAX, BAK, and BOK. Cell 2019; 173:1217-1230.e17. [PMID: 29775594 DOI: 10.1016/j.cell.2018.04.036] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/31/2018] [Accepted: 04/25/2018] [Indexed: 12/01/2022]
Abstract
Intrinsic apoptosis, reliant on BAX and BAK, has been postulated to be fundamental for morphogenesis, but its precise contribution to this process has not been fully explored in mammals. Our structural analysis of BOK suggests close resemblance to BAX and BAK structures. Notably, Bok-/-Bax-/-Bak-/- animals exhibited more severe defects and died earlier than Bax-/-Bak-/- mice, implying that BOK has overlapping roles with BAX and BAK during developmental cell death. By analyzing Bok-/-Bax-/-Bak-/- triple-knockout mice whose cells are incapable of undergoing intrinsic apoptosis, we identified tissues that formed well without this process. We provide evidence that necroptosis, pyroptosis, or autophagy does not substantially substitute for the loss of apoptosis. Albeit very rare, unexpected attainment of adult Bok-/-Bax-/-Bak-/- mice suggests that morphogenesis can proceed entirely without apoptosis mediated by these proteins and possibly without cell death in general.
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Affiliation(s)
- Francine F S Ke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia.
| | - Hannah K Vanyai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Angus D Cowan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Alex R D Delbridge
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Lachlan Whitehead
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Stephanie Grabow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia.
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia.
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14
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Lee EF, Smith NA, Soares da Costa TP, Meftahi N, Yao S, Harris TJ, Tran S, Pettikiriarachchi A, Perugini MA, Keizer DW, Evangelista M, Smith BJ, Fairlie WD. Structural insights into BCL2 pro-survival protein interactions with the key autophagy regulator BECN1 following phosphorylation by STK4/MST1. Autophagy 2019; 15:785-795. [PMID: 30626284 DOI: 10.1080/15548627.2018.1564557] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BECN1/Beclin 1 is a critical protein in the initiation of autophagosome formation. Recent studies have shown that phosphorylation of BECN1 by STK4/MST1 at threonine 108 (T108) within its BH3 domain blocks macroautophagy/autophagy by increasing BECN1 affinity for its negative regulators, the anti-apoptotic proteins BCL2/Bcl-2 and BCL2L1/Bcl-xL. It was proposed that this increased binding is due to formation of an electrostatic interaction with a conserved histidine residue on the anti-apoptotic molecules. Here, we performed biophysical studies which demonstrated that a peptide corresponding to the BECN1 BH3 domain in which T108 is phosphorylated (p-T108) does show increased affinity for anti-apoptotic proteins that is significant, though only minor (<2-fold). We also determined X-ray crystal structures of BCL2 and BCL2L1 with T108-modified BECN1 BH3 peptides, but only showed evidence of an interaction between the BH3 peptide and the conserved histidine residue when the histidine flexibility was restrained due to crystal contacts. These data, together with molecular dynamics studies, indicate that the histidine is highly flexible, even when complexed with BECN1 BH3. Binding studies also showed that detergent can increase the affinity of the interaction. Although this increase was similar for both the phosphorylated and non-phosphorylated peptides, it suggests factors such as membranes could impact on the interaction between BECN1 and BCL2 proteins, and therefore, on the regulation of autophagy. Hence, we propose that phosphorylation of BECN1 by STK4/MST1 can increase the affinity of the interaction between BECN1 and anti-apoptotic proteins and this interaction can be stabilized by local environmental factors. Abbreviations: asu: asymmetric unit; BH3: BCL2/Bcl-2 homology 3; DAPK: death associated protein kinase; MD: molecular dynamics; MST: microscale thermophoresis; NMR: nuclear magnetic resonance; PDB: protein data bank; p-T: phosphothreonine; SPR: surface plasmon resonance; STK4/MST1: serine/threonine kinase 4.
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Affiliation(s)
- Erinna F Lee
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia.,b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
| | - Nicholas A Smith
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | | | - Nastaran Meftahi
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - Shenggen Yao
- d Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Australia
| | - Tiffany J Harris
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia
| | - Sharon Tran
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
| | - Anne Pettikiriarachchi
- e Structural Biology Division , The Walter and Eliza Hall Institute of Medical Research , Parkville , Australia
| | - Matthew A Perugini
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - David W Keizer
- d Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Australia
| | - Marco Evangelista
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia
| | - Brian J Smith
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - W Douglas Fairlie
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia.,b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
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15
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Horne JE, Walko M, Calabrese AN, Levenstein MA, Brockwell DJ, Kapur N, Wilson AJ, Radford SE. Rapid Mapping of Protein Interactions Using Tag-Transfer Photocrosslinkers. Angew Chem Int Ed Engl 2018; 57:16688-16692. [PMID: 30393918 PMCID: PMC6348423 DOI: 10.1002/anie.201809149] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/30/2018] [Indexed: 12/31/2022]
Abstract
Analysing protein complexes by chemical crosslinking-mass spectrometry (XL-MS) is limited by the side-chain reactivities and sizes of available crosslinkers, their slow reaction rates, and difficulties in crosslink enrichment, especially for rare, transient or dynamic complexes. Here we describe two new XL reagents that incorporate a methanethiosulfonate (MTS) group to label a reactive cysteine introduced into the bait protein, and a residue-unbiased diazirine-based photoactivatable XL group to trap its interacting partner(s). Reductive removal of the bait transfers a thiol-containing fragment of the crosslinking reagent onto the target that can be alkylated and located by MS sequencing and exploited for enrichment, enabling the detection of low abundance crosslinks. Using these reagents and a bespoke UV LED irradiation platform, we show that maximum crosslinking yield is achieved within 10 seconds. The utility of this "tag and transfer" approach is demonstrated using a well-defined peptide/protein regulatory interaction (BID80-102 /MCL-1), and the dynamic interaction interface of a chaperone/substrate complex (Skp/OmpA).
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Affiliation(s)
- Jim E. Horne
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Martin Walko
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Antonio N. Calabrese
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Mark A. Levenstein
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- School of Mechanical EngineeringUniversity of LeedsLeedsLS2 9JTUK
| | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Nikil Kapur
- School of Mechanical EngineeringUniversity of LeedsLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
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16
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Horne JE, Walko M, Calabrese AN, Levenstein MA, Brockwell DJ, Kapur N, Wilson AJ, Radford SE. Rapid Mapping of Protein Interactions Using Tag‐Transfer Photocrosslinkers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jim E. Horne
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Martin Walko
- School of ChemistryUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Antonio N. Calabrese
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Mark A. Levenstein
- School of ChemistryUniversity of Leeds Leeds LS2 9JT UK
- School of Mechanical EngineeringUniversity of Leeds Leeds LS2 9JT UK
| | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Nikil Kapur
- School of Mechanical EngineeringUniversity of Leeds Leeds LS2 9JT UK
| | - Andrew J. Wilson
- School of ChemistryUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
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17
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Pohl SÖG, Agostino M, Dharmarajan A, Pervaiz S. Cross Talk Between Cellular Redox State and the Antiapoptotic Protein Bcl-2. Antioxid Redox Signal 2018; 29:1215-1236. [PMID: 29304561 DOI: 10.1089/ars.2017.7414] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE B cell lymphoma-2 (Bcl-2) was discovered over three decades ago and is the prototype antiapoptotic member of the Bcl-2 family that comprises proteins with contrasting effects on cell fate. First identified as a consequence of chromosomal translocation (t 14:18) in human lymphoma, subsequent studies have revealed mutations and/or gene copy number alterations as well as post-translational modifications of Bcl-2 in a variety of human cancers. The canonical function of Bcl-2 is linked to its ability to inhibit mitochondrial membrane permeabilization, thereby regulating apoptosome assembly and activation by blocking the cytosolic translocation of death amplification factors. Of note, the identification of specific domains within the Bcl-2 family of proteins (Bcl-2 homology domains; BH domains) has not only provided a mechanistic insight into the various interactions between the member proteins but has also been the impetus behind the design and development of small molecule inhibitors and BH3 mimetics for clinical use. Recent Advances: Aside from its role in maintaining mitochondrial integrity, recent evidence provides testimony to a novel facet in the biology of Bcl-2 that involves an intricate cross talk with cellular redox state. Bcl-2 overexpression modulates mitochondrial redox metabolism to create a "pro-oxidant" milieu, conducive for cell survival. However, under states of oxidative stress, overexpression of Bcl-2 functions as a redox sink to prevent excessive buildup of reactive oxygen species, thereby inhibiting execution signals. Emerging evidence indicates various redox-dependent transcriptional changes and post-translational modifications with different functional outcomes. CRITICAL ISSUES Understanding the complex interplay between Bcl-2 and the cellular redox milieu from the standpoint of cell fate signaling remains vital for a better understanding of pathological states associated with altered redox metabolism and/or aberrant Bcl-2 expression. FUTURE DIRECTIONS Based on its canonical functions, Bcl-2 has emerged as a potential druggable target. Small molecule inhibitors of Bcl-2 and/or other family members with similar function, as well as BH3 mimetics, are showing promise in the clinic. The emerging evidence for the noncanonical activity linked to cellular redox metabolism provides a novel avenue for the design and development of diagnostic and therapeutic strategies against cancers refractory to conventional chemotherapy by the overexpression of this prosurvival protein.
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Affiliation(s)
- Sebastian Öther-Gee Pohl
- 1 Stem Cell and Cancer Biology Laboratory, Curtin Health and Innovation Research Institute, Curtin University , Bentley, Western Australia .,2 School of Biomedical Sciences, Curtin University , Perth, Western Australia
| | - Mark Agostino
- 1 Stem Cell and Cancer Biology Laboratory, Curtin Health and Innovation Research Institute, Curtin University , Bentley, Western Australia .,2 School of Biomedical Sciences, Curtin University , Perth, Western Australia .,3 Curtin Institute for Computation, Curtin University , Perth, Western Australia
| | - Arun Dharmarajan
- 1 Stem Cell and Cancer Biology Laboratory, Curtin Health and Innovation Research Institute, Curtin University , Bentley, Western Australia .,2 School of Biomedical Sciences, Curtin University , Perth, Western Australia
| | - Shazib Pervaiz
- 2 School of Biomedical Sciences, Curtin University , Perth, Western Australia .,4 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore .,5 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore , Singapore, Singapore .,6 National University Cancer Institute, National University Health System , Singapore, Singapore
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18
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Maity A, Majumdar S, Ghosh Dastidar S. Flexibility enables to discriminate between ligands: Lessons from structural ensembles of Bcl-xl and Mcl-1. Comput Biol Chem 2018; 77:17-27. [PMID: 30195235 DOI: 10.1016/j.compbiolchem.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/24/2018] [Accepted: 08/17/2018] [Indexed: 12/19/2022]
Abstract
The proteins of Bcl-2 family, which are promising anti-cancer-drug targets, have substantial similarity in primary sequence and share homologous domains as well as similar structural folds. In spite of similarities in sequence and structures, the members of its pro- and anti- apoptotic subgroups form complexes with different type of partners with discriminating binding affinities. Understanding the origin of this discrimination is very important for designing ligands that can either selectively target a protein or could be made broad ranged as necessary. Using principal component analysis (PCA) of the available structures and from the analysis of the evolution of the binding pocket residues, the correlation has been investigated considering two important anti-apoptotic protein Bcl-xl and Mcl-1, which serve as two ideal representatives of this family. The flexibility of the receptor enables them to discriminate between the ligands or the binding partners. It has been observed that although Bcl-xl and Mcl-1 are classified as homologous proteins, through the course of evolution the binding pocket residues are highly conserved for Bcl-xl; whereas they have been substituted frequently in Mcl-1. The investigation has revealed that the Bcl-xl can adjust the backbone conformation of the binding pocket residues to a larger extent to complement with the shape of different binding partners whereas the Mcl-1 shows more variation in the side chain conformation of binding pocket residues for the same purpose.
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Affiliation(s)
- Atanu Maity
- Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
| | - Sarmistha Majumdar
- Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
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19
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Wu LH, Zhang Q, Zhang S, Meng LY, Wang YC, Sheng CJ. Effects of gene knockdown of CNP on ventricular remodeling after myocardial ischemia-reperfusion injury through NPRB/Cgmp signaling pathway in rats. J Cell Biochem 2017; 119:1804-1818. [PMID: 28796407 DOI: 10.1002/jcb.26341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/08/2017] [Indexed: 01/27/2023]
Abstract
This study aimed to explore effects of CNP on ventricular remodeling following myocardial ischemia-reperfusion (I/R) injury through the NPRB/cGMP signaling pathway. Rat cardiomyocytes were assigned into: control, I/R, I/R + CNP, and I/R + 8-Br-cGMP groups. ELISA, qRT-PCR, and Western blotting were used to detect cGMP content and expression, respectively. After model establishment of I/R rats, normal control, CNP-/- control, I/R, and CNP-/- groups were set. Indexes of heart were detected using echocardiography and hemodynamics. ELISA was used to measure serum CNP, cGMP, LDH, cTn I, CK-MB, TNF-α, and IL-6 levels. Myocardial infarct was identified by TTC staining, and apoptosis conditions by TUNEL staining. QRT-PCR and Western blotting were adopted to detect expressions of CNP, NPRB, cGMP, and apoptosis-related genes. Compared with control group, cGMP contents and expression in the I/R, I/R + CNP and I/R + 8-Br-cGMP groups were decreased. Levels of LVEDV, LVESV, LVDS, LVDD, IVSD, LVM, LVEDP, and LVSP were higher in the I/R, CNP-/- control, and CNP-/- groups than normal control group while LVEF, SV, CO, and ±dp/dtmax were lower. Compared with the normal control group, LDH, cTn I, CK-MB, TNF-α, and IL-6 were higher in the I/R, CNP-/- control and CNP-/- groups; pathological changes and myocardial infarction were observed in the I/R, CNP-/- control, and CNP-/- groups; expressions of apoptosis-related genes in those groups were higher; while CNP, NPRB, cGMP, and Bcl-2 expressions were decreased. We came to the conclusion that gene knockdown of CNP blocks the NPRB/cGMP signaling pathway, thereby aggravating myocardial I/R injury and causing ventricular remodeling in rats.
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Affiliation(s)
- Lian-He Wu
- Department of Cardiac Surgery, Jining No.1 People's Hospital, Jining, China
| | - Qi Zhang
- Department of Cardiology, Dongying City People's Hospital, Dongying, China
| | - Shen Zhang
- Department of Cardiac Surgery, Jining No.1 People's Hospital, Jining, China
| | - Lu-Yu Meng
- Department of Cardiac Surgery, Jining No.1 People's Hospital, Jining, China
| | - Yan-Chi Wang
- Department of Cardiac Surgery, Jining No.1 People's Hospital, Jining, China
| | - Cun-Jian Sheng
- Department of Cardiac Surgery, Jining No.1 People's Hospital, Jining, China
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20
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Marimuthu P, Singaravelu K. Deciphering the crucial residues involved in heterodimerization of Bak peptide and anti-apoptotic proteins for apoptosis. J Biomol Struct Dyn 2017; 36:1637-1648. [PMID: 28511583 DOI: 10.1080/07391102.2017.1331863] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
B-cell lymphoma 2 (Bcl-2) family proteins are the central regulators of apoptosis, functioning via mitochondrial outer membrane permeabilization. The family members are involved in several stages of apoptosis regulation. The overexpression of the anti-apoptotic proteins leads to several cancer pathological conditions. This overexpression is modulated or inhibited by heterodimerization of pro-apoptotic BH3 domain or BH3-only peptides to the hydrophobic groove present at the surface of anti-apoptotic proteins. Additionally, the heterodimerization displayed differences in binding affinity profile among the pro-apoptotic peptides binding to anti-apoptotic proteins. In light of discovering the novel peptide/drug molecules that contain the potential to inhibit specific anti-apoptotic protein, it is necessary to understand the molecular basis of recognition between the protein and its binding partner (peptide or ligand) along with its binding energies. Therefore, the present work focused on deciphering the molecular basis of recognition between pro-apoptotic Bak peptide binding to different anti-apoptotic (Bcl-xL, Bfl-1, Bcl-W, Mcl-1, and Bcl-2) proteins using advanced Molecular Dynamics (MD) approach such as Molecular Mechanics-Generalized Born Solvent Accessible. The results from our investigation revealed that the predicted binding free energies showed excellent correlation with the experimental values (r2 = .95). The electrostatic (ΔGele) contributions are the major component that drives the interaction between Bak peptides and different anti-apoptotic peptides. Additionally, van der Waals (ΔGvdw) energies also play an indispensible role in determining the binding free energy. Furthermore, the decomposition analysis highlighted the comprehensive information about the energy contributions of hotspot residues involved in stabilizing the interaction between Bak peptide and different anti-apoptotic proteins.
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Affiliation(s)
- Parthiban Marimuthu
- a Structural Bioinformatics Laboratory (SBL), Faculty of Science and Engineering, Biochemistry , Åbo Akademi University , Turku , FI , 20520 , Finland.,b Department of Biology , Albany State University , 504 College Drive, Albany , GA , USA
| | - Kalaimathy Singaravelu
- c Department of Information Technology , University of Turku , Turku , FI , 20520 , Finland
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Ivanov S, Huber R, Warwicker J, Bond P. Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity. Structure 2016; 24:2024-2033. [DOI: 10.1016/j.str.2016.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/05/2016] [Accepted: 09/28/2016] [Indexed: 12/21/2022]
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22
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Targeting BCL-2-like Proteins to Kill Cancer Cells. Trends Cancer 2016; 2:443-460. [PMID: 28741496 DOI: 10.1016/j.trecan.2016.07.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 02/01/2023]
Abstract
Mutations that impair apoptosis contribute to cancer development and reduce the effectiveness of conventional anti-cancer therapies. These insights and understanding of how the B cell lymphoma (BCL)-2 protein family governs apoptosis have galvanized the search for a new class of cancer drugs that target its pro-survival members by mimicking their natural antagonists, the BCL-2 homology (BH)3-only proteins. Successful initial clinical trials of the BH3 mimetic venetoclax/ABT-199, specific for BCL-2, have led to its recent licensing for refractory chronic lymphocytic leukemia and to multiple ongoing trials for other malignancies. Moreover, preclinical studies herald the potential of emerging BH3 mimetics targeting other BCL-2 pro-survival members, particularly myeloid cell leukemia (MCL)-1, for multiple cancer types. Thus, BH3 mimetics seem destined to become powerful new weapons in the arsenal against cancer. This review sketches the discovery of the BCL-2 family and its impact on cancer development and therapy; describes how interactions of family members trigger apoptosis; outlines the development of BH3 mimetic drugs; and discusses their potential to advance cancer therapy.
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23
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Luna-Vargas MP, Chipuk JE. The deadly landscape of pro-apoptotic BCL-2 proteins in the outer mitochondrial membrane. FEBS J 2016; 283:2676-89. [PMID: 26662859 PMCID: PMC4907887 DOI: 10.1111/febs.13624] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/11/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023]
Abstract
Apoptosis is a biological process that removes damaged, excess or infected cells through a genetically controlled mechanism. This process plays a crucial role in organismal development, immunity and tissue homeostasis, and alterations in apoptosis contribute to human diseases including cancer and auto-immunity. In the past two decades, significant efforts have focused on understanding the function of the BCL-2 proteins, a complex family of pro-survival and pro-apoptotic α-helical proteins that directly control the mitochondrial pathway of apoptosis. Diverse structural investigations of the BCL-2 family members have broadened our mechanistic understanding of their individual functions. However, an often over-looked aspect of the mitochondrial pathway of apoptosis is how the BCL-2 family specifically interacts with and targets the outer mitochondrial membrane to initiate apoptosis. Structural information on the relationship between the BCL-2 family and the outer mitochondrial membrane is missing; likewise, knowledge of the biophysical mechanisms by which the outer mitochondrial membrane affects and effects apoptosis is lacking. In this mini-review, we provide a current overview of the BCL-2 family members and discuss the latest structural insights into BAK/BAX activation and oligomerization in the context of the outer mitochondrial membrane and mitochondrial biology.
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Affiliation(s)
- Mark P.A. Luna-Vargas
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Jerry E. Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
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24
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Thébault S, Agez M, Chi X, Stojko J, Cura V, Telerman SB, Maillet L, Gautier F, Billas-Massobrio I, Birck C, Troffer-Charlier N, Karafin T, Honoré J, Senff-Ribeiro A, Montessuit S, Johnson CM, Juin P, Cianférani S, Martinou JC, Andrews DW, Amson R, Telerman A, Cavarelli J. TCTP contains a BH3-like domain, which instead of inhibiting, activates Bcl-xL. Sci Rep 2016; 6:19725. [PMID: 26813996 PMCID: PMC4728560 DOI: 10.1038/srep19725] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/17/2015] [Indexed: 01/28/2023] Open
Abstract
Translationally Controlled Tumor Protein (TCTP) is anti-apoptotic, key in development and cancer, however without the typical Bcl2 family members’ structure. Here we report that TCTP contains a BH3-like domain and forms heterocomplexes with Bcl-xL. The crystal structure of a Bcl-xL deletion variant-TCTP11–31 complex reveals that TCTP refolds in a helical conformation upon binding the BH3-groove of Bcl-xL, although lacking the h1-subregion interaction. Experiments using in vitro-vivo reconstituted systems and TCTP+/− mice indicate that TCTP activates the anti-apoptotic function of Bcl-xL, in contrast to all other BH3-proteins. Replacing the non-conserved h1 of TCTP by that of Bax drastically increases the affinity of this hybrid for Bcl-xL, modifying its biological properties. This work reveals a novel class of BH3-proteins potentiating the anti-apoptotic function of Bcl-xL.
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Affiliation(s)
- Stéphanie Thébault
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, INSERM U964, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France.,CNRS-UMR 8113, LBPA, École Normale Supérieure, 61 avenue du Président Wilson, 94235 Cachan, France
| | - Morgane Agez
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, INSERM U964, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France.,Institut Gustave Roussy, Unité Inserm U981, Bâtiment B2M, 114 rue Édouard-Vaillant, 94805 Villejuif, France
| | - Xiaoke Chi
- Sunnybrook Research Institute and Departments of Biochemistry and Medical Biophysics, University of Toronto, 2075 Bayview Ave., Toronto, Ontario, M4N 3M5, Canada.,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Ontario, L8N 3Z5, Canada
| | - Johann Stojko
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Vincent Cura
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, INSERM U964, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Stéphanie B Telerman
- King's College London Centre for Stem Cells and Regenerative Medicine, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Laurent Maillet
- Center for Cancer Research Nantes-Angers, UMR 892 Inserm - 6299 CNRS/Université de Nantes, IRS-UN, 8 Quai Moncousu - BP 70721, 44007 Nantes Cedex 1
| | - Fabien Gautier
- Center for Cancer Research Nantes-Angers, UMR 892 Inserm - 6299 CNRS/Université de Nantes, IRS-UN, 8 Quai Moncousu - BP 70721, 44007 Nantes Cedex 1.,Institut de Cancérologie de l'Ouest, Centre René Gauducheau Bd Jacques Monod, 44805 Saint Herblain-Nantes cedex
| | - Isabelle Billas-Massobrio
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, INSERM U964, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Catherine Birck
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, INSERM U964, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Nathalie Troffer-Charlier
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, INSERM U964, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Teele Karafin
- CNRS-UMR 8113, LBPA, École Normale Supérieure, 61 avenue du Président Wilson, 94235 Cachan, France.,Institut Gustave Roussy, Unité Inserm U981, Bâtiment B2M, 114 rue Édouard-Vaillant, 94805 Villejuif, France
| | - Joane Honoré
- Institut Gustave Roussy, Unité Inserm U981, Bâtiment B2M, 114 rue Édouard-Vaillant, 94805 Villejuif, France
| | - Andrea Senff-Ribeiro
- CNRS-UMR 8113, LBPA, École Normale Supérieure, 61 avenue du Président Wilson, 94235 Cachan, France.,Institut Gustave Roussy, Unité Inserm U981, Bâtiment B2M, 114 rue Édouard-Vaillant, 94805 Villejuif, France
| | - Sylvie Montessuit
- Department of Cell Biology, University of Geneva, 30, quai Ansermet, 1211 Geneva 4, Switzerland
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Philippe Juin
- Center for Cancer Research Nantes-Angers, UMR 892 Inserm - 6299 CNRS/Université de Nantes, IRS-UN, 8 Quai Moncousu - BP 70721, 44007 Nantes Cedex 1.,Institut de Cancérologie de l'Ouest, Centre René Gauducheau Bd Jacques Monod, 44805 Saint Herblain-Nantes cedex
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Jean-Claude Martinou
- Department of Cell Biology, University of Geneva, 30, quai Ansermet, 1211 Geneva 4, Switzerland
| | - David W Andrews
- Sunnybrook Research Institute and Departments of Biochemistry and Medical Biophysics, University of Toronto, 2075 Bayview Ave., Toronto, Ontario, M4N 3M5, Canada.,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Ontario, L8N 3Z5, Canada
| | - Robert Amson
- CNRS-UMR 8113, LBPA, École Normale Supérieure, 61 avenue du Président Wilson, 94235 Cachan, France.,Institut Gustave Roussy, Unité Inserm U981, Bâtiment B2M, 114 rue Édouard-Vaillant, 94805 Villejuif, France
| | - Adam Telerman
- CNRS-UMR 8113, LBPA, École Normale Supérieure, 61 avenue du Président Wilson, 94235 Cachan, France.,Institut Gustave Roussy, Unité Inserm U981, Bâtiment B2M, 114 rue Édouard-Vaillant, 94805 Villejuif, France
| | - Jean Cavarelli
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, INSERM U964, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
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25
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Abstract
High-resolution protein structures determined by X-ray crystallography or NMR have proven invaluable for deciphering the molecular mechanisms underlying the function of a vast range of proteins. Here, we describe methods to generate complexes of proteins belonging to the Bcl-2 family of proteins with either biological ligands or small molecule antagonists.
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Affiliation(s)
- Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Physical Sciences 4, Room 205, Kingsbury Drive, Bundoora, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia.
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26
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Abstract
The mitochondrion descends from a bacterium that, about two billion years ago, became endosymbiotic. This organelle represents a Pandora’s box whose opening triggers cytochrome-c release and apoptosis of cells from multicellular animals, which evolved much later, about six hundred million years ago. BCL-2 proteins, which are critical apoptosis regulators, were recruited at a certain time point in evolution to either lock or unlock this mitochondrial Pandora’s box. Hence, particularly intriguing is the issue of when and how the “BCL-2 proteins–mitochondria–apoptosis” triptych emerged. This chapter explains what it takes from an evolutionary perspective to evolve a BCL-2-regulated apoptotic pathway, by focusing on the events occurring upstream of mitochondria.
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27
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Lee EF, Perugini MA, Pettikiriarachchi A, Evangelista M, Keizer DW, Yao S, Fairlie WD. The BECN1 N-terminal domain is intrinsically disordered. Autophagy 2016; 12:460-71. [PMID: 27046249 PMCID: PMC4836020 DOI: 10.1080/15548627.2016.1140292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/16/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022] Open
Abstract
BECN1/Beclin 1 has a critical role in the early stages of autophagosome formation. Recently, structures of its central and C-terminal domains were reported, however, little structural information is available on the N-terminal domain, comprising a third of the protein. This lack of structural information largely stems from the inability to produce this region in a purified form. Here, we describe the expression and purification of the N-terminal domain of BECN1 (residues 1 to 150) and detailed biophysical characterization, including NMR spectroscopy. Combined, our studies demonstrated at the atomic level that the BECN1 N-terminal domain is intrinsically disordered, and apart from the BH3 subdomain, remains disordered following interaction with a binding partner, BCL2L1/BCL-XL. In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor. No significant interactions between N- and C-terminal domains were detected.
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Affiliation(s)
- Erinna F. Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Marco Evangelista
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - David W. Keizer
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shenggen Yao
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - W. Douglas Fairlie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
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28
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Dai Z, Ji J, Yan Y, Lin W, Li H, Chen F, Liu Y, Chen W, Bi Y, Xie Q. Role of gga-miR-221 and gga-miR-222 during Tumour Formation in Chickens Infected by Subgroup J Avian Leukosis Virus. Viruses 2015; 7:6538-51. [PMID: 26690468 PMCID: PMC4690879 DOI: 10.3390/v7122956] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/18/2015] [Accepted: 12/02/2015] [Indexed: 02/02/2023] Open
Abstract
Subgroup J avian leukosis virus (ALV-J) causes a neoplastic disease in infected chickens. Differential expression patterns of microRNAs (miRNAs) are closely related to the formation and growth of tumors. (1) Background: This study was undertaken to understand how miRNAs might be related to tumor growth during ALV-J infection. We chose to characterize the effects of miR-221 and miR-222 on cell proliferation, migration, and apoptosis based on previous microarray data. (2) Methods: In vivo, the expression levels of miR-221 and miR-222 were significantly increased in the liver of ALV-J infected chickens (p < 0.01). Over-expression of gga-miR-221 and gga-miR-222 promoted the proliferation, migration, and growth of DF-1 cells, and decreased the expression of BCL-2 modifying factor (BMF) making cells more resistant to apoptosis. (3) Results: Our results suggest that gga-miR-221 and gga-miR-222 may be tumour formation relevant gene in chicken that promote proliferation, migration, and growth of cancer cells, and inhibit apoptosis. BMF expression was significantly reduced in vivo 70 days after ALV-J infection. They may also play a pivotal role in tumorigenesis during ALV-J infection.
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Affiliation(s)
- Zhenkai Dai
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Jun Ji
- China-UK-NYNU-RRes Joint laboratory of Insect Biology, Nanyang Normal Universiy, Nanyang 473000, China.
| | - Yiming Yan
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Wencheng Lin
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Hongxin Li
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
| | - Feng Chen
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
| | - Yang Liu
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Weiguo Chen
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- China-UK-NYNU-RRes Joint laboratory of Insect Biology, Nanyang Normal Universiy, Nanyang 473000, China.
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
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29
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Redefining the BH3 Death Domain as a 'Short Linear Motif'. Trends Biochem Sci 2015; 40:736-748. [PMID: 26541461 PMCID: PMC5056427 DOI: 10.1016/j.tibs.2015.09.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/18/2015] [Accepted: 09/24/2015] [Indexed: 01/06/2023]
Abstract
B cell lymphoma-2 (BCL-2)-related proteins control programmed cell death through a complex network of protein–protein interactions mediated by BCL-2 homology 3 (BH3) domains. Given their roles as dynamic linchpins, the discovery of novel BH3-containing proteins has attracted considerable attention. However, without a clearly defined BH3 signature sequence the BCL-2 family has expanded to include a nebulous group of nonhomologous BH3-only proteins, now justified by an intriguing twist. We present evidence that BH3s from both ordered and disordered proteins represent a new class of short linear motifs (SLiMs) or molecular recognition features (MoRFs) and are diverse in their evolutionary histories. The implied corollaries are that BH3s have a broad phylogenetic distribution and could potentially bind to non-BCL-2-like structural domains with distinct functions. BCL-2 family interactions are mediated by evolutionarily diverse BH3 motifs to regulate apoptosis. Given their key roles, BH3 mimetics are in clinical trials as cancer therapies. The discovery of novel BH3-only proteins represents a major endeavor in the cell death field. As a result, BH3 motifs are reportedly present in a nebulous conglomerate of different proteins, both structured and intrinsically disordered. There is no rigorous definition of a BH3 motif. Currently available BH3 signatures are diverse and elusive for predicting new functional BH3-containing proteins. Redefining the BH3 motif as a new type of short linear motif (SLiM) or molecular recognition feature (MoRF) reconciles many puzzling features of this motif and opens up new avenues for research.
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30
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Crystal structure of Bax bound to the BH3 peptide of Bim identifies important contacts for interaction. Cell Death Dis 2015; 6:e1809. [PMID: 26158515 PMCID: PMC4650713 DOI: 10.1038/cddis.2015.141] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/22/2015] [Indexed: 11/20/2022]
Abstract
The BH3-only protein Bim is a potent direct activator of the proapoptotic effector protein Bax, but the structural basis for its activity has remained poorly defined. Here we describe the crystal structure of the BimBH3 peptide bound to BaxΔC26 and structure-based mutagenesis studies. Similar to BidBH3, the BimBH3 peptide binds into the cognate surface groove of Bax using the conserved hydrophobic BH3 residues h1–h4. However, the structure and mutagenesis data show that Bim is less reliant compared with Bid on its ‘h0' residues for activating Bax and that a single amino-acid difference between Bim and Bid encodes a fivefold difference in Bax-binding potency. Similar to the structures of BidBH3 and BaxBH3 bound to BaxΔC21, the structure of the BimBH3 complex with BaxΔC displays a cavity surrounded by Bax α1, α2, α5 and α8. Our results are consistent with a model in which binding of an activator BH3 domain to the Bax groove initiates separation of its core (α2–α5) and latch (α6–α8) domains, enabling its subsequent dimerisation and the permeabilisation of the mitochondrial outer membrane.
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31
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Rajan S, Choi M, Nguyen QT, Ye H, Liu W, Toh HT, Kang C, Kamariah N, Li C, Huang H, White C, Baek K, Grüber G, Yoon HS. Structural transition in Bcl-xL and its potential association with mitochondrial calcium ion transport. Sci Rep 2015; 5:10609. [PMID: 26023881 PMCID: PMC4448555 DOI: 10.1038/srep10609] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/21/2015] [Indexed: 11/17/2022] Open
Abstract
Bcl-2 family proteins are key regulators for cellular homeostasis in response to apoptotic stimuli. Bcl-xL, an antiapoptotic Bcl-2 family member, undergoes conformational transitions, which leads to two conformational states: the cytoplasmic and membrane-bound. Here we present the crystal and small-angle X-ray scattering (SAXS) structures of Bcl-xL treated with the mild detergent n-Octyl β-D-Maltoside (OM). The detergent-treated Bcl-xL forms a dimer through three-dimensional domain swapping (3DDS) by swapping helices α6-α8 between two monomers. Unlike Bax, a proapoptotic member of the Bcl-2 family, Bcl-xL is not converted to 3DDS homodimer upon binding BH3 peptides and ABT-737, a BH3 mimetic drug. We also designed Bcl-xL mutants which cannot dimerize and show that these mutants reduced mitochondrial calcium uptake in MEF cells. This illustrates the structural plasticity in Bcl-xL providing hints toward the probable molecular mechanism for Bcl-xL to play a regulatory role in mitochondrial calcium ion transport.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Minjoo Choi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Quoc Toan Nguyen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Wei Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Hui Ting Toh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore 138669
| | - Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671
| | - Chi Li
- Molecular Targets Program, James Graham Brown Center and Department of Medicine, Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
| | - Huiya Huang
- Department of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Carl White
- Department of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Kwanghee Baek
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
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32
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Foight GW, Keating AE. Locating Herpesvirus Bcl-2 Homologs in the Specificity Landscape of Anti-Apoptotic Bcl-2 Proteins. J Mol Biol 2015; 427:2468-2490. [PMID: 26009469 DOI: 10.1016/j.jmb.2015.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/13/2015] [Accepted: 05/17/2015] [Indexed: 12/31/2022]
Abstract
Viral homologs of the anti-apoptotic Bcl-2 proteins are highly diverged from their mammalian counterparts, yet they perform overlapping functions by binding and inhibiting BH3 (Bcl-2 homology 3)-motif-containing proteins. We investigated the BH3 binding properties of the herpesvirus Bcl-2 homologs KSBcl-2, BHRF1, and M11, as they relate to those of the human Bcl-2 homologs Mcl-1, Bfl-1, Bcl-w, Bcl-xL, and Bcl-2. Analysis of the sequence and structure of the BH3 binding grooves showed that, despite low sequence identity, M11 has structural similarities to Bcl-xL, Bcl-2, and Bcl-w. BHRF1 and KSBcl-2 are more structurally similar to Mcl-1 than to the other human proteins. Binding to human BH3-like peptides showed that KSBcl-2 has similar specificity to Mcl-1, and BHRF1 has a restricted binding profile; M11 binding preferences are distinct from those of Bcl-xL, Bcl-2, and Bcl-w. Because KSBcl-2 and BHRF1 are from human herpesviruses associated with malignancies, we screened computationally designed BH3 peptide libraries using bacterial surface display to identify selective binders of KSBcl-2 or BHRF1. The resulting peptides bound to KSBcl-2 and BHRF1 in preference to Bfl-1, Bcl-w, Bcl-xL, and Bcl-2 but showed only modest specificity over Mcl-1. Rational mutagenesis increased specificity against Mcl-1, resulting in a peptide with a dissociation constant of 2.9nM for binding to KSBcl-2 and >1000-fold specificity over other Bcl-2 proteins, as well as a peptide with >70-fold specificity for BHRF1. In addition to providing new insights into viral Bcl-2 binding specificity, this study will inform future work analyzing the interaction properties of homologous binding domains and designing specific protein interaction partners.
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Affiliation(s)
- Glenna Wink Foight
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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33
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Abstract
As mitochondria are the powerhouses of the cell, their damage during the cell suicide process of apoptosis is essentially responsible for cellular demise in most cells. A key family of proteins, the B-cell lymphoma-2 (BCL-2) family, determines the integrity of mitochondria in the face of apoptotic insult. A comprehensive understanding of the molecular details of how apoptosis is initiated and how it culminates is essential if apoptosis is to fulfil its undoubted potential as a therapeutic target to treat diseases ranging from cancer to neurodegenerative conditions. Recent advances have provided significant insight into the control of this fundamental process while prompting a re-evaluation of what was considered dogma in the field. Emerging evidence also points to a potential overarching control network that governs not only apoptosis but other fundamental mitochondrial processes, including mitochondrial fission/fusion and quality control.
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Affiliation(s)
- Mark Xiang Li
- Walter and Eliza Hall Institute of Medical Research1G Royal Parade, Parkville, Melbourne, Victoria 3052Australia
- Department of Medical Biology, University of MelbourneParkville, Victoria 3050Australia
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research1G Royal Parade, Parkville, Melbourne, Victoria 3052Australia
- Department of Medical Biology, University of MelbourneParkville, Victoria 3050Australia
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34
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Aouacheria A. [From dualism to multiplicity: seeing BCL-2 family proteins and cell death with new eyes]. Biol Aujourdhui 2015; 209:331-55. [PMID: 27021052 DOI: 10.1051/jbio/2016003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Indexed: 11/15/2022]
Abstract
The concept of cell death has many links to the concept of death itself, defined as the opposite of life. Achievements obtained through research on apoptosis have apparently allowed us to transcend this Manichean view. Death is no longer outside, but rather inside living systems, as a constitutive force at work within the living matter. Whereas the death of cells can be positive and breed "creation" (e.g. during morphogenesis), its dysregulation can also cause or contribute to fatal diseases including cancer. It is tempting to apply this biological discourse to illuminate the relations between life and death, taken in general terms, but does this generalization actually hold? Is this discourse not essentially a metaphor? If cell death is considered as a vital aspect of various biological processes, then are we not faced with some vitalistic conception of death? Are there one or more meanings to the word "death"? Does the power to self-destruct act in opposition to other key features of living entities, or rather in juxtaposition to them? In this article, we first describe how the field of cell death has been developed on the basis of perceived and built dichotomies, mirroring the original opposition between life and death. We detail the limitations of the current paradigm of apoptosis regulation by BCL-2 family proteins, which nicely illustrate the problem of binary thinking in biology. Last, we try to show a way out of this dualistic matrix, by drawing on the notions of multiplicity, complexity, diversity, evolution and contingency.
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Affiliation(s)
- Abdel Aouacheria
- LBMC - Laboratoire de Biologie Moléculaire de la Cellule, École Normale Supérieure de Lyon, UMR 5239, CNRS, Université Lyon 1, HCL, 46 Allée d'Italie, 69364 Lyon Cedex 07, France - ISEM - Institut des Sciences de l'Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, France
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