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Hernández-Sánchez A, Páez-Pérez ED, Alfaro-Saldaña E, García-Meza JV. Deciphering the enigmatic PilY1 of Acidithiobacillus thiooxidans: An in silico analysis. Biochem Biophys Rep 2024; 39:101797. [PMID: 39161578 PMCID: PMC11331964 DOI: 10.1016/j.bbrep.2024.101797] [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: 05/30/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/21/2024] Open
Abstract
Thirty years since the first report on the PilY1 protein in bacteria, only the C-terminal domain has been crystallized; there is no study in which the N-terminal domain, let alone the complete protein, has been crystallized. In our laboratory, we are interested in characterizing the Type IV Pili (T4P) of Acidithiobacillus thiooxidans. We performed an in silico characterization of PilY1 and other pilins of the T4P of this acidophilic bacterium. In silico characterization is crucial for understanding how proteins adapt and function under extreme conditions. By analyzing the primary and secondary structures of proteins through computational methods, researchers can gain valuable insights into protein stability, key structural features, and unique amino acid compositions that contribute to resilience in harsh environments. Here, it is presented a description of the particularities of At. thiooxidans PilY1 through predictor software and homology data. Our results suggest that PilY1 from At. thiooxidans may have the same role as has been described for other PilY1 associated with T4P in neutrophilic bacteria; also, its C-terminal interacts (interface interaction) with the minor pilins PilX, PilW and PilV. The N-terminal region comprises domains such as the vWA and the MIDAS, involved in signaling, ligand-binding, and protein-protein interaction. In fact, the vWA domain has intrinsically disordered regions that enable it to maintain its structure over a wide pH range, not only at extreme acidity to which At. thiooxidans is adapted. The results obtained helped us design the correct methodology for its heterologous expression. This allowed us partially experimentally characterize it by obtaining the N-terminal domain recombinantly and evaluating its acid stability through fluorescence spectroscopy. The data suggest that it remains stable across pH changes. This work thus provides guidance for the characterization of extracellular proteins from extremophilic organisms.
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Affiliation(s)
| | - Edgar D. Páez-Pérez
- Corresponding author. Geomicrobiología, Metalurgia, UASLP, Sierra Leona 550, San Luis Potosí, 78210, SLP, Mexico.
| | - Elvia Alfaro-Saldaña
- Geomicrobiología, Metalurgia, UASLP, Sierra Leona 550, San Luis Potosí, 78210, SLP, Mexico
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2
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Wang Q, Tian S, Zhang X, Zhang Y, Wang Y, Xie S. Insights into the tolerant function of VWA proteins in terms of expression analysis and RGLG5-VWA crystal structure. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108864. [PMID: 38943876 DOI: 10.1016/j.plaphy.2024.108864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
The VWA domain commonly functions as a crucial component of multiprotein complexes, facilitating protein-protein interactions. However, limited studies have focused on the systemic study of VWA proteins in plants. Here, we identified 28 VWA protein genes in Arabidopsis thaliana, categorized into three clades, with one tandem duplication event and four paralogous genes within collinearity blocks. Then, we determined their expression patterns under abiotic stresses by transcriptomic analysis. All five RGLG genes were found to be responsive to at least one kind of abiotic stress, and RGLG5 was identified as a multiple stress-responsive gene, coding an E3 ubiquitin ligase with a VWA domain and a C-terminal RING domain. Subsequently, we explored tolerant function of RGLG5 by determining the crystal structure of its VWA domain. The structural comparison revealed the allosteric regulation mechanism of RGLG5-VWA, wherein the deflection of α7 led to displacement of key residue binding metal ion within MIDAS motif. Our findings provide full-scale knowledge on VWA proteins, and insights into tolerant function of RGLG5-VWA in terms of crystal structure.
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Affiliation(s)
- Qin Wang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China.
| | - Shicheng Tian
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | | | - Yutong Zhang
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuran Wang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | - Shuyang Xie
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China.
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3
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Zhang M, Zhang J, Liang Y, Tian S, Xie S, Zhou T, Wang Q. The regulation of RGLG2-VWA by Ca 2+ ions. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140966. [PMID: 37734561 DOI: 10.1016/j.bbapap.2023.140966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
RGLG2, an E3 ubiquitin ligase in Arabidopsis thaliana, affects hormone signaling and participates in drought regulation. Here, we determined two crystal structures of RGLG2 VWA domain, representing two conformations, open and closed, respectively. The two structures reveal that Ca2+ ions are allosteric regulators of RGLG2-VWA, which adopts open state when NCBS1(Novel Calcium ions Binding Site 1) binds Ca2+ ions and switches to closed state after Ca2+ ions are removed. This mechanism of allosteric regulation is identical to RGLG1-VWA, but distinct from integrin α and β VWA domains. Therefore, our data provide a backdrop for understanding the role of the Ca2+ ions in conformational change of VWA domain. In addition, we found that RGLG2closed, corresponding to low affinity, can bind pseudo-ligand, which has never been observed in other VWA domains.
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Affiliation(s)
- MeiLing Zhang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China
| | - JiaXiang Zhang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China
| | - Yan Liang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China
| | - ShiCheng Tian
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China
| | - ShuYang Xie
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China
| | - Tong Zhou
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China
| | - Qin Wang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China.
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Boland AW, Gas-Pascual E, van der Wel H, Kim HW, West CM. Synergy between a cytoplasmic vWFA/VIT protein and a WD40-repeat F-box protein controls development in Dictyostelium. Front Cell Dev Biol 2023; 11:1259844. [PMID: 37779900 PMCID: PMC10539598 DOI: 10.3389/fcell.2023.1259844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Like most eukaryotes, the pre-metazoan social amoeba Dictyostelium depends on the SCF (Skp1/cullin-1/F-box protein) family of E3 ubiquitin ligases to regulate its proteome. In Dictyostelium, starvation induces a transition from unicellular feeding to a multicellular slug that responds to external signals to culminate into a fruiting body containing terminally differentiated stalk and spore cells. These transitions are subject to regulation by F-box proteins and O2-dependent posttranslational modifications of Skp1. Here we examine in greater depth the essential role of FbxwD and Vwa1, an intracellular vault protein inter-alpha-trypsin (VIT) and von Willebrand factor-A (vWFA) domain containing protein that was found in the FbxwD interactome by co-immunoprecipitation. Reciprocal co-IPs using gene-tagged strains confirmed the interaction and similar changes in protein levels during multicellular development suggested co-functioning. FbxwD overexpression and proteasome inhibitors did not affect Vwa1 levels suggesting a non-substrate relationship. Forced FbxwD overexpression in slug tip cells where it is normally enriched interfered with terminal cell differentiation by a mechanism that depended on its F-box and RING domains, and on Vwa1 expression itself. Whereas vwa1-disruption alone did not affect development, overexpression of either of its three conserved domains arrested development but the effect depended on Vwa1 expression. Based on structure predictions, we propose that the Vwa1 domains exert their negative effect by artificially activating Vwa1 from an autoinhibited state, which in turn imbalances its synergistic function with FbxwD. Autoinhibition or homodimerization might be relevant to the poorly understood tumor suppressor role of the evolutionarily related VWA5A/BCSC-1 in humans.
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Affiliation(s)
- Andrew W. Boland
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Elisabet Gas-Pascual
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Hanke van der Wel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Hyun W. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Christopher M. West
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
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5
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Zhang S, Wang F, Zhang D, Liu D, Ding W, Springer TA, Song G. Structural insights into MIC2 recognition by MIC2-associated protein in Toxoplasma gondii. Commun Biol 2023; 6:895. [PMID: 37652989 PMCID: PMC10471735 DOI: 10.1038/s42003-023-05277-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023] Open
Abstract
Microneme protein 2 (MIC2) and MIC2-associated protein (M2AP) play crucial roles in the gliding motility and host cell invasion of Toxoplasma gondii. Complex formation between MIC2 and M2AP is required for maturation and transport from the microneme to the parasite surface. Previous studies showed that M2AP associates with the 6th TSR domain of MIC2 (TSR6), but the detailed interaction remains unclear. In this study, we report crystal structures of M2AP alone and in complex with TSR6. TSR domains have an unusually thin, long structure with a layer of intercalated residues on one side. The non-layered side of TSR6 with hotspot residue His-620 at the center binds to M2AP. Remarkably, we show that TSR6 residue Y602 is dynamic; it equilibrates between being part of the layer (the layered state) and in a flipped-out state in the absence of M2AP. However, when bound to M2AP, Y602 shifts to the flipped-out state. Our findings provide insights into the association and stabilization of MIC2-M2AP complex, and may be used to develop new therapies to prevent infections caused by this parasite.
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Affiliation(s)
- Su Zhang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Fangfang Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Dujuan Zhang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Dongsheng Liu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Wei Ding
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, China
| | - Timothy A Springer
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Gaojie Song
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 200241, Shanghai, China.
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6
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Offley SR, Pfleiderer MM, Zucco A, Fraudeau A, Welsh SA, Razew M, Galej WP, Gardini A. A combinatorial approach to uncover an additional Integrator subunit. Cell Rep 2023; 42:112244. [PMID: 36920904 DOI: 10.1016/j.celrep.2023.112244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/15/2022] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
RNA polymerase II (RNAPII) controls expression of all protein-coding genes and most noncoding loci in higher eukaryotes. Calibrating RNAPII activity requires an assortment of polymerase-associated factors that are recruited at sites of active transcription. The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Integrator is known to be composed of 14 subunits that assemble and operate in a modular fashion. We employed proteomics and machine-learning structure prediction (AlphaFold2) to identify an additional Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS13/14/10 module and interfaces with the Int-PP2A module. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes. Our study shows that omics approaches combined with AlphaFold2-based predictions provide additional insights into the molecular architecture of large and dynamic multiprotein complexes.
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Affiliation(s)
- Sarah R Offley
- The Wistar Institute, Philadelphia, PA 19103, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Avery Zucco
- The Wistar Institute, Philadelphia, PA 19103, USA
| | - Angelique Fraudeau
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | | | - Michal Razew
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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7
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ANTXR1 as a potential sensor of extracellular mechanical cues. Acta Biomater 2023; 158:80-86. [PMID: 36638946 DOI: 10.1016/j.actbio.2023.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/18/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Cell adhesion molecules mediate cell-cell or cell-matrix interactions, some of which are mechanical sensors, such as integrins. Emerging evidence indicates that anthrax toxin receptor 1 (ANTXR1), a newly identified cell adhesion molecule, can also sense extracellular mechanical signals such as hydrostatic pressure and extracellular matrix (ECM) rigidity. ANTXR1 can interact with ECM through connecting intracellular cytoskeleton and ECM molecules (just like integrins) to regulate numerous biological processes, such as cell adhesion, cell migration or ECM homeostasis. Although with high structural similarity to integrins, its functions and downstream signal transduction are independent from those of integrins. In this perspective, based on existing evidence in literature, we analyzed the structural and functional evidence that ANTXR1 can act as a potential sensor for extracellular mechanical cues. To our knowledge, this is the first in-depth overview of ANTXR1 from the perspective of mechanobiology. STATEMENT OF SIGNIFICANCE: An overview of ANTXR1 from the perspective of mechanobiology; An analysis of mechanical sensitivity of ANTXR1 in structure and function; A summary of existing evidence of ANTXR1 as a potential mechanosensor.
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8
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Zhang T, Day NJ, Gaffrey M, Weitz KK, Attah K, Mimche PN, Paine R, Qian WJ, Helms MN. Regulation of hyperoxia-induced neonatal lung injury via post-translational cysteine redox modifications. Redox Biol 2022; 55:102405. [PMID: 35872399 PMCID: PMC9307955 DOI: 10.1016/j.redox.2022.102405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 07/11/2022] [Indexed: 12/17/2022] Open
Abstract
Preterm infants and patients with lung disease often have excess fluid in the lungs and are frequently treated with oxygen, however long-term exposure to hyperoxia results in irreversible lung injury. Although the adverse effects of hyperoxia are mediated by reactive oxygen species, the full extent of the impact of hyperoxia on redox-dependent regulation in the lung is unclear. In this study, neonatal mice overexpressing the beta-subunit of the epithelial sodium channel (β-ENaC) encoded by Scnn1b and their wild type (WT; C57Bl6) littermates were utilized to study the pathogenesis of high fraction inspired oxygen (FiO2)-induced lung injury. Results showed that O2-induced lung injury in transgenic Scnn1b mice is attenuated following chronic O2 exposure. To test the hypothesis that reversible cysteine-redox-modifications of proteins play an important role in O2-induced lung injury, we performed proteome-wide profiling of protein S-glutathionylation (SSG) in both WT and Scnn1b overexpressing mice maintained at 21% O2 (normoxia) or FiO2 85% (hyperoxia) from birth to 11-15 days postnatal. Over 7700 unique Cys sites with SSG modifications were identified and quantified, covering more than 3000 proteins in the lung. In both mouse models, hyperoxia resulted in a significant alteration of the SSG levels of Cys sites belonging to a diverse range of proteins. In addition, substantial SSG changes were observed in the Scnn1b overexpressing mice exposed to hyperoxia, suggesting that ENaC plays a critically important role in cellular regulation. Hyperoxia-induced SSG changes were further supported by the results observed for thiol total oxidation, the overall level of reversible oxidation on protein cysteine residues. Differential analyses reveal that Scnn1b overexpression may protect against hyperoxia-induced lung injury via modulation of specific processes such as cell adhesion, blood coagulation, and proteolysis. This study provides a landscape view of protein oxidation in the lung and highlights the importance of redox regulation in O2-induced lung injury.
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Affiliation(s)
- Tong Zhang
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nicholas J Day
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew Gaffrey
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kwame Attah
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Patrice N Mimche
- Division of Microbiology and Immunology, Department of Pathology, University of Utah Molecular Medicine Program, Salt Lake City, UT, USA
| | - Robert Paine
- Pulmonary Division, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Wei-Jun Qian
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - My N Helms
- Pulmonary Division, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA.
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Bin Dajem SM, Ahmed MA, Alghnnam FF, Alghannam SF, Deshmukh GY, Zaidi RH, Bohol MFF, Salam SS, Wazid SW, Shafeai MI, Rudiny FH, Motaen AM, Morsy K, Al-Qahtani AA. Genetic Diversity and Population Genetic Analysis of Plasmodium falciparum Thrombospondin Related Anonymous Protein (TRAP) in Clinical Samples from Saudi Arabia. Genes (Basel) 2022; 13:genes13071149. [PMID: 35885932 PMCID: PMC9319867 DOI: 10.3390/genes13071149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The thrombospondin related anonymous protein (TRAP) is considered one of the most important pre-erythrocytic vaccine targets. Earlier population genetic studies revealed the TRAP gene to be under strong balancing natural selection. This study is the first attempt to analyze genetic diversity, natural selection, phylogeography and population structure in 199 clinical samples from Saudi Arabia using the full-length PfTRAP gene. We found the rate of nonsynonymous substitutions to be significantly higher than that of synonymous substitutions in the clinical samples, indicating a strong positive or diversifying selection for the full-length gene and the Von Willebrand factor (VWF). The nucleotide diversity was found to be π~0.00789 for the full-length gene; however, higher nucleotide diversity was observed for the VWF compared to the thrombospondin repeat region (TSP). Deduction of the amino acid sequence alignment of the PNP repeat region in the Saudi samples revealed six genotypes characterized by tripeptide repeat motifs (PNP, ANP, ENP and SNP). Haplotype network, population structure and population differentiation analyses indicated four distinct sub-populations in spite of the low geographical distance between the sampling sites. Our results suggest the likeliness of independent parasite evolution, creating opportunities for further adaptation, including host transition, and making malaria control even more challenging.
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Affiliation(s)
- Saad M. Bin Dajem
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.M.B.D.); (K.M.)
| | - Md Atique Ahmed
- ICMR-Regional Medical Research Center, Dibrugarh 786010, Assam, India;
| | - Fatimah F. Alghnnam
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
| | - Shouq F. Alghannam
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
| | - Gauspasha Yusuf Deshmukh
- Department of Biotechnology and Microbiology, National College, Tiruchirapalli 620001, Tamil Nadu, India; (G.Y.D.); (R.H.Z.)
| | - Rehan Haider Zaidi
- Department of Biotechnology and Microbiology, National College, Tiruchirapalli 620001, Tamil Nadu, India; (G.Y.D.); (R.H.Z.)
| | - Marie Fe F. Bohol
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
| | - Syeda Sabiha Salam
- Department of Life Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India;
| | - Syeda Wasfeea Wazid
- Arogya Society of Health, Welfare and Support (ASHWAS), Dinsugia 785640, Assam, India;
| | - Mohammed I. Shafeai
- Sabya General Hospital, Sabya 85534, Saudi Arabia; (M.I.S.); (F.H.R.); (A.M.M.)
| | - Fuad H. Rudiny
- Sabya General Hospital, Sabya 85534, Saudi Arabia; (M.I.S.); (F.H.R.); (A.M.M.)
| | - Ali M. Motaen
- Sabya General Hospital, Sabya 85534, Saudi Arabia; (M.I.S.); (F.H.R.); (A.M.M.)
| | - Kareem Morsy
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.M.B.D.); (K.M.)
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Correspondence:
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Rajasekaran S, Tangavel C, Anand KSSV, Soundararajan DCR, Nayagam SM, Sunmathi R, Raveendran M, Shetty AP, Kanna RM, Pushpa BT. Can Scoliotic Discs Be Controls for Molecular Studies in Intervertebral Disc Research? Insights From Proteomics. Global Spine J 2022; 12:598-609. [PMID: 32945197 PMCID: PMC9109558 DOI: 10.1177/2192568220959038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
STUDY DESIGN Proteomic analysis of human intervertebral discs. OBJECTIVES To compare the characters of scoliotic discs and discs from magnetic resonance imaging (MRI)-normal voluntary organ donors controls used in disc research employing proteomics and establish "true controls" that can be utilized for future intervertebral disc (IVD) research. METHODS Eight MRI-normal discs from 8 brain-dead voluntary organ donors (ND) and 8 scoliotic discs (SD) from 3 patients who underwent anterior surgery for adolescent idiopathic scoliosis were subjected to tandem mass spectrometry, and further analysis was performed. RESULTS Mass spectrometry identified a total of 235 proteins in ND and 438 proteins in the SD group. Proteins involved in extracellular matrix integrity (Versican, keratins KRT6A, KRT14, KRT5, and KRT 13A1, A-kinase anchor protein 13, coagulation factor XIII A chain, proteoglycan 4) and proteins involved in transcription and DNA repair (Von Willebrand factor A domain-containing 3B, eukaryotic initiation factor 2B, histone H4, leukocyte cell-derived chemotaxin 2) were found to be downregulated in SD. Inflammatory proteins (C3, C1S), and oxidative stress response proteins (peroxiredoxin-2,6, catalase, myeloperoxidase, apolipoprotein E) were found to be upregulated in SD. These changes were reflected at the pathway level also. CONCLUSION Findings of our study confirm that scoliotic discs have an abundance of inflammatory, oxidative stress response proteins, which are either absent or downregulated in the ND group indicating that scoliotic discs are not pathologically inert. Furthermore, this study has established MRI-normal discs from voluntary organ donors as the "true" control for molecular studies in IVD research.
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Affiliation(s)
- S. Rajasekaran
- Ganga Hospital, Coimbatore, Tamil
Nadu, India,S. Rajasekaran, Department of Spine Surgery,
Ganga Hospital, 313, Mettupalayam Road, Coimbatore, 641043, Tamil Nadu India.
| | | | | | | | | | - R. Sunmathi
- Ganga Research Centre, Coimbatore,
Tamil Nadu, India
| | - M. Raveendran
- Tamil Nadu Agricultural University,
Coimbatore, Tamil Nadu, India
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11
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Inter-Alpha-Trypsin Inhibitor Heavy Chain 4 Plays an Important Role in the Development and Reproduction of Nilaparvata lugens. INSECTS 2022; 13:insects13030303. [PMID: 35323600 PMCID: PMC8951764 DOI: 10.3390/insects13030303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/07/2022] [Accepted: 03/15/2022] [Indexed: 12/18/2022]
Abstract
Simple Summary The brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae), is a destructive insect pest of rice. It causes reductions in rice yield and great economic losses. In this study, we used RNAi to explore the function of the inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) gene in the development and reproduction of the brown planthopper. Our results revealed that ITIH4 influences the survival, ovarian development, egg production, and egg hatching of this insect, indicating that ITIH4 plays important roles in development and reproduction. Considering the importance of ITIH4 in the brown planthopper, it may be a potential target for pest management. Abstract The brown planthopper, Nilaparvata lugens, is a difficult-to-control insect pest affecting rice yields in Asia. As a structural component of the inter-alpha-trypsin inhibitor (ITI), the inter-alpha-trypsin inhibitor heavy chain (ITIH) has been reported to be involved in various inflammatory or malignant disorders, ovarian development, and ovulation. To reveal the function of ITIH4 in N. lugens, the gene encoding N. lugens ITIH4 (NlITIH4) was cloned and characterized. NlITIH4 contains a signal peptide, a vault protein inter-alpha-trypsin domain, and a von Willebrand factor type A domain. qPCR analysis showed that NlITIH4 was expressed at all developmental stages and in all tissues (fat body, ovary, and gut), with the highest expression in the fat body. Double stranded NlITIH4 (dsNlITIH4) injection clearly led to an RNAi-mediated inhibition of the expression of NlITIH4 and resulted in reduced survival, delayed ovarian development, and reduced egg production and egg hatching. These results indicate that NlITIH4 plays an important role in the development and reproduction of N. lugens.
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C-type lectin binds envelope protein of white spot syndrome virus and induces antiviral peptides in red swamp crayfish. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2021; 2:100027. [DOI: 10.1016/j.fsirep.2021.100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022] Open
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Jia Y, Cheng Z, Bharath SR, Sun Q, Su N, Huang J, Song H. Crystal structure of the INTS3/INTS6 complex reveals the functional importance of INTS3 dimerization in DSB repair. Cell Discov 2021; 7:66. [PMID: 34400606 PMCID: PMC8368002 DOI: 10.1038/s41421-021-00283-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
SOSS1 is a single-stranded DNA (ssDNA)-binding protein complex that plays a critical role in double-strand DNA break (DSB) repair. SOSS1 consists of three subunits: INTS3, SOSSC, and hSSB1, with INTS3 serving as a scaffold to stabilize this complex. Moreover, the integrator complex subunit 6 (INTS6) participates in the DNA damage response through direct binding to INTS3, but how INTS3 interacts with INTS6, thereby impacting DSB repair, is not clear. Here, we determined the crystal structure of the C-terminus of INTS3 (INTS3c) in complex with the C-terminus of INTS6 (INTS6c) at a resolution of 2.4 Å. Structural analysis revealed that two INTS3c subunits dimerize and interact with INTS6c via conserved residues. Subsequent biochemical analyses confirmed that INTS3c forms a stable dimer and INTS3 dimerization is important for recognizing the longer ssDNA. Perturbation of INTS3c dimerization and disruption of the INTS3c/INTS6c interaction impair the DSB repair process. Altogether, these results unravel the underappreciated role of INTS3 dimerization and the molecular basis of INTS3/INTS6 interaction in DSB repair.
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Affiliation(s)
- Yu Jia
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zixiu Cheng
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore City, Singapore
| | - Qiangzu Sun
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Nannan Su
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Huang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Haiwei Song
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore City, Singapore. .,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore City, Singapore.
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Abstract
Ro60 ribonucleoproteins (RNPs), composed of the ring-shaped Ro 60-kDa (Ro60) protein and noncoding RNAs called Y RNAs, are present in all three domains of life. Ro60 was first described as an autoantigen in patients with rheumatic disease, and Ro60 orthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla. Their functions have been characterized primarily in Deinococcus radiodurans, the first sequenced bacterium with a recognizable ortholog. In D. radiodurans, the Ro60 ortholog enhances the ability of 3'-to-5' exoribonucleases to degrade structured RNA during several forms of environmental stress. Y RNAs are regulators that inhibit or allow the interactions of Ro60 with other proteins and RNAs. Studies of Ro60 RNPs in other bacteria hint at additional functions, since the most conserved Y RNA contains a domain that is a close tRNA mimic and Ro60 RNPs are often encoded adjacent to components of RNA repair systems.
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Affiliation(s)
- Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Kevin Hughes
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
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15
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Kant A, Palva A, von Ossowski I, Krishnan V. Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili. J Struct Biol 2020; 211:107571. [PMID: 32653644 DOI: 10.1016/j.jsb.2020.107571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
Adhesion to cell surfaces is an essential and early prerequisite for successful host colonization by bacteria, and in most instances involves the specificities of various adhesins. Among bacterial Gram-positives, some genera and species mediate attachment to host cells by using long non-flagellar appendages called sortase-dependent pili. A case in point is the beneficial Lactobacillus rhamnosus GG gut-adapted strain that produces the so-called SpaCBA pilus, a structure noted for its promiscuous binding to intestinal mucus and collagen. Structurally, SpaCBA pili are heteropolymers of three different pilin-protein subunits, each with its own location and function in the pilus: backbone SpaA for length, basal SpaB for anchoring, and tip SpaC for adhesion. Previously, we solved the SpaA tertiary structure by X-ray crystallography and also reported on the crystallization of SpaB and SpaC. Here, we reveal the full-length high-resolution (1.9 Å) crystal structure of SpaC, a first for a sortase-dependent pilus-bearing commensal. The SpaC structure, unlike the representative four-domain architecture of other Gram-positive tip pilins, espouses an atypically longer five-domain arrangement that includes N-terminal 'binding' and C-terminal 'stalk' regions of two and three domains, respectively. With the prospect of establishing new mechanistic insights, we provide a structural basis for the multi-substrate binding nature of SpaC, as well as a structural model that reconciles its exclusive localization at the SpaCBA pilus tip.
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Affiliation(s)
- Abhiruchi Kant
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 122016, India; Department of Biotechnology, Manipal University, Karnataka 576104, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki FIN-00014, Finland
| | - Ingemar von Ossowski
- Department of Veterinary Biosciences, University of Helsinki, Helsinki FIN-00014, Finland
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 122016, India.
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Sabath K, Stäubli ML, Marti S, Leitner A, Moes M, Jonas S. INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module. Nat Commun 2020; 11:3422. [PMID: 32647223 PMCID: PMC7347597 DOI: 10.1038/s41467-020-17232-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/18/2020] [Indexed: 11/18/2022] Open
Abstract
The Integrator complex processes 3′-ends of spliceosomal small nuclear RNAs (snRNAs). Furthermore, it regulates transcription of protein coding genes by terminating transcription after unstable pausing. The molecular basis for Integrator’s functions remains obscure. Here, we show that INTS10, Asunder/INTS13 and INTS14 form a separable, functional Integrator module. The structure of INTS13-INTS14 reveals a strongly entwined complex with a unique chain interlink. Unexpected structural homology to the Ku70-Ku80 DNA repair complex suggests nucleic acid affinity. Indeed, the module displays affinity for DNA and RNA but prefers RNA hairpins. While the module plays an accessory role in snRNA maturation, it has a stronger influence on transcription termination after pausing. Asunder/INTS13 directly binds Integrator’s cleavage module via a conserved C-terminal motif that is involved in snRNA processing and required for spermatogenesis. Collectively, our data establish INTS10-INTS13-INTS14 as a nucleic acid-binding module and suggest that it brings cleavage module and target transcripts into proximity. The Integrator complex (INT) is responsible for the 3′-end processing of several classes of non-coding RNAs. Here the authors show that the INTS10-INTS13-INTS14 complex forms a distinct submodule of INT and suggest it facilitates RNA substrate targeting.
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Affiliation(s)
- Kevin Sabath
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Melanie L Stäubli
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Sabrina Marti
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Murielle Moes
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland.
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Ca 2+-based allosteric switches and shape shifting in RGLG1 VWA domain. Comput Struct Biotechnol J 2020; 18:821-833. [PMID: 32308929 PMCID: PMC7155146 DOI: 10.1016/j.csbj.2020.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
RGLG1 is an E3 ubiquitin ligase in Arabidopsis thaliana that participates in ABA signaling and regulates apical dominance. Here, we present crystal structures of RGLG1 VWA domain, revealing two novel calcium ions binding sites (NCBS1 and NCBS2). Furthermore, the structures with guided mutagenesis in NCBS1 prove that Ca2+ ions play important roles in controlling conformational change of VWA, which is stabilized in open state with Ca2+ bound and converted to closed state after Ca2+ removal. This allosteric regulation mechanism is distinct from the ever reported one involving the C-terminal helix in integrin α and β I domains. The mutation of a key residue in NCBS2 do not abolish its Ca2+-binding potential, with no conformational change. MD simulations reveals that open state of RGLG1 VWA has higher ligand affinity than its closed state, consisting with integrin. Structural comparison of ion-free-MIDAS with Mg2+-MIDAS reveals that Mg2+ binding to MIDAS does not induce conformational change. With acquisition of first structure of plant VWA domain in both open state and closed state, we carefully analyze the conformational change and propose a totally new paradigm for its transition of open-closed states, which will be of great value for guiding future researches on VWA proteins and their important biological significance.
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18
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Berry KN, Brett TJ. Structural and Biophysical Analysis of the CLCA1 VWA Domain Suggests Mode of TMEM16A Engagement. Cell Rep 2020; 30:1141-1151.e3. [PMID: 31995732 PMCID: PMC7050472 DOI: 10.1016/j.celrep.2019.12.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/14/2019] [Accepted: 12/16/2019] [Indexed: 01/09/2023] Open
Abstract
The secreted protein calcium-activated chloride channel regulator 1 (CLCA1) utilizes a von Willebrand factor type A (VWA) domain to bind to and potentiate the calcium-activated chloride channel TMEM16A. To gain insight into this unique potentiation mechanism, we determined the 2.0-Å crystal structure of human CLCA1 VWA bound to Ca2+. The structure reveals the metal-ion-dependent adhesion site (MIDAS) in a high-affinity "open" conformation, engaging in crystal contacts that likely mimic how CLCA1 engages TMEM16A. The CLCA1 VWA contains a disulfide bond between α3 and α4 in close proximity to the MIDAS that is invariant in the CLCA family and unique in VWA structures. Further biophysical studies indicate that CLCA1 VWA is preferably stabilized by Mg2+ over Ca2+ and that α6 atypically extends from the VWA core. Finally, an analysis of TMEM16A structures suggests residues likely to mediate interaction with CLCA1 VWA.
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Affiliation(s)
- Kayla N Berry
- Immunology Program and Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Internal Medicine, Division of Pulmonary and Critical Care, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tom J Brett
- Department of Internal Medicine, Division of Pulmonary and Critical Care, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Investigation of Membrane Excitability Diseases (CIMED), Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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19
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Lancellotti S, Sacco M, Basso M, De Cristofaro R. Mechanochemistry of von Willebrand factor. Biomol Concepts 2019; 10:194-208. [PMID: 31778361 DOI: 10.1515/bmc-2019-0022] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022] Open
Abstract
Von Willebrand factor (VWF), a blood multimeric protein with a very high molecular weight, plays a crucial role in the primary haemostasis, the physiological process characterized by the adhesion of blood platelets to the injured vessel wall. Hydrodynamic forces are responsible for extensive conformational transitions in the VWF multimers that change their structure from a globular form to a stretched linear conformation. This feature makes this protein particularly prone to be investigated by mechanochemistry, the branch of the biophysical chemistry devoted to investigating the effects of shear forces on protein conformation. This review describes the structural elements of the VWF molecule involved in the biochemical response to shear forces. The stretched VWF conformation favors the interaction with the platelet GpIb and at the same time with ADAMTS-13, the zinc-protease that cleaves VWF in the A2 domain, limiting its prothrombotic capacity. The shear-induced conformational transitions favor also a process of self-aggregation, responsible for the formation of a spider-web like network, particularly efficient in the trapping process of flowing platelets. The investigation of the biophysical effects of shear forces on VWF conformation contributes to unraveling the molecular mechanisms of many types of thrombotic and haemorrhagic syndromes.
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Affiliation(s)
- Stefano Lancellotti
- Servizio Malattie Emorragiche e Trombotiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma, Italy
| | - Monica Sacco
- Istituto di Medicina Interna e Geriatria, Facoltà di Medicina e Chirurgia "A. Gemelli", Università Cattolica S. Cuore, Roma, Italy
| | - Maria Basso
- Servizio Malattie Emorragiche e Trombotiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma, Italy
| | - Raimondo De Cristofaro
- Servizio Malattie Emorragiche e Trombotiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma, Italy.,Istituto di Medicina Interna e Geriatria, Facoltà di Medicina e Chirurgia "A. Gemelli", Università Cattolica S. Cuore, Roma, Italy
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20
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Nyström EEL, Arike L, Ehrencrona E, Hansson GC, Johansson MEV. Calcium-activated chloride channel regulator 1 (CLCA1) forms non-covalent oligomers in colonic mucus and has mucin 2-processing properties. J Biol Chem 2019; 294:17075-17089. [PMID: 31570526 PMCID: PMC6851300 DOI: 10.1074/jbc.ra119.009940] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/23/2019] [Indexed: 12/18/2022] Open
Abstract
Calcium-activated chloride channel regulator 1 (CLCA1) is one of the major nonmucin proteins found in intestinal mucus. It is part of a larger family of CLCA proteins that share highly conserved features and domain architectures. The CLCA domain arrangement is similar to proteins belonging to the ADAM (a disintegrin and metalloproteinase) family, known to process extracellular matrix proteins. Therefore, CLCA1 is an interesting candidate in the search for proteases that process intestinal mucus. Here, we investigated CLCA1's biochemical properties both in vitro and in mucus from mouse and human colon biopsy samples. Using immunoblotting with CLCA1-specific antibodies and recombinant proteins, we observed that the CLCA1 C-terminal self-cleavage product forms a disulfide-linked dimer that noncovalently interacts with the N-terminal part of CLCA1, which further interacts to form oligomers. We also characterized a second, more catalytically active, N-terminal product of CLCA1, encompassing the catalytic domain together with its von Willebrand domain type A (VWA). This fragment was unstable but could be identified in freshly prepared mucus. Furthermore, we found that CLCA1 can cleave the N-terminal part of the mucus structural component MUC2. We propose that CLCA1 regulates the structural arrangement of the mucus and thereby takes part in the regulation of mucus processing.
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Affiliation(s)
- Elisabeth E L Nyström
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Liisa Arike
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Erik Ehrencrona
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Malin E V Johansson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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Lee D, Park K, Yoon GJ, Lee HJ, Lee J, Park YS, Park J, Lee G, Chung CP, Park YJ. Identification of cell‐penetrating osteogenic peptide from copine‐7 protein and its delivery system for enhanced bone formation. J Biomed Mater Res A 2019; 107:2392-2402. [DOI: 10.1002/jbm.a.36746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/09/2019] [Accepted: 06/03/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Dongwoo Lee
- Department of Oral BiochemistryDental Regenerative Bioengineering Major and Dental Research Institute, School of Dentistry, Seoul National University Seoul Republic of Korea
- Central Research Institute, Nano Intelligent Biomedical Engineering Corporation (NIBEC) Seoul Republic of Korea
| | - Kwang‐Sook Park
- Department of Oral BiochemistryDental Regenerative Bioengineering Major and Dental Research Institute, School of Dentistry, Seoul National University Seoul Republic of Korea
| | - Gook Jin Yoon
- Department of Oral BiochemistryDental Regenerative Bioengineering Major and Dental Research Institute, School of Dentistry, Seoul National University Seoul Republic of Korea
| | - Hyun Jung Lee
- Department of Oral BiochemistryDental Regenerative Bioengineering Major and Dental Research Institute, School of Dentistry, Seoul National University Seoul Republic of Korea
| | - Jue‐Yeon Lee
- Central Research Institute, Nano Intelligent Biomedical Engineering Corporation (NIBEC) Seoul Republic of Korea
| | - Yoon Shin Park
- Major in MicrobiologySchool of Biological Sciences, College of Natural Sciences, Chungbuk National University Cheongju Republic of Korea
| | - Joo‐Cheol Park
- Department of Oral Histology‐Developmental Biology and Dental Research InstituteSchool of Dentistry, Seoul National University Seoul Republic of Korea
| | - Gene Lee
- Department of Oral BiochemistryDental Regenerative Bioengineering Major and Dental Research Institute, School of Dentistry, Seoul National University Seoul Republic of Korea
| | - Chong Pyoung Chung
- Central Research Institute, Nano Intelligent Biomedical Engineering Corporation (NIBEC) Seoul Republic of Korea
| | - Yoon Jeong Park
- Department of Oral BiochemistryDental Regenerative Bioengineering Major and Dental Research Institute, School of Dentistry, Seoul National University Seoul Republic of Korea
- Central Research Institute, Nano Intelligent Biomedical Engineering Corporation (NIBEC) Seoul Republic of Korea
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Boccitto M, Wolin SL. Ro60 and Y RNAs: structure, functions, and roles in autoimmunity. Crit Rev Biochem Mol Biol 2019; 54:133-152. [PMID: 31084369 DOI: 10.1080/10409238.2019.1608902] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ro60, also known as SS-A or TROVE2, is an evolutionarily conserved RNA-binding protein that is found in most animal cells, approximately 5% of sequenced prokaryotic genomes and some archaea. Ro60 is present in cells as both a free protein and as a component of a ribonucleoprotein complex, where its best-known partners are members of a class of noncoding RNAs called Y RNAs. Structural and biochemical analyses have revealed that Ro60 is a ring-shaped protein that binds Y RNAs on its outer surface. In addition to Y RNAs, Ro60 binds misfolded and aberrant noncoding RNAs in some animal cell nuclei. Although the fate of these defective Ro60-bound noncoding RNAs in animal cells is not well-defined, a bacterial Ro60 ortholog functions with 3' to 5' exoribonucleases to assist structured RNA degradation. Studies of Y RNAs have revealed that these RNAs regulate the subcellular localization of Ro60, tether Ro60 to effector proteins and regulate the access of other RNAs to its central cavity. As both mammalian cells and bacteria lacking Ro60 are sensitized to ultraviolet irradiation, Ro60 function may be important during exposure to some environmental stressors. Here we summarize the current knowledge regarding the functions of Ro60 and Y RNAs in animal cells and bacteria. Because the Ro60 RNP is a clinically important target of autoantibodies in patients with rheumatic diseases such as Sjogren's syndrome, systemic lupus erythematosus, and neonatal lupus, we also discuss potential roles for Ro60 RNPs in the initiation and pathogenesis of systemic autoimmune rheumatic disease.
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Affiliation(s)
- Marco Boccitto
- a RNA Biology Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , MD , USA
| | - Sandra L Wolin
- a RNA Biology Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , MD , USA
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Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts. mBio 2019; 10:mBio.00715-19. [PMID: 31064832 PMCID: PMC6509191 DOI: 10.1128/mbio.00715-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Diverse and highly variable systems involved in biological conflicts and self-versus-nonself discrimination are ubiquitous in bacteria but much less studied in archaea. We performed comprehensive comparative genomic analyses of the archaeal systems that share components with analogous bacterial systems and propose an approach to identify new systems that could be involved in these functions. We predict polymorphic toxin systems in 141 archaeal genomes and identify new, archaea-specific toxin and immunity protein families. These systems are widely represented in archaea and are predicted to play major roles in interactions between species and in intermicrobial conflicts. This work is expected to stimulate experimental research to advance the understanding of poorly characterized major aspects of archaeal biology. Numerous, diverse, highly variable defense and offense genetic systems are encoded in most bacterial genomes and are involved in various forms of conflict among competing microbes or their eukaryotic hosts. Here we focus on the offense and self-versus-nonself discrimination systems encoded by archaeal genomes that so far have remained largely uncharacterized and unannotated. Specifically, we analyze archaeal genomic loci encoding polymorphic and related toxin systems and ribosomally synthesized antimicrobial peptides. Using sensitive methods for sequence comparison and the “guilt by association” approach, we identified such systems in 141 archaeal genomes. These toxins can be classified into four major groups based on the structure of the components involved in the toxin delivery. The toxin domains are often shared between and within each system. We revisit halocin families and substantially expand the halocin C8 family, which was identified in diverse archaeal genomes and also certain bacteria. Finally, we employ features of protein sequences and genomic locus organization characteristic of archaeocins and polymorphic toxins to identify candidates for analogous but not necessarily homologous systems among uncharacterized protein families. This work confidently predicts that more than 1,600 archaeal proteins, currently annotated as “hypothetical” in public databases, are components of conflict and self-versus-nonself discrimination systems.
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Autonomous conformational regulation of β 3 integrin and the conformation-dependent property of HPA-1a alloantibodies. Proc Natl Acad Sci U S A 2018; 115:E9105-E9114. [PMID: 30209215 DOI: 10.1073/pnas.1806205115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Integrin α/β heterodimer adopts a compact bent conformation in the resting state, and upon activation undergoes a large-scale conformational rearrangement. During the inside-out activation, signals impinging on the cytoplasmic tail of β subunit induce the α/β separation at the transmembrane and cytoplasmic domains, leading to the extended conformation of the ectodomain with the separated leg and the opening headpiece that is required for the high-affinity ligand binding. It remains enigmatic which integrin subunit drives the bent-to-extended conformational rearrangement in the inside-out activation. The β3 integrins, including αIIbβ3 and αVβ3, are the prototypes for understanding integrin structural regulation. The Leu33Pro polymorphism located at the β3 PSI domain defines the human platelet-specific alloantigen (HPA) 1a/b, which provokes the alloimmune response leading to clinically important bleeding disorders. Some, but not all, anti-HPA-1a alloantibodies can distinguish the αIIbβ3 from αVβ3 and affect their functions with unknown mechanisms. Here we designed a single-chain β3 subunit that mimics a separation of α/β heterodimer on inside-out activation. Our crystallographic and functional studies show that the single-chain β3 integrin folds into a bent conformation in solution but spontaneously extends on the cell surface. This demonstrates that the β3 subunit autonomously drives the membrane-dependent conformational rearrangement during integrin activation. Using the single-chain β3 integrin, we identified the conformation-dependent property of anti-HPA-1a alloantibodies, which enables them to differently recognize the β3 in the bent state vs. the extended state and in the complex with αIIb vs. αV This study provides deeper understandings of integrin conformational activation on the cell surface.
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25
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Zhou D, Thinn AMM, Zhao Y, Wang Z, Zhu J. Structure of an extended β 3 integrin. Blood 2018; 132:962-972. [PMID: 30018079 PMCID: PMC6117741 DOI: 10.1182/blood-2018-01-829572] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/10/2018] [Indexed: 12/23/2022] Open
Abstract
Cells use adhesion receptor integrins to communicate with their surroundings. Integrin activation and cellular signaling are coupled with change from bent to extended conformation. β3 integrins, including αIIbβ3, which is essential for the function of platelets in hemostasis and thrombosis, and αVβ3, which plays multiple roles in diverse cell types, have been prototypes in understanding integrin structure and function. Despite extensive structural studies, a high-resolution integrin structure in an extended conformation remains to be determined. The human β3 Leu33Pro polymorphism, located at the PSI domain, defines human platelet-specific alloantigens 1a and 1b (HPA-1a/b), immune response to which is a cause of posttransfusion purpura and fetal/neonatal alloimmune thrombocytopenia. Leu33Pro substitution has also been suggested to be a risk factor for thrombosis. Here we report the crystal structure of the β3 headpiece in either Leu33 or Pro33 form, both of which reveal intermediate and fully extended conformations coexisting in 1 crystal. These were used to build high-resolution structures of full-length β3 integrin in the intermediate and fully extended states, agreeing well with the corresponding conformations observed by electron microscopy. Our structures reveal how β3 integrin becomes extended at its β-knee region and how the flexibility of β-leg domains is determined. In addition, our structures reveal conformational changes of the PSI and I-EGF1 domains upon β3 extension, which may affect the binding of conformation-dependent anti-HPA-1a alloantibodies. Our structural and functional data show that Leu33Pro substitution does not directly alter the conformation or ligand binding of β3 integrin.
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Affiliation(s)
- Dongwen Zhou
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
| | - Aye Myat Myat Thinn
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI; and
| | - Yan Zhao
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
- Department of Physiology, School of Basic Medical Science, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhengli Wang
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
| | - Jieqing Zhu
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI; and
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26
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Klychnikov OI, Shamorkina TM, Weeks SD, van Leeuwen HC, Corver J, Drijfhout JW, van Veelen PA, Sluchanko NN, Strelkov SV, Hensbergen PJ. Discovery of a new Pro-Pro endopeptidase, PPEP-2, provides mechanistic insights into the differences in substrate specificity within the PPEP family. J Biol Chem 2018; 293:11154-11165. [PMID: 29794027 DOI: 10.1074/jbc.ra118.003244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/22/2018] [Indexed: 12/20/2022] Open
Abstract
Pro-Pro endopeptidases (PPEPs) belong to a recently discovered family of proteases capable of hydrolyzing a Pro-Pro bond. The first member from the bacterial pathogen Clostridium difficile (PPEP-1) cleaves two C. difficile cell-surface proteins involved in adhesion, one of which is encoded by the gene adjacent to the ppep-1 gene. However, related PPEPs may exist in other bacteria and may shed light on substrate specificity in this enzyme family. Here, we report on the homolog of PPEP-1 in Paenibacillus alvei, which we denoted PPEP-2. We found that PPEP-2 is a secreted metalloprotease, which likewise cleaved a cell-surface protein encoded by an adjacent gene. However, the cleavage motif of PPEP-2, PLP↓PVP, is distinct from that of PPEP-1 (VNP↓PVP). As a result, an optimal substrate peptide for PPEP-2 was not cleaved by PPEP-1 and vice versa. To gain insight into the specificity mechanism of PPEP-2, we determined its crystal structure at 1.75 Å resolution and further confirmed the structure in solution using small-angle X-ray scattering (SAXS). We show that a four-amino-acid loop, which is distinct in PPEP-1 and -2 (GGST in PPEP-1 and SERV in PPEP-2), plays a crucial role in substrate specificity. A PPEP-2 variant, in which the four loop residues had been swapped for those from PPEP-1, displayed a shift in substrate specificity toward PPEP-1 substrates. Our results provide detailed insights into the PPEP-2 structure and the structural determinants of substrate specificity in this new family of PPEP proteases.
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Affiliation(s)
- Oleg I Klychnikov
- From the Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | | | - Stephen D Weeks
- From the Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | | | | | - Jan W Drijfhout
- Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 Leiden, The Netherlands
| | | | - Nikolai N Sluchanko
- the A. N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia, and.,the Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergei V Strelkov
- From the Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
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27
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Contribution of Pili of S. Pneumoniae in the Onset of Meningitis. FOLIA VETERINARIA 2018. [DOI: 10.2478/fv-2018-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Bacterial meningitis is a devastating worldwide disease. Half of the survivors of meningitis remain with permanent neurological sequelae. The pathogenesis of meningitis is based on a complex host-pathogen interaction. Streptococcus pneumoniae is a life-threatening neuroinvasive pathogen that asymptomatically colonizes the upper respiratory tract. Adherence of pneumococci to the host epithelium is a prerequisite in the onset of streptococcal infections; such adherence is favored by the formation of bacterial pili. In this article, we will describe the pneumococcal pili and its contribution to the onset of meningitis.
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Briot J, Mailhot O, Bourdin B, Tétreault MP, Najmanovich R, Parent L. A three-way inter-molecular network accounts for the Ca Vα2δ1-induced functional modulation of the pore-forming Ca V1.2 subunit. J Biol Chem 2018; 293:7176-7188. [PMID: 29588365 DOI: 10.1074/jbc.ra118.001902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Indexed: 12/17/2022] Open
Abstract
L-type CaV1.2 channels are essential for the excitation-contraction coupling in cardiomyocytes and are hetero-oligomers of a pore-forming CaVα1C assembled with CaVβ and CaVα2δ1 subunits. A direct interaction between CaVα2δ1 and Asp-181 in the first extracellular loop of CaVα1 reproduces the native properties of the channel. A 3D model of the von Willebrand factor type A (VWA) domain of CaVα2δ1 complexed with the voltage sensor domain of CaVα1C suggests that Ser-261 and Ser-263 residues in the metal ion-dependent adhesion site (MIDAS) motif are determinant in this interaction, but this hypothesis is untested. Here, coimmunoprecipitation assays and patch-clamp experiments of single-substitution variants revealed that CaVα2δ1 Asp-259 and Ser-261 are the two most important residues in regard to protein interactions and modulation of CaV1.2 currents. In contrast, mutating the side chains of CaVα2δ1 Ser-263, Thr-331, and Asp-363 with alanine did not completely prevent channel function. Molecular dynamics simulations indicated that the carboxylate side chain of CaVα2δ1 Asp-259 coordinates the divalent cation that is further stabilized by the oxygen atoms from the hydroxyl side chain of CaVα2δ1 Ser-261 and the carboxylate group of CaVα1C Asp-181. In return, the hydrogen atoms contributed by the side chain of Ser-261 and the main chain of Ser-263 bonded the oxygen atoms of CaV1.2 Asp-181. We propose that CaVα2δ1 Asp-259 promotes Ca2+ binding necessary to produce the conformation of the VWA domain that locks CaVα2δ1 Ser-261 and Ser-263 within atomic distance of CaVα1C Asp-181. This three-way network appears to account for the CaVα2δ1-induced modulation of CaV1.2 currents.
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Affiliation(s)
- Julie Briot
- Départements de Pharmacologie et Physiologie, Faculté de Médecine, Montréal, Québec H1T 1C8, Canada; Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Olivier Mailhot
- Départements de Pharmacologie et Physiologie, Faculté de Médecine, Montréal, Québec H1T 1C8, Canada; Biochimie et Médecine Moléculaire, Faculté de Médecine, Montréal, Québec H1T 1C8, Canada
| | - Benoîte Bourdin
- Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Marie-Philippe Tétreault
- Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Rafael Najmanovich
- Départements de Pharmacologie et Physiologie, Faculté de Médecine, Montréal, Québec H1T 1C8, Canada
| | - Lucie Parent
- Départements de Pharmacologie et Physiologie, Faculté de Médecine, Montréal, Québec H1T 1C8, Canada; Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H1T 1C8, Canada.
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29
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Rienzo M, Casamassimi A. Integrator complex and transcription regulation: Recent findings and pathophysiology. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1269-80. [PMID: 27427483 DOI: 10.1016/j.bbagrm.2016.07.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 12/20/2022]
Abstract
In the last decade, a novel molecular complex has been added to the RNA polymerase II-mediated transcription machinery as one of the major components. This multiprotein complex, named Integrator, plays a pivotal role in the regulation of most RNA Polymerase II-dependent genes. This complex consists of at least 14 different subunits. However, studies investigating its structure and composition are still lacking. Although it was originally discovered as a complex implicated in the 3'-end formation of noncoding small nuclear RNAs, recent studies indicate additional roles for Integrator in transcription regulation, for example during transcription pause-release and elongation of polymerase, in the biogenesis of transcripts derived from enhancers, as well as in DNA and RNA metabolism for some of its components. Noteworthy, several subunits have been emerging to play roles during development and differentiation; more importantly, their alterations are likely to be involved in several human pathologies, including cancer and lung diseases.
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Affiliation(s)
- Monica Rienzo
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Amelia Casamassimi
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy.
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30
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Scavenius C, Nikolajsen CL, Stenvang M, Thøgersen IB, Wyrożemski Ł, Wisniewski HG, Otzen DE, Sanggaard KW, Enghild JJ. The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations. J Biol Chem 2016; 291:4658-70. [PMID: 26728454 DOI: 10.1074/jbc.m115.678748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Indexed: 11/06/2022] Open
Abstract
Inter-α-inhibitor is a proteoglycan of unique structure. The protein consists of three subunits, heavy chain 1, heavy chain 2, and bikunin covalently joined by a chondroitin sulfate chain originating at Ser-10 of bikunin. Inter-α-inhibitor interacts with an inflammation-associated protein, tumor necrosis factor-inducible gene 6 protein, in the extracellular matrix. This interaction leads to transfer of the heavy chains from the chondroitin sulfate of inter-α-inhibitor to hyaluronan and consequently to matrix stabilization. Divalent cations and heavy chain 2 are essential co-factors in this transfer reaction. In the present study, we have investigated how divalent cations in concert with the chondroitin sulfate chain influence the structure and stability of inter-α-inhibitor. The results showed that Mg(2+) or Mn(2+), but not Ca(2+), induced a conformational change in inter-α-inhibitor as evidenced by a decrease in the Stokes radius and a bikunin chondroitin sulfate-dependent increase of the thermodynamic stability. This structure was shown to be essential for the ability of inter-α-inhibitor to participate in extracellular matrix stabilization. In addition, the data revealed that bikunin was positioned adjacent to both heavy chains and that the two heavy chains also were in close proximity. The chondroitin sulfate chain interacted with all protein components and inter-α-inhibitor dissociated when it was degraded. Conventional purification protocols result in the removal of the Mg(2+) found in plasma and because divalent cations influence the conformation and affect function it is important to consider this when characterizing the biological activity of inter-α-inhibitor.
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Affiliation(s)
- Carsten Scavenius
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Camilla Lund Nikolajsen
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
| | - Marcel Stenvang
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
| | - Ida B Thøgersen
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Łukasz Wyrożemski
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Hans-Georg Wisniewski
- the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Daniel E Otzen
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
| | - Kristian W Sanggaard
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Jan J Enghild
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
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31
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Friedrich T, Dekovic DK, Burschel S. Assembly of the Escherichia coli NADH:ubiquinone oxidoreductase (respiratory complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:214-23. [PMID: 26682761 DOI: 10.1016/j.bbabio.2015.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022]
Abstract
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples the electron transfer from NADH to ubiquinone with the translocation of four protons across the membrane. The Escherichia coli complex I is made up of 13 different subunits encoded by the so-called nuo-genes. The electron transfer is catalyzed by nine cofactors, a flavin mononucleotide and eight iron-sulfur (Fe/S)-clusters. The individual subunits and the cofactors have to be assembled together in a coordinated way to guarantee the biogenesis of the active holoenzyme. Only little is known about the assembly of the bacterial complex compared to the mitochondrial one. Due to the presence of so many Fe/S-clusters the assembly of complex I is intimately connected with the systems responsible for the biogenesis of these clusters. In addition, a few other proteins have been reported to be required for an effective assembly of the complex in other bacteria. The proposed role of known bacterial assembly factors is discussed and the information from other bacterial species is used in this review to draw an as complete as possible model of bacterial complex I assembly. In addition, the supramolecular organization of the complex in E. coli is briefly described. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof. Conrad Mullineaux.
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Affiliation(s)
- Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany.
| | - Doris Kreuzer Dekovic
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany
| | - Sabrina Burschel
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany
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32
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Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Mol Cell 2015; 59:794-806. [PMID: 26340423 DOI: 10.1016/j.molcel.2015.07.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/10/2015] [Accepted: 07/17/2015] [Indexed: 10/23/2022]
Abstract
TFIIH is essential for both RNA polymerase II transcription and DNA repair, and mutations in TFIIH can result in human disease. Here, we determine the molecular architecture of human and yeast TFIIH by an integrative approach using chemical crosslinking/mass spectrometry (CXMS) data, biochemical analyses, and previously published electron microscopy maps. We identified four new conserved "topological regions" that function as hubs for TFIIH assembly and more than 35 conserved topological features within TFIIH, illuminating a network of interactions involved in TFIIH assembly and regulation of its activities. We show that one of these conserved regions, the p62/Tfb1 Anchor region, directly interacts with the DNA helicase subunit XPD/Rad3 in native TFIIH and is required for the integrity and function of TFIIH. We also reveal the structural basis for defects in patients with xeroderma pigmentosum and trichothiodystrophy, with mutations found at the interface between the p62 Anchor region and the XPD subunit.
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Affiliation(s)
- Jie Luo
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Peter Cimermancic
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shruthi Viswanath
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christopher C Ebmeier
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Bong Kim
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Marine Dehecq
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, PO Box 19024, Mailstop A1-162, Seattle, WA 98109, USA; Génétique des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3525, 25-28 rue du docteur Roux, 75015 Paris, France
| | - Vishnu Raman
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Charles H Greenberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Steven Hahn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, PO Box 19024, Mailstop A1-162, Seattle, WA 98109, USA
| | - Jeff Ranish
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA.
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33
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Makarova KS, Galperin MY, Koonin EV. Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems. Biochimie 2015; 118:302-12. [PMID: 25583072 PMCID: PMC5898192 DOI: 10.1016/j.biochi.2015.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/02/2015] [Indexed: 01/03/2023]
Abstract
A systematic comparative genomic analysis of all archaeal membrane proteins that have been projected to the last archaeal common ancestor gene set led to the identification of several novel components of predicted secretion, membrane remodeling, and protein glycosylation systems. Among other findings, most crenarchaea have been shown to encode highly diverged orthologs of the membrane insertase YidC, which is nearly universal in bacteria, eukaryotes, and euryarchaea. We also identified a vast family of archaeal proteins, including the C-terminal domain of N-glycosylation protein AglD, as membrane flippases homologous to the flippase domain of bacterial multipeptide resistance factor MprF, a bifunctional lysylphosphatidylglycerol synthase and flippase. Additionally, several proteins were predicted to function as membrane transporters. The results of this work, combined with our previous analyses, reveal an unexpected diversity of putative archaeal membrane-associated functional systems that remain to be functionally characterized. A more general conclusion from this work is that the currently available collection of archaeal (and bacterial) genomes could be sufficient to identify (almost) all widespread functional modules and develop experimentally testable predictions of their functions.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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34
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Nam HJ, Kim I, Bowie JU, Kim S. Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. Sci Rep 2015; 5:9576. [PMID: 25923201 PMCID: PMC4894438 DOI: 10.1038/srep09576] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/09/2015] [Indexed: 12/15/2022] Open
Abstract
A central question in animal evolution is how multicellular animals evolved from unicellular ancestors. We hypothesize that membrane proteins must be key players in the development of multicellularity because they are well positioned to form the cell-cell contacts and to provide the intercellular communication required for the creation of complex organisms. Here we find that a major mechanism for the necessary increase in membrane protein complexity in the transition from non-metazoan to metazoan life was the new incorporation of domains from soluble proteins. The membrane proteins that have incorporated soluble domains in metazoans are enriched in many of the functions unique to multicellular organisms such as cell-cell adhesion, signaling, immune defense and developmental processes. They also show enhanced protein-protein interaction (PPI) network complexity and centrality, suggesting an important role in the cellular diversification found in complex organisms. Our results expose an evolutionary mechanism that contributed to the development of higher life forms.
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Affiliation(s)
- Hyun-Jun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Inhae Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095-1570, United States
| | - Sanguk Kim
- 1] School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Korea [2] Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
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35
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Becker AKA, Mikolajek H, Werner JM, Paulsson M, Wagener R. Characterization of recombinantly expressed matrilin VWA domains. Protein Expr Purif 2015; 107:20-8. [PMID: 25462806 PMCID: PMC4294422 DOI: 10.1016/j.pep.2014.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/13/2014] [Accepted: 11/15/2014] [Indexed: 11/01/2022]
Abstract
VWA domains are the predominant independent folding units within matrilins and mediate protein-protein interactions. Mutations in the matrilin-3 VWA domain cause various skeletal diseases. The analysis of the pathological mechanisms is hampered by the lack of detailed structural information on matrilin VWA domains. Attempts to resolve their structures were hindered by low solubility and a tendency to aggregation. We therefore took a comprehensive approach to improve the recombinant expression of functional matrilin VWA domains to enable X-ray crystallography and nuclear magnetic resonance (NMR) studies. The focus was on expression in Escherichia coli, as this allows incorporation of isotope-labeled amino acids, and on finding conditions that enhance solubility. Indeed, circular dichroism (CD) and NMR measurements indicated a proper folding of the bacterially expressed domains and, interestingly, expression of zebrafish matrilin VWA domains and addition of N-ethylmaleimide yielded the most stable proteins. However, such proteins did still not crystallize and allowed only partial peak assignment in NMR. Moreover, bacterially expressed matrilin VWA domains differ in their solubility and functional properties from the same domains expressed in eukaryotic cells. Structural studies of matrilin VWA domains will depend on the use of eukaryotic expression systems.
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Affiliation(s)
- Ann-Kathrin A Becker
- Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, D-50931, Germany
| | - Halina Mikolajek
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton SO17 1BJ, UK
| | - Jörn M Werner
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton SO17 1BJ, UK
| | - Mats Paulsson
- Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, D-50931, Germany
| | - Raimund Wagener
- Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, D-50931, Germany.
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Sinha A, Datta SP, Ray A, Sarkar S. A reduced VWA domain-containing proteasomal ubiquitin receptor of Giardia lamblia localizes to the flagellar pore regions in microtubule-dependent manner. Parasit Vectors 2015; 8:120. [PMID: 25888841 PMCID: PMC4352536 DOI: 10.1186/s13071-015-0737-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/13/2015] [Indexed: 11/22/2022] Open
Abstract
Background Giardia lamblia switches its lifecycle between trophozoite and cyst forms and the proteasome plays a pivotal role in this switching event. Compared to most model eukaryotes, the proteasome of this parasite has already been documented to have certain variations. This study was undertaken to characterize the ubiquitin receptor, GlRpn10, of the 19S regulatory particle of the Giardia proteasome and determine its cellular localization in trophozoites, encysting trophozoites and cysts. Method Sequence alignment and domain architecture analyses were performed to characterize GlRpn10. In vitro ubiquitin binding assay, functional complementation and biochemical studies verified the protein’s ability to function as ubiquitin receptor in the context of the yeast proteasome. Immunofluorescence localization was performed with antibody against GlRpn10 to determine its distribution in trophozoites, encysting trophozoites and cysts. Real-time PCR and Western blotting were performed to monitor the expression pattern of GlRpn10 during encystation. Result GlRpn10 contained a functional ubiquitin interacting motif, which was capable of binding to ubiquitin. Although it contained a truncated VWA domain, it was still capable of partially complementing the function of the yeast Rpn10 orthologue. Apart from localizing to the nucleus and cytosol, GlRpn10 was also present at flagellar pores of trophozoites and this localization was microtubule-dependent. Although there was no change in the cellular levels of GlRpn10 during encystation, its selective distribution at the flagellar pores was absent. Conclusion GlRpn10 contains a noncanonical VWA domain that is partially functional in yeast. Besides the expected nuclear and cytosolic distribution, the protein displays microtubule-dependent flagellar pore localization in trophozoites. While the protein remained in the nucleus and cytosol in encysting trophozoites, it could no longer be detected at the flagellar pores. This absence at the flagellar pore regions in encysting trophozoites is likely to involve redistribution of the protein, rather than decreased gene expression or selective protein degradation. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0737-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abhishek Sinha
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Shankari Prasad Datta
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Atrayee Ray
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Srimonti Sarkar
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
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Kim JS, Saint-André C, Lim HS, Hwang CS, Egly JM, Cho Y. Crystal structure of the Rad3/XPD regulatory domain of Ssl1/p44. J Biol Chem 2015; 290:8321-30. [PMID: 25681444 DOI: 10.1074/jbc.m115.636514] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Ssl1/p44 subunit is a core component of the yeast/mammalian general transcription factor TFIIH, which is involved in transcription and DNA repair. Ssl1/p44 binds to and stimulates the Rad3/XPD helicase activity of TFIIH. To understand the helicase stimulatory mechanism of Ssl1/p44, we determined the crystal structure of the N-terminal regulatory domain of Ssl1 from Saccharomyces cerevisiae. Ssl1 forms a von Willebrand factor A fold in which a central six-stranded β-sheet is sandwiched between three α helices on both sides. Structural and biochemical analyses of Ssl1/p44 revealed that the β4-α5 loop, which is frequently found at the interface between von Willebrand factor A family proteins and cellular counterparts, is critical for the stimulation of Rad3/XPD. Yeast genetics analyses showed that double mutation of Leu-239 and Ser-240 in the β4-α5 loop of Ssl1 leads to lethality of a yeast strain, demonstrating the importance of the Rad3-Ssl1 interactions to cell viability. Here, we provide a structural model for the Rad3/XPD-Ssl1/p44 complex and insights into how the binding of Ssl1/p44 contributes to the helicase activity of Rad3/XPD and cell viability.
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Affiliation(s)
- Jin Seok Kim
- From the Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea and
| | - Charlotte Saint-André
- the Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, BP163, 67404 Illkirch Cedex, C.U. Strasbourg, France
| | - Hye Seong Lim
- From the Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea and
| | - Cheol-Sang Hwang
- From the Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea and
| | - Jean Marc Egly
- the Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, BP163, 67404 Illkirch Cedex, C.U. Strasbourg, France
| | - Yunje Cho
- From the Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea and
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Zwolanek D, Flicker M, Kirstätter E, Zaucke F, van Osch GJVM, Erben RG. β1 Integrins Mediate Attachment of Mesenchymal Stem Cells to Cartilage Lesions. Biores Open Access 2015; 4:39-53. [PMID: 26309781 PMCID: PMC4497673 DOI: 10.1089/biores.2014.0055] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mesenchymal stem cells (MSC) may have great potential for cell-based therapies of osteoarthritis. However, after injection in the joint, only few cells adhere to defective articular cartilage and contribute to cartilage regeneration. Little is known about the molecular mechanisms of MSC attachment to defective articular cartilage. Here, we developed an ex vivo attachment system, using rat osteochondral explants with artificially created full-thickness cartilage defects in combination with genetically labeled MSC isolated from bone marrow of human placental alkaline phosphatase transgenic rats. Binding of MSC to full-thickness cartilage lesions was improved by serum, but not hyaluronic acid, and was dependent on the presence of divalent cations. Additional in vitro tests showed that rat MSC attach, in a divalent cation-dependent manner, to collagen I, collagen II, and fibronectin, but not to collagen XXII or cartilage oligomeric matrix protein (COMP). RGD peptides partially blocked the adhesion of MSC to fibronectin in vitro and to cartilage lesions ex vivo. Furthermore, the attachment of MSC to collagen I and II in vitro and to cartilage lesions ex vivo was almost completely abolished in the presence of a β1 integrin blocking antibody. In conclusion, our data suggest that attachment of MSC to ex vivo full-thickness cartilage lesions is almost entirely β1 integrin-mediated, whereby both RGD- and collagen-binding integrins are involved. These findings suggest a key role of integrins during MSC attachment to defective cartilage and may pave the way for improved MSC-based therapies in the future.
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Affiliation(s)
- Daniela Zwolanek
- Department of Biomedical Sciences, University of Veterinary Medicine , Vienna, Austria
| | - Magdalena Flicker
- Department of Biomedical Sciences, University of Veterinary Medicine , Vienna, Austria
| | - Elisabeth Kirstätter
- Department of Biomedical Sciences, University of Veterinary Medicine , Vienna, Austria
| | - Frank Zaucke
- Center for Biochemistry and Cologne Center for Musculoskeletal Biomechanics, Medical Faculty, University of Cologne , Cologne, Germany
| | - Gerjo J V M van Osch
- Department of Orthopaedics and Otorhinolaryngology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands
| | - Reinhold G Erben
- Department of Biomedical Sciences, University of Veterinary Medicine , Vienna, Austria
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Grundy GJ, Moulding HA, Caldecott KW, Rulten SL. One ring to bring them all--the role of Ku in mammalian non-homologous end joining. DNA Repair (Amst) 2014; 17:30-8. [PMID: 24680220 DOI: 10.1016/j.dnarep.2014.02.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/25/2014] [Indexed: 12/26/2022]
Abstract
The repair of DNA double strand breaks is essential for cell survival and several conserved pathways have evolved to ensure their rapid and efficient repair. The non-homologous end joining pathway is initiated when Ku binds to the DNA break site. Ku is an abundant nuclear heterodimer of Ku70 and Ku80 with a toroidal structure that allows the protein to slide over the broken DNA end and bind with high affinity. Once locked into placed, Ku acts as a tool-belt to recruit multiple interacting proteins, forming one or more non-homologous end joining complexes that act in a regulated manner to ensure efficient repair of DNA ends. Here we review the structure and functions of Ku and the proteins with which it interacts during non-homologous end joining.
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Affiliation(s)
- Gabrielle J Grundy
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
| | - Hayley A Moulding
- School of Biochemistry, Medical Sciences, University Walk, Bristol BS8 1TD, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
| | - Stuart L Rulten
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
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40
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Collagen XXII binds to collagen-binding integrins via the novel motifs GLQGER and GFKGER. Biochem J 2014; 459:217-27. [DOI: 10.1042/bj20130642] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cell attachment to collagens is mediated by integrins. In the present study, we define two new integrin-binding motifs, GLQGER and GFKGER, within the collagen XXII triple helical domain. Mutation of the two motifs in collagen XXII abolishes the binding to HaCaT cells completely.
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41
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Houston S, Russell S, Hof R, Roberts AK, Cullen P, Irvine K, Smith DS, Borchers CH, Tonkin ML, Boulanger MJ, Cameron CE. The multifunctional role of the pallilysin-associated Treponema pallidum protein, Tp0750, in promoting fibrinolysis and extracellular matrix component degradation. Mol Microbiol 2014; 91:618-34. [PMID: 24303899 PMCID: PMC3954913 DOI: 10.1111/mmi.12482] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2013] [Indexed: 12/25/2022]
Abstract
The mechanisms that facilitate dissemination of the highly invasive spirochaete, Treponema pallidum, are incompletely understood. Previous studies showed the treponemal metalloprotease pallilysin (Tp0751) possesses fibrin clot degradation capability, suggesting a role in treponemal dissemination. In the current study we report characterization of the functionally linked protein Tp0750. Structural modelling predicts Tp0750 contains a von Willebrand factor type A (vWFA) domain, a protein-protein interaction domain commonly observed in extracellular matrix (ECM)-binding proteins. We report Tp0750 is a serine protease that degrades the major clot components fibrinogen and fibronectin. We also demonstrate Tp0750 cleaves a matrix metalloprotease (MMP) peptide substrate that is targeted by several MMPs, enzymes central to ECM remodelling. Through proteomic analyses we show Tp0750 binds the endothelial fibrinolytic receptor, annexin A2, in a specific and dose-dependent manner. These results suggest Tp0750 constitutes a multifunctional protein that is able to (1) degrade infection-limiting clots by both inhibiting clot formation through degradation of host coagulation cascade proteins and promoting clot dissolution by complexing with host proteins involved in the fibrinolytic cascade and (2) facilitate ECM degradation via MMP-like proteolysis of host components. We propose that through these activities Tp0750 functions in concert with pallilysin to enable T. pallidum dissemination.
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Affiliation(s)
- Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Shannon Russell
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Rebecca Hof
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Alanna K. Roberts
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Paul Cullen
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Kyle Irvine
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Derek S. Smith
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia, Canada, V8Z 7X8
| | - Christoph H. Borchers
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia, Canada, V8Z 7X8
| | - Michelle L. Tonkin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Martin J. Boulanger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Caroline E. Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
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A structure of a collagen VI VWA domain displays N and C termini at opposite sides of the protein. Structure 2013; 22:199-208. [PMID: 24332716 PMCID: PMC3919171 DOI: 10.1016/j.str.2013.06.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 05/27/2013] [Accepted: 11/07/2013] [Indexed: 11/23/2022]
Abstract
Von Willebrand factor A (VWA) domains are versatile protein interaction domains with N and C termini in close proximity placing spatial constraints on overall protein structure. The 1.2 Å crystal structures of a collagen VI VWA domain and a disease-causing point mutant show C-terminal extensions that place the N and C termini at opposite ends. This allows a “beads-on-a-string” arrangement of multiple VWA domains as observed for ten N-terminal domains of the collagen VI α3 chain. The extension is linked to the core domain by a salt bridge and two hydrophobic patches. Comparison of the wild-type and a muscular dystrophy-associated mutant structure identifies a potential perturbation of a protein interaction interface and indeed, the secretion of mutant collagen VI tetramers is affected. Homology modeling is used to locate a number of disease-associated mutations and analyze their structural impact, which will allow mechanistic analysis of collagen-VI-associated muscular dystrophy phenotypes. The structure of a VWA domain (N5) of collagen VI at 1.2 Å is presented N and C termini of the domain are at opposite ends The structure with a myopathy-causing mutation shows altered interaction interface The impact of mutations in collagen VI VWA domains was analyzed
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43
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Liu G, Fang Y, Wu J. A mechanism for localized dynamics-driven affinity regulation of the binding of von Willebrand factor to platelet glycoprotein Ibα. J Biol Chem 2013; 288:26658-67. [PMID: 23902764 DOI: 10.1074/jbc.m113.453803] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Binding of the A1 domain of von Willebrand factor (vWF) to glycoprotein Ibα (GPIbα) results in platelet adhesion, activation, and aggregation that initiates primary hemostasis. Both the elevated shear stress and the mutations associated with type 2B von Willebrand disease enhance the interaction between A1 and GPIbα. Through molecular dynamics simulations for wild-type vWF-A1 and its eight gain of function mutants (R543Q, I546V, ΔSS, etc.), we found that the gain of function mutations destabilize the N-terminal arm, increase a clock pendulum-like movement of the α2-helix, and turn a closed A1 conformation into a partially open one favoring binding to GPIbα. The residue Arg(578) at the α2-helix behaves as a pivot in the destabilization of the N-terminal arm and a consequent dynamic change of the α2-helix. These results suggest a localized dynamics-driven affinity regulation mechanism for vWF-GPIbα interaction. Allosteric drugs controlling this intrinsic protein dynamics may be effective in blocking the GPIb-vWF interaction.
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Affiliation(s)
- Guangjian Liu
- From the Institute of Biomechanics, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
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44
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Lea SM, Johnson S. Putting the structure into complement. Immunobiology 2013; 217:1117-21. [PMID: 22964238 DOI: 10.1016/j.imbio.2012.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 07/13/2012] [Accepted: 07/15/2012] [Indexed: 11/25/2022]
Abstract
In a field where structure has finally begun to have a real impact, a series of new structures over the last two years have further extended our understanding of some of the critical regulatory events of the complement system. Notably, information has begun to flow from larger assemblies of components which allow insight into the often transient assemblies critical to complement regulation at the cell surface. This review will summarise the key structures determined since the last International Complement Workshop and the insights these have given us, before highlighting some questions that still require molecular frameworks to drive understanding.
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Affiliation(s)
- Susan M Lea
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK.
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45
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46
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Shape change in the receptor for gliding motility in Plasmodium sporozoites. Proc Natl Acad Sci U S A 2012; 109:21420-5. [PMID: 23236185 DOI: 10.1073/pnas.1218581109] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Sporozoite gliding motility and invasion of mosquito and vertebrate host cells in malaria is mediated by thrombospondin repeat anonymous protein (TRAP). Tandem von Willebrand factor A (VWA) and thrombospondin type I repeat (TSR) domains in TRAP connect through proline-rich stalk, transmembrane, and cytoplasmic domains to the parasite actin-dependent motility apparatus. We crystallized fragments containing the VWA and TSR domains from Plasmodium vivax and Plasmodium falciparum in different crystal lattices. TRAP VWA domains adopt closed and open conformations, and bind a Mg(2+) ion at a metal ion-dependent adhesion site implicated in ligand binding. Metal ion coordination in the open state is identical to that seen in the open high-affinity state of integrin I domains. The closed VWA conformation associates with a disordered TSR domain. In contrast, the open VWA conformation crystallizes with an extensible β ribbon and ordered TSR domain. The extensible β ribbon is composed of disulfide-bonded segments N- and C-terminal to the VWA domain that are largely drawn out of the closed VWA domain in a 15 Å movement to the open conformation. The extensible β ribbon and TSR domain overlap at a conserved interface. The VWA, extensible β ribbon, and TSR domains adopt a highly elongated overall orientation that would be stabilized by tensile force exerted across a ligand-receptor complex by the actin motility apparatus of the sporozoite. Our results provide insights into regulation of "stick-and-slip" parasite motility and for development of sporozoite subunit vaccines.
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47
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Danne C, Dramsi S. Pili of gram-positive bacteria: roles in host colonization. Res Microbiol 2012; 163:645-58. [PMID: 23116627 DOI: 10.1016/j.resmic.2012.10.012] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 10/11/2012] [Indexed: 02/06/2023]
Abstract
In the last decade, pili, which are encoded within pathogenicity islands, have been found in many Gram-positive bacteria, including the major streptococcal and enterococcal pathogens. These long proteinaceous polymers extending from the bacterial surface are constituted of covalently linked pilin subunits, which play major roles in adhesion and host colonization. They are also involved in biofilm formation, a characteristic life-style of the bacteria constituting the oral flora. Pili are highly immunogenic structures that are under the selective pressure of host immune responses. Indeed, pilus expression was found to be heterogeneous in several bacteria with the co-existence of two subpopulations expressing various levels of pili. The molecular mechanisms underlying this complex regulation are poorly characterized except for Streptococcus pneumoniae. In this review, we will discuss the roles of Gram-positive bacteria pili in adhesion to host extracellular matrix proteins, tissue tropism, biofilm formation, modulation of innate immune responses and their contribution to virulence, and in a second part the regulation of their expression. This overview should help to understand the rise of pili as an intensive field of investigation and pinpoints the areas that need further study.
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Affiliation(s)
- Camille Danne
- Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram-positif, Paris F-75015, France
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48
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α2δ expression sets presynaptic calcium channel abundance and release probability. Nature 2012; 486:122-5. [PMID: 22678293 PMCID: PMC3376018 DOI: 10.1038/nature11033] [Citation(s) in RCA: 275] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 03/13/2012] [Indexed: 11/08/2022]
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Forneris F, Wu J, Gros P. The modular serine proteases of the complement cascade. Curr Opin Struct Biol 2012; 22:333-41. [PMID: 22560446 DOI: 10.1016/j.sbi.2012.04.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 04/05/2012] [Indexed: 11/30/2022]
Abstract
Modular serine proteases are central to the complement cascade of the mammalian humoral immune system. These proteases form protein complexes through multi-domain interactions to achieve their proteolytic activity. We review the structural insights into complement initiation by auto-activation of the hetero-tetrameric proteases of the large danger-recognition protein complexes, amplification and labelling of particles by the formation and activity of C3 convertases, and regulation by convertase dissociation and degradation to prevent 'bystander' damage to healthy host cells and tissues. The data reveal that complex formation and large domain-domain rearrangements underlie the proteolytic reactions of the complement cascade, which enables the host to recognize and clear invading microbes and host debris from its blood and fluids surrounding tissues.
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Affiliation(s)
- Federico Forneris
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Novel structural and functional insights into the MoxR family of AAA+ ATPases. J Struct Biol 2012; 179:211-21. [PMID: 22491058 DOI: 10.1016/j.jsb.2012.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/21/2012] [Accepted: 03/25/2012] [Indexed: 11/23/2022]
Abstract
The MoxR family of AAA+ ATPases is widespread among bacteria and archaea, although their cellular functions are not well characterized. Based on recent studies, MoxR ATPases are proposed to have chaperone-like function for the maturation of specific protein complexes or for the insertion of cofactors into proteins. MoxR proteins have been found to be important modulators of multiple stress response pathways in different organisms. For example, the respective MoxR proteins have been found to play important roles in the cell envelope stress response in Rhizobium leguminosarum, in the oxidative stress, acid stress, and heat stress responses in Francisella tularensis, in the acid stress and stringent responses in Escherichia coli, in viral tail formation in the crenarchaeal Acidianus two-tailed virus, and in the utilization of carbon monoxide as the sole carbon source by the Gram-negative chemolithoautotrophe Oligotropha carboxidovorans. Recent structural studies on the MoxR proteins from E. coli and Cytophaga hutchinsonii show the unique spatial arrangement of the αβα and all-α subdomains of the AAA+ domain in these proteins compared to the typical arrangement found in canonical AAA+ proteins such as HslU. The spatial organization of the subdomains in the AAA+ domain of MoxR proteins is similar to that found in the ATPase component of the magnesium chelatase complexes, possibly suggesting a similar mechanism of function. In this review, we provide an overview of the newly identified functions and the newly obtained structures of MoxR AAA+ ATPases.
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