1
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Brady ST, Mesnard-Hoaglin NA, Mays S, Priego M, Dziechciowska J, Morris S, Kang M, Tsai MY, Purks JL, Klein A, Gaona A, Melloni A, Connors T, Hyman B, Song Y, Morfini GA. Toxic effects of mutant huntingtin in axons are mediated by its proline-rich domain. Brain 2024; 147:2098-2113. [PMID: 37633260 PMCID: PMC11146425 DOI: 10.1093/brain/awad280] [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] [Revised: 05/13/2023] [Accepted: 07/17/2023] [Indexed: 08/28/2023] Open
Abstract
Huntington's disease results from expansion of a polyglutamine tract (polyQ) in mutant huntingtin (mHTT) protein, but mechanisms underlying polyQ expansion-mediated toxic gain-of-mHTT function remain elusive. Here, deletion and antibody-based experiments revealed that a proline-rich domain (PRD) adjacent to the polyQ tract is necessary for mHTT to inhibit fast axonal transport and promote axonal pathology in cultured mammalian neurons. Further, polypeptides corresponding to subregions of the PRD sufficed to elicit the toxic effect on fast axonal transport, which was mediated by c-Jun N-terminal kinases (JNKs) and involved PRD binding to one or more SH3-domain containing proteins. Collectively, these data suggested a mechanism whereby polyQ tract expansion in mHTT promotes aberrant PRD exposure and interactions of this domain with SH3 domain-containing proteins including some involved in activation of JNKs. In support, biochemical and immunohistochemical experiments linked aberrant PRD exposure to increased JNK activation in striatal tissues of the zQ175 mouse model and from post-mortem Huntington's disease patients. Together, these findings support a critical role of PRD on mHTT toxicity, suggesting a novel framework for the potential development of therapies aimed to halt or reduce axonal pathology in Huntington's disease.
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Affiliation(s)
- Scott T Brady
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | | | - Sarah Mays
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Mercedes Priego
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Joanna Dziechciowska
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Sarah Morris
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Minsu Kang
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Ming Ying Tsai
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | | | - Alison Klein
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Angelica Gaona
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Alexandra Melloni
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Theresa Connors
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Bradley Hyman
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02129, USA
| | - Yuyu Song
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02129, USA
| | - Gerardo A Morfini
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
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2
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Kazemein Jasemi NS, Mehrabipour M, Magdalena Estirado E, Brunsveld L, Dvorsky R, Ahmadian MR. Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily. Cells 2024; 13:195. [PMID: 38275820 PMCID: PMC10814857 DOI: 10.3390/cells13020195] [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: 12/12/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
SRC homology 3 (SH3) domains are critical interaction modules that orchestrate the assembly of protein complexes involved in diverse biological processes. They facilitate transient protein-protein interactions by selectively interacting with proline-rich motifs (PRMs). A database search revealed 298 SH3 domains in 221 human proteins. Multiple sequence alignment of human SH3 domains is useful for phylogenetic analysis and determination of their selectivity towards PRM-containing peptides (PRPs). However, a more precise functional classification of SH3 domains is achieved by constructing a phylogenetic tree only from PRM-binding residues and using existing SH3 domain-PRP structures and biochemical data to determine the specificity within each of the 10 families for particular PRPs. In addition, the C-terminal proline-rich domain of the RAS activator SOS1 covers 13 of the 14 recognized proline-rich consensus sequence motifs, encompassing differential PRP pattern selectivity among all SH3 families. To evaluate the binding capabilities and affinities, we conducted fluorescence dot blot and polarization experiments using 25 representative SH3 domains and various PRPs derived from SOS1. Our analysis has identified 45 interacting pairs, with binding affinities ranging from 0.2 to 125 micromolar, out of 300 tested and potential new SH3 domain-SOS1 interactions. Furthermore, it establishes a framework to bridge the gap between SH3 and PRP interactions and provides predictive insights into the potential interactions of SH3 domains with PRMs based on sequence specifications. This novel framework has the potential to enhance the understanding of protein networks mediated by SH3 domain-PRM interactions and be utilized as a general approach for other domain-peptide interactions.
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Affiliation(s)
- Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands; (E.M.E.); (L.B.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands; (E.M.E.); (L.B.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
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3
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Mehrabipour M, Jasemi NSK, Dvorsky R, Ahmadian MR. A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling. Cells 2023; 12:2054. [PMID: 37626864 PMCID: PMC10453029 DOI: 10.3390/cells12162054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
SRC homology 3 (SH3) domains are fundamental modules that enable the assembly of protein complexes through physical interactions with a pool of proline-rich/noncanonical motifs from partner proteins. They are widely studied modular building blocks across all five kingdoms of life and viruses, mediating various biological processes. The SH3 domains are also implicated in the development of human diseases, such as cancer, leukemia, osteoporosis, Alzheimer's disease, and various infections. A database search of the human proteome reveals the existence of 298 SH3 domains in 221 SH3 domain-containing proteins (SH3DCPs), ranging from 13 to 720 kilodaltons. A phylogenetic analysis of human SH3DCPs based on their multi-domain architecture seems to be the most practical way to classify them functionally, with regard to various physiological pathways. This review further summarizes the achievements made in the classification of SH3 domain functions, their binding specificity, and their significance for various diseases when exploiting SH3 protein modular interactions as drug targets.
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Affiliation(s)
- Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, 040 01 Košice, Slovakia
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
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4
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Experimental Characterization of the Interaction between the N-Terminal SH3 Domain of Crkl and C3G. Int J Mol Sci 2021; 22:ijms222413174. [PMID: 34947971 PMCID: PMC8705818 DOI: 10.3390/ijms222413174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Crkl is a protein involved in the onset of several cancer pathologies that exerts its function only through its protein-protein interaction domains, a SH2 domain and two SH3 domains. SH3 domains are small protein interaction modules that mediate the binding and recognition of proline-rich sequences. One of the main physiological interactors of Crkl is C3G (also known as RAPGEF1), an interaction with key implications in regulating cellular growth and differentiation, cell morphogenesis and adhesion processes. Thus, understanding the interaction between Crkl and C3G is fundamental to gaining information about the molecular determinants of the several cancer pathologies in which these proteins are involved. In this paper, through a combination of fast kinetics at different experimental conditions and site-directed mutagenesis, we characterize the binding reaction between the N-SH3 domain of Crkl and a peptide mimicking a specific portion of C3G. Our results show a clear effect of pH on the stability of the complex, due to the protonation of negatively charged residues in the binding pocket of N-SH3. Our results are discussed under the light of previous work on SH3 domains.
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5
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Jaufmann J, Franke FC, Sperlich A, Blumendeller C, Kloos I, Schneider B, Sasaki D, Janssen KP, Beer-Hammer S. The emerging and diverse roles of the SLy/SASH1-protein family in health and disease-Overview of three multifunctional proteins. FASEB J 2021; 35:e21470. [PMID: 33710696 DOI: 10.1096/fj.202002495r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/22/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022]
Abstract
Intracellular adaptor proteins are indispensable for the transduction of receptor-derived signals, as they recruit and connect essential downstream effectors. The SLy/SASH1-adaptor family comprises three highly homologous proteins, all of them sharing conserved structural motifs. The initial characterization of the first member SLy1/SASH3 (SH3 protein expressed in lymphocytes 1) in 2001 was rapidly followed by identification of SLy2/HACS1 (hematopoietic adaptor containing SH3 and SAM domains 1) and SASH1/SLy3 (SAM and SH3 domain containing 1). Based on their pronounced sequence similarity, they were subsequently classified as one family of intracellular scaffold proteins. Despite their obvious homology, the three SLy/SASH1-members fundamentally differ with regard to their expression and function in intracellular signaling. On the contrary, growing evidence clearly demonstrates an important role of all three proteins in human health and disease. In this review, we systematically summarize what is known about the SLy/SASH1-adaptors in the field of molecular cell biology and immunology. To this end, we recapitulate current research about SLy1/SASH3, SLy2/HACS1, and SASH1/SLy3, with an emphasis on their similarities and differences.
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Affiliation(s)
- Jennifer Jaufmann
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomik and ICePhA, University of Tuebingen, Tuebingen, Germany
| | - Fabian Christoph Franke
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Andreas Sperlich
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Carolin Blumendeller
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomik and ICePhA, University of Tuebingen, Tuebingen, Germany
| | - Isabel Kloos
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomik and ICePhA, University of Tuebingen, Tuebingen, Germany
| | - Barbara Schneider
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomik and ICePhA, University of Tuebingen, Tuebingen, Germany
| | - Daisuke Sasaki
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.,Medical SC New Technology Strategy Office, General Research Institute, Nitto Boseki, Co., Ltd, Tokyo, Japan
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Sandra Beer-Hammer
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomik and ICePhA, University of Tuebingen, Tuebingen, Germany
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6
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Kaur G, Iyer LM, Burroughs AM, Aravind L. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. eLife 2021; 10:70394. [PMID: 34061031 PMCID: PMC8195603 DOI: 10.7554/elife.70394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022] Open
Abstract
Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptotic processes to counter-invader immunity, in prokaryotes with a multicellular habit. However, the provenance of key adaptor domains, namely those of the Death-like and TRADD-N superfamilies, a quintessential feature of metazoan apoptotic systems, remained murky. Here, we use sensitive sequence analysis and comparative genomics methods to identify unambiguous bacterial homologs of the Death-like and TRADD-N superfamilies. We show the former to have arisen as part of a radiation of effector-associated α-helical adaptor domains that likely mediate homotypic interactions bringing together diverse effector and signaling domains in predicted bacterial apoptosis- and counter-invader systems. Similarly, we show that the TRADD-N domain defines a key, widespread signaling bridge that links effector deployment to invader-sensing in multicellular bacterial and metazoan counter-invader systems. TRADD-N domains are expanded in aggregating marine invertebrates and point to distinctive diversifying immune strategies probably directed both at RNA and retroviruses and cellular pathogens that might infect such communities. These TRADD-N and Death-like domains helped identify several new bacterial and metazoan counter-invader systems featuring underappreciated, common functional principles: the use of intracellular invader-sensing lectin-like (NPCBM and FGS), transcription elongation GreA/B-C, glycosyltransferase-4 family, inactive NTPase (serving as nucleic acid receptors), and invader-sensing GTPase switch domains. Finally, these findings point to the possibility of multicellular bacteria-stem metazoan symbiosis in the emergence of the immune/apoptotic systems of the latter.
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Affiliation(s)
- Gurmeet Kaur
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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7
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Ding W, Tan HY, Zhang JX, Wilczek LA, Hsieh KR, Mulkin JA, Bianco PR. The mechanism of Single strand binding protein-RecG binding: Implications for SSB interactome function. Protein Sci 2020; 29:1211-1227. [PMID: 32196797 PMCID: PMC7184773 DOI: 10.1002/pro.3855] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023]
Abstract
The Escherichia coli single-strand DNA binding protein (SSB) is essential to viability where it functions to regulate SSB interactome function. Here it binds to single-stranded DNA and to target proteins that comprise the interactome. The region of SSB that links these two essential protein functions is the intrinsically disordered linker. Key to linker function is the presence of three, conserved PXXP motifs that mediate binding to oligosaccharide-oligonucleotide binding folds (OB-fold) present in SSB and its interactome partners. Not surprisingly, partner OB-fold deletions eliminate SSB binding. Furthermore, single point mutations in either the PXXP motifs or, in the RecG OB-fold, obliterate SSB binding. The data also demonstrate that, and in contrast to the view currently held in the field, the C-terminal acidic tip of SSB is not required for interactome partner binding. Instead, we propose the tip has two roles. First, and consistent with the proposal of Dixon, to regulate the structure of the C-terminal domain in a biologically active conformation that prevents linkers from binding to SSB OB-folds until this interaction is required. Second, as a secondary binding domain. Finally, as OB-folds are present in SSB and many of its partners, we present the SSB interactome as the first family of OB-fold genome guardians identified in prokaryotes.
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Affiliation(s)
- Wenfei Ding
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Hui Yin Tan
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndianaUnited States
| | - Jia Xiang Zhang
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Luke A. Wilczek
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of ChemistryBrown UniversityProvidenceRhode IslandUnited States
| | - Karin R. Hsieh
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Jeffrey A. Mulkin
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Piero R. Bianco
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
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8
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Bianco PR. DNA Helicase-SSB Interactions Critical to the Regression and Restart of Stalled DNA Replication forks in Escherichia coli. Genes (Basel) 2020; 11:E471. [PMID: 32357475 PMCID: PMC7290993 DOI: 10.3390/genes11050471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 01/25/2023] Open
Abstract
In Escherichia coli, DNA replication forks stall on average once per cell cycle. When this occurs, replisome components disengage from the DNA, exposing an intact, or nearly intact fork. Consequently, the fork structure must be regressed away from the initial impediment so that repair can occur. Regression is catalyzed by the powerful, monomeric DNA helicase, RecG. During this reaction, the enzyme couples unwinding of fork arms to rewinding of duplex DNA resulting in the formation of a Holliday junction. RecG works against large opposing forces enabling it to clear the fork of bound proteins. Following subsequent processing of the extruded junction, the PriA helicase mediates reloading of the replicative helicase DnaB leading to the resumption of DNA replication. The single-strand binding protein (SSB) plays a key role in mediating PriA and RecG functions at forks. It binds to each enzyme via linker/OB-fold interactions and controls helicase-fork loading sites in a substrate-dependent manner that involves helicase remodeling. Finally, it is displaced by RecG during fork regression. The intimate and dynamic SSB-helicase interactions play key roles in ensuring fork regression and DNA replication restart.
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Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, University at Buffalo, SUNY, Buffalo, NY 14221, USA
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9
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Pattaro Júnior JR, Caruso ÍP, de Lima Neto QA, Duarte Junior FF, dos Santos Rando F, Gerhardt ECM, Fernandez MA, Seixas FAV. Biophysical characterization and molecular phylogeny of human KIN protein. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:645-657. [DOI: 10.1007/s00249-019-01390-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/07/2019] [Accepted: 07/06/2019] [Indexed: 11/24/2022]
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10
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Zhao H, Liu B, Li J. LIM and SH3 protein 1 knockdown suppresses proliferation and metastasis of colorectal carcinoma cells via inhibition of the mitogen-activated protein kinase signaling pathway. Oncol Lett 2018; 15:6839-6844. [PMID: 29731863 PMCID: PMC5920965 DOI: 10.3892/ol.2018.8222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/13/2017] [Indexed: 12/15/2022] Open
Abstract
LIM and SH3 protein 1 (Lasp-1), a focal adhesion protein, serves a critical role in the regulation of cell proliferation and migration. The role of Lasp-1, as well as the intracellular signaling pathways involved in metastasis and progression of colorectal carcinoma, remains unclear. In the present study, the regulatory effect of Lasp-1 and the underlying molecular mechanism involved in migration and invasion of colorectal carcinoma were investigated. RNA interference and overexpression in SW480 cells were performed to elucidate the role of Lasp-1. Reverse transcription-quantitative polymerase chain reaction, western blotting and immunofluorescence were conducted to determine the mRNA and protein levels of Lasp-1 and extracellular-signal-regulated kinase 1/2 (ERK1/2) in SW480 cells as well as tumor and adjacent normal tissues obtained from 20 patients with colorectal carcinoma. Furthermore, a cell proliferation assay, flow cytometric analysis, and cell migration and invasion assays were performed to examine the effect of Lasp-1 on cell growth. The results of the present study demonstrated that Lasp-1 and ERK1/2 were upregulated in tumor tissue compared with adjacent normal colorectal mucosa. Cell-based in vitro assays demonstrated that Lasp-1 knockdown suppressed the expression and activation of ERK1/2, whereas Lasp-1 overexpression resulted in ERK1/2 upregulation. Additionally, Lasp-1 knockdown inhibited cell proliferation, migration, and invasion and induced cellular apoptosis and G0/G1 cell-cycle arrest. The results of the present study indicate that Lasp-1 serves a critical role in the progression of colorectal carcinoma regulating the activation of the mitogen-activated protein kinase signaling pathway.
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Affiliation(s)
- Hongpeng Zhao
- Department of Gastrointestinal Surgery, Shandong Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Bo Liu
- Department of Gastrointestinal Surgery, Shandong Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Jie Li
- Department of Hepatobiliary Surgery, Shandong Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
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11
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Baker EG, Williams C, Hudson KL, Bartlett GJ, Heal JW, Porter Goff KL, Sessions RB, Crump MP, Woolfson DN. Engineering protein stability with atomic precision in a monomeric miniprotein. Nat Chem Biol 2017; 13:764-770. [PMID: 28530710 DOI: 10.1038/nchembio.2380] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/27/2017] [Indexed: 02/04/2023]
Abstract
Miniproteins simplify the protein-folding problem, allowing the dissection of forces that stabilize protein structures. Here we describe PPα-Tyr, a designed peptide comprising an α-helix buttressed by a polyproline II helix. PPα-Tyr is water soluble and monomeric, and it unfolds cooperatively with a midpoint unfolding temperature (TM) of 39 °C. NMR structures of PPα-Tyr reveal proline residues docked between tyrosine side chains, as designed. The stability of PPα is sensitive to modifications in the aromatic residues: replacing tyrosine with phenylalanine, i.e., changing three solvent-exposed hydroxyl groups to protons, reduces the TM to 20 °C. We attribute this result to the loss of CH-π interactions between the aromatic and proline rings, which we probe by substituting the aromatic residues with nonproteinogenic side chains. In analyses of natural protein structures, we find a preference for proline-tyrosine interactions over other proline-containing pairs, and observe abundant CH-π interactions in biologically important complexes between proline-rich ligands and SH3 and similar domains.
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Affiliation(s)
- Emily G Baker
- School of Chemistry, University of Bristol, Bristol, UK
| | - Christopher Williams
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | | | | | - Jack W Heal
- School of Chemistry, University of Bristol, Bristol, UK
| | | | - Richard B Sessions
- BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
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12
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Gustafsson MO, Mohammad DK, Ylösmäki E, Choi H, Shrestha S, Wang Q, Nore BF, Saksela K, Smith CIE. ANKRD54 preferentially selects Bruton's Tyrosine Kinase (BTK) from a Human Src-Homology 3 (SH3) domain library. PLoS One 2017; 12:e0174909. [PMID: 28369144 PMCID: PMC5378395 DOI: 10.1371/journal.pone.0174909] [Citation(s) in RCA: 2] [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: 07/01/2016] [Accepted: 03/17/2017] [Indexed: 11/19/2022] Open
Abstract
Bruton's Tyrosine Kinase (BTK) is a cytoplasmic protein tyrosine kinase with a fundamental role in B-lymphocyte development and activation. The nucleocytoplasmic shuttling of BTK is specifically modulated by the Ankyrin Repeat Domain 54 (ANKRD54) protein and the interaction is known to be exclusively SH3-dependent. To identify the spectrum of the ANKRD54 SH3-interactome, we applied phage-display screening of a library containing all the 296 human SH3 domains. The BTK-SH3 domain was the prime interactor. Quantitative western blotting analysis demonstrated the accuracy of the screening procedure. Revealing the spectrum and specificity of ANKRD54-interactome is a critical step toward functional analysis in cells and tissues.
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Affiliation(s)
- Manuela O. Gustafsson
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE Stockholm, Sweden
| | - Dara K. Mohammad
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE Stockholm, Sweden
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Kurdistan Region-Iraq
| | - Erkko Ylösmäki
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hyunseok Choi
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Subhash Shrestha
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Qing Wang
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE Stockholm, Sweden
| | - Beston F. Nore
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE Stockholm, Sweden
- Department of Biochemistry, School of Medicine, Faculty of Medical Sciences, University of Sulaimani, Sulaimani, Iraq
- Department of Health, Kurdistan Institution for Strategic Studies and Scientific Research (KISSSR), Sulaimani, Kurdistan-Iraq
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - C. I. Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE Stockholm, Sweden
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Ko TP, Tseng ST, Lai SJ, Chen SC, Guan HH, Shin Yang C, Jung Chen C, Chen Y. SH3-like motif-containing C-terminal domain of staphylococcal teichoic acid transporter suggests possible function. Proteins 2016; 84:1328-32. [DOI: 10.1002/prot.25074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 04/25/2016] [Accepted: 05/10/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica; Taipei Taiwan
| | - Shih-Ting Tseng
- Department of Food and Nutrition; Providence University; Taichung City Taiwan
- Department of Endocrinology and Metabolism; Kuang Tien General Hospital; Taiwan
| | - Shu-Jung Lai
- Institute of Biological Chemistry, Academia Sinica; Taipei Taiwan
| | - Sheng-Chia Chen
- Department of Biotechnology; Hungkuang University; Taichung Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division; National Synchrotron Radiation Research Center; Hsinchu 30076 Taiwan
| | - Chia Shin Yang
- Department of Biotechnology; Hungkuang University; Taichung Taiwan
- Taiwan Advance Biopharm (TABP) Inc; Xizhi City, New Taipei City Taiwan
| | - Chun Jung Chen
- Life Science Group, Scientific Research Division; National Synchrotron Radiation Research Center; Hsinchu 30076 Taiwan
- Institute of Biotechnology and Center for Bioscience and Biotechnology; National Cheng Kung University; Tainan City 701 Taiwan
- Department of Physics; National Tsing Hua University; Hsinchu 30043 Taiwan
| | - Yeh Chen
- Department of Biotechnology; Hungkuang University; Taichung Taiwan
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Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Arch Biochem Biophys 2016; 602:116-126. [PMID: 26924596 DOI: 10.1016/j.abb.2016.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.
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Krishnan S, Collett M, Robinson PJ. SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity. PLoS One 2015; 10:e0144609. [PMID: 26659814 PMCID: PMC4687643 DOI: 10.1371/journal.pone.0144609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/20/2015] [Indexed: 11/19/2022] Open
Abstract
Dynamin I is a highly regulated GTPase enzyme enriched in nerve terminals which mediates vesicle fission during synaptic vesicle endocytosis. One regulatory mechanism involves its interactions with proteins containing Src homology 3 (SH3) domains. At least 30 SH3 domain-containing proteins bind dynamin at its proline-rich domain (PRD). Those that stimulate dynamin activity act by promoting its oligomerisation. We undertook a systematic parallel screening of 13 glutathione-S-transferase (GST)-tagged endocytosis-related SH3 domains on dynamin binding, GTPase activity and oligomerisation. No correlation was found between dynamin binding and their potency to stimulate GTPase activity. There was limited correlation between the extent of their ability to stimulate dynamin activity and the level of oligomerisation, indicating an as yet uncharacterised allosteric coupling of the PRD and G domain. We examined the two variants, dynamin Iab and Ibb, which differ in the alternately splice middle domain α2 helix. They responded differently to the panel of SH3s, with the extent of stimulation between the splice variants varying greatly between the SH3s. This study reveals that SH3 binding can act as a heterotropic allosteric regulator of the G domain via the middle domain α2 helix, suggesting an involvement of this helix in communicating the PRD-mediated allostery. This indicates that SH3 binding both stabilises multiple conformations of the tetrameric building block of dynamin, and promotes assembly of dynamin-SH3 complexes with distinct rates of GTP hydrolysis.
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Affiliation(s)
- Sai Krishnan
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia
| | - Michael Collett
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia
| | - Phillip J. Robinson
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia
- * E-mail:
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16
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Domain function dissection and catalytic properties of Listeria monocytogenes p60 protein with bacteriolytic activity. Appl Microbiol Biotechnol 2015; 99:10527-37. [PMID: 26363556 DOI: 10.1007/s00253-015-6967-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/12/2015] [Accepted: 08/23/2015] [Indexed: 02/07/2023]
Abstract
The major extracellular protein p60 of Listeria monocytogenes (Lm-p60) is an autolysin that can hydrolyze the peptidoglycan of bacterial cell wall and has been shown to be required for L. monocytogenes virulence. The predicted three-dimensional structure of Lm-p60 showed that Lm-p60 could be split into two independent structural domains at the amino acid residue 270. Conserved motif analysis showed that V30, D207, S395, and H444 are the key amino acid residues of the corresponding motifs. However, not only the actual functions of these two domains but also the catalytic properties of Lm-p60 are unclear. We try to express recombinant Lm-p60 and identify the functions of two domains by residue substitution (V30A, D207A, S395A, and H444A) and peptide truncation. The C-terminal domain was identified as catalytic element and N-terminal domain as substrate recognition and binding element. Either N-terminal domain truncation or C-terminal domain truncation presents corresponding biological activity. The catalytic activity of Lm-p60 with a malfunctioned substrate-binding domain was decreased, while the substrate binding was not affected by a mulfunctioned catalytic domain. With turbidimetric method, we determined the optimal conditions for the bacteriolytic activity of Lm-p60 against Micrococcus lysodeikficus. The assay for the effect of Lm-p60 on the bacteriolytic activity of lysozyme revealed that the combined use of Lm-p60 protein with lysozyme showed a strong synergistic effect on the bacteriolytic activity.
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17
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Orth MF, Cazes A, Butt E, Grunewald TGP. An update on the LIM and SH3 domain protein 1 (LASP1): a versatile structural, signaling, and biomarker protein. Oncotarget 2015; 6:26-42. [PMID: 25622104 PMCID: PMC4381576 DOI: 10.18632/oncotarget.3083] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/28/2014] [Indexed: 01/15/2023] Open
Abstract
The gene encoding the LIM and SH3 domain protein (LASP1) was cloned two decades ago from a cDNA library of breast cancer metastases. As the first protein of a class comprising one N-terminal LIM and one C-terminal SH3 domain, LASP1 founded a new LIM-protein subfamily of the nebulin group. Since its discovery LASP1 proved to be an extremely versatile protein because of its exceptional structure allowing interaction with various binding partners, its ubiquitous expression in normal tissues, albeit with distinct expression patterns, and its ability to transmit signals from the cytoplasm into the nucleus. As a result, LASP1 plays key roles in cell structure, physiological processes, and cell signaling. Furthermore, LASP1 overexpression contributes to cancer aggressiveness hinting to a potential value of LASP1 as a cancer biomarker. In this review we summarize published data on structure, regulation, function, and expression pattern of LASP1, with a focus on its role in human cancer and as a biomarker protein. In addition, we provide a comprehensive transcriptome analysis of published microarrays (n=2,780) that illustrates the expression profile of LASP1 in normal tissues and its overexpression in a broad range of human cancer entities.
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Affiliation(s)
- Martin F Orth
- Institute for Clinical Biochemistry and Pathobiochemistry, University Clinic of Würzburg, Grombühlstrasse, Würzburg, Germany
| | - Alex Cazes
- Institute for Clinical Biochemistry and Pathobiochemistry, University Clinic of Würzburg, Grombühlstrasse, Würzburg, Germany
| | - Elke Butt
- Institute for Clinical Biochemistry and Pathobiochemistry, University Clinic of Würzburg, Grombühlstrasse, Würzburg, Germany
| | - Thomas G P Grunewald
- Laboratory for Pediatric Sarcoma Biology, Institute of Pathology of the LMU Munich, Thalkirchner Strasse, Munich, Germany
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18
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Grubb DR, Luo J, Woodcock EA. Phospholipase Cβ1b directly binds the SH3 domain of Shank3 for targeting and activation in cardiomyocytes. Biochem Biophys Res Commun 2015; 461:519-24. [DOI: 10.1016/j.bbrc.2015.04.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/10/2015] [Indexed: 12/24/2022]
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Grose JH, Jensen GL, Burnett SH, Breakwell DP. Correction: genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity. BMC Genomics 2014; 15:1184. [PMID: 25547158 PMCID: PMC4464726 DOI: 10.1186/1471-2164-15-1184] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/04/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. RESULTS Whole genome nucleotide and proteome comparison of the 83 extant, fully sequenced Bacillus phages revealed 10 distinct clusters, 24 subclusters and 15 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,442 protein families (phams) of which only 894 (20%) had a predicted function. In addition, 2,583 (58%) of phams were orphams (phams containing a single member). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains. CONCLUSIONS This analysis provides a basis for understanding and characterizing Bacillus and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.
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Affiliation(s)
- Julianne H Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA.
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20
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Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity. BMC Genomics 2014; 15:855. [PMID: 25280881 PMCID: PMC4197329 DOI: 10.1186/1471-2164-15-855] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023] Open
Abstract
Background The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. Results Whole genome nucleotide and proteome comparison of the 93 extant Bacillus phages revealed 12 distinct clusters, 28 subclusters and 14 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member of the group. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,922 protein families (phams) of which only 951 (19%) had a predicted function. In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains. Conclusions This analysis provides a basis for understanding and characterizing Bacillus phages and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.
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21
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He P, Wu W, Wang HD, Liao KL, Zhang W, Lv FL, Yang K. Why ligand cross-reactivity is high within peptide recognition domain families? A case study on human c-Src SH3 domain. J Theor Biol 2014; 340:30-7. [DOI: 10.1016/j.jtbi.2013.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/26/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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Bacarizo J, Camara-Artigas A. Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:756-66. [PMID: 23633584 DOI: 10.1107/s0907444913001522] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/15/2013] [Indexed: 12/20/2022]
Abstract
The atomic resolution crystal structures of complexes between the SH3 domain of the c-Src tyrosine kinase and two high-affinity peptides belonging to class I and class II have been solved. The crystals of the Thr98Asp and Thr98Glu mutants in complex with the APP12 peptide (APPLPPRNRPRL) belonged to the trigonal space group P3121 and in both cases the asymmetric unit was composed of one molecule of the SH3-APP12 complex. The crystals of the Thr98Glu mutant in complex with the VSL12 peptide (VSLARRPLPLP) belonged to the trigonal space group P3221 and the asymmetric unit was also composed of a single molecule of the SH3-VSL12 complex. All crystals were obtained in the presence of PEG 300 under the same conditions as reported for the intertwined dimeric structure of the c-Src SH3 domain, but the presence of the peptide stabilizes the monomeric form of the domain. These structures allow a detailed analysis of the role of salt bridges, cation-π interactions and hydrogen bonds in the binding of proline-rich motifs to the c-Src SH3 domain. Moreover, these crystallographic structures allow the role of water molecules in the binding of these motifs to the c-Src SH3 domain to be studied for the first time.
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Affiliation(s)
- Julio Bacarizo
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence, Carretera de Sacramento, 04120 Almería, Spain
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Pesti S, Balázs A, Udupa R, Szabó B, Fekete A, Bőgel G, Buday L. Complex formation of EphB1/Nck/Caskin1 leads to tyrosine phosphorylation and structural changes of the Caskin1 SH3 domain. Cell Commun Signal 2012. [PMID: 23181695 PMCID: PMC3549760 DOI: 10.1186/1478-811x-10-36] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Scaffold proteins have an important role in the regulation of signal propagation. These proteins do not possess any enzymatic activity but can contribute to the formation of multiprotein complexes. Although scaffold proteins are present in all cell types, the nervous system contains them in the largest amount. Caskin proteins are typically present in neuronal cells, particularly, in the synapses. However, the signaling mechanisms by which Caskin proteins are regulated are largely unknown. Results Here we demonstrate that EphB1 receptor tyrosine kinase can recruit Caskin1 through the adaptor protein Nck. Upon activation of the receptor kinase, the SH2 domain of Nck binds to one of its tyrosine residues, while Nck SH3 domains interact with the proline-rich domain of Caskin1. Complex formation of the receptor, adaptor and scaffold proteins results in the tyrosine phosphorylation of Caskin1 on its SH3 domain. The phosphorylation sites were identified by mass-spectrometry as tyrosines 296 and 336. To reveal the structural consequence of this phosphorylation, CD spectroscopy was performed. This measurement suggests that upon tyrosine phosphorylation the structure of the Caskin1 SH3 domain changes significantly. Conclusion Taken together, we propose that the scaffold protein Caskin1 can form a complex with the EphB1 tyrosine kinase via the Nck protein as a linker. Complex formation results in tyrosine phosphorylation of the Caskin1 SH3 domain. Although we were not able to identify any physiological partner of the SH3 domain so far, we could demonstrate that phosphorylation on conserved tyrosine residues results in marked changes in the structure of the SH3 domain.
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Affiliation(s)
- Szabolcs Pesti
- From the Department of Medical Chemistry, Semmelweis University Medical School, Budapest, 1094, Hungary.
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