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Yang Y, Ahmad E, Premkumar V, Liu A, Ashikur Rahman SM, Nikolovska‐Coleska Z. Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors. Protein Sci 2024; 33:e5019. [PMID: 38747396 PMCID: PMC11094776 DOI: 10.1002/pro.5019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/19/2024]
Abstract
AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL-rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP-AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1-2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein-inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.
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Affiliation(s)
- Yuting Yang
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Ejaz Ahmad
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Vidhya Premkumar
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Alicen Liu
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - S. M. Ashikur Rahman
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Zaneta Nikolovska‐Coleska
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
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2
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [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: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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3
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Bruley A, Bitard-Feildel T, Callebaut I, Duprat E. A sequence-based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum. Proteins 2023; 91:466-484. [PMID: 36306150 DOI: 10.1002/prot.26441] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Order and disorder govern protein functions, but there is a great diversity in disorder, from regions that are-and stay-fully disordered to conditional order. This diversity is still difficult to decipher even though it is encoded in the amino acid sequences. Here, we developed an analytic Python package, named pyHCA, to estimate the foldability of a protein segment from the only information of its amino acid sequence and based on a measure of its density in regular secondary structures associated with hydrophobic clusters, as defined by the hydrophobic cluster analysis (HCA) approach. The tool was designed by optimizing the separation between foldable segments from databases of disorder (DisProt) and order (SCOPe [soluble domains] and OPM [transmembrane domains]). It allows to specify the ratio between order, embodied by regular secondary structures (either participating in the hydrophobic core of well-folded 3D structures or conditionally formed in intrinsically disordered regions) and disorder. We illustrated the relevance of pyHCA with several examples and applied it to the sequences of the proteomes of 21 species ranging from prokaryotes and archaea to unicellular and multicellular eukaryotes, for which structure models are provided in the AlphaFold protein structure database. Cases of low-confidence scores related to disorder were distinguished from those of sequences that we identified as foldable but are still excluded from accurate modeling by AlphaFold2 due to a lack of sequence homologs or to compositional biases. Overall, our approach is complementary to AlphaFold2, providing guides to map structural innovations through evolutionary processes, at proteome and gene scales.
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Affiliation(s)
- Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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4
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Peil K, Värv S, Ilves I, Kristjuhan K, Jürgens H, Kristjuhan A. Transcriptional regulator Taf14 binds DNA and is required for the function of transcription factor TFIID in the absence of histone H2A.Z. J Biol Chem 2022; 298:102369. [PMID: 35970389 PMCID: PMC9478928 DOI: 10.1016/j.jbc.2022.102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptional regulator Taf14 is a component of multiple protein complexes involved in transcription initiation and chromatin remodeling in yeast cells. Although Taf14 is not required for cell viability, it becomes essential in conditions where the formation of the transcription preinitiation complex is hampered. The specific role of Taf14 in mediating transcription initiation and preinitiation complex formation is unclear. Here, we explored its role in the general transcription factor IID by mapping Taf14 genetic and proteomic interactions and found that it was needed for the function of the complex if Htz1, the yeast homolog of histone H2A.Z, was absent from chromatin. Dissecting the functional domains of Taf14 revealed that the linker region between the YEATS and ET domains was required for cell viability in the absence of Htz1 protein. We further show that the linker region of Taf14 interacts with DNA. We propose that providing additional DNA binding capacity might be a general role of Taf14 in the recruitment of protein complexes to DNA and chromatin.
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Affiliation(s)
- Kadri Peil
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Signe Värv
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Ivar Ilves
- Institute of Technology, University of Tartu; Nooruse 1, Tartu 50411, Estonia
| | - Kersti Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Henel Jürgens
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Arnold Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia.
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5
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Noncanonical function of Capicua as a growth termination signal in Drosophila oogenesis. Proc Natl Acad Sci U S A 2022; 119:e2123467119. [PMID: 35881788 PMCID: PMC9351367 DOI: 10.1073/pnas.2123467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Capicua (Cic) proteins are conserved HMG-box transcriptional repressors that control receptor tyrosine kinase (RTK) signaling responses and are implicated in human neurological syndromes and cancer. While Cic is known to exist as short (Cic-S) and long (Cic-L) isoforms with identical HMG-box and associated core regions but distinct N termini, most previous studies have focused on Cic-S, leaving the function of Cic-L unexplored. Here we show that Cic-L acts in two capacities during Drosophila oogenesis: 1) as a canonical sensor of RTK signaling in somatic follicle cells, and 2) as a regulator of postmitotic growth in germline nurse cells. In these latter cells, Cic-L behaves as a temporal signal that terminates endoreplicative growth before they dump their contents into the oocyte. We show that Cic-L is necessary and sufficient for nurse cell endoreplication arrest and induces both stabilization of CycE and down-regulation of Myc. Surprisingly, this function depends mainly on the Cic-L-specific N-terminal module, which is capable of acting independently of the Cic HMG-box-containing core. Mirroring these observations, basal metazoans possess truncated Cic-like proteins composed only of Cic-L N-terminal sequences, suggesting that this module plays unique, ancient roles unrelated to the canonical function of Cic.
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Papadopoulos C, Chevrollier N, Lopes A. Exploring the Peptide Potential of Genomes. Methods Mol Biol 2022; 2405:63-82. [PMID: 35298808 DOI: 10.1007/978-1-0716-1855-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent studies attribute a central role to the noncoding genome in the emergence of novel genes. The widespread transcription of noncoding regions and the pervasive translation of the resulting RNAs offer to the organisms a vast reservoir of novel peptides. Although the majority of these peptides are anticipated as deleterious or neutral, and thereby expected to be degraded right away or short-lived in evolutionary history, some of them can confer an advantage to the organism. The latter can be further subjected to natural selection and be established as novel genes. In any case, characterizing the structural properties of these pervasively translated peptides is crucial to understand (1) their impact on the cell and (2) how some of these peptides, derived from presumed noncoding regions, can give rise to structured and functional de novo proteins. Therefore, we present a protocol that aims to explore the potential of a genome to produce novel peptides. It consists in annotating all the open reading frames (ORFs) of a genome (i.e., coding and noncoding ones) and characterizing the fold potential and other structural properties of their corresponding potential peptides. Here, we apply our protocol to a small genome and show how to apply it to very large genomes. Finally, we present a case study which aims to probe the fold potential of a set of 721 translated ORFs in mouse lncRNAs, identified with ribosome profiling experiments. Interestingly, we show that the distribution of their fold potential is different from that of the nontranslated lncRNAs and more generally from the other noncoding ORFs of the mouse.
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Affiliation(s)
- Chris Papadopoulos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, cedex, France
| | - Nicolas Chevrollier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, cedex, France
| | - Anne Lopes
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, cedex, France.
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7
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Papadopoulos C, Callebaut I, Gelly JC, Hatin I, Namy O, Renard M, Lespinet O, Lopes A. Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution. Genome Res 2021; 31:2303-2315. [PMID: 34810219 PMCID: PMC8647833 DOI: 10.1101/gr.275638.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/23/2021] [Indexed: 01/08/2023]
Abstract
The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic open reading frames (ORFs) of S. cerevisiae with the aim of (1) exploring whether the structural states' diversity of proteomes is already present in noncoding sequences, and (2) estimating the potential of the noncoding genome to produce novel protein bricks that could either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural state diversity of canonical proteins, with the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by reconstructing the ancestral sequences of 70 yeast de novo genes and characterized the sequence and structural properties of intergenic ORFs with a strong translation signal. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.
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Affiliation(s)
- Chris Papadopoulos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Jean-Christophe Gelly
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015 Paris, France
- Laboratoire d'Excellence GR-Ex, 75015 Paris, France
- Institut National de la Transfusion Sanguine, F-75015 Paris, France
| | - Isabelle Hatin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Namy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maxime Renard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Lespinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Anne Lopes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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8
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Saito M, Ladha A, Strecker J, Faure G, Neumann E, Altae-Tran H, Macrae RK, Zhang F. Dual modes of CRISPR-associated transposon homing. Cell 2021; 184:2441-2453.e18. [PMID: 33770501 PMCID: PMC8276595 DOI: 10.1016/j.cell.2021.03.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/25/2021] [Accepted: 03/02/2021] [Indexed: 12/23/2022]
Abstract
Tn7-like transposons have co-opted CRISPR systems, including class 1 type I-F, I-B, and class 2 type V-K. Intriguingly, although these CRISPR-associated transposases (CASTs) undergo robust CRISPR RNA (crRNA)-guided transposition, they are almost never found in sites targeted by the crRNAs encoded by the cognate CRISPR array. To understand this paradox, we investigated CAST V-K and I-B systems and found two distinct modes of transposition: (1) crRNA-guided transposition and (2) CRISPR array-independent homing. We show distinct CAST systems utilize different molecular mechanisms to target their homing site. Type V-K CAST systems use a short, delocalized crRNA for RNA-guided homing, whereas type I-B CAST systems, which contain two distinct target selector proteins, use TniQ for RNA-guided DNA transposition and TnsD for homing to an attachment site. These observations illuminate a key step in the life cycle of CAST systems and highlight the diversity of molecular mechanisms mediating transposon homing.
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Affiliation(s)
- Makoto Saito
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alim Ladha
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan Strecker
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guilhem Faure
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edwin Neumann
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Han Altae-Tran
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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9
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Hezroni H, Ben-Tov Perry R, Gil N, Degani N, Ulitsky I. Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus. EMBO Rep 2020; 21:e51264. [PMID: 32969152 DOI: 10.15252/embr.202051264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/09/2022] Open
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs), yet the biological functions of most of them remain unknown. A particularly rich repertoire of lncRNAs found in mammalian brain and in the early embryo. We used RNA-seq and computational analysis to prioritize lncRNAs that may regulate commitment of pluripotent cells to a neuronal fate and perturbed their expression prior to neuronal differentiation. Knockdown by RNAi of two highly conserved and well-expressed lncRNAs, Reno1 (2810410L24Rik) and lnc-Nr2f1, decreased the expression of neuronal markers and led to massive changes in gene expression in the differentiated cells. We further show that the Reno1 locus forms increasing spatial contacts during neurogenesis with its adjacent protein-coding gene Bahcc1. Loss of either Reno1 or Bahcc1 leads to an early arrest in neuronal commitment, failure to induce a neuronal gene expression program, and to global reduction in chromatin accessibility at regions that are marked by the H3K4me3 chromatin mark at the onset of differentiation. Reno1 and Bahcc1 thus form a previously uncharacterized circuit required for the early steps of neuronal commitment.
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Affiliation(s)
| | | | - Noa Gil
- Weizmann Institute of Science, Rehovot, Israel
| | - Neta Degani
- Weizmann Institute of Science, Rehovot, Israel
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10
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Chen G, Wang D, Wu B, Yan F, Xue H, Wang Q, Quan S, Chen Y. Taf14 recognizes a common motif in transcriptional machineries and facilitates their clustering by phase separation. Nat Commun 2020; 11:4206. [PMID: 32826896 PMCID: PMC7442819 DOI: 10.1038/s41467-020-18021-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
Saccharomyces cerevisiae TBP associated factor 14 (Taf14) is a well-studied transcriptional regulator that controls diverse physiological processes and that physically interacts with at least seven nuclear complexes in yeast. Despite multiple previous Taf14 structural studies, the nature of its disparate transcriptional regulatory functions remains opaque. Here, we demonstrate that the extra-terminal (ET) domain of Taf14 (Taf14ET) recognizes a common motif in multiple transcriptional coactivator proteins from several nuclear complexes, including RSC, SWI/SNF, INO80, NuA3, TFIID, and TFIIF. Moreover, we show that such partner binding promotes liquid-liquid phase separation (LLPS) of Taf14ET, in a mechanism common to YEATS-associated ET domains (e.g., AF9ET) but not Bromo-associated ET domains from BET-family proteins. Thus, beyond identifying the molecular mechanism by which Taf14ET associates with many transcriptional regulators, our study suggests that Taf14 may function as a versatile nuclear hub that orchestrates transcriptional machineries to spatiotemporally regulate diverse cellular pathways. S. cerevisiae TBP associated factor 14 (Taf14) is a transcriptional regulator that interacts with multiple nuclear complexes. Here, the authors report that the extra-terminal domain of Taf14 (Taf14ET) recognizes a common motif in various transcriptional coactivator proteins and they solve the NMR structure of Taf14ET bound the ET-binding motif of Sth1, the catalytic subunit of the RSC (Remodel the Structure of Chromatin) complex, and furthermore show that Taf14ET undergoes liquid-liquid phase separation, which is enhanced by Taf14 interaction partners.
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Affiliation(s)
- Guochao Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Duo Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Fuxiang Yan
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Quanmeng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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11
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Marichal L, Klein G, Armengaud J, Boulard Y, Chédin S, Labarre J, Pin S, Renault JP, Aude JC. Protein Corona Composition of Silica Nanoparticles in Complex Media: Nanoparticle Size does not Matter. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E240. [PMID: 32013169 PMCID: PMC7075126 DOI: 10.3390/nano10020240] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 12/30/2022]
Abstract
Biomolecules, and particularly proteins, bind on nanoparticle (NP) surfaces to form the so-called protein corona. It is accepted that the corona drives the biological distribution and toxicity of NPs. Here, the corona composition and structure were studied using silica nanoparticles (SiNPs) of different sizes interacting with soluble yeast protein extracts. Adsorption isotherms showed that the amount of adsorbed proteins varied greatly upon NP size with large NPs having more adsorbed proteins per surface unit. The protein corona composition was studied using a large-scale label-free proteomic approach, combined with statistical and regression analyses. Most of the proteins adsorbed on the NPs were the same, regardless of the size of the NPs. To go beyond, the protein physicochemical parameters relevant for the adsorption were studied: electrostatic interactions and disordered regions are the main driving forces for the adsorption on SiNPs but polypeptide sequence length seems to be an important factor as well. This article demonstrates that curvature effects exhibited using model proteins are not determining factors for the corona composition on SiNPs, when dealing with complex biological media.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
| | - Géraldine Klein
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin, AgroSup Dijon, Université de Bourgogne Franche-Comté, rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, 30207 Bagnols-sur-Cèze, France;
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
| | - Stéphane Chédin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
| | - Jean Labarre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
| | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
| | - Jean-Philippe Renault
- Université Paris-Saclay, CEA, CNRS, NIMBE, Laboratoire Interdisciplinaire sur l’Organisation Nanométrique et Supramoléculaire, 91191 Gif-sur-Yvette, France; (S.P.); (J.-P.R.)
| | - Jean-Christophe Aude
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (G.K.); (Y.B.); (S.C.); (J.L.)
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12
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Masuko K, Fuse N, Komaba K, Katsuyama T, Nakajima R, Furuhashi H, Kurata S. winged eye Induces Transdetermination of Drosophila Imaginal Disc by Acting in Concert with a Histone Methyltransferase, Su(var)3-9. Cell Rep 2019; 22:206-217. [PMID: 29298422 DOI: 10.1016/j.celrep.2017.11.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 07/12/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022] Open
Abstract
Drosophila imaginal disc cells exhibit a remarkable ability to convert cell fates in response to various perturbations, a phenomenon called transdetermination (TD). We previously identified winged eye (wge) as a factor that induces eye-to-wing TD upon overexpression in eye imaginal discs, but the molecular mechanisms underlying TD have remained largely unclear. Here, we found that wge induces various histone modifications and enhances the methylation of Lys9 on histone H3 (H3K9), a feature of heterochromatin. A histone methyltransferase, Su(var)3-9, is required for wge-mediated H3K9 methylation and eye-to-wing TD. Su(var)3-9 is also required for classical wound-induced TD but not for normal development, suggesting its involvement in several types of imaginal disc TDs. Transcriptome analysis revealed that wge represses eye identity genes independently of Su(var)3-9 and activates TD-related genes by acting together with Su(var)3-9. These findings provide new insights into diverse types of chromatin regulation at progressive steps of cell-fate conversions.
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Affiliation(s)
- Keita Masuko
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Naoyuki Fuse
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Kanae Komaba
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Tomonori Katsuyama
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Rumi Nakajima
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Hirofumi Furuhashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Shoichiro Kurata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
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13
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Faure G, Jézéquel K, Roisné-Hamelin F, Bitard-Feildel T, Lamiable A, Marcand S, Callebaut I. Discovery and Evolution of New Domains in Yeast Heterochromatin Factor Sir4 and Its Partner Esc1. Genome Biol Evol 2019; 11:572-585. [PMID: 30668669 PMCID: PMC6394760 DOI: 10.1093/gbe/evz010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2019] [Indexed: 12/22/2022] Open
Abstract
Sir4 is a core component of heterochromatin found in yeasts of the Saccharomycetaceae family, whose general hallmark is to harbor a three-loci mating-type system with two silent loci. However, a large part of the Sir4 amino acid sequences has remained unexplored, belonging to the dark proteome. Here, we analyzed the phylogenetic profile of yet undescribed foldable regions present in Sir4 as well as in Esc1, an Sir4-interacting perinuclear anchoring protein. Within Sir4, we identified a new conserved motif (TOC) adjacent to the N-terminal KU-binding motif. We also found that the Esc1-interacting region of Sir4 is a Dbf4-related H-BRCT domain, only present in species possessing the HO endonuclease and in Kluveryomyces lactis. In addition, we found new motifs within Esc1 including a motif (Esc1-F) that is unique to species where Sir4 possesses an H-BRCT domain. Mutagenesis of conserved amino acids of the Sir4 H-BRCT domain, known to play a critical role in the Dbf4 function, shows that the function of this domain is separable from the essential role of Sir4 in transcriptional silencing and the protection from HO-induced cutting in Saccharomyces cerevisiae. In the more distant methylotrophic clade of yeasts, which often harbor a two-loci mating-type system with one silent locus, we also found a yet undescribed H-BRCT domain in a distinct protein, the ISWI2 chromatin-remodeling factor subunit Itc1. This study provides new insights on yeast heterochromatin evolution and emphasizes the interest of using sensitive methods of sequence analysis for identifying hitherto ignored functional regions within the dark proteome.
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Affiliation(s)
- Guilhem Faure
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Kévin Jézéquel
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Florian Roisné-Hamelin
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Alexis Lamiable
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Stéphane Marcand
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,Sorbonne Université, UMR CNRS 7238, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France.,Sorbonne Université, UMR CNRS 7238, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
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14
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Bitard‐Feildel T, Lamiable A, Mornon J, Callebaut I. Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences. Proteomics 2018; 18:e1800054. [PMID: 30299594 PMCID: PMC7168002 DOI: 10.1002/pmic.201800054] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/29/2018] [Indexed: 12/17/2022]
Abstract
Hydrophobic cluster analysis (HCA) is an original approach for protein sequence analysis, which provides access to the foldable repertoire of the protein universe, including yet unannotated protein segments ("dark proteome"). Foldable segments correspond to ordered regions, as well as to intrinsically disordered regions (IDRs) undergoing disorder to order transitions. In this review, how HCA can be used to give insight into this last category of foldable segments is illustrated, with examples matching known 3D structures. After reviewing the HCA principles, examples of short foldable segments are given, which often contain short linear motifs, typically matching hydrophobic clusters. These segments become ordered upon contact with partners, with secondary structure preferences generally corresponding to those observed in the 3D structures within the complexes. Such small foldable segments are sometimes larger than the segments of known 3D structures, including flanking hydrophobic clusters that may be critical for interaction specificity or regulation, as well as intervening sequences allowing fuzziness. Cases of larger conditionally disordered domains are also presented, with lower density in hydrophobic clusters than well-folded globular domains or with exposed hydrophobic patches, which are stabilized by interaction with partners.
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Affiliation(s)
- Tristan Bitard‐Feildel
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
- Laboratoire de Biologie Computationnelle et Quantitative (LCQB)Institute of Biology Paris‐Seine (IBPS)Centre national de la recherche scientifique (CNRS)Sorbonne Université75005ParisFrance
| | - Alexis Lamiable
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
| | - Jean‐Paul Mornon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
| | - Isabelle Callebaut
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
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15
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Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PLoS One 2018; 13:e0205267. [PMID: 30307988 PMCID: PMC6181354 DOI: 10.1371/journal.pone.0205267] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 09/02/2018] [Indexed: 12/24/2022] Open
Abstract
BAF250a and BAF250b are subunits of the SWI/SNF chromatin-remodeling complex that recruit the complex to chromatin allowing transcriptional activation of several genes. Despite being the central subunits of the SWI/SNF complex, the structural and functional annotation of BAF250a/b remains poorly understood. BAF250a (nearly 2200 residues protein) harbors an N-terminal DNA binding ARID (~110 residues) and a C-terminal folded region (~250 residues) of unknown structure and function, recently annotated as BAF250_C. Using hydrophobic core analysis, fold prediction and comparative modeling, here we have defined a domain boundary and associate a β-catenin like ARM-repeat fold to the C-terminus of BAF250a that encompass BAF250_C. The N-terminal DNA-binding ARID is found in diverse domain combinations in proteins imparting unique functions. We used a comparative sequence analysis based approach to study the ARIDs from diverse domain contexts and identified conserved residue positions that are important to preserve its core structure. Supporting this, mutation of one such conserved residue valine, at position 1067, to glycine, resulted in destabilization, loss of structural integrity and DNA binding affinity of ARID. Additionally, we identified a set of conserved and surface-exposed residues unique to the ARID when it co-occurs with the ARM repeat containing BAF250_C in BAF250a. Several of these residues are found mutated in somatic cancers. We predict that these residues in BAF250a may play important roles in mediating protein-DNA and protein-protein interactions in the BAF complex.
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16
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Hausrath AC, Kingston RL. Conditionally disordered proteins: bringing the environment back into the fold. Cell Mol Life Sci 2017; 74:3149-3162. [PMID: 28597298 PMCID: PMC11107710 DOI: 10.1007/s00018-017-2558-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
For many proteins, biological function requires the folding of the polypeptide chain into a unique and persistent tertiary structure. This review concerns proteins that adopt a specific tertiary structure to function, but are otherwise partially or completely disordered. The biological cue for protein folding is environmental perturbation or minor post-translational modification. Hence, we term these proteins conditionally disordered. Many of these proteins recognize and bind other molecules, and conditional disorder has been hypothesized to allow for more nuanced control and regulation of binding processes. However, this remains largely unproven. The sequences of conditionally disordered proteins suggest their propensity to fold; yet, under the standard laboratory conditions, they do not do so, which may appear surprising. We argue that the surprise results from the failure to consider the role of the environment in protein structure formation and that conditional disorder arises as a natural consequence of the marginal stability of the folded state.
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Affiliation(s)
- Andrew C Hausrath
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand.
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17
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Nemet J, Vidan N, Sopta M. A meta-analysis reveals complex regulatory properties at Taf14-repressed genes. BMC Genomics 2017; 18:175. [PMID: 28209126 PMCID: PMC5312515 DOI: 10.1186/s12864-017-3544-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regulation of gene transcription in response to stress is central to a cell's ability to cope with environmental challenges. Taf14 is a YEATS domain protein in S.cerevisiae that physically associates with several transcriptionally relevant multisubunit complexes including the general transcription factors TFIID and TFIIF and the chromatin-modifying complexes SWI/SNF, INO80, RSC and NuA3. TAF14 deletion strains are sensitive to a variety of stresses suggesting that it plays a role in the transcriptional stress response. RESULTS In this report we survey published genome-wide transcriptome and occupancy data to define regulatory properties associated with Taf14-dependent genes. Our transcriptome analysis reveals that stress related, TATA-containing and SAGA-dependent genes were much more affected by TAF14 deletion than were TFIID-dependent genes. Comparison of Taf14 and multiple transcription factor occupancy at promoters genome-wide identified a group of proteins whose occupancy correlates with that of Taf14 and whose proximity to Taf14 suggests functional interactions. We show that Taf14-repressed genes tend to be extensively regulated, positively by SAGA complex and the stress dependent activators, Msn2/4 and negatively by a wide number of repressors that act upon promoter chromatin and TBP. CONCLUSIONS Taken together our analyses suggest a novel role for Taf14 in repression and derepression of stress induced genes, most probably as part of a regulatory network which includes Cyc8-Tup1, Srb10 and histone modifying enzymes.
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Affiliation(s)
- Josipa Nemet
- Department of molecular biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Nikolina Vidan
- Department of molecular biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Mary Sopta
- Department of molecular biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.
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18
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Exploring the dark foldable proteome by considering hydrophobic amino acids topology. Sci Rep 2017; 7:41425. [PMID: 28134276 PMCID: PMC5278394 DOI: 10.1038/srep41425] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022] Open
Abstract
The protein universe corresponds to the set of all proteins found in all organisms. A way to explore it is by taking into account the domain content of the proteins. However, some part of sequences and many entire sequences remain un-annotated despite a converging number of domain families. The un-annotated part of the protein universe is referred to as the dark proteome and remains poorly characterized. In this study, we quantify the amount of foldable domains within the dark proteome by using the hydrophobic cluster analysis methodology. These un-annotated foldable domains were grouped using a combination of remote homology searches and domain annotations, leading to define different levels of darkness. The dark foldable domains were analyzed to understand what make them different from domains stored in databases and thus difficult to annotate. The un-annotated domains of the dark proteome universe display specific features relative to database domains: shorter length, non-canonical content and particular topology in hydrophobic residues, higher propensity for disorder, and a higher energy. These features make them hard to relate to known families. Based on these observations, we emphasize that domain annotation methodologies can still be improved to fully apprehend and decipher the molecular evolution of the protein universe.
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19
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Zhang S, Pondarre C, Pennarun G, Labussiere-Wallet H, Vera G, France B, Chansel M, Rouvet I, Revy P, Lopez B, Soulier J, Bertrand P, Callebaut I, de Villartay JP. A nonsense mutation in the DNA repair factor Hebo causes mild bone marrow failure and microcephaly. J Exp Med 2016; 213:1011-28. [PMID: 27185855 PMCID: PMC4886357 DOI: 10.1084/jem.20151183] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 04/12/2016] [Indexed: 11/05/2022] Open
Abstract
de Villartay et al. describe a patient with a DNA repair factor mutation that leads to an increased sensitivity to DNA-damaging agents and, ultimately, to mild bone marrow failure and microcephaly. Inherited bone marrow failure syndromes are human conditions in which one or several cell lineages of the hemopoietic system are affected. They are present at birth or may develop progressively. They are sometimes accompanied by other developmental anomalies. Three main molecular causes have been recognized to result in bone marrow failure syndromes: (1) defects in the Fanconi anemia (FA)/BRCA DNA repair pathway, (2) defects in telomere maintenance, and (3) abnormal ribosome biogenesis. We analyzed a patient with mild bone marrow failure and microcephaly who did not present with the typical FA phenotype. Cells from this patient showed increased sensitivity to ionizing radiations and phleomycin, attesting to a probable DNA double strand break (dsb) repair defect. Linkage analysis and whole exome sequencing revealed a homozygous nonsense mutation in the ERCC6L2 gene. We identified a new ERCC6L2 alternative transcript encoding the DNA repair factor Hebo, which is critical for complementation of the patient’s DNAdsb repair defect. Sequence analysis revealed three structured regions within Hebo: a TUDOR domain, an adenosine triphosphatase domain, and a new domain, HEBO, specifically present in Hebo direct orthologues. Hebo is ubiquitously expressed, localized in the nucleus, and rapidly recruited to DNAdsb’s in an NBS1-dependent manner.
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Affiliation(s)
- Shu Zhang
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Corinne Pondarre
- Institut d'Hématologie et d'Oncologie Pédiatrique, 69008 Lyon, France
| | - Gaelle Pennarun
- Commisariat à l'Energie Atomique, Division des Sciences du Vivant, Institut National de la Santé et de la Recherche Médicale, UMR 967 CEA, Université Paris Diderot, 75013 Paris, France Institut de Radiobiologie Cellulaire et Moléculaire Fontenay-aux-Roses, Université Paris Sud, 91400 Orsay, France
| | - Helene Labussiere-Wallet
- Service d'Hématologie, Groupement Hospitalier Lyon Sud, Hospices Civils de Lyon, 69002 Lyon, France
| | - Gabriella Vera
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Benoit France
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Marie Chansel
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Isabelle Rouvet
- Biotechnology Department, Hospices Civils de Lyon, 69002 Lyon, France
| | - Patrick Revy
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Bernard Lopez
- Institut de Cancérologie Gustave Roussy, Centre National de la Recherche Scientifique, UMR 8200, Université Paris Sud, 91400 Orsay, France
| | - Jean Soulier
- Institute of Hematology, Institut National de la Santé et de la Recherche Médicale, UMR 944, Centre National de la Recherche Scientifique, UMR 7212, Saint-Louis Hospital and Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Pascale Bertrand
- Commisariat à l'Energie Atomique, Division des Sciences du Vivant, Institut National de la Santé et de la Recherche Médicale, UMR 967 CEA, Université Paris Diderot, 75013 Paris, France
| | - Isabelle Callebaut
- Centre National de la Recherche Scientifique, UMR 7590, Université Pierre et Marie Curie, Museum National d'Histoire Naturelle, Institut de recherche pour le développement, Institut Universitaire de Cancérologie, Sorbonne Universités, 75005 Paris, France
| | - Jean-Pierre de Villartay
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
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20
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Rebehmed J, Quintus F, Mornon JP, Callebaut I. The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis. Proteins 2016; 84:624-38. [DOI: 10.1002/prot.25012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Joseph Rebehmed
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
| | - Flavien Quintus
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
| | - Jean-Paul Mornon
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
| | - Isabelle Callebaut
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
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21
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Bitard-Feildel T, Heberlein M, Bornberg-Bauer E, Callebaut I. Detection of orphan domains in Drosophila using "hydrophobic cluster analysis". Biochimie 2015; 119:244-53. [PMID: 25736992 DOI: 10.1016/j.biochi.2015.02.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/20/2015] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Comparative genomics has become an important strategy in life science research. While many genes, and the proteins they code for, can be well characterized by assigning orthologs, a significant amount of proteins or domains remain obscure "orphans". Some orphans are overlooked by current computational methods because they rapidly diverged, others emerged relatively recently (de novo). Recent research has demonstrated the importance of orphans, and of de novo proteins and domains for development of new phenotypic traits and adaptation. New approaches for detecting novel domains are thus of paramount importance. RESULTS The hydrophobic cluster analysis (HCA) method delineates globular-like domains from the information of a protein sequence and thereby allows bypassing some of the established methods limitations based on conserved sequence similarity. In this study, HCA is tested for orphan domain detection on 12 Drosophila genomes. After their detection, the oprhan domains are classified into two categories, depending on their presence/absence in distantly related species. The two categories show significantly different physico-chemical properties when compared to previously characterized domains from the Pfam database. The newly detected domains have a higher degree of intrinsic disorder and a particular hydrophobic cluster composition. The older the domains are, the more similar their hydrophobic cluster content is to the cluster content of Pfam domains. The results suggest that, over time, newly created domains acquire a canonical set of hydrophobic clusters but conserve some features of intrinsically disordered regions. CONCLUSION Our results agree with previous findings on orphan domains and suggest that the physico-chemical properties of domains change over evolutionary long time scale. The presented HCA-based method is able to detect domains with unusual properties without relying on prior knowledge, such as the availability of homologs. Therefore, the method has large potential for complementing existing strategies to annotate genomes, and for better understanding how molecular features emerge.
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Affiliation(s)
- Tristan Bitard-Feildel
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Huefferstrasse 1, D-48149, Germany
| | - Magdalena Heberlein
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Huefferstrasse 1, D-48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Huefferstrasse 1, D-48149, Germany.
| | - Isabelle Callebaut
- IMPMC, Sorbonne Universités - UMR CNRS 7590, UPMC Univ Paris 06, Muséum National d'Histoire Naturelle, IRD UMR 206, IUC 4 Place Jussieu, F-75005 Paris, France.
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Expanding the SRI domain family: a common scaffold for binding the phosphorylated C-terminal domain of RNA polymerase II. FEBS Lett 2014; 588:4431-7. [PMID: 25448681 DOI: 10.1016/j.febslet.2014.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/07/2014] [Accepted: 10/12/2014] [Indexed: 11/21/2022]
Abstract
The SRI domain is a small three-helix domain originally discovered near the C-terminus of both histone methyltransferase SETD2 and helicase RECQL5. The SRI domain binds to the C-terminal repeat domain of the largest subunit of RNA polymerase II, allowing SETD2 and RECQL5 to regulate various mechanisms associated with RNA transcription. Using original tools to detect common patterns in distantly related sequences, we have identified SRI domains in several additional proteins, most of which are involved in RNA metabolism. Combining sequence analysis with structural prediction, we show that this domain family is more diverse than previously thought and we predict critical structural and functional features.
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Faure G, Revy P, Schertzer M, Londono-Vallejo A, Callebaut I. The C-terminal extension of human RTEL1, mutated in Hoyeraal-Hreidarsson syndrome, contains harmonin-N-like domains. Proteins 2013; 82:897-903. [PMID: 24130156 DOI: 10.1002/prot.24438] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/13/2013] [Accepted: 09/26/2013] [Indexed: 12/28/2022]
Abstract
Several studies have recently shown that germline mutations in RTEL1, an essential DNA helicase involved in telomere regulation and DNA repair, cause Hoyeraal-Hreidarsson syndrome (HHS), a severe form of dyskeratosis congenita. Using original new softwares, facilitating the delineation of the different domains of the protein and the identification of remote relationships for orphan domains, we outline here that the C-terminal extension of RTEL1, downstream of its catalytic domain and including several HHS-associated mutations, contains a yet unidentified tandem of harmonin-N-like domains, which may serve as a hub for partner interaction. This finding highlights the potential critical role of this region for the function of RTEL1 and gives insights into the impact that the identified mutations would have on the structure and function of these domains.
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Affiliation(s)
- Guilhem Faure
- CNRS, UPMC University Paris 6, IMPMC, UMR7590-IUC, F-75005, Paris, France
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Faure G, Callebaut I. Comprehensive repertoire of foldable regions within whole genomes. PLoS Comput Biol 2013; 9:e1003280. [PMID: 24204229 PMCID: PMC3812050 DOI: 10.1371/journal.pcbi.1003280] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 08/15/2013] [Indexed: 11/30/2022] Open
Abstract
In order to get a comprehensive repertoire of foldable domains within whole proteomes, including orphan domains, we developed a novel procedure, called SEG-HCA. From only the information of a single amino acid sequence, SEG-HCA automatically delineates segments possessing high densities in hydrophobic clusters, as defined by Hydrophobic Cluster Analysis (HCA). These hydrophobic clusters mainly correspond to regular secondary structures, which together form structured or foldable regions. Genome-wide analyses revealed that SEG-HCA is opposite of disorder predictors, both addressing distinct structural states. Interestingly, there is however an overlap between the two predictions, including small segments of disordered sequences, which undergo coupled folding and binding. SEG-HCA thus gives access to these specific domains, which are generally poorly represented in domain databases. Comparison of the whole set of SEG-HCA predictions with the Conserved Domain Database (CDD) also highlighted a wide proportion of predicted large (length >50 amino acids) segments, which are CDD orphan. These orphan sequences may either correspond to highly divergent members of already known families or belong to new families of domains. Their comprehensive description thus opens new avenues to investigate new functional and/or structural features, which remained so far uncovered. Altogether, the data described here provide new insights into the protein architecture and organization throughout the three kingdoms of life. Spontaneous or induced folding into a specific 3D structure is a key property of proteins to perform their biological functions. Folded 3D structures of proteins perform specific functions, including interactions with other proteins. Intrinsically disordered regions also mediate interaction, gaining structure only when bound to a target protein. In both cases, hydrophobicity generally plays a major role in the protein segment “foldability”. Here, we developed an original procedure to identify foldable segments from only the information of a single amino acid sequence and to explore protein structures at a proteomic scale. Our approach goes beyond the simple consideration of mean hydrophobicity, by including the secondary structure information through the use of a two-dimensional transposition of the sequence. The developed procedure, combined with disorder predictors, may facilitate the specific identification of small segments that undergo coupled folding and binding. Combined with the analysis of specific domain databases, it also highlights orphan foldable segments, which remain yet uncharacterized.
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Affiliation(s)
- Guilhem Faure
- CNRS, UPMC Univ Paris 6, IMPMC, UMR7590 - IUC, Paris, France
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