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Wang CR, Gong JH, Zhao ZB, Zhu Q, Shu B, Hu JJ, Cai D, Liu XY, Dai X, Qiu C, Gong JP, Zhong GC. m 6A demethylation of FOSL1 mRNA protects hepatoma cells against necrosis under glucose deprivation. Cell Death Differ 2024; 31:1029-1043. [PMID: 38762597 PMCID: PMC11303728 DOI: 10.1038/s41418-024-01308-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
Stress-adaptive mechanisms enabling cancer cells to survive under glucose deprivation remain elusive. N6-methyladenosine (m6A) modification plays important roles in determining cancer cell fate and cellular stress response to nutrient deficiency. However, whether m6A modification functions in the regulation of cancer cell survival under glucose deprivation is unknown. Here, we found that glucose deprivation reduced m6A modification levels. Increasing m6A modification resulted in increased hepatoma cell necrosis under glucose deprivation, whereas decreasing m6A modification had an opposite effect. Integrated m6A-seq and RNA-seq revealed potential targets of m6A modification under glucose deprivation, including the transcription factor FOSL1; further, glucose deprivation upregulated FOSL1 by inhibiting FOSL1 mRNA decay in an m6A-YTHDF2-dependent manner through reducing m6A modification in its exon1 and 5'-UTR regions. Functionally, FOSL1 protected hepatoma cells against glucose deprivation-induced necrosis in vitro and in vivo. Mechanistically, FOSL1 transcriptionally repressed ATF3 by binding to its promoter. Meanwhile, ATF3 and MAFF interacted via their leucine zipper domains to form a heterodimer, which competed with NRF2 for binding to antioxidant response elements in the promoters of NRF2 target genes, thereby inhibiting their transcription. Consequently, FOSL1 reduced the formation of the ATF3-MAFF heterodimer, thereby enhancing NRF2 transcriptional activity and the antioxidant capacity of glucose-deprived-hepatoma cells. Thus, FOSL1 alleviated the necrosis-inducing effect of glucose deprivation-induced reactive oxygen species accumulation. Collectively, our study uncovers the protective role of m6A-FOSL1-ATF3 axis in hepatoma cell necrosis under glucose deprivation, and may provide new targets for cancer therapy.
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Affiliation(s)
- Chun-Rui Wang
- Department of Infectious Diseases, Institute for Viral Hepatitis, the Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun-Hua Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Bo Zhao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qian Zhu
- Department of Nutrition and Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Bian Shu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie-Jun Hu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Cai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin-Yi Liu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Dai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chan Qiu
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian-Ping Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guo-Chao Zhong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Zhang X, Tseo Y, Bai Y, Chen F, Uhler C. Prediction of protein subcellular localization in single cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605178. [PMID: 39091825 PMCID: PMC11291118 DOI: 10.1101/2024.07.25.605178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The subcellular localization of a protein is important for its function and interaction with other molecules, and its mislocalization is linked to numerous diseases. While atlas-scale efforts have been made to profile protein localization across various cell lines, existing datasets only contain limited pairs of proteins and cell lines which do not cover all human proteins. We present a method that uses both protein sequences and cellular landmark images to perform P redictions of U nseen P roteins' S ubcellular localization ( PUPS ), which can generalize to both proteins and cell lines not used for model training. PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images for protein localization prediction. The protein sequence input enables generalization to unseen proteins and the cellular image input enables cell type specific prediction that captures single-cell variability. PUPS' ability to generalize to unseen proteins and cell lines enables us to assess the variability in protein localization across cell lines as well as across single cells within a cell line and to identify the biological processes associated with the proteins that have variable localization. Experimental validation shows that PUPS can be used to predict protein localization in newly performed experiments outside of the Human Protein Atlas used for training. Collectively, PUPS utilizes both protein sequences and cellular images to predict protein localization in unseen proteins and cell lines with the ability to capture single-cell variability.
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3
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Georgi JA, Stasik S, Kramer M, Meggendorfer M, Röllig C, Haferlach T, Valk P, Linch D, Herold T, Duployez N, Taube F, Middeke JM, Platzbecker U, Serve H, Baldus CD, Muller-Tidow C, Haferlach C, Koch S, Berdel WE, Woermann BJ, Krug U, Braess J, Hiddemann W, Spiekermann K, Boertjes EL, Hills RK, Burnett A, Ehninger G, Metzeler K, Rothenberg-Thurley M, Dufour A, Dombret H, Pautas C, Preudhomme C, Fenwarth L, Bornhäuser M, Gale R, Thiede C. Prognostic impact of CEBPA mutational subgroups in adult AML. Leukemia 2024; 38:281-290. [PMID: 38228680 PMCID: PMC10844079 DOI: 10.1038/s41375-024-02140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Despite recent refinements in the diagnostic and prognostic assessment of CEBPA mutations in AML, several questions remain open, i.e. implications of different types of basic region leucin zipper (bZIP) mutations, the role of co-mutations and the allelic state. Using pooled primary data analysis on 1010 CEBPA-mutant adult AML patients, a comparison was performed taking into account the type of mutation (bZIP: either typical in-frame insertion/deletion (InDel) mutations (bZIPInDel), frameshift InDel or nonsense mutations inducing translational stop (bZIPSTOP) or single base-pair missense alterations (bZIPms), and transcription activation domain (TAD) mutations) and the allelic state (single (smCEBPA) vs. double mutant (dmCEBPA)). Only bZIPInDel patients had significantly higher rates of complete remission and longer relapse free and overall survival (OS) compared with all other CEBPA-mutant subgroups. Moreover, co-mutations in bZIPInDel patients (e.g. GATA2, FLT3, WT1 as well as ELN2022 adverse risk aberrations) had no independent impact on OS, whereas in non-bZIPInDel patients, grouping according to ELN2022 recommendations added significant prognostic information. In conclusion, these results demonstrate bZIPInDel mutations to be the major independent determinant of outcome in CEBPA-mutant AML, thereby refining current classifications according to WHO (including all dmCEBPA and smCEBPA bZIP) as well as ELN2022 and ICC recommendations (including CEBPA bZIPms).
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Affiliation(s)
- Julia-Annabell Georgi
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sebastian Stasik
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | | | - Christoph Röllig
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Peter Valk
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - David Linch
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Nicolas Duployez
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Franziska Taube
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jan Moritz Middeke
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Uwe Platzbecker
- Klinik und Poliklinik fur Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Hubert Serve
- Medizinische Klinik 2, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | - Claudia D Baldus
- Klinik für Innere Medizin II, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Carsten Muller-Tidow
- Klinik für Hämatologie, Onkologie und Rheumatologie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | | | - Sarah Koch
- MLL Münchner Leukämielabor GmbH, Munich, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | | | - Utz Krug
- Department of Medicine 3, Klinikum Leverkusen, Leverkusen, Germany
| | - Jan Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital LMU Munich, Munich, Germany
| | | | | | - Robert K Hills
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Alan Burnett
- Department of Haematology, Cardiff University, University Hospital of Wales, Cardiff, UK
| | | | - Klaus Metzeler
- Klinik und Poliklinik fur Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | | | - Annika Dufour
- Department of Medicine III, University Hospital LMU Munich, Munich, Germany
| | - Hervé Dombret
- Hôpital Saint-Louis (AP-HP), EA 3518, Université de Paris, Paris, France
| | - Cecile Pautas
- Service d'Hématologie et de thérapie cellulaire, Hôpital Henri Mondor, Créteil, France
| | - Claude Preudhomme
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Laurene Fenwarth
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Martin Bornhäuser
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Nationales Zentrum für Tumorerkrankungen (NCT), Dresden, Germany
| | - Rosemary Gale
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Christian Thiede
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- AgenDix GmbH, Dresden, Germany.
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4
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Paquette AR, Boddy CN. Double Stranded DNA Binding Stapled Peptides: An Emerging Tool for Transcriptional Regulation. Chembiochem 2023; 24:e202300594. [PMID: 37750576 DOI: 10.1002/cbic.202300594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
Stapled peptides have rapidly established themselves as a powerful technique to mimic α-helical interactions with a short peptide sequence. There are many examples of stapled peptides that successfully disrupt α-helix-mediated protein-protein interactions, with an example currently in clinical trials. DNA-protein interactions are also often mediated by α-helices and are involved in all transcriptional regulation processes. Unlike DNA-binding small molecules, which typically lack DNA sequence selectivity, DNA-binding proteins bind with high affinity and high selectivity. These are ideal candidates for the design DNA-binding stapled peptides. Despite the parallel to protein-protein interaction disrupting stapled peptides and the need for sequence specific DNA binders, there are very few DNA-binding stapled peptides. In this review we examine all the known DNA-binding stapled peptides. Their design concepts are compared to stapled peptides that disrupt protein-protein interactions and based on the few examples in the literature, DNA-binding stapled peptide trends are discussed.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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5
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Kostel Bal S, Giuliani S, Block J, Repiscak P, Hafemeister C, Shahin T, Kasap N, Ransmayr B, Miao Y, van de Wetering C, Frohne A, Jimenez Heredia R, Schuster M, Zoghi S, Hertlein V, Thian M, Bykov A, Babayeva R, Bilgic Eltan S, Karakoc-Aydiner E, Shaw LE, Chowdhury I, Varjosalo M, Argüello RJ, Farlik M, Ozen A, Serfling E, Dupré L, Bock C, Halbritter F, Hannich JT, Castanon I, Kraakman MJ, Baris S, Boztug K. Biallelic NFATC1 mutations cause an inborn error of immunity with impaired CD8+ T-cell function and perturbed glycolysis. Blood 2023; 142:827-845. [PMID: 37249233 DOI: 10.1182/blood.2022018303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 04/27/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023] Open
Abstract
The nuclear factor of activated T cells (NFAT) family of transcription factors plays central roles in adaptive immunity in murine models; however, their contribution to human immune homeostasis remains poorly defined. In a multigenerational pedigree, we identified 3 patients who carry germ line biallelic missense variants in NFATC1, presenting with recurrent infections, hypogammaglobulinemia, and decreased antibody responses. The compound heterozygous NFATC1 variants identified in these patients caused decreased stability and reduced the binding of DNA and interacting proteins. We observed defects in early activation and proliferation of T and B cells from these patients, amenable to rescue upon genetic reconstitution. Stimulation induced early T-cell activation and proliferation responses were delayed but not lost, reaching that of healthy controls at day 7, indicative of an adaptive capacity of the cells. Assessment of the metabolic capacity of patient T cells revealed that NFATc1 dysfunction rendered T cells unable to engage in glycolysis after stimulation, although oxidative metabolic processes were intact. We hypothesized that NFATc1-mutant T cells could compensate for the energy deficit due to defective glycolysis by using enhanced lipid metabolism as an adaptation, leading to a delayed, but not lost, activation responses. Indeed, we observed increased 13C-labeled palmitate incorporation into citrate, indicating higher fatty acid oxidation, and we demonstrated that metformin and rosiglitazone improved patient T-cell effector functions. Collectively, enabled by our molecular dissection of the consequences of loss-of-function NFATC1 mutations and extending the role of NFATc1 in human immunity beyond receptor signaling, we provide evidence of metabolic plasticity in the context of impaired glycolysis observed in patient T cells, alleviating delayed effector responses.
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Affiliation(s)
- Sevgi Kostel Bal
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Sarah Giuliani
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Jana Block
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Repiscak
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | | | - Tala Shahin
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Nurhan Kasap
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Bernhard Ransmayr
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Yirun Miao
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cheryl van de Wetering
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Frohne
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Raul Jimenez Heredia
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Samaneh Zoghi
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Vanessa Hertlein
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marini Thian
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Aleksandr Bykov
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Royala Babayeva
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Sevgi Bilgic Eltan
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Rafael J Argüello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Ahmet Ozen
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Edgar Serfling
- Department of Molecular Pathology, Institute of Pathology, and Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Loïc Dupré
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Toulouse Institute for Infectious and Inflammatory Diseases, INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
| | - Christoph Bock
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | | | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Irinka Castanon
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Michael J Kraakman
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Safa Baris
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Kaan Boztug
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St. Anna Children's Hospital, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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6
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Coñuecar R, Asela I, Rivera M, Galaz-Davison P, González-Higueras J, Hamilton GL, Engelberger F, Ramírez-Sarmiento CA, Babul J, Sanabria H, Medina E. DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 2023; 26:107228. [PMID: 37485372 PMCID: PMC10362293 DOI: 10.1016/j.isci.2023.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
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Affiliation(s)
- Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - George L. Hamilton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Felipe Engelberger
- Institute for Drug Discovery, Leipzig University Medical School, 04107 Leipzig, Germany
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
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7
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Cruz P, Paredes N, Asela I, Kolimi N, Molina JA, Ramírez-Sarmiento CA, Goutam R, Huang G, Medina E, Sanabria H. Domain tethering impacts dimerization and DNA-mediated allostery in the human transcription factor FoxP1. J Chem Phys 2023; 158:2890482. [PMID: 37184020 DOI: 10.1063/5.0138782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
Transcription factors are multidomain proteins with specific DNA binding and regulatory domains. In the human FoxP subfamily (FoxP1, FoxP2, FoxP3, and FoxP4) of transcription factors, a 90 residue-long disordered region links a Leucine Zipper (ZIP)-known to form coiled-coil dimers-and a Forkhead (FKH) domain-known to form domain swapping dimers. We used replica exchange discrete molecular dynamics simulations, single-molecule fluorescence experiments, and other biophysical tools to understand how domain tethering in FoxP1 impacts dimerization at ZIP and FKH domains and how DNA binding allosterically regulates their dimerization. We found that domain tethering promotes FoxP1 dimerization but inhibits a FKH domain-swapped structure. Furthermore, our findings indicate that the linker mediates the mutual organization and dynamics of ZIP and FKH domains, forming closed and open states with and without interdomain contacts, thus highlighting the role of the linkers in multidomain proteins. Finally, we found that DNA allosterically promotes structural changes that decrease the dimerization propensity of FoxP1. We postulate that, upon DNA binding, the interdomain linker plays a crucial role in the gene regulatory function of FoxP1.
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Affiliation(s)
- Perla Cruz
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Nicolás Paredes
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Narendar Kolimi
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - José Alejandro Molina
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 7820436, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 7820436, Chile
| | - Rajen Goutam
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Gangton Huang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
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8
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Bentley EP, Scholl D, Wright PE, Deniz AA. Coupling of binding and differential subdomain folding of the intrinsically disordered transcription factor CREB. FEBS Lett 2023; 597:917-932. [PMID: 36480418 PMCID: PMC10089947 DOI: 10.1002/1873-3468.14554] [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: 08/18/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The cyclic AMP response element binding protein (CREB) contains a basic leucine zipper motif (bZIP) that forms a coiled coil structure upon dimerization and specific DNA binding. Although this state is well characterized, key features of CREB bZIP binding and folding are not well understood. We used single-molecule Förster resonance energy transfer (smFRET) to probe conformations of CREB bZIP subdomains. We found differential folding of the basic region and leucine zipper in response to different binding partners; a strong and previously unreported DNA-independent dimerization affinity; folding upon binding to nonspecific DNA; and evidence of long-range interdomain interactions in full-length CREB that modulate DNA binding. These studies provide new insights into DNA binding and dimerization and have implications for CREB function.
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Affiliation(s)
- Emily P. Bentley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Daniel Scholl
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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9
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Sengoku T, Shiina M, Suzuki K, Hamada K, Sato K, Uchiyama A, Kobayashi S, Oguni A, Itaya H, Kasahara K, Moriwaki H, Watanabe C, Honma T, Okada C, Baba S, Ohta T, Motohashi H, Yamamoto M, Ogata K. Structural basis of transcription regulation by CNC family transcription factor, Nrf2. Nucleic Acids Res 2022; 50:12543-12557. [PMID: 36454022 PMCID: PMC9756947 DOI: 10.1093/nar/gkac1102] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/22/2022] [Accepted: 11/02/2022] [Indexed: 12/05/2022] Open
Abstract
Several basic leucine zipper (bZIP) transcription factors have accessory motifs in their DNA-binding domains, such as the CNC motif of CNC family or the EHR motif of small Maf (sMaf) proteins. CNC family proteins heterodimerize with sMaf proteins to recognize CNC-sMaf binding DNA elements (CsMBEs) in competition with sMaf homodimers, but the functional role of the CNC motif remains elusive. In this study, we report the crystal structures of Nrf2/NFE2L2, a CNC family protein regulating anti-stress transcriptional responses, in a complex with MafG and CsMBE. The CNC motif restricts the conformations of crucial Arg residues in the basic region, which form extensive contact with the DNA backbone phosphates. Accordingly, the Nrf2-MafG heterodimer has approximately a 200-fold stronger affinity for CsMBE than canonical bZIP proteins, such as AP-1 proteins. The high DNA affinity of the CNC-sMaf heterodimer may allow it to compete with the sMaf homodimer on target genes without being perturbed by other low-affinity bZIP proteins with similar sequence specificity.
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Affiliation(s)
- Toru Sengoku
- To whom correspondence should be addressed. Tel: +81 45 787 2590; Fax: +81 45 784 4530;
| | | | - Kae Suzuki
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Ko Sato
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Akiko Uchiyama
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shunsuke Kobayashi
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Asako Oguni
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hayato Itaya
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan,JST PRESTO, Yokohama 230-0045, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Chikako Okada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shiho Baba
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tsutomu Ohta
- Department of Physical Therapy, Faculty of Health and Medical Sciences, Tokoha University, Hamamatsu 431-2102, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8575, Japan
| | - Kazuhiro Ogata
- Correspondence may also be addressed to Kazuhiro Ogata. Tel: +81 45 787 2590; Fax: +81 45 784 4530;
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10
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Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N 6-methyladenine. Sci Rep 2022; 12:19583. [PMID: 36380112 PMCID: PMC9666514 DOI: 10.1038/s41598-022-23585-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Covalent modifications of standard DNA/RNA nucleobases affect epigenetic regulation of gene expression by modulating interactions between nucleic acids and protein readers. We derive here the absolute binding free energies and analyze the binding modalities between key modified nucleobases 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (m6A) and all non-prolyl/non-glycyl protein side chains using molecular dynamics simulations and umbrella sampling in both water and methanol, the latter mimicking the low dielectric environment at the dehydrated nucleic-acid/protein interfaces. We verify the derived affinities by comparing against a comprehensive set of high-resolution structures of nucleic-protein complexes involving 5mC. Our analysis identifies protein side chains that are highly tuned for detecting cytosine methylation as a function of the environment and can thus serve as microscopic readers of epigenetic marks. Conversely, we show that the relative ordering of sidechain affinities for 5hmC and m6A does not differ significantly from those for their precursor bases, cytosine and adenine, respectively, especially in the low dielectric environment. For those two modified bases, the effect is more nuanced and manifests itself primarily at the level of absolute changes in the binding free energy. Our results contribute towards establishing a quantitative foundation for understanding, predicting and modulating the interactions between modified nucleic acids and proteins at the atomistic level.
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11
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Kumar A, Aglyamova G, Yim Y, Bailey AO, Lynch H, Powell R, Nguyen N, Rosenthal Z, Zhao WN, Li Y, Chen J, Fan S, Lee H, Russell W, Stephan C, Robison A, Haggarty S, Nestler E, Zhou J, Machius M, Rudenko G. Chemically targeting the redox switch in AP1 transcription factor ΔFOSB. Nucleic Acids Res 2022; 50:9548-9567. [PMID: 36039764 PMCID: PMC9458432 DOI: 10.1093/nar/gkac710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022] Open
Abstract
The AP1 transcription factor ΔFOSB, a splice variant of FOSB, accumulates in the brain in response to chronic insults such as exposure to drugs of abuse, depression, Alzheimer's disease and tardive dyskinesias, and mediates subsequent long-term neuroadaptations. ΔFOSB forms heterodimers with other AP1 transcription factors, e.g. JUND, that bind DNA under control of a putative cysteine-based redox switch. Here, we reveal the structural basis of the redox switch by determining a key missing crystal structure in a trio, the ΔFOSB/JUND bZIP domains in the reduced, DNA-free form. Screening a cysteine-focused library containing 3200 thiol-reactive compounds, we identify specific compounds that target the redox switch, validate their activity biochemically and in cell-based assays, and show that they are well tolerated in different cell lines despite their general potential to bind to cysteines covalently. A crystal structure of the ΔFOSB/JUND bZIP domains in complex with a redox-switch-targeting compound reveals a deep compound-binding pocket near the DNA-binding site. We demonstrate that ΔFOSB, and potentially other, related AP1 transcription factors, can be targeted specifically and discriminately by exploiting unique structural features such as the redox switch and the binding partner to modulate biological function despite these proteins previously being thought to be undruggable.
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Affiliation(s)
| | | | - Yun Young Yim
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Haley M Lynch
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Reid T Powell
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Nghi D Nguyen
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Zachary Rosenthal
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianping Chen
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shanghua Fan
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hubert Lee
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Clifford Stephan
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Alfred J Robison
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mischa Machius
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gabby Rudenko
- To whom correspondence should be addressed. Tel: +1 409 772 6292; Fax: +1 409 772 9642;
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12
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Tsuji A, Yamashita H, Hisatomi O, Abe M. Dimerization processes for light-regulated transcription factor Photozipper visualized by high-speed atomic force microscopy. Sci Rep 2022; 12:12903. [PMID: 35941201 PMCID: PMC9359980 DOI: 10.1038/s41598-022-17228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Dimerization is critical for transcription factors (TFs) to bind DNA and regulate a wide variety of cellular functions; however, the molecular mechanisms remain to be completely elucidated. Here, we used high-speed atomic force microscopy (HS-AFM) to observe the dimerization process for a photoresponsive TF Photozipper (PZ), which consists of light–oxygen–voltage-sensing (LOV) and basic-region-leucine-zipper (bZIP) domains. HS-AFM visualized not only the oligomeric states of PZ molecules forming monomers and dimers under controlled dark–light conditions but also the domain structures within each molecule. Successive AFM movies captured the dimerization process for an individual PZ molecule and the monomer–dimer reversible transition during dark–light cycling. Detailed AFM images of domain structures in PZ molecules demonstrated that the bZIP domain entangled under dark conditions was loosened owing to light illumination and fluctuated around the LOV domain. These observations revealed the role of the bZIP domain in the dimerization processes of a TF.
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Affiliation(s)
- Akihiro Tsuji
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Hayato Yamashita
- Graduate School of Engineering Science, Osaka University, Osaka, Japan.
| | - Osamu Hisatomi
- Graduate School of Science, Osaka University, Osaka, Japan
| | - Masayuki Abe
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
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13
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Learte-Aymamí S, Martin-Malpartida P, Roldán-Martín L, Sciortino G, Couceiro JR, Maréchal JD, Macias MJ, Mascareñas JL, Vázquez ME. Controlling oncogenic KRAS signaling pathways with a Palladium-responsive peptide. Commun Chem 2022; 5:75. [PMID: 36697641 PMCID: PMC9814687 DOI: 10.1038/s42004-022-00691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/10/2022] [Indexed: 01/28/2023] Open
Abstract
RAS oncoproteins are molecular switches associated with critical signaling pathways that regulate cell proliferation and differentiation. Mutations in the RAS family, mainly in the KRAS isoform, are responsible for some of the deadliest cancers, which has made this protein a major target in biomedical research. Here we demonstrate that a designed bis-histidine peptide derived from the αH helix of the cofactor SOS1 binds to KRAS with high affinity upon coordination to Pd(II). NMR spectroscopy and MD studies demonstrate that Pd(II) has a nucleating effect that facilitates the access to the bioactive α-helical conformation. The binding can be suppressed by an external metal chelator and recovered again by the addition of more Pd(II), making this system the first switchable KRAS binder, and demonstrates that folding-upon-binding mechanisms can operate in metal-nucleated peptides. In vitro experiments show that the metallopeptide can efficiently internalize into living cells and inhibit the MAPK kinase cascade.
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Affiliation(s)
- Soraya Learte-Aymamí
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Pau Martin-Malpartida
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain
| | - Lorena Roldán-Martín
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Giuseppe Sciortino
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain ,grid.473715.30000 0004 6475 7299Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, 43007 Spain
| | - José R. Couceiro
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Jean-Didier Maréchal
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Maria J. Macias
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010 Spain
| | - José L. Mascareñas
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - M. Eugenio Vázquez
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
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14
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Almutairi ZM. In Silico Identification and Characterization of B12D Family Proteins in Viridiplantae. Evol Bioinform Online 2022; 18:11769343221106795. [PMID: 35721582 PMCID: PMC9201304 DOI: 10.1177/11769343221106795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
B12D family proteins are transmembrane proteins that contain the B12D
domain involved in membrane trafficking. Plants comprise several
members of the B12D family, but these members’ numbers and specific
functions are not determined. This study aims to identify and
characterize the members of B12D protein family in plants. Phytozome
database was retrieved for B12D proteins from 14 species. The total 66
B12D proteins were analyzed in silico for gene structure, motifs, gene
expression, duplication events, and phylogenetics. In general, B12D
proteins are between 86 and 98 aa in length, have 2 or 3 exons, and
comprise a single transmembrane helix. Motif prediction and multiple
sequence alignment show strong conservation among B12D proteins of 11
flowering plants species. Despite that, the phylogenetic tree revealed
a distinct cluster of 16 B12D proteins that have high conservation
across flowering plants. Motif prediction revealed 41 aa motif
conserved in 58 of the analyzed B12D proteins similar to the bZIP
motif, confirming that in the predicted biological process and
molecular function, B12D proteins are DNA-binding proteins.
Cis-regulatory elements screening in putative
B12D promoters found various responsive
elements for light, abscisic acid, methyl jasmonate, cytokinin,
drought, and heat. Despite that, there is specific elements for cold
stress, cell cycle, circadian, auxin, salicylic acid, and gibberellic
acid in the promoter of a few B12D genes indicating
for functional diversification for B12D family members. The digital
expression shows that B12D genes of Glycine
max have similar expression patterns consistent with
their clustering in the phylogenetic tree. However, the expression of
B12D genes of Hordeum vulgure
appears inconsistent with their clustering in the tree. Despite the
strong conservation of the B12D proteins of Viridiplantae, gene
association analysis, promoter analysis, and digital expression
indicate different roles for the members of the B12D family during
plant developmental stages.
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Affiliation(s)
- Zainab M Almutairi
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-kharj, Saudi Arabia
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15
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Zhao K, Liu L, Huang S. Genome-Wide Identification and Functional Analysis of the bZIP Transcription Factor Family in Rice Bakanae Disease Pathogen, Fusarium fujikuroi. Int J Mol Sci 2022; 23:ijms23126658. [PMID: 35743103 PMCID: PMC9223689 DOI: 10.3390/ijms23126658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 12/10/2022] Open
Abstract
Fungal basic leucine zipper (bZIP) proteins play a vital role in biological processes such as growth, biotic/abiotic stress responses, nutrient utilization, and invasion. In this study, genome-wide identification of bZIP genes in the fungus Fusarium fujikuroi, the pathogen of bakanae disease, was carried out. Forty-four genes encoding bZIP transcription factors (TFs) from the genome of F. fujikuroi (FfbZIP) were identified and functionally characterized. Structures, domains, and phylogenetic relationships of the sequences were analyzed by bioinformatic approaches. Based on the phylogenetic relationships with the FfbZIP proteins of eight other fungi, the bZIP genes can be divided into six groups (A–F). The additional conserved motifs have been identified and their possible functions were predicted. To analyze functions of the bZIP genes, 11 FfbZIPs were selected according to different motifs they contained and were knocked out by genetic recombination. Results of the characteristic studies revealed that these FfbZIPs were involved in oxygen stress, osmotic stress, cell wall selection pressure, cellulose utilization, cell wall penetration, and pathogenicity. In conclusion, this study enhanced understandings of the evolution and regulatory mechanism of the FfbZIPs in fungal growth, abiotic/biotic stress resistance, and pathogenicity, which could be the reference for other fungal bZIP studies.
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16
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Huber EM, Hortschansky P, Scheven MT, Misslinger M, Haas H, Brakhage AA, Groll M. Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX. Structure 2022; 30:934-946.e4. [PMID: 35472306 DOI: 10.1016/j.str.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
The heterotrimeric CCAAT-binding complex (CBC) is a fundamental eukaryotic transcription factor recognizing the CCAAT box. In certain fungi, like Aspergilli, the CBC cooperates with the basic leucine zipper HapX to control iron metabolism. HapX functionally depends on the CBC, and the stable interaction of both requires DNA. To study this cooperative effect, X-ray structures of the CBC-HapX-DNA complex were determined. Downstream of the CCAAT box, occupied by the CBC, a HapX dimer binds to the major groove. The leash-like N terminus of the distal HapX subunit contacts the CBC, and via a flexible polyproline type II helix mediates minor groove interactions that stimulate sequence promiscuity. In vitro and in vivo mutagenesis suggest that the structural and functional plasticity of HapX results from local asymmetry and its ability to target major and minor grooves simultaneously. The latter feature may also apply to related transcription factors such as yeast Hap4 and distinct Yap family members.
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Affiliation(s)
- Eva M Huber
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (Leibniz-HKI), Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Mareike T Scheven
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (Leibniz-HKI), Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Matthias Misslinger
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (Leibniz-HKI), Adolf-Reichwein-Straße 23, 07745 Jena, Germany; Institute for Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany.
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17
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Zeke A, Schád É, Horváth T, Abukhairan R, Szabó B, Tantos A. Deep structural insights into RNA-binding disordered protein regions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1714. [PMID: 35098694 PMCID: PMC9539567 DOI: 10.1002/wrna.1714] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022]
Abstract
Recent efforts to identify RNA binding proteins in various organisms and cellular contexts have yielded a large collection of proteins that are capable of RNA binding in the absence of conventional RNA recognition domains. Many of the recently identified RNA interaction motifs fall into intrinsically disordered protein regions (IDRs). While the recognition mode and specificity of globular RNA binding elements have been thoroughly investigated and described, much less is known about the way IDRs can recognize their RNA partners. Our aim was to summarize the current state of structural knowledge on the RNA binding modes of disordered protein regions and to propose a classification system based on their sequential and structural properties. Through a detailed structural analysis of the complexes that contain disordered protein regions binding to RNA, we found two major binding modes that represent different recognition strategies and, most likely, functions. We compared these examples with DNA binding disordered proteins and found key differences stemming from the nucleic acids as well as similar binding strategies, implying a broader substrate acceptance by these proteins. Due to the very limited number of known structures, we integrated molecular dynamics simulations in our study, whose results support the proposed structural preferences of specific RNA‐binding IDRs. To broaden the scope of our review, we included a brief analysis of RNA‐binding small molecules and compared their structural characteristics and RNA recognition strategies to the RNA‐binding IDRs. This article is categorized under:RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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Affiliation(s)
- András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Rawan Abukhairan
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Beáta Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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18
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Proteins That Read DNA Methylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:269-293. [DOI: 10.1007/978-3-031-11454-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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IFP35 Is a Relevant Factor in Innate Immunity, Multiple Sclerosis, and Other Chronic Inflammatory Diseases: A Review. BIOLOGY 2021; 10:biology10121325. [PMID: 34943240 PMCID: PMC8698480 DOI: 10.3390/biology10121325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 02/03/2023]
Abstract
Simple Summary In this review, we focused on the emerging role of IFP35, a highly conserved leucine zipper protein from fish to humans, with a still unknown biological function. The considered literature indicates this protein as a key-pleiotropic factor reflecting JAK-STAT and DAMPs pathways activation in innate immunity-dependent inflammation, as well as in the physiology and general pathology of a wide range of phylogenetically distant organisms. These findings also indicate IFP35 as a biologically relevant molecule in human demyelinating diseases of the central nervous system, including Multiple Sclerosis, and other organ-specific chronic inflammatory disorders. Abstract Discovered in 1993 by Bange et al., the 35-kDa interferon-induced protein (IFP35) is a highly conserved cytosolic interferon-induced leucine zipper protein with a 17q12-21 coding gene and unknown function. Belonging to interferon stimulated genes (ISG), the IFP35 reflects the type I interferon (IFN) activity induced through the JAK-STAT phosphorylation, and it can homodimerize with N-myc-interactor (NMI) and basic leucine zipper transcription factor (BATF), resulting in nuclear translocation and a functional expression. Casein kinase 2-interacting protein-1 (CKIP-1), retinoic acid-inducible gene I (RIG-I), and laboratory of genetics and physiology 2 Epinephelus coioides (EcLGP2) are thought to regulate IFP35, via the innate immunity pathway. Several in vitro and in vivo studies on fish and mammals have confirmed the IFP35 as an ISG factor with antiviral and antiproliferative functions. However, in a mice model of sepsis, IFP35 was found working as a damage associated molecular pattern (DAMP) molecule, which enhances inflammation by acting in the innate immune-mediated way. In human pathology, the IFP35 expression level predicts disease outcome and response to therapy in Multiple Sclerosis (MS), reflecting IFN activity. Specifically, IFP35 was upregulated in Lupus Nephritis (LN), Rheumatoid Arthritis (RA), and untreated MS. However, it normalized in the MS patients undergoing therapy. The considered data indicate IFP35 as a pleiotropic factor, suggesting it as biologically relevant in the innate immunity, general pathology, and human demyelinating diseases of the central nervous system.
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20
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Ng JCK, Peng JHC, Chen AYS, Tian T, Zhou JS, Smith TJ. Plasticity of the lettuce infectious yellows virus minor coat protein (CPm) in mediating the foregut retention and transmission of a chimeric CPm mutant by whitefly vectors. J Gen Virol 2021; 102:001652. [PMID: 34494949 PMCID: PMC8567426 DOI: 10.1099/jgv.0.001652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/16/2021] [Indexed: 01/04/2023] Open
Abstract
Transmission of the crinivirus, lettuce infectious yellows virus (LIYV), is determined by a minor coat protein (CPm)-mediated virion retention mechanism located in the foregut of its whitefly vector. To better understand the functions of LIYV CPm, chimeric CPm mutants engineered with different lengths of the LIYV CPm amino acid sequence and that of the crinivirus, lettuce chlorosis virus (LCV), were constructed based on bioinformatics and sequence alignment data. The 485 amino acid-long chimeric CPm of LIYV mutant, CPmP-1, contains 60 % (from position 3 to 294) of LCV CPm amino acids. The chimeric CPm of mutants CPmP-2, CPmP-3 and CPmP-4 contains 46 (position 3 to 208), 51 (position 3 to 238) and 41 % (position 261 to 442) of LCV CPm amino acids, respectively. All four mutants moved systemically, expressed the chimeric CPm and formed virus particles. However, following acquisition feeding of the virus preparations, only CPmP-1 was retained in the foreguts of a significant number of vectors and transmitted. In immuno-gold labelling transmission electron microscopy (IGL-TEM) analysis, CPmP-1 particles were distinctly labelled by antibodies directed against the LCV but not LIYV CPm. In contrast, CPmP-4 particles were not labelled by antibodies directed against the LCV or LIYV CPm, while CPmP-2 and -3 particles were weakly labelled by anti-LIYV CPm but not anti-LCV CPm antibodies. The unique antibody recognition and binding pattern of CPmP-1 was also displayed in the foreguts of whitefly vectors that fed on CPmP-1 virions. These results are consistent with the hypothesis that the chimeric CPm of CPmP-1 is incorporated into functional virions, with the LCV CPm region being potentially exposed on the surface and accessible to anti-LCV CPm antibodies.
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Affiliation(s)
- James C. K. Ng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
- Center for Infectious Disease and Vector Research, University of California, Riverside, CA 92521, USA
| | - James H. C. Peng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Angel Y. S. Chen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Tongyan Tian
- California Department of Food and Agriculture, Sacramento, CA 95832, USA
| | - Jaclyn S. Zhou
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Thomas J. Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, TX, 77555, USA
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21
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John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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22
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Podder S, Ghosh A, Ghosh T. Mutations in membrane-fusion subunit of spike glycoprotein play crucial role in the recent outbreak of COVID-19. J Med Virol 2021; 93:2790-2798. [PMID: 33090493 PMCID: PMC7675664 DOI: 10.1002/jmv.26598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/14/2020] [Accepted: 10/11/2020] [Indexed: 01/06/2023]
Abstract
Coronavirus disease‐2019 (COVID‐19), the ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a major threat to the entire human race. It is reported that SARS‐CoV‐2 seems to have relatively low pathogenicity and higher transmissibility than previously outbroke SARS‐CoV. To explore the reason of the increased transmissibility of SARS‐CoV‐2 compared with SARS‐CoV, we have performed a comparative analysis on the structural proteins (spike, envelope, membrane, and nucleoprotein) of two viruses. Our analysis revealed that extensive substitutions of hydrophobic to polar and charged amino acids in spike glycoproteins of SARS‐CoV2 creates an intrinsically disordered region (IDR) at the beginning of membrane‐fusion subunit and intrinsically disordered residues in fusion peptide. IDR provides a potential site for proteolysis by furin and enriched disordered residues facilitate prompt fusion of the SARS‐CoV2 with host membrane by recruiting molecular recognition features. Here, we have hypothesized that mutation‐driven accumulation of intrinsically disordered residues in spike glycoproteins play dual role in enhancing viral transmissibility than previous SARS‐coronavirus. These analyses may help in epidemic surveillance and preventive measures against COVID‐19. Spike glycoprotein of SARS‐CoV2 experiences higher synonymous and non‐synonymous substitution rates than other three structural (E, M, N) proteins. Extensive hydrophobic to polar and charged amino acid substitutions in S proteins during evolution from SARS‐CoV generate intrinsically disordered residues in the membrane fusion subunit (S2) of S protein. Intrinsically disordered region at the beginning of S2 offers cleavage site of furin protease and by virtue of their flexible nature, they provide sensitive site for efficient proteolysis to activate the fusion peptide. Enrichment of intrinsically disordered residues in fusion peptide prompts rapid fusion of viral envelop with host membrane by recruiting several MoRFs. Intrinsic disorderness in spike glycoproteins in SARS‐CoV2 play dual role in enhancing their transmissibility than previous SARS‐corona virus.
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Affiliation(s)
- Soumita Podder
- Department of Microbiology, Raiganj University, Uttar Dinajpur, West Bengal, India
| | - Avishek Ghosh
- Department of Microbiology, Maulana Azad College, Kolkata, West Bengal, India
| | - Tapash Ghosh
- Department of Microbiology, Raiganj University, Uttar Dinajpur, West Bengal, India.,Department of Bioinformatics, Bose Institute, Kolkata, West Bengal, India
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23
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Bartas M, Červeň J, Guziurová S, Slychko K, Pečinka P. Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins. Int J Mol Sci 2021; 22:ijms22020922. [PMID: 33477647 PMCID: PMC7831508 DOI: 10.3390/ijms22020922] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.
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24
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Shahmir F, Pauls KP. Identification, Gene Structure, and Expression of BnMicEmUP: A Gene Upregulated in Embryogenic Brassica napus Microspores. FRONTIERS IN PLANT SCIENCE 2021; 11:576008. [PMID: 33519838 PMCID: PMC7845737 DOI: 10.3389/fpls.2020.576008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Microspores of Brassica napus can be diverted from normal pollen development into embryogenesis by treating them with a mild heat shock. As microspore embryogenesis closely resembles zygotic embryogenesis, it is used as model for studying the molecular mechanisms controlling embryo formation. A previous study comparing the transcriptomes of three-day-old sorted embryogenic and pollen-like (non-embryogenic) microspores identified a gene homologous to AT1G74730 of unknown function that was upregulated 8-fold in the embryogenic cells. In the current study, the gene was isolated and sequenced from B. napus and named BnMicEmUP (B. napus microspore embryogenesis upregulated gene). Four forms of BnMicEmUP mRNA and three forms of genomic DNA were identified. BnMicEmUP2,3 was upregulated more than 7-fold by day 3 in embryogenic microspore cultures compared to non-induced cultures. BnMicEmUP1,4 was highly expressed in leaves. Transient expression studies of BnMicEmUP3::GFP fusion protein in Nicotiana benthamiana and in stable Arabidopsis transgenics showed that it accumulates in chloroplasts. The features of the BnMicEmUP protein, which include a chloroplast targeting region, a basic region, and a large region containing 11 complete leucine-rich repeats, suggest that it is similar to a bZIP PEND (plastid envelope DNA-binding protein) protein, a DNA binding protein found in the inner envelope membrane of developing chloroplasts. Here, we report that the BnMicEmUP3 overexpression in Arabidopsis increases the sensitivity of seedlings to exogenous abscisic acid (ABA). The BnMicEmUP proteins appear to be transcription factors that are localized in plastids and are involved in plant responses to biotic and abiotic environmental stresses; as well as the results obtained from this study can be used to improve crop yield.
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25
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Ray S, Tillo D, Ufot A, Assad N, Durell S, Vinson C. bZIP Dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun Prefer to Bind to Some Double-Stranded DNA Sequences Containing 5-Formylcytosine and 5-Carboxylcytosine. Biochemistry 2020; 59:3529-3540. [PMID: 32902247 DOI: 10.1021/acs.biochem.0c00475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In mammalian cells, 5-methylcytosine (5mC) occurs in genomic double-stranded DNA (dsDNA) and is enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), then to 5-formylcytosine (5fC), and finally to 5-carboxylcytosine (5caC). These cytosine modifications are enriched in regulatory regions of the genome. The effect of these oxidative products on five bZIP dimers (CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun) binding to five types of dsDNA was measured using protein binding microarrays. The five dsDNAs contain either cytosine in both DNA strands or cytosine in one strand and either 5mC, 5hmC, 5fC, or 5caC in the second strand. Some sequences containing the CEBP half-site GCAA are bound more strongly by all five bZIP domains when dsDNA contains 5mC, 5hmC, or 5fC. dsDNA containing 5caC in some TRE (AP-1)-like sequences, e.g., TGACTAA, is better bound by Zta, ATF3|cJun, and cFos|cJun.
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26
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Pogenberg V, Ballesteros-Álvarez J, Schober R, Sigvaldadóttir I, Obarska-Kosinska A, Milewski M, Schindl R, Ögmundsdóttir MH, Steingrímsson E, Wilmanns M. Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif. Nucleic Acids Res 2020; 48:934-948. [PMID: 31777941 PMCID: PMC6954422 DOI: 10.1093/nar/gkz1104] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/01/2019] [Accepted: 11/25/2019] [Indexed: 12/01/2022] Open
Abstract
Interrupted dimeric coiled coil segments are found in a broad range of proteins and generally confer selective functional properties such as binding to specific ligands. However, there is only one documented case of a basic-helix–loop–helix leucine zipper transcription factor—microphthalmia-associated transcription factor (MITF)—in which an insertion of a three-residue stammer serves as a determinant of conditional partner selectivity. To unravel the molecular principles of this selectivity, we have analyzed the high-resolution structures of stammer-containing MITF and an engineered stammer-less MITF variant, which comprises an uninterrupted symmetric coiled coil. Despite this fundamental difference, both MITF structures reveal identical flanking in-phase coiled coil arrangements, gained by helical over-winding and local asymmetry in wild-type MITF across the stammer region. These conserved structural properties allow the maintenance of a proper functional readout in terms of nuclear localization and binding to specific DNA-response motifs regardless of the presence of the stammer. By contrast, MITF heterodimer formation with other bHLH-Zip transcription factors is only permissive when both factors contain either the same type of inserted stammer or no insert. Our data illustrate a unique principle of conditional partner selectivity within the wide arsenal of transcription factors with specific partner-dependent functional readouts.
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Affiliation(s)
| | - Josué Ballesteros-Álvarez
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Romana Schober
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Gruberstraße 40, A-4020 Linz, Austria
| | - Ingibjörg Sigvaldadóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Agnieszka Obarska-Kosinska
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany.,Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Morlin Milewski
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Rainer Schindl
- Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria
| | - Margrét Helga Ögmundsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Matthias Wilmanns
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany.,University Hamburg Clinical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
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27
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Yin Z, Venkannagari H, Lynch H, Aglyamova G, Bhandari M, Machius M, Nestler EJ, Robison AJ, Rudenko G. Self-assembly of the bZIP transcription factor ΔFosB. Curr Res Struct Biol 2019; 2:1-13. [PMID: 32542236 PMCID: PMC7295165 DOI: 10.1016/j.crstbi.2019.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
ΔFosB is a highly stable transcription factor that accumulates in specific brain regions upon chronic exposure to drugs of abuse, stress, or seizures, and mediates lasting behavioral responses. ΔFosB reportedly heterodimerizes with JunD forming a canonical bZIP leucine zipper coiled coil that clamps onto DNA. However, the striking accumulation of ΔFosB protein in brain upon chronic insult has brought its molecular status into question. Here, we demonstrate through a series of crystal structures that the ΔFosB bZIP domain self-assembles into stable oligomeric assemblies that defy the canonical arrangement. The ΔFosB bZIP domain also self-assembles in solution, and in neuron-like Neuro 2a cells it is trapped into molecular arrangements that are consistent with our structures. Our data suggest that, as ΔFosB accumulates in brain in response to chronic insult, it forms non-canonical assemblies. These species may be at the root of ΔFosB's striking protein stability, and its unique transcriptional and behavioral consequences.
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Affiliation(s)
- Zhou Yin
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Harikanth Venkannagari
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Haley Lynch
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Galina Aglyamova
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mukund Bhandari
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mischa Machius
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Eric J. Nestler
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L Levy Place, New York, NY 10029, USA
| | - Alfred J. Robison
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Gabby Rudenko
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA,Corresponding author.
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28
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Abstract
Structural disorder is widespread in regulatory protein networks. Weak and transient interactions render disordered proteins particularly sensitive to fluctuations in solution conditions such as ion and crowder concentrations. How this sensitivity alters folding coupled binding reactions, however, has not been fully understood. Here, we demonstrate that salt jointly modulates polymer properties and binding affinities of 5 disordered proteins from a transcription factor network. A combination of single-molecule Förster resonance energy transfer experiments, polymer theory, and molecular simulations shows that all 5 proteins expand with increasing ionic strengths due to Debye-Hückel charge screening. Simultaneously, pairwise affinities between the proteins increase by an order of magnitude within physiological salt limits. A quantitative analysis shows that 50% of the affinity increase can be explained by changes in the disordered state. Disordered state properties therefore have a functional relevance even if these states are not directly involved in biological functions. Numerical solutions of coupled binding equilibria with our results show that networks of homologous disordered proteins can function surprisingly robustly in fluctuating cellular environments, despite the sensitivity of its individual proteins.
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29
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Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. Annu Rev Cell Dev Biol 2019; 35:357-379. [PMID: 31283382 DOI: 10.1146/annurev-cellbio-100617-062719] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell partly resolves this specificity paradox through combinatorial strategies and the use of low-affinity binding sites, which are better able to distinguish between similar TFs. However, because these sites have low affinity, it is challenging to understand how TFs recognize them in vivo. Here, we summarize recent findings and technological advancements that allow for the quantification and mechanistic interpretation of TF recognition across a wide range of affinities. We propose a model that integrates insights from the fields of genetics and cell biology to provide further conceptual understanding of TF binding specificity. We argue that in eukaryotes, target specificity is driven by an inhomogeneous 3D nuclear distribution of TFs and by variation in DNA binding affinity such that locally elevated TF concentration allows low-affinity binding sites to be functional.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Richard S Mann
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA; .,Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10031, USA.,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
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30
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Kopra K, Tong-Ochoa N, Laine M, Eskonen V, Koskinen PJ, Härmä H. Homogeneous peptide-break assay for luminescent detection of enzymatic protein post-translational modification activity utilizing charged peptides. Anal Chim Acta 2019; 1055:126-132. [PMID: 30782363 DOI: 10.1016/j.aca.2018.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022]
Abstract
We have developed a rapid and sensitive universal peptide-based time-resolved luminescence assay for detection of enzymatic post-translational modifications (PTMs). PTMs play essential roles in intracellular signaling and cell regulation, thus providing functional protein diversity in cell. Due this, impaired PTM patterns have been linked to multiple disease states. Clear link between PTMs and pathological conditions have also driven assay development further, but still today most of the methodologies are based on single-specificity or group-specific PTM-recognition. We have previously introduced leuzine-zipper based peptide-break technology as a viable option for universal PTM detection. Here, we introduce peptide-break technology utilizing single-label homogeneous quenching resonance energy transfer (QRET) and charge-based peptide-peptide interaction. We demonstrate the functionality of the new assay concept in phosphorylation, deacetylation, and citrullination. In a comparable study between previously introduced leucine-zipper and the novel charge-based approach, we found equal PTM detection performance and sensitivity, but the peptide design for new targets is simplified with the charged peptides. The new concept allows the use of short <20 amino acid peptides without limitations rising from the leucine-zipper coiled-coil structure. Introduced methodology enables wash-free PTM detection in a 384-well plate format, using low nanomolar enzyme concentrations. Potentially, the peptide-break technique using charged peptides may be applicable for natural peptide sequences directly obtained from the target protein.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland.
| | - Natalia Tong-Ochoa
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Mari Laine
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Päivi J Koskinen
- Section of Physiology and Genetics, Department of Biology, University of Turku, Vesilinnantie 5, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
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Bannister S, Böhm E, Zinn T, Hellweg T, Kottke T. Arguments for an additional long-lived intermediate in the photocycle of the full-length aureochrome 1c receptor: A time-resolved small-angle X-ray scattering study. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:034701. [PMID: 31263739 PMCID: PMC6588521 DOI: 10.1063/1.5095063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Aureochromes (AUREO) act as blue-light photoreceptors in algae. They consist of a light-, oxygen-, voltage-sensitive (LOV) domain and a DNA-binding basic region/leucine zipper. Illumination of the flavin cofactor in LOV leads to the formation of an adduct, followed by global structural changes. Here, we first applied UV/vis spectroscopy to characterize the photocycle of full-length aureochrome 1c (PtAUREO1c) from the diatom Phaeodactylum tricornutum. With a time constant of 850 s and a quantum yield of 23%, PtAUREO1c reveals a faster recovery time and a much lower sensitivity toward light than PtAUREO1a, pointing to its role as a high light sensor in vivo. UV/vis spectroscopy offers details on the local recovery of the flavin chromophore. However, kinetic information on the global structural recovery of full-length AUREO or any other multidomain LOV protein is missing. This information is essential not least for the photoreceptors' applications as optogenetic devices. Therefore, we established a procedure to apply small-angle X-ray scattering on PtAUREO1c in a time-resolved manner employing an in-house setup. In combination with UV/vis spectroscopy under similar conditions, we revealed a discrepancy between the recovery of the global protein structure and the adduct lifetime. Accordingly, we propose to supplement the photocycle by an intermediate state (I447), which decays with a time constant of about 800 s and prolongs the lifetime of the signaling state.
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Affiliation(s)
- Saskia Bannister
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Elena Böhm
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Thomas Zinn
- ESRF–The European Synchrotron, 71, Avenue des Martyrs, 38043 Grenoble Cedex 9, France
| | - Thomas Hellweg
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
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Ray S, Ufot A, Assad N, Singh J, Durell SR, Porollo A, Tillo D, Vinson C. The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:486-492. [PMID: 30825655 DOI: 10.1016/j.bbagrm.2019.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/09/2019] [Accepted: 02/05/2019] [Indexed: 12/25/2022]
Abstract
The bZIP homodimers CEBPB and CREB1 bind DNA containing methylated cytosines differently. CREB1 binds stronger to the C/EBP half-site GCAA when the cytosine is methylated. For CEBPB, methylation of the same cytosine does not affect DNA binding. The X-ray structure of CREB1 binding the half site GTCA identifies an alanine in the DNA binding region interacting with the methyl group of T, structurally analogous to the methyl group of methylated C. This alanine is replaced with a valine in CEBPB. To explore the contribution of this amino acid to binding with methylated cytosine of the GCAA half-site, we made the reciprocal mutants CEBPB(V285A) and CREB1(A297V) and used protein binding microarrays (PBM) to examine binding to four types of double-stranded DNA (dsDNA): 1) DNA with cytosine in both strands (DNA(C|C)), 2) DNA with 5-methylcytosine (M) in one strand and cytosine in the second strand (DNA(M|C)), 3) DNA with 5-hydroxymethylcytosine (H) in one strand and cytosine in the second strand (DNA(H|C)), and 4) DNA with both cytosines in all CG dinucleotides containing 5-methylcytosine (DNA(5mCG)). When binding to DNA(C|C), CEBPB (V285A) preferentially binds the CRE consensus motif (TGACGTCA), similar to CREB1. The reciprocal mutant, CREB1(A297V) binds DNA with some similarity to CEBPB, with strongest binding to the methylated PAR site 8-mer TTACGTAA. These data demonstrate that V285 residue inhibits CEBPB binding to methylated cytosine of the GCAA half-site.
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Affiliation(s)
- Sreejana Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Aniekanabasi Ufot
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Nima Assad
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Jocelyn Singh
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Aleksey Porollo
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States of America; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, United States of America
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America.
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Hsu A, Ferrage F, Palmer AG. Analysis of NMR Spin-Relaxation Data Using an Inverse Gaussian Distribution Function. Biophys J 2018; 115:2301-2309. [PMID: 30503534 DOI: 10.1016/j.bpj.2018.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 10/24/2018] [Indexed: 02/08/2023] Open
Abstract
Spin relaxation in solution-state NMR spectroscopy is a powerful approach to explore the conformational dynamics of biological macromolecules. Probability distribution functions for overall or internal correlation times have been used previously to model spectral density functions central to spin-relaxation theory. Applications to biological macromolecules rely on transverse relaxation rate constants, and when studying nanosecond timescale motions, sampling at ultralow frequencies is often necessary. Consequently, appropriate distribution functions necessitate spectral density functions that are accurate and convergent as frequencies approach zero. In this work, the inverse Gaussian probability distribution function is derived from general properties of spectral density functions at low and high frequencies for macromolecules in solution, using the principle of maximal entropy. This normalized distribution function is first used to calculate the correlation function, followed by the spectral density function. The resulting model-free spectral density functions are finite at a frequency of zero and can be used to describe distributions of either overall or internal correlation times using the model-free ansatz. To validate the approach, 15N spin-relaxation data for the bZip transcription factor domain of the Saccharomyces cerevisiae protein GCN4, in the absence of cognate DNA, were analyzed using the inverse Gaussian probability distribution for intramolecular correlation times. The results extend previous models for the conformational dynamics of the intrinsically disordered, DNA-binding region of the bZip transcription factor domain.
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Affiliation(s)
- Andrew Hsu
- Department of Chemistry, Columbia University, New York, New York
| | - Fabien Ferrage
- Laboratoire des Biomolécules, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
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Zhu YP, Wang M, Xiang Y, Qiu L, Hu S, Zhang Z, Mattjus P, Zhu X, Zhang Y. Nach Is a Novel Subgroup at an Early Evolutionary Stage of the CNC-bZIP Subfamily Transcription Factors from the Marine Bacteria to Humans. Int J Mol Sci 2018; 19:ijms19102927. [PMID: 30261635 PMCID: PMC6213907 DOI: 10.3390/ijms19102927] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/19/2018] [Accepted: 09/22/2018] [Indexed: 02/07/2023] Open
Abstract
Normal growth and development, as well as adaptive responses to various intracellular and environmental stresses, are tightly controlled by transcriptional networks. The evolutionarily conserved genomic sequences across species highlights the architecture of such certain regulatory elements. Among them, one of the most conserved transcription factors is the basic-region leucine zipper (bZIP) family. Herein, we have performed phylogenetic analysis of these bZIP proteins and found, to our surprise, that there exist a few homologous proteins of the family members Jun, Fos, ATF2, BATF, C/EBP and CNC (cap’n’collar) in either viruses or bacteria, albeit expansion and diversification of this bZIP superfamily have occurred in vertebrates from metazoan. Interestingly, a specific group of bZIP proteins is identified, designated Nach (Nrf and CNC homology), because of their strong conservation with all the known CNC and NF-E2 p45 subunit-related factors Nrf1 and Nrf2. Further experimental evidence has also been provided, revealing that Nach1 and Nach2 from the marine bacteria exert distinctive functions, when compared with human Nrf1 and Nrf2, in the transcriptional regulation of antioxidant response element (ARE)-battery genes. Collectively, further insights into these Nach/CNC-bZIP subfamily transcription factors provide a novel better understanding of distinct biological functions of these factors expressed in distinct species from the marine bacteria to humans.
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Affiliation(s)
- Yu-Ping Zhu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Meng Wang
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Yuancai Xiang
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Lu Qiu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Shaofan Hu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Zhengwen Zhang
- Institute of Neuroscience and Psychology, School of Life Sciences, University of Glasgow, 42 Western Common Road, Glasgow G22 5PQ, Scotland, UK.
| | - Peter Mattjus
- Department of Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Artillerigatan 6A, III, BioCity, FI-20520 Turku, Finland.
| | - Xiaomei Zhu
- Shanghai Center for Quantitative Life Science and Department of Physics, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
| | - Yiguo Zhang
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
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The Unfolded Protein Response Pathway in the Yeast Kluyveromyces lactis. A Comparative View among Yeast Species. Cells 2018; 7:cells7080106. [PMID: 30110882 PMCID: PMC6116095 DOI: 10.3390/cells7080106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/04/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic cells have evolved signalling pathways that allow adaptation to harmful conditions that disrupt endoplasmic reticulum (ER) homeostasis. When the function of the ER is compromised in a condition known as ER stress, the cell triggers the unfolded protein response (UPR) in order to restore ER homeostasis. Accumulation of misfolded proteins due to stress conditions activates the UPR pathway. In mammalian cells, the UPR is composed of three branches, each containing an ER sensor (PERK, ATF6 and IRE1). However, in yeast species, the only sensor present is the inositol-requiring enzyme Ire1. To cope with unfolded protein accumulation, Ire1 triggers either a transcriptional response mediated by a transcriptional factor that belongs to the bZIP transcription factor family or an mRNA degradation process. In this review, we address the current knowledge of the UPR pathway in several yeast species: Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida glabrata, Cryptococcus neoformans, and Candida albicans. We also include unpublished data on the UPR pathway of the budding yeast Kluyveromyces lactis. We describe the basic components of the UPR pathway along with similarities and differences in the UPR mechanism that are present in these yeast species.
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36
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Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Cell Rep 2018; 19:2383-2395. [PMID: 28614722 DOI: 10.1016/j.celrep.2017.05.069] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 04/07/2017] [Accepted: 05/22/2017] [Indexed: 01/25/2023] Open
Abstract
Although DNA modifications play an important role in gene regulation, the underlying mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of transcription factor binding to DNA modification in vitro using massively parallel sequencing. Feature-based modeling quantifies the effect of cytosine methylation (5mC) on binding free energy in a position-specific manner. Application to the human bZIP proteins ATF4 and C/EBPβ and three different Pbx-Hox complexes shows that 5mCpG can both increase and decrease affinity, depending on where the modification occurs within the protein-DNA interface. The TF paralogs tested vary in their methylation sensitivity, for which we provide a structural rationale. We show that 5mCpG can also enhance in vitro p53 binding and provide evidence for increased in vivo p53 occupancy at methylated binding sites, correlating with primed enhancer histone marks. Our results establish a powerful strategy for dissecting the epigenomic modulation of protein-DNA interactions and their role in gene regulation.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Siying Chen
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Gabriella D Martini
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - William A Freed-Pastor
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Richard S Mann
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA.
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Takai T, Matsuda T, Matsuura Y, Inoue K, Suzuki E, Kanno A, Kimura-Koyanagi M, Asahara SI, Hatano N, Ogawa W, Kido Y. Casein kinase 2 phosphorylates and stabilizes C/EBPβ in pancreatic β cells. Biochem Biophys Res Commun 2018; 497:451-456. [PMID: 29448105 DOI: 10.1016/j.bbrc.2018.02.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/11/2018] [Indexed: 12/27/2022]
Abstract
During the development of type 2 diabetes, endoplasmic reticulum (ER) stress leads to pancreatic β cell failure. CCAAT/enhancer-binding protein (C/EBP) β is highly induced by ER stress and AMP-activated protein kinase (AMPK) suppression in pancreatic β cells, and its accumulation reduces pancreatic β cell mass. We investigated the phosphorylation state of C/EBPβ under these conditions. Casein kinase 2 (CK2) was found to co-localize with C/EBPβ in MIN6 cells. It phosphorylated S222 of C/EBPβ, a previously unidentified phosphorylation site. We found that C/EBPβ is phosphorylated by CK2 under AMPK suppression and ER stress, which are important from the viewpoint of the worsening pathological condition of type 2 diabetes, such as decreased insulin secretion and apoptosis of pancreatic β cells.
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Affiliation(s)
- Tomoko Takai
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomokazu Matsuda
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuki Matsuura
- Division of Metabolism and Disease, Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Kaho Inoue
- Division of Metabolism and Disease, Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Emi Suzuki
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ayumi Kanno
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Maki Kimura-Koyanagi
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shun-Ichiro Asahara
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Naoya Hatano
- The Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Wataru Ogawa
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoshiaki Kido
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan; Division of Metabolism and Disease, Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan.
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Boga S, Bouzada D, García Peña D, Vázquez López M, Vázquez ME. Sequence-Specific DNA Recognition with Designed Peptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Boga
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Diego García Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Inorgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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Patel S. Pathogenicity-associated protein domains: The fiercely-conserved evolutionary signatures. GENE REPORTS 2017; 7:127-141. [PMID: 32363241 PMCID: PMC7185390 DOI: 10.1016/j.genrep.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/15/2022]
Abstract
Proteins have highly conserved domains that determine their functionality. Out of the thousands of domains discovered so far across all living forms, some of the predominant clinically-relevant domains include IENR1, HNHc, HELICc, Pro-kuma_activ, Tryp_SPc, Lactamase_B, PbH1, ChtBD3, CBM49, acidPPc, G3P_acyltransf, RPOL8c, KbaA, HAMP, HisKA, Hr1, Dak2, APC2, Citrate_ly_lig, DALR, VKc, YARHG, WR1, PWI, ZnF_BED, TUDOR, MHC_II_beta, Integrin_B_tail, Excalibur, DISIN, Cadherin, ACTIN, PROF, Robl_LC7, MIT, Kelch, GAS2, B41, Cyclin_C, Connexin_CCC, OmpH, Bac_rhodopsin, AAA, Knot1, NH, Galanin, IB, Elicitin, ACTH, Cache_2, CHASE, AgrB, PRP, IGR, and Antimicrobial21. These domains are distributed in nucleases/helicases, proteases, esterases, lipases, glycosylase, GTPases, phosphatases, methyltransferases, acyltransferase, acetyltransferase, polymerase, kinase, ligase, synthetase, oxidoreductase, protease inhibitors, nucleic acid binding proteins, adhesion and immunity-related proteins, cytoskeletal component-manipulating proteins, lipid biosynthesis and metabolism proteins, membrane-associated proteins, hormone-like and signaling proteins, etc. These domains are ubiquitous stretches or folds of the proteins in pathogens and allergens. Pathogenesis alleviation efforts can benefit enormously if the characteristics of these domains are known. Hence, this review catalogs and discusses the role of such pivotal domains, suggesting hypotheses for better understanding of pathogenesis at molecular level. Proteins have highly conserved regions or domains across pathogens and allergens. Knowledge on these critical domains can facilitate our understanding of pathogenesis mechanisms. Such immune manipulation-related domains include IENR1, HNHc, HELICc, ACTIN, PROF, Robl_LC7, OmpH etc. These domains are presnt in enzyme, transcription regulators, adhesion proteins, and hormones. This review discusses and hypothesizes on these domains.
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Key Words
- CARDs, caspase activation and recruitment domains
- CBM, carbohydrate binding module
- CTD, C-terminal domain
- ChtBD, chitin-binding domain
- Diversification
- HNHc, homing endonucleases
- HTH, helix-turn-helix
- IENR1, intron-encoded endonuclease repeat
- Immune manipulation
- PAMPs, pathogen associated molecular patterns
- Pathogenesis
- Phylogenetic conservation
- Protein domains
- SMART, Simple Modular Architecture Research Tool
- Shuffling
- UDG, uracil DNA glycosylase
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA
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40
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Fang Y, Tyler BM. Nuclear localization of a putative Phytophthora sojae bZIP1 transcription factor is mediated by multiple targeting motifs. Mol Microbiol 2017; 104:621-635. [PMID: 28213898 DOI: 10.1111/mmi.13652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2017] [Indexed: 11/28/2022]
Abstract
Oomycetes are fungal-like eukaryotic microbes in the kingdom Stramenopila. We recently found that the oomycete plant pathogen Phytophthora sojae uses nuclear localization signals (NLSs) for translocation of proteins into the nucleus that differ from conventional well-characterized NLSs from mammals and yeast. Here, we have characterized in depth the NLSs of a P. sojae basic leucine zipper transcription factor, PsbZIP1. Nuclear localization of PsbZIP1 was determined by a central conserved region overlapping the DNA binding domain. Mutational analysis of this region identified four distinct elements that contributed multiplicatively to nuclear localization, but the conserved DNA binding residues were not required. Three of the elements showed autonomous NLS activity and the fourth served as a nuclear localization enhancer. Sequences within two of the nuclear localization elements defined a new form of bipartite NLS consisting of a triplet of basic residues followed by a tail of scattered basic amino acids.
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Affiliation(s)
- Yufeng Fang
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics & Computational Biology, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, 24061, USA.,Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brett M Tyler
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics & Computational Biology, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, 24061, USA.,Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
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Shammas SL. Mechanistic roles of protein disorder within transcription. Curr Opin Struct Biol 2017; 42:155-161. [PMID: 28262589 DOI: 10.1016/j.sbi.2017.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 12/28/2022]
Abstract
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.
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Affiliation(s)
- Sarah L Shammas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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42
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Rodríguez-Martínez JA, Reinke AW, Bhimsaria D, Keating AE, Ansari AZ. Combinatorial bZIP dimers display complex DNA-binding specificity landscapes. eLife 2017; 6:e19272. [PMID: 28186491 PMCID: PMC5349851 DOI: 10.7554/elife.19272] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 02/06/2017] [Indexed: 01/06/2023] Open
Abstract
How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or 'emergent' sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers. These binding sites were biochemically validated by EMSA-FRET analysis and validated in vivo by ChIP-seq data from human cell lines. Focusing on ATF3, we observed distinct cognate site preferences conferred by different bZIP partners, and demonstrated that genome-wide binding of ATF3 is best explained by considering many dimers in which it participates. Importantly, our compendium of bZIP-DNA interactomes predicted bZIP binding to 156 disease associated SNPs, of which only 20 were previously annotated with known bZIP motifs.
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Affiliation(s)
| | - Aaron W Reinke
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, Unites States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
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43
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Patel S. In silico analysis of Hepatitis C virus (HCV) polyprotein domains and their comparison with other pathogens and allergens to gain insight on pathogenicity mechanisms. Comput Biol Chem 2016; 65:91-102. [DOI: 10.1016/j.compbiolchem.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/12/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022]
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Gill ML, Byrd RA, Palmer AG. Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region. Phys Chem Chem Phys 2016; 18:5839-49. [PMID: 26661739 PMCID: PMC4894059 DOI: 10.1039/c5cp06197k] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are known to play important roles in regulatory and signaling pathways. A critical aspect of these functions is the ability of IDP/IDRs to form highly specific complexes with target molecules. However, elucidation of the contributions of conformational dynamics to function has been limited by challenges associated with structural heterogeneity of IDP/IDRs. Using NMR spin relaxation parameters ((15)N R1, (15)N R2, and {(1)H}-(15)N heteronuclear NOE) collected at four static magnetic fields ranging from 14.1 to 21.1 T, we have analyzed the backbone dynamics of the basic leucine-zipper (bZip) domain of the Saccharomyces cerevisiae transcription factor GCN4, whose DNA binding domain is intrinsically disordered in the absence of DNA substrate. We demonstrate that the extended model-free analysis can be applied to proteins with IDRs such as apo GCN4 and that these results significantly extend previous NMR studies of GCN4 dynamics performed using a single static magnetic field of 11.74 T [Bracken, et al., J. Mol. Biol., 1999, 285, 2133-2146] and correlate well with molecular dynamics simulations [Robustelli, et al., J. Chem. Theory Comput., 2013, 9, 5190-5200]. In contrast to the earlier work, data at multiple static fields allows the time scales of internal dynamics of GCN4 to be reliably quantified. Large amplitude dynamic fluctuations in the DNA-binding region have correlation times (τs ≈ 1.4-2.5 ns) consistent with a two-step mechanism in which partially ordered bZip conformations of GCN4 form initial encounter complexes with DNA and then rapidly rearrange to the high affinity state with fully formed basic region recognition helices.
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Affiliation(s)
- Michelle L Gill
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. and Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - R Andrew Byrd
- Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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45
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Jindrich K, Degnan BM. The diversification of the basic leucine zipper family in eukaryotes correlates with the evolution of multicellularity. BMC Evol Biol 2016; 16:28. [PMID: 26831906 PMCID: PMC4736632 DOI: 10.1186/s12862-016-0598-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/19/2016] [Indexed: 01/01/2023] Open
Abstract
Background Multicellularity evolved multiple times in eukaryotes. In all cases, this required an elaboration of the regulatory mechanisms controlling gene expression. Amongst the conserved eukaryotic transcription factor families, the basic leucine zipper (bZIP) superfamily is one of the most ancient and best characterised. This gene family plays a diversity of roles in the specification, differentiation and maintenance of cell types in plants and animals. bZIPs are also involved in stress responses and the regulation of cell proliferation in fungi, amoebozoans and heterokonts. Results Using 49 sequenced genomes from across the Eukaryota, we demonstrate that the bZIP superfamily has evolved from a single ancestral eukaryotic gene and undergone multiple independent expansions. bZIP family diversification is largely restricted to multicellular lineages, consistent with bZIPs contributing to the complex regulatory networks underlying differential and cell type-specific gene expression in these lineages. Analyses focused on the Metazoa suggest an elaborate bZIP network was in place in the most recent shared ancestor of all extant animals that was comprised of 11 of the 12 previously recognized families present in modern taxa. In addition this analysis identifies three bZIP families that appear to have been lost in mammals. Thus the ancestral metazoan and eumetazoan bZIP repertoire consists of 12 and 16 bZIPs, respectively. These diversified from 7 founder genes present in the holozoan ancestor. Conclusions Our results reveal the ancestral opisthokont, holozoan and metazoan bZIP repertoire and provide insights into the progressive expansion and divergence of bZIPs in the five main eukaryotic kingdoms, suggesting that the early diversification of bZIPs in multiple eukaryotic lineages was a prerequisite for the evolution of complex multicellular organisms. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0598-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katia Jindrich
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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46
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Khakpour S, Wilhelmsen K, Hellman J. Vascular endothelial cell Toll-like receptor pathways in sepsis. Innate Immun 2015; 21:827-46. [DOI: 10.1177/1753425915606525] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/11/2015] [Indexed: 12/20/2022] Open
Abstract
The endothelium forms a vast network that dynamically regulates vascular barrier function, coagulation pathways and vasomotor tone. Microvascular endothelial cells are uniquely situated to play key roles during infection and injury, owing to their widespread distribution throughout the body and their constant interaction with circulating blood. While not viewed as classical immune cells, endothelial cells express innate immune receptors, including the Toll-like receptors (TLRs), which activate intracellular inflammatory pathways mediated through NF-κB and the MAP kinases. TLR agonists, including LPS and bacterial lipopeptides, directly upregulate microvascular endothelial cell expression of inflammatory mediators. Intriguingly, TLR activation also modulates microvascular endothelial cell permeability and the expression of coagulation pathway intermediaries. Microvascular thrombi have been hypothesized to trap microorganisms thereby limiting the spread of infection. However, dysregulated activation of endothelial inflammatory pathways is also believed to lead to coagulopathy and increased vascular permeability, which together promote sepsis-induced organ failure. This article reviews vascular endothelial cell innate immune pathways mediated through the TLRs as they pertain to sepsis, highlighting links between TLRs and coagulation and permeability pathways, and their role in healthy and pathologic responses to infection and sepsis.
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Affiliation(s)
- Samira Khakpour
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
- Biomedical Sciences and Immunology Programs, University of California, San Francisco, CA, USA
| | - Kevin Wilhelmsen
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
| | - Judith Hellman
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
- Biomedical Sciences and Immunology Programs, University of California, San Francisco, CA, USA
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47
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Conformational ensembles explored dynamically from disordered peptides targeting chemokine receptor CXCR4. Int J Mol Sci 2015; 16:12159-73. [PMID: 26030674 PMCID: PMC4490436 DOI: 10.3390/ijms160612159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/20/2015] [Indexed: 11/17/2022] Open
Abstract
This work reports on the design and the synthesis of two short linear peptides both containing a few amino acids with disorder propensity and an allylic ester group at the C-terminal end. Their structural properties were firstly analyzed by means of experimental techniques in solution such as CD and NMR methods that highlighted peptide flexibility. These results were further confirmed by MD simulations that demonstrated the ability of the peptides to assume conformational ensembles. They revealed a network of transient and dynamic H-bonds and interactions with water molecules. Binding assays with a well-known drug-target, i.e., the CXCR4 receptor, were also carried out in an attempt to verify their biological function and the possibility to use the assays to develop new specific targets for CXCR4. Moreover, our data indicate that these peptides represent useful tools for molecular recognition processes in which a flexible conformation is required in order to obtain an interaction with a specific target.
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48
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Xu H, Malinin NL, Awasthi N, Schwarz RE, Schwarz MA. The N terminus of pro-endothelial monocyte-activating polypeptide II (EMAP II) regulates its binding with the C terminus, arginyl-tRNA synthetase, and neurofilament light protein. J Biol Chem 2015; 290:9753-66. [PMID: 25724651 DOI: 10.1074/jbc.m114.630533] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 12/17/2022] Open
Abstract
Pro-endothelial monocyte-activating polypeptide II (EMAP II), one component of the multi-aminoacyl tRNA synthetase complex, plays multiple roles in physiological and pathological processes of protein translation, signal transduction, immunity, lung development, and tumor growth. Recent studies have determined that pro-EMAP II has an essential role in maintaining axon integrity in central and peripheral neural systems where deletion of the C terminus of pro-EMAP II has been reported in a consanguineous Israeli Bedouin kindred suffering from Pelizaeus-Merzbacher-like disease. We hypothesized that the N terminus of pro-EMAP II has an important role in the regulation of protein-protein interactions. Using a GFP reporter system, we defined a putative leucine zipper in the N terminus of human pro-EMAP II protein (amino acid residues 1-70) that can form specific strip-like punctate structures. Through GFP punctum analysis, we uncovered that the pro-EMAP II C terminus (amino acids 147-312) can repress GFP punctum formation. Pulldown assays confirmed that the binding between the pro-EMAP II N terminus and its C terminus is mediated by a putative leucine zipper. Furthermore, the pro-EMAP II 1-70 amino acid region was identified as the binding partner of arginyl-tRNA synthetase, a polypeptide of the multi-aminoacyl tRNA synthetase complex. We also determined that the punctate GFP pro-EMAP II 1-70 amino acid aggregate colocalizes and binds to the neurofilament light subunit protein that is associated with pathologic neurofilament network disorganization and degeneration of motor neurons. These findings indicate the structure and binding interaction of pro-EMAP II protein and suggest a role of this protein in pathological neurodegenerative diseases.
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Affiliation(s)
- Haiming Xu
- From the Department of Pediatrics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 and
| | - Nikolay L Malinin
- the Indiana University School of Medicine, South Bend, Indiana 46617
| | - Niranjan Awasthi
- the Indiana University School of Medicine, South Bend, Indiana 46617
| | | | - Margaret A Schwarz
- From the Department of Pediatrics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 and the Indiana University School of Medicine, South Bend, Indiana 46617
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49
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Cukier RI. Dihedral angle entropy measures for intrinsically disordered proteins. J Phys Chem B 2015; 119:3621-34. [PMID: 25679039 DOI: 10.1021/jp5102412] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein stability is based on a delicate balance between energetic and entropic factors. Intrinsically disordered proteins (IDPs) interacting with a folded partner protein in the act of binding can order the IDP to form the correct functional interface by decrease in the overall free energy. In this work, we evaluate the part of the entropic cost of ordering an IDP arising from their dihedral states. The IDP studied is a leucine zipper dimer that we simulate with molecular dynamics and find that it does show disorder in six phi and psi dihedral angles of the N terminal sequence of one monomer. Essential to ascertain is the degree of disorder in the IDP, and we do so by considering the entire, discretized probability distribution function of N dihedrals with M conformers per dihedral. A compositional clustering method is introduced, whereby the NS = N(M) states are formed from the Cartesian product of each dihedral's conformational space. Clustering is carried out with a version of a k-means algorithm that accounts for the circular nature of dihedral angles. For the 12 dihedrals each found to have three conformers, among the resulting 531441 states, their populations show that the first 100 (500) most populated states account for ∼65% (∼90%) of the entire population, indicating that there are strong dependencies among the dihedrals' conformations. These state populations are used to evaluate a Kullback-Leibler divergence entropy measure and obtain the dihedral configurational entropy S. At 300 K, TS ∼ 3 kcal/mol, showing that IDP entropy, while roughly half that would be expected from independently distributed dihedrals, can be a decisive contributor to the free energy of this IDP binding and ordering.
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Affiliation(s)
- Robert I Cukier
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824-1322, United States
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50
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Hortschansky P, Ando E, Tuppatsch K, Arikawa H, Kobayashi T, Kato M, Haas H, Brakhage AA. Deciphering the combinatorial DNA-binding code of the CCAAT-binding complex and the iron-regulatory basic region leucine zipper (bZIP) transcription factor HapX. J Biol Chem 2015; 290:6058-70. [PMID: 25589790 DOI: 10.1074/jbc.m114.628677] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The heterotrimeric CCAAT-binding complex (CBC) is evolutionarily conserved in eukaryotic organisms, including fungi, plants, and mammals. The CBC consists of three subunits, which are named in the filamentous fungus Aspergillus nidulans HapB, HapC, and HapE. HapX, a fourth CBC subunit, was identified exclusively in fungi, except for Saccharomyces cerevisiae and the closely related Saccharomycotina species. The CBC-HapX complex acts as the master regulator of iron homeostasis. HapX belongs to the class of basic region leucine zipper transcription factors. We demonstrated that the CBC and HapX bind cooperatively to bipartite DNA motifs with a general HapX/CBC/DNA 2:1:1 stoichiometry in a class of genes that are repressed by HapX-CBC in A. nidulans during iron limitation. This combinatorial binding mode requires protein-protein interaction between the N-terminal domain of HapE and the N-terminal CBC binding domain of HapX as well as sequence-specific DNA binding of both the CBC and HapX. Initial binding of the CBC to CCAAT boxes is mandatory for DNA recognition of HapX. HapX specifically targets the minimal motif 5'-GAT-3', which is located at a distance of 11-12 bp downstream of the respective CCAAT box. Single nucleotide substitutions at the 5'- and 3'-end of the GAT motif as well as different spacing between the CBC and HapX DNA-binding sites revealed a remarkable promiscuous DNA-recognition mode of HapX. This flexible DNA-binding code may have evolved as a mechanism for fine-tuning the transcriptional activity of CBC-HapX at distinct target promoters.
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Affiliation(s)
- Peter Hortschansky
- From the Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, D-07745 Jena, Germany
| | - Eriko Ando
- the Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Katja Tuppatsch
- From the Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, D-07745 Jena, Germany
| | - Hisashi Arikawa
- the Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Tetsuo Kobayashi
- the Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masashi Kato
- the Faculty of Agriculture, Meijo University, Shiogama-guchi 1-501, Nagoya 468-8502, Japan
| | - Hubertus Haas
- the Division of Molecular Biology, Biocenter, Innsbruck Medical University, A-6020 Innsbruck, Austria, and
| | - Axel A Brakhage
- From the Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, D-07745 Jena, Germany, the Department of Microbiology and Molecular Biology, Institute for Microbiology, Friedrich Schiller University, D-07743 Jena, Germany
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