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Guiza Beltran D, Wan T, Zhang L. WhiB-like proteins: Diversity of structure, function and mechanism. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119787. [PMID: 38879133 PMCID: PMC11365794 DOI: 10.1016/j.bbamcr.2024.119787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/20/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
The WhiB-Like (Wbl) proteins are a large family of iron-sulfur (Fe-S) cluster-containing transcription factors exclusively found in the phylum Actinobacteria, including the notable genera like Mycobacteria, Streptomycetes and Corynebacteria. These proteins play pivotal roles in diverse biological processes, such as cell development, redox stress response and antibiotic resistance. Members of the Wbl family exhibit remarkable diversity in their sequences, structures and functions, attracting great attention since their first discovery. This review highlights the most recent breakthroughs in understanding the structural and mechanistic aspects of Wbl-dependent transcriptional regulation.
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Affiliation(s)
- Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA
| | - Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA
| | - LiMei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA.
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2
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Battista S, Fedele M, Secco L, Ingo AMD, Sgarra R, Manfioletti G. Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove. Int J Mol Sci 2024; 25:8863. [PMID: 39201549 PMCID: PMC11354804 DOI: 10.3390/ijms25168863] [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: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
The "AT-hook" is a peculiar DNA-binding domain that interacts with DNA in the minor groove in correspondence to AT-rich sequences. This domain has been first described in the HMGA protein family of architectural factors and later in various transcription factors and chromatin proteins, often in association with major groove DNA-binding domains. In this review, using a literature search, we identified about one hundred AT-hook-containing proteins, mainly chromatin proteins and transcription factors. After considering the prototypes of AT-hook-containing proteins, the HMGA family, we review those that have been studied in more detail and that have been involved in various pathologies with a particular focus on cancer. This review shows that the AT-hook is a domain that gives proteins not only the ability to interact with DNA but also with RNA and proteins. This domain can have enzymatic activity and can influence the activity of the major groove DNA-binding domain and chromatin docking modules when present, and its activity can be modulated by post-translational modifications. Future research on the function of AT-hook-containing proteins will allow us to better decipher their function and contribution to the different pathologies and to eventually uncover their mutual influences.
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Affiliation(s)
- Sabrina Battista
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Luca Secco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | - Guidalberto Manfioletti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
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3
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Wilhelm E, Poirier M, Da Rocha M, Bédard M, McDonald PP, Lavigne P, Hunter CL, Bell B. Mitotic deacetylase complex (MiDAC) recognizes the HIV-1 core promoter to control activated viral gene expression. PLoS Pathog 2024; 20:e1011821. [PMID: 38781120 PMCID: PMC11115230 DOI: 10.1371/journal.ppat.1011821] [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: 11/15/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
The human immunodeficiency virus (HIV) integrates into the host genome forming latent cellular reservoirs that are an obstacle for cure or remission strategies. Viral transcription is the first step in the control of latency and depends upon the hijacking of the host cell RNA polymerase II (Pol II) machinery by the 5' HIV LTR. Consequently, "block and lock" or "shock and kill" strategies for an HIV cure depend upon a full understanding of HIV transcriptional control. The HIV trans-activating protein, Tat, controls HIV latency as part of a positive feed-forward loop that strongly activates HIV transcription. The recognition of the TATA box and adjacent sequences of HIV essential for Tat trans-activation (TASHET) of the core promoter by host cell pre-initiation complexes of HIV (PICH) has been shown to be necessary for Tat trans-activation, yet the protein composition of PICH has remained obscure. Here, DNA-affinity chromatography was employed to identify the mitotic deacetylase complex (MiDAC) as selectively recognizing TASHET. Using biophysical techniques, we show that the MiDAC subunit DNTTIP1 binds directly to TASHET, in part via its CTGC DNA motifs. Using co-immunoprecipitation assays, we show that DNTTIP1 interacts with MiDAC subunits MIDEAS and HDAC1/2. The Tat-interacting protein, NAT10, is also present in HIV-bound MiDAC. Gene silencing revealed a functional role for DNTTIP1, MIDEAS, and NAT10 in HIV expression in cellulo. Furthermore, point mutations in TASHET that prevent DNTTIP1 binding block the reactivation of HIV by latency reversing agents (LRA) that act via the P-TEFb/7SK axis. Our data reveal a key role for MiDAC subunits DNTTIP1, MIDEAS, as well as NAT10, in Tat-activated HIV transcription and latency. DNTTIP1, MIDEAS and NAT10 emerge as cell cycle-regulated host cell transcription factors that can control activated HIV gene expression, and as new drug targets for HIV cure strategies.
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Affiliation(s)
| | | | - Morgane Da Rocha
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Mikaël Bédard
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Patrick P. McDonald
- Pulmonary Division, Medicine Faculty, Université de Sherbrooke; and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Pierre Lavigne
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | | | - Brendan Bell
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
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4
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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [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: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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5
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Blanc-Mathieu R, Dumas R, Turchi L, Lucas J, Parcy F. Plant-TFClass: a structural classification for plant transcription factors. TRENDS IN PLANT SCIENCE 2024; 29:40-51. [PMID: 37482504 DOI: 10.1016/j.tplants.2023.06.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.
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Affiliation(s)
- Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France.
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6
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Porter RS, Nagai M, An S, Gavilan MC, Murata-Nakamura Y, Bonefas KM, Zhou B, Dionne O, Manuel JM, St-Germain J, Browning L, Laurent B, Cho US, Iwase S. A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563357. [PMID: 37904995 PMCID: PMC10614952 DOI: 10.1101/2023.10.20.563357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A -n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.
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7
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Kuwayama N, Kujirai T, Kishi Y, Hirano R, Echigoya K, Fang L, Watanabe S, Nakao M, Suzuki Y, Ishiguro KI, Kurumizaka H, Gotoh Y. HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation. Nat Commun 2023; 14:6420. [PMID: 37828010 PMCID: PMC10570362 DOI: 10.1038/s41467-023-42094-9] [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: 01/09/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Identification of factors that regulate chromatin condensation is important for understanding of gene regulation. High-mobility group AT-hook (HMGA) proteins 1 and 2 are abundant nonhistone chromatin proteins that play a role in many biological processes including tissue stem-progenitor cell regulation, but the nature of their protein function remains unclear. Here we show that HMGA2 mediates direct condensation of polynucleosomes and forms droplets with nucleosomes. Consistently, most endogenous HMGA2 localized to transposase 5- and DNase I-inaccessible chromatin regions, and its binding was mostly associated with gene repression, in mouse embryonic neocortical cells. The AT-hook 1 domain was necessary for chromatin condensation by HMGA2 in vitro and in cellulo, and an HMGA2 mutant lacking this domain was defective in the ability to maintain neuronal progenitors in vivo. Intrinsically disordered regions of other proteins could substitute for the AT-hook 1 domain in promoting this biological function of HMGA2. Taken together, HMGA2 may regulate neural cell fate by its chromatin condensation activity.
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Grants
- This research was supported by AMED-CREST and AMED-PRIME of the Japan Agency for Medical Research and Development (JP22gm1310004, JP22gm6110021), SECOM Science and Technology Foundation SECOM Science and Technology Foundation (for Y.K.), Platform Project for Supporting Drug Discovery and Life Science Research from AMED JP21am0101076 and (for H.K.), Research Support Project for Life Science and Drug Discovery from AMED JP22ama121009 (for H.K.), Japan Science and Technology Agency ERATO JPMJER1901 (for H.K.) and by KAKENHI grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan and the Japan Society for the Promotion of Science (JP21J14115 for N.K.; JP22K15033 for T.K.;16H06279, 20H03179, 21H00242 and 22H04687 for Y.K.; 20K07589 for S.W.; JP20H00449, JP18H05534 for H.K.; JP22H00431, JP16H06279 and JP22H04925 for Y.G.)
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Affiliation(s)
- Naohiro Kuwayama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Kishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rina Hirano
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Kenta Echigoya
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Lingyan Fang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Sugiko Watanabe
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Mitsuyoshi Nakao
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Kei-Ichiro Ishiguro
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, 113-0033, Japan.
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8
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Mori M, Ghirga F, Amato B, Secco L, Quaglio D, Romeo I, Gambirasi M, Bergamo A, Covaceuszach S, Sgarra R, Botta B, Manfioletti G. Selection of Natural Compounds with HMGA-Interfering Activities and Cancer Cell Cytotoxicity. ACS OMEGA 2023; 8:32424-32431. [PMID: 37720761 PMCID: PMC10500574 DOI: 10.1021/acsomega.3c02043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/30/2023] [Indexed: 09/19/2023]
Abstract
HMGA proteins are intrinsically disordered (ID) chromatin architectural factors characterized by three DNA binding domains (AT-hooks) that allow them to bind into the DNA minor groove of AT-rich stretches. HMGA are functionally involved in regulating transcription, RNA processing, DNA repair, and chromatin remodeling and dynamics. These proteins are highly expressed and play essential functions during embryonic development. They are almost undetectable in adult tissues but are re-expressed at high levels in all cancers where they are involved in neoplastic transformation and cancer progression. We focused on identifying new small molecules capable of binding into the minor groove of AT-rich DNA sequences that could compete with HMGA for DNA binding and, thus, potentially interfere with their activities. Here, a docking-based virtual screening of a unique high diversity in-house library composed of around 1000 individual natural products identified 16 natural compounds as potential minor groove binders that could inhibit the interaction between HMGA and DNA. To verify the ability of these selected compounds to compete with HMGA proteins, we screened them using electrophoretic mobility shift assays. We identified Sorocein C, a Diels-Alder (D-A)-type adducts, isolated from Sorocea ilicifolia and Sorocea bonplandii with an HMGA/DNA-displacing activity and compared its activity with that of two structurally related compounds, Sorocein A and Sorocein B. All these compounds showed a cytotoxicity effect on cancer cells, suggesting that the Sorocein-structural family may provide new and yet unexplored chemotypes for the development of minor groove binders to be evaluated as anticancer agents.
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Affiliation(s)
- Mattia Mori
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Francesca Ghirga
- Department
of Chemistry and Technology of Drugs, Sapienza-University
of Rome, Rome 00185, Italy
| | - Beatrice Amato
- Department
of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Luca Secco
- Department
of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Deborah Quaglio
- Department
of Chemistry and Technology of Drugs, Sapienza-University
of Rome, Rome 00185, Italy
| | - Isabella Romeo
- Department
of Chemistry and Technology of Drugs, Sapienza-University
of Rome, Rome 00185, Italy
| | - Marta Gambirasi
- Department
of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Alberta Bergamo
- Department
of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Sonia Covaceuszach
- Institute
of Crystallography, National Research Council, Trieste Outstation, Basovizza, Trieste 34149, Italy
| | - Riccardo Sgarra
- Department
of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Bruno Botta
- Department
of Chemistry and Technology of Drugs, Sapienza-University
of Rome, Rome 00185, Italy
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Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL. Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA. RSC Chem Biol 2023; 4:486-493. [PMID: 37415868 PMCID: PMC10320839 DOI: 10.1039/d3cb00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
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Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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10
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Wan T, Horová M, Khetrapal V, Li S, Jones C, Schacht A, Sun X, Zhang L. Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis. J Biol Chem 2023; 299:104777. [PMID: 37142222 PMCID: PMC10245118 DOI: 10.1016/j.jbc.2023.104777] [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: 07/29/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) WhiB3 is an iron-sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σA4) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σA4 to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σA4 complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σA4 complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σA4 and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Vimmy Khetrapal
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Camden Jones
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Andrew Schacht
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - LiMei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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11
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DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing. Nat Commun 2023; 14:874. [PMID: 36797253 PMCID: PMC9935910 DOI: 10.1038/s41467-023-36600-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Expanding mitochondrial base editing tools with broad sequence compatibility is of high need for both research and therapeutic purposes. In this study, we identify a DddA homolog from Simiaoa sunii (Ddd_Ss) which can efficiently deaminate cytosine in DC context in double-stranded DNA (dsDNA). We successfully develop Ddd_Ss-derived cytosine base editors (DdCBE_Ss) and introduce mutations at multiple mitochondrial DNA (mtDNA) loci including disease-associated mtDNA mutations in previously inaccessible GC context. Finally, by introducing a single amino acid substitution from Ddd_Ss, we successfully improve the activity and sequence compatibility of DdCBE derived from DddA of Burkholderia cenocepacia (DdCBE_Bc). Our study expands mtDNA editing tool boxes and provides resources for further screening and engineering dsDNA base editors for biological and therapeutic applications.
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12
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Wang J, Yang B, Zhang X, Liu S, Pan X, Ma C, Ma S, Yu D, Wu W. Chromobox proteins in cancer: Multifaceted functions and strategies for modulation (Review). Int J Oncol 2023; 62:36. [PMID: 36734270 PMCID: PMC9937689 DOI: 10.3892/ijo.2023.5484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 02/01/2023] Open
Abstract
Chromobox (CBX) proteins are important epigenetic regulatory proteins and are widely involved in biological processes, such as embryonic development, the maintenance of stem cell characteristics and the regulation of cell proliferation and apoptosis. Disorder and dysfunction of CBXs in cancer usually lead to the blockade or ectoptic activation of developmental pathways, promoting the occurrence, development and progression of cancer. In the present review, the characteristics and functions of CBXs were first introduced. Subsequently, the expression of CBXs in cancers and the relationship between CBXs and clinical characteristics (mainly cancer grade, stage, metastasis and relapse) and prognosis were discussed. Finally, it was described how CBXs regulate cell proliferation and self‑renewal, apoptosis and the acquisition of malignant phenotypes, such as invasion, migration and chemoresistance, through mechanisms involving epigenetic modification, nuclear translocation, noncoding RNA interactions, transcriptional regulation, posttranslational modifications, protein‑protein interactions, signal transduction and metabolic reprogramming. The study also focused on cancer therapies targeting CBXs. The present review provides new insight and a comprehensive basis for follow‑up research on CBXs and cancer.
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Affiliation(s)
- Jian Wang
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Bo Yang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xiuhang Zhang
- Department of Burn Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shuhan Liu
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xiaoqiang Pan
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Changkai Ma
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shiqiang Ma
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Dehai Yu
- Department of Public Research Platform, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China,Professor Dehai Yu, Public Research Platform, The First Hospital of Jilin University, 1 Xinmin Street, Changchun, Jilin 130021, P.R. China, E-mail:
| | - Wei Wu
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China,Correspondence to: Professor Wei Wu, Department of Neurovascular Surgery, The First Hospital of Jilin University, 1 Xinmin Street, Changchun, Jilin 130021, P.R. China, E-mail:
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13
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Sipe SN, Jeanne Dit Fouque K, Garabedian A, Leng F, Fernandez-Lima F, Brodbelt JS. Exploring the Conformations and Binding Location of HMGA2·DNA Complexes Using Ion Mobility Spectrometry and 193 nm Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1092-1102. [PMID: 35687872 PMCID: PMC9274541 DOI: 10.1021/jasms.2c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Although it is widely accepted that protein function is largely dependent on its structure, intrinsically disordered proteins (IDPs) lack defined structure but are essential in proper cellular processes. Mammalian high mobility group proteins (HMGA) are one such example of IDPs that perform a number of crucial nuclear activities and have been highly studied due to their involvement in the proliferation of a variety of disease and cancers. Traditional structural characterization methods have had limited success in understanding HMGA proteins and their ability to coordinate to DNA. Ion mobility spectrometry and mass spectrometry provide insights into the diversity and heterogeneity of structures adopted by IDPs and are employed here to interrogate HMGA2 in its unbound states and bound to two DNA hairpins. The broad distribution of collision cross sections observed for the apo-protein are restricted when HMGA2 is bound to DNA, suggesting that increased protein organization is promoted in the holo-form. Ultraviolet photodissociation was utilized to probe the changes in structures for the compact and elongated structures of HMGA2 by analyzing backbone cleavage propensities and solvent accessibility based on charge-site analysis, which revealed a spectrum of conformational possibilities. Namely, preferential binding of the DNA hairpins with the second of three AT-hooks of HMGA2 is suggested based on the suppression of backbone fragmentation and distribution of DNA-containing protein fragments.
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Affiliation(s)
- Sarah N Sipe
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
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14
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Jeanne Dit Fouque K, Sipe SN, Garabedian A, Mejia G, Su L, Hossen ML, Chapagain PP, Leng F, Brodbelt JS, Fernandez-Lima F. Exploring the Conformational and Binding Dynamics of HMGA2·DNA Complexes Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1103-1112. [PMID: 35687119 PMCID: PMC9280850 DOI: 10.1021/jasms.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is an intrinsically disordered DNA-binding protein expressed during embryogenesis. In the present work, the conformational and binding dynamics of HMGA2 and HMGA2 in complex with a 22-nt (DNA22) and a 50-nt (DNA50) AT-rich DNA hairpin were investigated using trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) under native starting solvent conditions (e.g., 100 mM aqueous NH4Ac) and collision-induced unfolding/dissociation (CIU/CID) as well as solution fluorescence anisotropy to assess the role of the DNA ligand when binding to the HMGA2 protein. CIU-TIMS-CID-MS/MS experiments showed a significant reduction of the conformational space and charge-state distribution accompanied by an energy stability increase of the native HMGA2 upon DNA binding. Fluorescence anisotropy experiments and CIU-TIMS-CID-MS/MS demonstrated for the first time that HMGA2 binds with high affinity to the minor groove of AT-rich DNA oligomers and with lower affinity to the major groove of AT-rich DNA oligomers (minor groove occupied by a minor groove binder Hoechst 33258). The HMGA2·DNA22 complex (18.2 kDa) 1:1 and 1:2 stoichiometry suggests that two of the AT-hook sites are accessible for DNA binding, while the other AT-hook site is probably coordinated by the C-terminal motif peptide (CTMP). The HMGA2 transition from disordered to ordered upon DNA binding is driven by the interaction of the three basic AT-hook residues with the minor and/or major grooves of AT-rich DNA oligomers.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Sarah N Sipe
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - German Mejia
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Linjia Su
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Md Lokman Hossen
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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15
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Gómez-González J, Martínez-Castro L, Tolosa-Barrilero J, Alcalde-Ordóñez A, Learte-Aymamí S, Mascareñas JL, García-Martínez JC, Martínez-Costas J, Maréchal JD, Vázquez López M, Vázquez ME. Selective recognition of A/T-rich DNA 3-way junctions with a three-fold symmetric tripeptide. Chem Commun (Camb) 2022; 58:7769-7772. [PMID: 35730795 DOI: 10.1039/d2cc02874c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Non-canonical DNA structures, particularly 3-Way Junctions (3WJs) that are transiently formed during DNA replication, have recently emerged as promising chemotherapeutic targets. Here, we describe a new approach to target 3WJs that relies on the cooperative and sequence-selective recognition of A/T-rich duplex DNA branches by three AT-Hook peptides attached to a three-fold symmetric and fluorogenic 1,3,5-tristyrylbenzene core.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - Laura Martínez-Castro
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Juan Tolosa-Barrilero
- Department of Inorganic, Organic Chemistry and Biochemistry, Faculty of Pharmacy, University of Castilla-La Mancha, 02071 Albacete, Spain.,Regional Center for Biomedical Research (CRIB), 02071 Albacete, Spain
| | - Ana Alcalde-Ordóñez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - Joaquín C García-Martínez
- Department of Inorganic, Organic Chemistry and Biochemistry, Faculty of Pharmacy, University of Castilla-La Mancha, 02071 Albacete, Spain.,Regional Center for Biomedical Research (CRIB), 02071 Albacete, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
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16
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Garabedian A, Jeanne Dit Fouque K, Chapagain PP, Leng F, Fernandez-Lima F. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2431-2439. [PMID: 35212375 PMCID: PMC8934665 DOI: 10.1093/nar/gkac115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/30/2021] [Accepted: 02/08/2022] [Indexed: 11/25/2022] Open
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) houses three motifs that preferentially bind short stretches of AT-rich DNA regions. These DNA binding motifs, known as ‘AT-hooks’, are traditionally characterized as being unstructured. Upon binding to AT-rich DNA, they form ordered assemblies. It is this disordered-to-ordered transition that has implicated HMGA2 as a protein actively involved in many biological processes, with abnormal HMGA expression linked to a variety of health problems including diabetes, obesity, and oncogenesis. In the current work, the solution binding dynamics of the three ‘AT-hook’ peptides (ATHPs) with AT-rich DNA hairpin substrates were studied using DNA UV melting studies, fluorescence spectroscopy, native ion mobility spectrometry-mass spectrometry (IMS-MS), solution isothermal titration calorimetry (ITC) and molecular modeling. Results showed that the ATHPs bind to the DNA to form a single, 1:1 and 2:1, ‘key-locked’ conformational ensemble. The molecular models showed that 1:1 and 2:1 complex formation is driven by the capacity of the ATHPs to bind to the minor and major grooves of the AT-rich DNA oligomers. Complementary solution ITC results confirmed that the 2:1 stoichiometry of ATHP: DNA is originated under native conditions in solution.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, 33199, USA
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, 33199, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, 33199, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, 33199, USA
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17
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The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival. Chromosoma 2021; 130:215-234. [PMID: 34331109 PMCID: PMC8426247 DOI: 10.1007/s00412-021-00762-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
The Drosophila Trithorax group (TrxG) protein ASH1 remains associated with mitotic chromatin through mechanisms that are poorly understood. ASH1 dimethylates histone H3 at lysine 36 via its SET domain. Here, we identify domains of the TrxG protein ASH1 that are required for mitotic chromatin attachment in living Drosophila. Quantitative live imaging demonstrates that ASH1 requires AT hooks and the BAH domain but not the SET domain for full chromatin binding in metaphase, and that none of these domains are essential for interphase binding. Genetic experiments show that disruptions of the AT hooks and the BAH domain together, but not deletion of the SET domain alone, are lethal. Transcriptional profiling demonstrates that intact ASH1 AT hooks and the BAH domain are required to maintain expression levels of a specific set of genes, including several involved in cell identity and survival. This study identifies in vivo roles for specific ASH1 domains in mitotic binding, gene regulation, and survival that are distinct from its functions as a histone methyltransferase.
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18
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Lilic M, Darst SA, Campbell EA. Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7. Mol Cell 2021; 81:2875-2886.e5. [PMID: 34171296 PMCID: PMC8311663 DOI: 10.1016/j.molcel.2021.05.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/22/2021] [Accepted: 05/12/2021] [Indexed: 01/25/2023]
Abstract
In pathogenic mycobacteria, transcriptional responses to antibiotics result in induced antibiotic resistance. WhiB7 belongs to the Actinobacteria-specific family of Fe-S-containing transcription factors and plays a crucial role in inducible antibiotic resistance in mycobacteria. Here, we present cryoelectron microscopy structures of Mycobacterium tuberculosis transcriptional regulatory complexes comprising RNA polymerase σA-holoenzyme, global regulators CarD and RbpA, and WhiB7, bound to a WhiB7-regulated promoter. The structures reveal how WhiB7 interacts with σA-holoenzyme while simultaneously interacting with an AT-rich sequence element via its AT-hook. Evidently, AT-hooks, rare elements in bacteria yet prevalent in eukaryotes, bind to target AT-rich DNA sequences similarly to the nuclear chromosome binding proteins. Unexpectedly, a subset of particles contained a WhiB7-stabilized closed promoter complex, revealing this intermediate's structure, and we apply kinetic modeling and biochemical assays to rationalize how WhiB7 activates transcription. Altogether, our work presents a comprehensive view of how WhiB7 serves to activate gene expression leading to antibiotic resistance.
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Affiliation(s)
- Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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19
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Wan T, Horová M, Beltran DG, Li S, Wong HX, Zhang LM. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Mol Cell 2021; 81:2887-2900.e5. [PMID: 34171298 DOI: 10.1016/j.molcel.2021.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Huey-Xian Wong
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Li-Mei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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20
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Duan B, Ding P, Navarre WW, Liu J, Xia B. Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol 2021; 38:4135-4148. [PMID: 34003286 PMCID: PMC8476142 DOI: 10.1093/molbev/msab136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
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21
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Acosta-Reyes FJ, Pagan M, Fonfría-Subirós E, Saperas N, Subirana JA, Campos JL. The influence of Ni 2+ and other ions on the trigonal structure of DNA. Biopolymers 2020; 112:e23397. [PMID: 32898299 DOI: 10.1002/bip.23397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/19/2022]
Abstract
We present a new structure of a DNA dodecamer obtained in the presence of Ni2+ ions. The DNA forms Ni-guanine cross-links between neighboring molecules. Our results show that an adequate dosage of Ni2+ may help to form well-defined DNA nanostructures. We also compare our structure with other dodecamers which present unique features and also crystallize in trigonal unit cells, strongly influenced by the counterions associated with DNA. In all cases, the DNA duplexes form parallel pseudo-helical columns in the crystal, similar to DNA-protamine and native DNA fibers.
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Affiliation(s)
| | - Mireia Pagan
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Elsa Fonfría-Subirós
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Núria Saperas
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Juan A Subirana
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - J Lourdes Campos
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
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22
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Kohl B, Zhong X, Herrmann C, Stoll R. Phosphorylation orchestrates the structural ensemble of the intrinsically disordered protein HMGA1a and modulates its DNA binding to the NFκB promoter. Nucleic Acids Res 2020; 47:11906-11920. [PMID: 31340016 PMCID: PMC7145567 DOI: 10.1093/nar/gkz614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/14/2019] [Accepted: 07/05/2019] [Indexed: 12/27/2022] Open
Abstract
High Mobility Group Protein A1a (HMGA1a) is a highly abundant nuclear protein, which plays a crucial role during embryogenesis, cell differentiation, and neoplasia. Here, we present the first ever NMR-based structural ensemble of full length HMGA1a. Our results show that the protein is not completely random coil but adopts a compact structure consisting of transient long-range contacts, which is regulated by post-translational phosphorylation. The CK2-, cdc2- and cdc2/CK2-phosphorylated forms of HMGA1a each exhibit a different binding affinity towards the PRD2 element of the NFκB promoter. Our study identifies connected regions between phosphorylation sites in the wildtype ensemble that change considerably upon phosphorylation, indicating that these posttranslational modifications sites are part of an electrostatic contact network that alters the structural ensemble by shifting the conformational equilibrium. Moreover, ITC data reveal that the CK2-phosphorylated HMGA1a exhibits a different DNA promoter binding affinity for the PRD2 element. Furthermore, we present the first structural model for AT-hook 1 of HMGA1a that can adopt a transient α-helical structure, which might serve as an additional regulatory mechanism in HMAG1a. Our findings will help to develop new therapeutic strategies against HMGA1a-associated cancers by taking posttranslational modifications into consideration.
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Affiliation(s)
- Bastian Kohl
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Xueyin Zhong
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Christian Herrmann
- Faculty of Chemistry and Biochemistry, Protein Interactions, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy, Ruhr University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
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23
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The Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2): Biochemical and Biophysical Properties, and Its Association with Adipogenesis. Int J Mol Sci 2020; 21:ijms21103710. [PMID: 32466162 PMCID: PMC7279267 DOI: 10.3390/ijms21103710] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mammalian high-mobility-group protein AT-hook 2 (HMGA2) is a small DNA-binding protein and consists of three “AT-hook” DNA-binding motifs and a negatively charged C-terminal motif. It is a multifunctional nuclear protein directly linked to obesity, human height, stem cell youth, human intelligence, and tumorigenesis. Biochemical and biophysical studies showed that HMGA2 is an intrinsically disordered protein (IDP) and could form homodimers in aqueous buffer solution. The “AT-hook” DNA-binding motifs specifically bind to the minor groove of AT-rich DNA sequences and induce DNA-bending. HMGA2 plays an important role in adipogenesis most likely through stimulating the proliferative expansion of preadipocytes and also through regulating the expression of transcriptional factor Peroxisome proliferator-activated receptor γ (PPARγ) at the clonal expansion step from preadipocytes to adipocytes. Current evidence suggests that a main function of HMGA2 is to maintain stemness and renewal capacity of stem cells by which HMGA2 binds to chromosome and lock chromosome into a specific state, to allow the human embryonic stem cells to maintain their stem cell potency. Due to the importance of HMGA2 in adipogenesis and tumorigenesis, HMGA2 is considered a potential therapeutic target for anticancer and anti-obesity drugs. Efforts are taken to identify inhibitors targeting HMGA2.
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24
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Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine. Nucleic Acids Res 2019; 47:8375-8387. [PMID: 31081034 PMCID: PMC6895265 DOI: 10.1093/nar/gkz381] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/11/2022] Open
Abstract
The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome-an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5'-0CG-1CA-2CG-3TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2CG has very little effect on TCF4 binding, E-box 1CA modification has a negative influence on binding, while modification of the flanking 0CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.
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Affiliation(s)
- Jie Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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25
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Jangal M, Lebeau B, Witcher M. Beyond EZH2: is the polycomb protein CBX2 an emerging target for anti-cancer therapy? Expert Opin Ther Targets 2019; 23:565-578. [PMID: 31177918 DOI: 10.1080/14728222.2019.1627329] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Epigenetic modifications are important regulators of transcription and appropriate gene expression answering an environmental stimulus. In cancer, these epigenetic modifications are altered, which impact the transcriptome, promoting initiation and cancer progression. Thus, targeting epigenetic machinery has proven to be an efficient cancer therapy. Areas covered: We review CBX2 as a therapeutic target. CBX2 is a polycomb protein, responsible for polycomb-repressive complex 1 (PRC1) targeting to chromatin via recognition of the repressive mark H3K27me3. Mechanistically, CBX2 overexpression may be implicated in poor survival by maintaining cancer stem cells in an undifferentiated state and via repression of tumor suppressors. We discuss strategies used to target CBX proteins and provide insights into biomarker considerations that may be important when targeting CBX family members for anti-cancer therapy. Expert opinion: CBX2 inhibition is a promising approach for the targeting of polycomb complexes in the cancer stem cell niche. However, extensive optimization of the current field of small molecules targeting CBX family proteins will be critical to reach in vivo, or clinical, utility.
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Affiliation(s)
- Maïka Jangal
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
| | - Benjamin Lebeau
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
| | - Michael Witcher
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
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26
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Pedone F, Mazzei F, Santoni D. A study of the impact of DNA helical rise on protein-DNA interaction. Genomics 2018; 111:1620-1628. [PMID: 30453062 DOI: 10.1016/j.ygeno.2018.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/26/2018] [Accepted: 11/10/2018] [Indexed: 11/19/2022]
Abstract
Nucleosomes are not uniformly distributed along DNA and their positioning (termed "nucleosomal landscape") can be derived using data available for several genomes. In this study we analyzed DNA helical rise profiles through a tetranucleotide code, and we defined the nucleosomal landscape of several sequences forming dinucleosomes and of the sequences of huntingtin, myotonic dystrophy type 1 and fragile mental retardation 2 genes, which contained several repeated sequences. We also analyzed the profiles of some sequences interacting with transcription factors or with RNA polymerase II. In the genomes of Cenorhabditis elegans, Mus musculus and Homo sapiens we found profiles with extremely low helical rise values, characteristic of nucleosome free regions. We defined these regions as "holes" and found that their presence correlates with lamina associated domains sequences. Altogether, this study shows that DNA helical rise profile may have a role in gene expression modulation and in shaping chromosomal structure.
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Affiliation(s)
- Francesco Pedone
- Department of Biology and Biotechnology, "Sapienza" University, P.le A. Moro 5, Rome 00185, Italy.
| | - Filomena Mazzei
- Environment and Health Department, Istituto Superiore di Sanità,V.le Regina Elena 299, Rome 00161, Italy.
| | - Daniele Santoni
- National Research Council of Italy, Institute for System Analysis and Computer Science "Antonio Ruberti", Via dei Taurini 19, Rome 00185, Italy.
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27
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Garabedian A, Bolufer A, Leng F, Fernandez-Lima F. Peptide Sequence Influence on the Conformational Dynamics and DNA binding of the Intrinsically Disordered AT-Hook 3 Peptide. Sci Rep 2018; 8:10783. [PMID: 30018295 PMCID: PMC6050235 DOI: 10.1038/s41598-018-28956-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
The intrinsically disordered ATHP3 was studied at native conditions and in complex with DNA using single amino acid substitutions and high-resolution ion mobility spectrometry coupled to mass spectrometry (trapped IMS-MS). Results showed that ATHP3 can exist in multiple conformations at native conditions (at least 10 conformers were separated), with a variety of proline cis/trans orientations, side chain orientations and protonation sites. When in complex with AT rich DNA hairpins, the -RGRP- core is essential for stabilizing the ATHP3: DNA complex. In particular, the arginine in the sixth position plays an important role during binding to AT-rich regions of hairpin DNA, in good agreement with previous NMR and X-ray data. Mobility based correlation matrices are proposed as a way to reveal differences in structural motifs across the peptide mutants based on the conformational space and relative conformer abundance.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Alexander Bolufer
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States. .,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States.
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28
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Ejlersen M, Christensen NJ, Sørensen KK, Jensen KJ, Wengel J, Lou C. Synergy of Two Highly Specific Biomolecular Recognition Events: Aligning an AT-Hook Peptide in DNA Minor Grooves via Covalent Conjugation to 2'-Amino-LNA. Bioconjug Chem 2018; 29:1025-1029. [PMID: 29505242 DOI: 10.1021/acs.bioconjchem.8b00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.
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Affiliation(s)
- Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Kasper K Sørensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Knud J Jensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
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29
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Nanoscale Assembly of High-Mobility Group AT-Hook 2 Protein with DNA Replication Fork. Biophys J 2018; 113:2609-2620. [PMID: 29262356 DOI: 10.1016/j.bpj.2017.10.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/24/2017] [Accepted: 10/12/2017] [Indexed: 01/31/2023] Open
Abstract
High mobility group AT-hook 2 (HMGA2) protein is composed of three AT-hook domains. HMGA2 expresses at high levels in both embryonic stem cells and cancer cells, where it interacts with and stabilizes replication forks (RFs), resulting in elevated cell proliferation rates. In this study, we demonstrated that HMGA2 knockdown reduces cell proliferation. To understand the features required for interaction between HMGA2 and RFs, we studied the solution structure of HMGA2, free and in complex with RFs, using an integrated host of biophysical techniques. Circular dichroism and NMR experiments confirmed the disordered state of unbound HMGA2. Dynamic light scattering and sedimentation velocity experiments demonstrated that HMGA2 and RF are monodisperse in solution, and form an equimolar complex. Small-angle x-ray scattering studies revealed that HMGA2 binds in a side-by-side orientation to RF where 3 AT-hooks act as a clamp to wrap around a distorted RF. Thus, our data provide insights into how HMGA2 interacts with stalled RFs and the function of the process.
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30
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Chiefari E, Foti DP, Sgarra R, Pegoraro S, Arcidiacono B, Brunetti FS, Greco M, Manfioletti G, Brunetti A. Transcriptional Regulation of Glucose Metabolism: The Emerging Role of the HMGA1 Chromatin Factor. Front Endocrinol (Lausanne) 2018; 9:357. [PMID: 30034366 PMCID: PMC6043803 DOI: 10.3389/fendo.2018.00357] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/13/2018] [Indexed: 02/06/2023] Open
Abstract
HMGA1 (high mobility group A1) is a nonhistone architectural chromosomal protein that functions mainly as a dynamic regulator of chromatin structure and gene transcription. As such, HMGA1 is involved in a variety of fundamental cellular processes, including gene expression, epigenetic regulation, cell differentiation and proliferation, as well as DNA repair. In the last years, many reports have demonstrated a role of HMGA1 in the transcriptional regulation of several genes implicated in glucose homeostasis. Initially, it was proved that HMGA1 is essential for normal expression of the insulin receptor (INSR), a critical link in insulin action and glucose homeostasis. Later, it was demonstrated that HMGA1 is also a downstream nuclear target of the INSR signaling pathway, representing a novel mediator of insulin action and function at this level. Moreover, other observations have indicated the role of HMGA1 as a positive modulator of the Forkhead box protein O1 (FoxO1), a master regulatory factor for gluconeogenesis and glycogenolysis, as well as a positive regulator of the expression of insulin and of a series of circulating proteins that are involved in glucose counterregulation, such as the insulin growth factor binding protein 1 (IGFBP1), and the retinol binding protein 4 (RBP4). Thus, several lines of evidence underscore the importance of HMGA1 in the regulation of glucose production and disposal. Consistently, lack of HMGA1 causes insulin resistance and diabetes in humans and mice, while variations in the HMGA1 gene are associated with the risk of type 2 diabetes and metabolic syndrome, two highly prevalent diseases that share insulin resistance as a common pathogenetic mechanism. This review intends to give an overview about our current knowledge on the role of HMGA1 in glucose metabolism. Although research in this field is ongoing, many aspects still remain elusive. Future directions to improve our insights into the pathophysiology of glucose homeostasis may include epigenetic studies and the use of "omics" strategies. We believe that a more comprehensive understanding of HMGA1 and its networks may reveal interesting molecular links between glucose metabolism and other biological processes, such as cell proliferation and differentiation.
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Affiliation(s)
- Eusebio Chiefari
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Daniela P. Foti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Silvia Pegoraro
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Francesco S. Brunetti
- Department of Medical and Surgical Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Manfredi Greco
- Department of Clinical and Experimental Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | | | - Antonio Brunetti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti
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31
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Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content. PLoS Genet 2017; 13:e1007102. [PMID: 29267285 PMCID: PMC5756049 DOI: 10.1371/journal.pgen.1007102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 01/05/2018] [Accepted: 11/04/2017] [Indexed: 11/26/2022] Open
Abstract
Genomic location can inform on potential function and recruitment signals for chromatin-associated proteins. High mobility group (Hmg) proteins are of similar size as histones with Hmga1 and Hmga2 being particularly abundant in replicating normal tissues and in cancerous cells. While several roles for Hmga proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA-binding domain mutants. Comparative analysis of the genome-wide distribution of Hmga proteins reveals pervasive binding, a feature that critically depends on a functional DNA-binding domain and which is shared by both Hmga proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness, defined as high frequency of A or T bases, as the major criterion for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on Hmga binding both in stem and differentiated cells. As a consequence, Hmga proteins are preferentially found at AT-rich regions such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model, we show that genetic deletion of Hmga proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors. Overall our comparative study describing the in vivo binding modality of Hmga1 and Hmga2 identifies the proteins’ preference for AT-rich DNA genome-wide and argues against a suggested function of Hmga at regulatory regions. Instead we discover pervasive binding with enrichment at regions of higher AT content irrespective of local variation in chromatin modifications. We investigated the chromosomal location of a group of highly abundant nuclear proteins. Our genome-wide results for Hmga1 and Hmga2 reveal a unique binding modality indicating preference for DNA rich in A or T bases in vivo. Importantly this preferential binding to AT-rich sequences occurs throughout the genome irrespectively of other local chromatin features. Genomic location and loss of function experiments challenge the view that Hmga proteins act as local modulators of transcriptional regulation but rather argue for a role as structural components of chromatin.
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32
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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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33
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Millan CR, Acosta-Reyes FJ, Lagartera L, Ebiloma GU, Lemgruber L, Nué Martínez JJ, Saperas N, Dardonville C, de Koning HP, Campos JL. Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast. Nucleic Acids Res 2017. [PMID: 28637278 PMCID: PMC5737332 DOI: 10.1093/nar/gkx521] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Trypanosoma brucei, the causative agent of sleeping sickness (Human African Trypanosomiasis, HAT), contains a kinetoplast with the mitochondrial DNA (kDNA), comprising of >70% AT base pairs. This has prompted studies of drugs interacting with AT-rich DNA, such as the N-phenylbenzamide bis(2-aminoimidazoline) derivatives 1 [4-((4,5-dihydro-1H-imidazol-2-yl)amino)-N-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzamide dihydrochloride] and 2 [N-(3-chloro-4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)-4-((4,5-dihydro-1H-imidazol-2-yl)amino)benzamide] as potential drugs for HAT. Both compounds show in vitro effects against T. brucei and in vivo curative activity in a mouse model of HAT. The main objective was to identify their cellular target inside the parasite. We were able to demonstrate that the compounds have a clear effect on the S-phase of T. brucei cell cycle by inflicting specific damage on the kinetoplast. Surface plasmon resonance (SPR)–biosensor experiments show that the drug can displace HMG box-containing proteins essential for kDNA function from their kDNA binding sites. The crystal structure of the complex of the oligonucleotide d[AAATTT]2 with compound 1 solved at 1.25 Å (PDB-ID: 5LIT) shows that the drug covers the minor groove of DNA, displaces bound water and interacts with neighbouring DNA molecules as a cross-linking agent. We conclude that 1 and 2 are powerful trypanocides that act directly on the kinetoplast, a structure unique to the order Kinetoplastida.
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Affiliation(s)
- Cinthia R Millan
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, 08019 Barcelona, Spain
| | - Francisco J Acosta-Reyes
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, 08019 Barcelona, Spain
| | | | - Godwin U Ebiloma
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Leandro Lemgruber
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.,The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | | | - Núria Saperas
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, 08019 Barcelona, Spain
| | | | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - J Lourdes Campos
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, 08019 Barcelona, Spain
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34
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Normanno D, Négrel A, de Melo AJ, Betzi S, Meek K, Modesti M. Mutational phospho-mimicry reveals a regulatory role for the XRCC4 and XLF C-terminal tails in modulating DNA bridging during classical non-homologous end joining. eLife 2017; 6. [PMID: 28500754 PMCID: PMC5468090 DOI: 10.7554/elife.22900] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/12/2017] [Indexed: 12/23/2022] Open
Abstract
XRCC4 and DNA Ligase 4 (LIG4) form a tight complex that provides DNA ligase activity for classical non-homologous end joining (the predominant DNA double-strand break repair pathway in higher eukaryotes) and is stimulated by XLF. Independently of LIG4, XLF also associates with XRCC4 to form filaments that bridge DNA. These XRCC4/XLF complexes rapidly load and connect broken DNA, thereby stimulating intermolecular ligation. XRCC4 and XLF both include disordered C-terminal tails that are functionally dispensable in isolation but are phosphorylated in response to DNA damage by DNA-PK and/or ATM. Here we concomitantly modify the tails of XRCC4 and XLF by substituting fourteen previously identified phosphorylation sites with either alanine or aspartate residues. These phospho-blocking and -mimicking mutations impact both the stability and DNA bridging capacity of XRCC4/XLF complexes, but without affecting their ability to stimulate LIG4 activity. Implicit in this finding is that phosphorylation may regulate DNA bridging by XRCC4/XLF filaments.
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Affiliation(s)
- Davide Normanno
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Aurélie Négrel
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Abinadabe J de Melo
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Stéphane Betzi
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Katheryn Meek
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, United States
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
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35
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A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence. Sci Rep 2016; 6:31210. [PMID: 27502833 PMCID: PMC4977486 DOI: 10.1038/srep31210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/04/2016] [Indexed: 11/08/2022] Open
Abstract
DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed.
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36
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Lyst MJ, Connelly J, Merusi C, Bird A. Sequence-specific DNA binding by AT-hook motifs in MeCP2. FEBS Lett 2016; 590:2927-33. [PMID: 27461740 PMCID: PMC5028900 DOI: 10.1002/1873-3468.12328] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 11/11/2022]
Abstract
MeCP2 is a chromatin‐associated protein that is mutated in Rett syndrome. Its methyl‐CpG‐binding domain interacts with DNA containing methylated cytosine, but other modes of recruitment to the genome have also been proposed. Here, we use in vitro and in vivo assays to investigate the DNA binding specificity of two AT‐hook motifs in MeCP2. One exhibits robust sequence‐specific DNA binding, whereas the other is a much weaker AT‐hook. Our data indicate that these motifs are secondary contributors to DNA binding by MeCP2, and this view is supported by the absence of disease‐causing missense mutations at these sites.
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Affiliation(s)
- Matthew J Lyst
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - John Connelly
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Cara Merusi
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Adrian Bird
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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37
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Rodríguez J, Mosquera J, García-Fandiño R, Vázquez ME, Mascareñas JL. A designed DNA binding motif that recognizes extended sites and spans two adjacent major grooves. Chem Sci 2016; 7:3298-3303. [PMID: 27252825 PMCID: PMC4885664 DOI: 10.1039/c6sc00045b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/01/2016] [Indexed: 12/28/2022] Open
Abstract
We report the rational design of a DNA-binding peptide construct composed of the DNA-contacting regions of two transcription factors (GCN4 and GAGA) linked through an AT-hook DNA anchor. The resulting chimera, which represents a new, non-natural DNA binding motif, binds with high affinity and selectivity to a long composite sequence of 13 base pairs (TCAT-AATT-GAGAG).
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Rebeca García-Fandiño
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
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38
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Abstract
'Epigenome' refers to the panoply of chemical modifications borne by DNA and its associated proteins that locally affect genome function. Epigenomic patterns are thought to be determined by external constraints resulting from development, disease and the environment, but DNA sequence is also a potential influence. We propose that domains of relatively uniform DNA base composition may modulate the epigenome through cell type-specific proteins that recognize short, frequent sequence motifs. Differential recruitment of epigenomic modifiers may adjust gene expression in multigene blocks as an alternative to tuning the activity of each gene separately, thus simplifying gene expression programming.
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39
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Abstract
The high mobility group protein A1 (HMGA1) is a master regulator of chromatin structure mediating its major gene regulatory activity by direct interactions with A/T-rich DNA sequences located in the promoter and enhancer regions of a large variety of genes. HMGA1 DNA-binding through three AT-hook motifs results in an open chromatin structure and subsequently leads to changes in gene expression. Apart from its significant expression during development, HMGA1 is over-expressed in virtually every cancer, where HMGA1 expression levels correlate with tumor malignancy. The exogenous overexpression of HMGA1 can lead to malignant cell transformation, assigning the protein a key role during cancerogenesis. Recent studies have unveiled highly specific competitive interactions of HMGA1 with cellular and viral RNAs also through an AT-hook domain of the protein, significantly impacting the HMGA1-dependent gene expression. In this review, we discuss the structure and function of HMGA1-RNA complexes during transcription and epigenomic regulation and their implications in HMGA1-related diseases.
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40
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Lee S, Wang C, Song J, Kim DG, Oh Y, Ko W, Lee J, Park J, Lee HS, Jo K. Investigation of various fluorescent protein–DNA binding peptides for effectively visualizing large DNA molecules. RSC Adv 2016. [DOI: 10.1039/c6ra08683g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-molecule DNA visualization with fluorescent protein DNA binding peptides.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Cong Wang
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Junghyun Song
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Do-geun Kim
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Yeeun Oh
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Wooseok Ko
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jinyong Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jungyul Park
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Hyun Soo Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
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41
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Zaleska M, Fogl C, Kho AL, Ababou A, Ehler E, Pfuhl M. The Cardiac Stress Response Factor Ms1 Can Bind to DNA and Has a Function in the Nucleus. PLoS One 2015; 10:e0144614. [PMID: 26656831 PMCID: PMC4682817 DOI: 10.1371/journal.pone.0144614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/21/2015] [Indexed: 11/21/2022] Open
Abstract
Ms1 (also known as STARS and ABRA) has been shown to act as an early stress response gene in processes as different as hypertrophy in skeletal and cardiac muscle and growth of collateral blood vessels. It is important for cardiac development in zebrafish and is upregulated in mouse models for cardiac hypertrophy as well as in human failing hearts. Ms1 possesses actin binding sites at its C-terminus and is usually found in the cell bound to actin filaments in the cytosol or in sarcomeres. We determined the NMR structure of the only folded domain of Ms1 comprising the second actin binding site called actin binding domain 2 (ABD2, residues 294-375), and found that it is similar to the winged helix-turn-helix fold adopted mainly by DNA binding domains of transcriptional factors. In vitro experiments show specific binding of this domain, in combination with a newly discovered AT-hook motif located N-terminally, to the sequence (A/C/G)AAA(C/A). NMR and fluorescence titration experiments confirm that this motif is indeed bound specifically by the recognition helix. In neonatal rat cardiomyocytes endogenous Ms1 is found in the nucleus in a spotted pattern, reminiscent of PML bodies. In adult rat cardiomyocytes Ms1 is exclusively found in the sarcomere. A nuclear localisation site in the N-terminus of the protein is required for nuclear localisation. This suggests that Ms1 has the potential to act directly in the nucleus through specific interaction with DNA in development and potentially as a response to stress in adult tissues.
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Affiliation(s)
- Mariola Zaleska
- Cardiovascular and Randall Division, King's College London, London, United Kingdom
| | - Claudia Fogl
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester, United Kingdom
| | - Ay Lin Kho
- Cardiovascular and Randall Division, King's College London, London, United Kingdom
| | - Abdessamad Ababou
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Elisabeth Ehler
- Cardiovascular and Randall Division, King's College London, London, United Kingdom
| | - Mark Pfuhl
- Cardiovascular and Randall Division, King's College London, London, United Kingdom
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42
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Lopez MB, Garcia MN, Grasso D, Bintz J, Molejon MI, Velez G, Lomberk G, Neira JL, Urrutia R, Iovanna J. Functional Characterization of Nupr1L, A Novel p53-Regulated Isoform of the High-Mobility Group (HMG)-Related Protumoral Protein Nupr1. J Cell Physiol 2015; 230:2936-50. [PMID: 25899918 DOI: 10.1002/jcp.25022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/15/2015] [Indexed: 12/18/2022]
Abstract
We have previously demonstrated a crucial role of nuclear protein 1 (NUPR1) in tumor development and progression. In this work, we report the functional characterization of a novel Nupr1-like isoform (NUPR1L) and its functional interaction with the protumoral factor NUPR1. Through the use of primary sequence analysis, threading, and homology-based molecular modeling, as well as expression and immunolocalization, studies reveal that NUPR1L displays properties, which are similar to member of the HMG-like family of chromatin regulators, including its ability to translocate to the cell nucleus and bind to DNA. Analysis of the NUPR1L promoter showed the presence of two p53-response elements at positions -37 and -7, respectively. Experiments using reporter assays combined with site-directed mutagenesis and using cells with controllable p53 expression demonstrate that both of these sequences are responsible for the regulation of NUPR1L expression by p53. Congruently, NUPR1L gene expression is activated in response to DNA damage induced by oxaliplatin treatment or cell cycle arrest induced by serum starvation, two well-validated methods to achieve p53 activation. Interestingly, expression of NUPR1L downregulates the expression of NUPR1, its closely related protumoral isoform, by a mechanism that involves the inhibition of its promoter activity. At the cellular level, overexpression of NUPR1L induces G1 cell cycle arrest and a decrease in their cell viability, an effect that is mediated, at least in part, by downregulating NUPR1 expression. Combined, these experiments constitute the first functional characterization of NUPR1L as a new p53-induced gene, which negatively regulates the protumoral factor NUPR1.
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Affiliation(s)
- Maria Belen Lopez
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Maria Noé Garcia
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Daniel Grasso
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Jennifer Bintz
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Maria Inés Molejon
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Gabriel Velez
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Biophysics, and Medicine, Mayo Clinic, Rochester, Minnesota
| | - Gwen Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Biophysics, and Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jose Luis Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
| | - Raul Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Biophysics, and Medicine, Mayo Clinic, Rochester, Minnesota
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
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43
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A Non-Synonymous HMGA2 Variant Decreases Height in Shetland Ponies and Other Small Horses. PLoS One 2015; 10:e0140749. [PMID: 26474182 PMCID: PMC4608717 DOI: 10.1371/journal.pone.0140749] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/30/2015] [Indexed: 11/19/2022] Open
Abstract
The identification of quantitative trait loci (QTL) such as height and their underlying causative variants is still challenging and often requires large sample sizes. In humans hundreds of loci with small effects control the heritable portion of height variability. In domestic animals, typically only a few loci with comparatively large effects explain a major fraction of the heritability. We investigated height at withers in Shetland ponies and mapped a QTL to ECA 6 by genome-wide association (GWAS) using a small cohort of only 48 animals and the Illumina equine SNP70 BeadChip. Fine-mapping revealed a shared haplotype block of 793 kb in small Shetland ponies. The HMGA2 gene, known to be associated with height in horses and many other species, was located in the associated haplotype. After closing a gap in the equine reference genome we identified a non-synonymous variant in the first exon of HMGA2 in small Shetland ponies. The variant was predicted to affect the functionally important first AT-hook DNA binding domain of the HMGA2 protein (c.83G>A; p.G28E). We assessed the functional impact and found impaired DNA binding of a peptide with the mutant sequence in an electrophoretic mobility shift assay. This suggests that the HMGA2 variant also affects DNA binding in vivo and thus leads to reduced growth and a smaller stature in Shetland ponies. The identified HMGA2 variant also segregates in several other pony breeds but was not found in regular-sized horse breeds. We therefore conclude that we identified a quantitative trait nucleotide for height in horses.
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44
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Rodríguez J, Mosquera J, Couceiro JR, Vázquez ME, Mascareñas JL. The AT-Hook motif as a versatile minor groove anchor for promoting DNA binding of transcription factor fragments. Chem Sci 2015; 6:4767-4771. [PMID: 26290687 PMCID: PMC4538796 DOI: 10.1039/c5sc01415h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022] Open
Abstract
We report the development of chimeric DNA binding peptides comprising a DNA binding fragment of natural transcription factors (the basic region of a bZIP protein or a monomeric zinc finger module) and an AT-Hook peptide motif. The resulting peptide conjugates display high DNA affinity and excellent sequence selectivity. Furthermore, the AT-Hook motif also favors the cell internalization of the conjugates.
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - Jose R. Couceiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
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45
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Frost L, Baez MAM, Harrilal C, Garabedian A, Fernandez-Lima F, Leng F. The Dimerization State of the Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2). PLoS One 2015; 10:e0130478. [PMID: 26114780 PMCID: PMC4482583 DOI: 10.1371/journal.pone.0130478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/20/2015] [Indexed: 01/06/2023] Open
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is a chromosomal architectural transcription factor involved in cell transformation and oncogenesis. It consists of three positively charged “AT-hooks” and a negatively charged C-terminus. Sequence analyses, circular dichroism experiments, and gel-filtration studies showed that HMGA2, in the native state, does not have a defined secondary or tertiary structure. Surprisingly, using combined approaches of 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) chemical cross-linking, analytical ultracentrifugation, fluorescence resonance energy transfer (FRET), and mass spectrometry, we discovered that HMGA2 is capable of self-associating into homodimers in aqueous buffer solution. Our results showed that electrostatic interactions between the positively charged “AT-hooks” and the negatively charged C-terminus greatly contribute to the homodimer formation.
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Affiliation(s)
- Lorraine Frost
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Maria A. M. Baez
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Christopher Harrilal
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Alyssa Garabedian
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Francisco Fernandez-Lima
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- * E-mail:
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46
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Mosquera J, Sánchez MI, Valero J, Mendoza JD, Vázquez ME, Mascareñas JL. Sequence-selective DNA binding with cell-permeable oligoguanidinium–peptide conjugates. Chem Commun (Camb) 2015; 51:4811-4. [DOI: 10.1039/c4cc09525a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Conjugation of a short peptide fragment from a bZIP protein to an oligoguanidinium tail results in a DNA-binding miniprotein that selectively interacts with composite sequences containing the peptide-binding site next to an A/T-rich tract.
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Affiliation(s)
- Jesús Mosquera
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Mateo I. Sánchez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Julián Valero
- Institute of Chemical Research of Catalonia (ICIQ)
- 43007 Tarragona
- Spain
| | - Javier de Mendoza
- Institute of Chemical Research of Catalonia (ICIQ)
- 43007 Tarragona
- Spain
| | - M. Eugenio Vázquez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - José L. Mascareñas
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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47
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Dunker AK, Oldfield CJ. Back to the Future: Nuclear Magnetic Resonance and Bioinformatics Studies on Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:1-34. [PMID: 26387098 DOI: 10.1007/978-3-319-20164-1_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
From the 1970s to the present, regions of missing electron density in protein structures determined by X-ray diffraction and the characterization of the functions of these regions have suggested that not all protein regions depend on prior 3D structure to carry out function. Motivated by these observations, in early 1996 we began to use bioinformatics approaches to study these intrinsically disordered proteins (IDPs) and IDP regions. At just about the same time, several laboratory groups began to study a collection of IDPs and IDP regions using nuclear magnetic resonance. The temporal overlap of the bioinformatics and NMR studies played a significant role in the development of our understanding of IDPs. Here the goal is to recount some of this history and to project from this experience possible directions for future work.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
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48
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Acosta-Reyes FJ, Subirana JA, Pous J, Sánchez-Giraldo R, Condom N, Baldini R, Malinina L, Campos JL. Polymorphic crystal structures of an all-AT DNA dodecamer. Biopolymers 2014; 103:123-33. [DOI: 10.1002/bip.22565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/12/2022]
Affiliation(s)
| | - Juan A. Subirana
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Joan Pous
- Plataforma Automatitzada de Cristal·lografia; IBMB-CSIC and Institut de Recerca Biomédica de Barcelona; 08028 Barcelona Spain
| | - Raquel Sánchez-Giraldo
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Núria Condom
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Roberto Baldini
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Lucy Malinina
- Structural Biology Unit, CIC bioGUNE; Technology Park of Bizkaia; 48160 Derio Bilbao Spain
| | - J. Lourdes Campos
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
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Evidence supporting the existence of a NUPR1-like family of helix-loop-helix chromatin proteins related to, yet distinct from, AT hook-containing HMG proteins. J Mol Model 2014; 20:2357. [PMID: 25056123 PMCID: PMC4139591 DOI: 10.1007/s00894-014-2357-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 06/15/2014] [Indexed: 12/29/2022]
Abstract
NUPR1, a small chromatin protein, plays a critical role in cancer development, progression, and resistance to therapy. Here, using a combination of structural bioinformatics and molecular modeling methods, we report several novel findings that enhance our understanding of the biochemical function of this protein. We find that NUPR1 has been conserved throughout evolution, and over time it has undergone duplications and transpositions to form other transcriptional regulators. Using threading, homology-based molecular modeling, molecular mechanics calculations, and molecular dynamics simulations, we generated structural models for four of these proteins: NUPR1a, NUPR1b, NUPR2, and the NUPR-like domain of GTF2-I. Comparative analyses of these models combined with extensive linear motif identification reveal that these four proteins, though similar in their propensities for folding, differ in size, surface changes, and sites amenable for posttranslational modification. Lastly, taking NUPR1a as the paradigm for this family, we built models of a NUPR–DNA complex. Additional structural comparisons revealed that NUPR1 defines a new family of small-groove-binding proteins that share structural features with, yet are distinct from, helix-loop-helix AT-hook-containing HMG proteins. These models and inferences should lead to a better understanding of the function of this group of chromatin proteins, which play a critical role in the development of human malignant diseases.
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Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain. Proc Natl Acad Sci U S A 2013; 110:E4688-97. [PMID: 24218605 DOI: 10.1073/pnas.1219277110] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Arabidopsis thaliana genome encodes 29 AT-hook motif containing nuclear localized (AHL) genes, which evolved into two phylogenic clades. The AHL proteins contain one or two AT-hook motif(s) and one plant and prokaryote conserved (PPC)/domain of unknown function #296 (DUF296) domain. Seedlings lacking both SOB3/AHL29 and ESC/AHL27 confer a subtle long-hypocotyl phenotype compared with the WT or either single-null mutant. In contrast, the missense allele sob3-6 confers a dramatic long-hypocotyl phenotype in the light. In this study, we examined the dominant-negative feature of sob3-6 and found that it encodes a protein with a disrupted AT-hook motif that abolishes binding to AT-rich DNA. A loss-of-function approach demonstrated different, yet redundant, contributions of additional AHL genes in suppressing hypocotyl elongation in the light. We showed that AHL proteins interact with each other and themselves via the PPC/DUF296 domain. AHLs also share interactions with other nuclear proteins, such as transcription factors, suggesting that these interactions also contribute to the functional redundancy within this gene family. The coordinated action of AHLs requires an AT-hook motif capable of binding AT-rich DNA, as well as a PPC/DUF296 domain containing a conserved Gly-Arg-Phe-Glu-Ile-Leu region. Alteration of this region abolished SOB3/AHL29's physical interaction with transcription factors and resulted in a dominant-negative allele in planta that was phenotypically similar to sob3-6. We propose a molecular model where AHLs interact with each other and themselves, as well as other nuclear proteins, to form complexes which modulate plant growth and development.
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