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Gaspar JP, Takahashi MB, Teixeira AF, Nascimento ALTO. In silico analysis and functional characterization of a leucine-rich repeat protein of Leptospira interrogans. Int J Med Microbiol 2024; 316:151633. [PMID: 39232290 DOI: 10.1016/j.ijmm.2024.151633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024] Open
Abstract
Pathogenic spirochetes of the genus Leptospira are the causative agent of leptospirosis, a widely disseminated zoonosis that affects humans and animals. The ability of leptospires to quickly cross host barriers causing infection is not yet fully understood. Thus, understanding the mechanisms of pathogenicity is important to combat leptospiral infection. Outer membrane proteins are interesting targets to study as they are able to interact with host molecules. Proteins containing leucine-rich repeat (LRR) domains are characterized by the presence of multiple regions containing leucine residues and they have putative functions related to host-pathogen interactions. Hence, the present study aimed to clone and express the recombinant protein encoded by the LIC11098 gene, an LRR protein of L. interrogans serovar Copenhageni. In silico analyses predicted that the target protein is conserved among pathogenic strains of Leptospira, having a signal peptide and multiple LRR domains. The DNA sequence encoding the LRR protein was cloned in frame into the pAE vector, expressed without mutations in Escherichia coli and purified by His-tag chromatography. Circular dichroism (CD) spectrum showed that the recombinant protein was predominantly composed of β-sheets. A dose-dependent interaction was observed with cellular and plasma fibronectins, laminin and the complement system component C9, suggesting a possible role of the protein encoded by LIC11098 gene at the initial stages of infection.
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Affiliation(s)
- João P Gaspar
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, São Paulo, SP, Brazil; Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, SP, Brazil
| | - Maria B Takahashi
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, São Paulo, SP, Brazil
| | - Aline F Teixeira
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, São Paulo, SP, Brazil
| | - Ana L T O Nascimento
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, São Paulo, SP, Brazil.
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2
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Surdel MC, Coburn J. Leptospiral adhesins: from identification to future perspectives. Front Microbiol 2024; 15:1458655. [PMID: 39206373 PMCID: PMC11350617 DOI: 10.3389/fmicb.2024.1458655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Leptospirosis is a significant zoonosis worldwide, with disease severity ranging from a mild non-specific illness to multi-organ dysfunction and hemorrhage. The disease is caused by pathogenic bacteria of the genus Leptospira, which are classified into pathogenic and saprophytic clades. Bacterial binding to host molecules and cells, coordinated by adhesin proteins, is an important step in pathogenesis. While many leptospiral adhesins have been identified, the vast majority have not been characterized in vivo. Herein, we present an overview of the current methodologies and successes in identifying adhesins in Leptospira, including known biological roles in vivo. We will also identify and discuss potential areas for future research.
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Affiliation(s)
- Matthew C. Surdel
- Division of Infectious Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jenifer Coburn
- Division of Infectious Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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3
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Hsu SH, Wu CT, Sun YJ, Chang MY, Li C, Ko YC, Chou LF, Yang CW. Crystal structure of Leptospira LSS_01692 reveals a dimeric structure and induces inflammatory responses through Toll-like receptor 2-dependent NF-κB and MAPK signal transduction pathways. FEBS J 2023; 290:4513-4532. [PMID: 37243454 DOI: 10.1111/febs.16874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/12/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023]
Abstract
Leptospirosis is a commonly overlooked zoonotic disease that occurs in tropical and subtropical regions. Recent studies have divided the Leptospira spp. into three groups based on virulence, including pathogenic, intermediate, and saprophytic species. Pathogenic species express a protein family with leucine-rich repeat (LRR) domains, which are less expressed or absent in nonpathogenic species, highlighting the importance of this protein family in leptospirosis. However, the role of LRR domain proteins in the pathogenesis of leptospirosis is still unknown and requires further investigation. In this study, the 3D structure of LSS_01692 (rLRR38) was obtained using X-ray crystallography at a resolution of 3.2 Å. The results showed that rLRR38 forms a typical horseshoe structure with 11 α-helices and 11 β-sheets and an antiparallel dimeric structure. The interactions of rLRR38 with extracellular matrix and cell surface receptors were evaluated using ELISA and single-molecule atomic force microscopy. The results showed that rLRR38 interacted with fibronectin, collagen IV, and Toll-like receptor 2 (TLR2). Incubating HK2 cells with rLRR38 induced two downstream inflammation responses (IL-6 and MCP-1) in the TLR2 signal transduction pathway. The TLR2-TLR1 complex showed the most significant upregulation effects under rLRR38 treatment. Inhibitors also significantly inhibited nuclear factor κB and mitogen-activated protein kinases signals transduction under rLRR38 stimulation. In conclusion, rLRR38 was determined to be a novel LRR domain protein in 3D structure and demonstrated as a TLR2-binding protein that induces inflammatory responses. These structural and functional studies provide a deeper understanding of the pathogenesis of leptospirosis.
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Affiliation(s)
- Shen-Hsing Hsu
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Che-Ting Wu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
| | - Yuh-Ju Sun
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
| | - Ming-Yang Chang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chien Li
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ching Ko
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Li-Fang Chou
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chih-Wei Yang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
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4
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Chawla U, Chopra D. Structural Advancement in Shoc2‐MAPK Signaling Pathways in the Treatment of Cancer and Other Diseases. ChemistrySelect 2022. [DOI: 10.1002/slct.202203791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Udeep Chawla
- Innovation and Incubation Centre for Entrepreneurship Indian Institute of Science Education and Research Bhopal Bhopal 462066 Madhya Pradesh India
- The University of Arizona, Department of Chemistry and Biochemistry Tucson AZ85721 United States
| | - Deepak Chopra
- Innovation and Incubation Centre for Entrepreneurship Indian Institute of Science Education and Research Bhopal Bhopal 462066 Madhya Pradesh India
- Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal 462066 Madhya Pradesh India
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5
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Leptospiral Leucine-Rich Repeat Protein-Based Lateral Flow for Assessment of Canine Leptospiral Immunoglobulin G. Trop Med Infect Dis 2022; 7:tropicalmed7120427. [PMID: 36548682 PMCID: PMC9787837 DOI: 10.3390/tropicalmed7120427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
The recombinant, modified leucine-rich repeat protein rhKU_Sej_LRR_2271 has been suggested as a candidate for leptospiral vaccine development since it was predicted to be a transmembrane protein containing leucine-rich repeat motifs and immunogenic epitopes. The immunogenic epitopes showed binding affinities with lower IC50 values than peptides of known antigenic proteins, e.g., LipL32. Moreover, this protein was immunoreactive with hyperimmune sera against several serovars. In this study, we aimed to develop a lateral flow strip test using the rhKU_Sej_LRR_2271 protein for the detection of anti-leptospiral IgG in dogs. The lateral flow assay was performed with 184 dog plasma samples and evaluated with a culture method, 16S ribosomal RNA gene (rss) analysis real-time PCR, and LipL32 ELISA. The culture method failed to detect leptospires in the dog blood samples. Six of nine symptomatic dogs gave positive results with the real-time PCR assay. The lateral flow assay and LipL32 ELISA gave positive results with 59 and 50 dogs, respectively. The sensitivity, specificity, and accuracy of the rhKU_Sej_LRR_2271 lateral flow strip test were 70.00, 82.09, and 78.80%, respectively, when compared with LipL32 ELISA. There was a significant association between the LipL32 ELISA and the rhKU_Sej_LRR_2271 lateral flow assay. The rhKU_Sej_LRR_2271 lateral flow strip test has therefore demonstrated a good potential to detect anti-leptospiral IgG in dogs.
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Matsushima N, Kretsinger RH. Numerous variants of leucine rich repeats in proteins from nucleo-cytoplasmic large DNA viruses. Gene X 2022; 817:146156. [PMID: 35032616 DOI: 10.1016/j.gene.2021.146156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/15/2021] [Indexed: 11/04/2022] Open
Abstract
Leucine rich repeats (LRRs) occurring in tandem are 20-29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species. Directly before, metagenome data of nucleo-cytoplasmic large dsDNA viruses (NCLDVs) have been published; the 2,074 NCLDVs encode 199,021 proteins. From the NCLDVs 547 LRR proteins were identified and 502 were used for analysis. Various variants of known LRR types were identified in viral LRRs. A comprehensive analysis of TpLRR and FNIP that belong to an LRR type was first performed. The repeating unit lengths (RULs) in five types are 19 residues which is the shortest among all LRRs. The RULs of eight LRR types including FNIP are one to five residues shorter than those of the known, corresponding LRR types. The conserved hydrophobic residues such as Leu, Val or Ile in the consensus sequences are frequently substituted by cysteine at one or two positions. Four unique LRR motifs that are different from those identified previously are observed. The present study enhances the previous result. An evolutionary scenario of short or unique LRR was discussed.
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Affiliation(s)
- Norio Matsushima
- Division of Bioinformatics, Institute of Tandem Repeats, Noboribetsu 059-0464, Japan; Center for Medical Education, Sapporo Medical University, Sapporo 060-8556, Japan.
| | - Robert H Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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7
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Hsu SH, Yang CW. Insight into the Structure, Functions, and Dynamics of the Leptospira Outer Membrane Proteins with the Pathogenicity. MEMBRANES 2022; 12:membranes12030300. [PMID: 35323775 PMCID: PMC8951592 DOI: 10.3390/membranes12030300] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 02/01/2023]
Abstract
Leptospirosis is a widespread zoonosis that frequently occurs in tropical and subtropical countries. Leptospira enters the host through wounds or mucous membranes and spreads to the whole body through the blood, causing systemic infection. Kidneys are the preferential site where Leptospira accumulates, especially in the renal interstitium and renal tubule epithelial cells. Clinical symptoms in humans include high fever, jaundice, renal failure, and severe multiple-organ failure (Weil’s syndrome). Surface-exposed antigens are located at the outermost layer of Leptospira and these potential virulence factors are likely involved in primary host-pathogen interactions, adhesion, and/or invasion. Using the knockout/knockdown techniques to the evaluation of pathogenicity in the virulence factor are the most direct and effective methods and many virulence factors are evaluated including lipopolysaccharides (LPS), Leptospira lipoprotein 32 (LipL32), Leptospira ompA domain protein 22 (Loa22), LipL41, LipL71, Leptospira immunoglobulin-like repeat A (LigA), LigB, and LipL21. In this review, we will discuss the structure, functions, and dynamics of these virulence factors and the roles of these virulence factors in Leptospira pathogenicity. In addition, a protein family with special Leucine-rich repeat (LRR) will also be discussed for their vital role in Leptospira pathogenicity. Finally, these surface-exposed antigens are discussed in the application of the diagnosis target for leptospirosis and compared with the serum microscope agglutination test (MAT), the gold standard for leptospirosis.
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Coburn J, Picardeau M, Woods CW, Veldman T, Haake DA. Pathogenesis insights from an ancient and ubiquitous spirochete. PLoS Pathog 2021; 17:e1009836. [PMID: 34673833 PMCID: PMC8530280 DOI: 10.1371/journal.ppat.1009836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jenifer Coburn
- Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | | | - Christopher W. Woods
- Duke University Medical Center, Durham, North Carolina, United States of America
- Durham VA Medical Center, Durham, North Carolina, United States of America
| | - Timothy Veldman
- Duke University Medical Center, Durham, North Carolina, United States of America
| | - David A. Haake
- VA Greater Los Angeles Healthcare System, Los Angeles, California, United States of America
- The David Geffen School of Medicine at the University of California, Los Angeles, California, United States of America
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9
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Chen Y, Khazina E, Izaurralde E, Weichenrieder O. Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex. Nucleic Acids Res 2021; 49:6489-6510. [PMID: 34038562 PMCID: PMC8216464 DOI: 10.1093/nar/gkab414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 01/07/2023] Open
Abstract
The CCR4 and CAF1 deadenylases physically interact to form the CCR4-CAF1 complex and function as the catalytic core of the larger CCR4-NOT complex. Together, they are responsible for the eventual removal of the 3′-poly(A) tail from essentially all cellular mRNAs and consequently play a central role in the posttranscriptional regulation of gene expression. The individual properties of CCR4 and CAF1, however, and their respective contributions in different organisms and cellular environments are incompletely understood. Here, we determined the crystal structure of a human CCR4-CAF1 complex and characterized its enzymatic and substrate recognition properties. The structure reveals specific molecular details affecting RNA binding and hydrolysis, and confirms the CCR4 nuclease domain to be tethered flexibly with a considerable distance between both enzyme active sites. CCR4 and CAF1 sense nucleotide identity on both sides of the 3′-terminal phosphate, efficiently differentiating between single and consecutive non-A residues. In comparison to CCR4, CAF1 emerges as a surprisingly tunable enzyme, highly sensitive to pH, magnesium and zinc ions, and possibly allowing distinct reaction geometries. Our results support a picture of CAF1 as a primordial deadenylase, which gets assisted by CCR4 for better efficiency and by the assembled NOT proteins for selective mRNA targeting and regulation.
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Affiliation(s)
- Ying Chen
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
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10
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Fukuda K, Lu F, Qin J. Molecular basis for Ras suppressor-1 binding to PINCH-1 in focal adhesion assembly. J Biol Chem 2021; 296:100685. [PMID: 33891945 PMCID: PMC8141872 DOI: 10.1016/j.jbc.2021.100685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 10/29/2022] Open
Abstract
Ras suppressor-1 (Rsu-1) is a leucine-rich repeat (LRR)-containing protein that is crucial for regulating cell adhesion and is involved in such physiological and pathological processes as focal adhesion assembly and tumor metastasis. Rsu-1 interacts with zinc-finger type multi-LIM domain-containing adaptor protein PINCH-1, known to be involved in the integrin-mediated consensus adhesome, but not with its highly homologous family member PINCH-2. However, the structural basis for and regulatory mechanisms of this specific interaction remain unclear. Here, we determined the crystal structures of Rsu-1 and its complex with the PINCH-1 LIM4-5 domains. Rsu-1 displays an arc-shaped solenoid architecture, with eight LRRs shielded by N- and C-terminal capping modules. We showed that the conserved concave surface of the Rsu-1 LRR domain binds and stabilizes the PINCH-1 LIM5 domain via salt bridge and hydrophobic interactions, while the C-terminal non-LIM region of PINCH-2 sterically disfavors Rsu-1 binding. We also showed that Rsu-1 can be assembled, via PINCH-1-binding, into a heteropentamer complex comprising Rsu-1, PINCH-1, ILK, Parvin, and Kindlin-2, which constitute a major consensus integrin adhesome crucial for focal adhesion assembly. Our mutagenesis and cell biological data emphasize the significance of the Rsu-1/PINCH-1 interaction in focal adhesion assembly and cell spreading, providing crucial molecular insights into Rsu-1-mediated cell adhesion with implications for disease development.
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Affiliation(s)
- Koichi Fukuda
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA
| | - Fan Lu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jun Qin
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
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11
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Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses. Arch Virol 2020; 166:43-64. [PMID: 33052487 DOI: 10.1007/s00705-020-04820-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
Leucine-rich repeats (LRRs) are present in over 563,000 proteins from viruses to eukaryotes. LRRs repeat in tandem and have been classified into fifteen classes in which the repeat unit lengths range from 20 to 29 residues. Most LRR proteins are involved in protein-protein or ligand interactions. The amount of genome sequence data from viruses is increasing rapidly, and although viral LRR proteins have been identified, a comprehensive sequence analysis has not yet been done, and their structures, functions, and evolution are still unknown. In the present study, we characterized viral LRRs by sequence analysis and identified over 600 LRR proteins from 89 virus species. Most of these proteins were from double-stranded DNA (dsDNA) viruses, including nucleocytoplasmic large dsDNA viruses (NCLDVs). We found that the repeating unit lengths of 11 types are one to five residues shorter than those of the seven known corresponding LRR classes. The repeating units of six types are 19 residues long and are thus the shortest among all LRRs. In addition, two of the LRR types are unique and have not been observed in bacteria, archae or eukaryotes. Conserved strongly hydrophobic residues such as Leu, Val or Ile in the consensus sequences are replaced by Cys with high frequency. Phylogenetic analysis indicated that horizontal gene transfer of some viral LRR genes had occurred between the virus and its host. We suggest that the shortening might contribute to the survival strategy of viruses. The present findings provide a new perspective on the origin and evolution of LRRs.
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12
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Merski M, Młynarczyk K, Ludwiczak J, Skrzeczkowski J, Dunin-Horkawicz S, Górna MW. Self-analysis of repeat proteins reveals evolutionarily conserved patterns. BMC Bioinformatics 2020; 21:179. [PMID: 32381046 PMCID: PMC7204011 DOI: 10.1186/s12859-020-3493-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/15/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution. We noted that the patterns derived from traditional "dot plot" protein sequence self-similarity analysis tended to be conserved in sets of related repeat proteins and this conservation could be quantitated using a Jaccard metric. RESULTS Comparison of these dot plots obviated the issues due to sequence similarity for analysis of repeat proteins. A high Jaccard similarity score was suggestive of a conserved relationship between closely related repeat proteins. The dot plot patterns decayed quickly in the absence of selective pressure with an expected loss of 50% of Jaccard similarity due to a loss of 8.2% sequence identity. To perform method testing, we assembled a standard set of 79 repeat proteins representing all the subgroups in RepeatsDB. Comparison of known repeat and non-repeat proteins from the PDB suggested that the information content in dot plots could be used to identify repeat proteins from pure sequence with no requirement for structural information. Analysis of the UniRef90 database suggested that 16.9% of all known proteins could be classified as repeat proteins. These 13.3 million putative repeat protein chains were clustered and a significant amount (82.9%) of clusters containing between 5 and 200 members were of a single functional type. CONCLUSIONS Dot plot analysis of repeat proteins attempts to obviate issues that arise due to the sequence degeneracy of repeat proteins. These results show that this kind of analysis can efficiently be applied to analyze repeat proteins on a large scale.
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Affiliation(s)
- Matthew Merski
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Krzysztof Młynarczyk
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Jakub Skrzeczkowski
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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13
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Batkhishig D, Enkhbayar P, Kretsinger RH, Matsushima N. A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats. Proteins 2020; 88:840-852. [DOI: 10.1002/prot.25876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/03/2020] [Accepted: 01/25/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dashdavaa Batkhishig
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied SciencesNational University of Mongolia Ulaanbaatar Mongolia
- Department of Physics, School of Mathematics and Natural SciencesMongolian National University of Education Ulaanbaatar Mongolia
| | - Purevjav Enkhbayar
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied SciencesNational University of Mongolia Ulaanbaatar Mongolia
| | | | - Norio Matsushima
- Division of Bioinformatics, Institute of Tandem Repeats Noboribetsu Japan
- Center for Medical Education, Sapporo Medical University Sapporo Japan
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14
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Baudin M, Schreiber KJ, Martin EC, Petrescu AJ, Lewis JD. Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:352-370. [PMID: 31557357 DOI: 10.1111/tpj.14547] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 05/26/2023]
Abstract
NLR (nucleotide-binding [NB] leucine-rich repeat [LRR] receptor) proteins are critical for inducing immune responses in response to pathogen proteins, and must be tightly modulated to prevent spurious activation in the absence of a pathogen. The ZAR1 NLR recognizes diverse effector proteins from Pseudomonas syringae, including HopZ1a, and Xanthomonas species. Receptor-like cytoplasmic kinases (RLCKs) such as ZED1, interact with ZAR1 and provide specificity for different effector proteins, such as HopZ1a. We previously developed a transient expression system in Nicotiana benthamiana that allowed us to demonstrate that ZAR1 function is conserved from the Brassicaceae to the Solanaceae. Here, we combined structural modelling of ZAR1, with molecular and functional assays in our transient system, to show that multiple intramolecular and intermolecular interactions modulate ZAR1 activity. We identified determinants required for the formation of the ZARCC oligomer and its activity. Lastly, we characterized intramolecular interactions between ZAR1 subdomains that participate in keeping ZAR1 immune complexes inactive. This work identifies molecular constraints on immune receptor function and activation.
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Affiliation(s)
- Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Karl J Schreiber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Andrei J Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, USA
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15
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Burdett H, Bentham AR, Williams SJ, Dodds PN, Anderson PA, Banfield MJ, Kobe B. The Plant "Resistosome": Structural Insights into Immune Signaling. Cell Host Microbe 2019; 26:193-201. [PMID: 31415752 DOI: 10.1016/j.chom.2019.07.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plant innate immunity is triggered via direct or indirect recognition of pathogen effectors by the NLR family immune receptors. Mechanistic understanding of plant NLR function has relied on structural information from individual NLR domains and inferences from studies on animal NLRs. Recent reports of the cryo-EM structures of the Arabidopsis plant immune receptor ZAR1 in monomeric inactive and transition states, as well as the active oligomeric state or the "resistosome," have afforded a quantum leap in our understanding of how plant NLRs function. In this Review, we outline the recent structural findings and examine their implications for the activation of plant immune receptors more broadly. We also discuss how NLR signaling in plants, as illustrated by the ZAR1 structure, is analogous to innate immune receptor signaling mechanisms across kingdoms, drawing particular attention to the concept of signaling by cooperative assembly formation.
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Affiliation(s)
- Hayden Burdett
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Adam R Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra 2601, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Peter A Anderson
- College of Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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16
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Matsushima N, Takatsuka S, Miyashita H, Kretsinger RH. Leucine Rich Repeat Proteins: Sequences, Mutations, Structures and Diseases. Protein Pept Lett 2019; 26:108-131. [PMID: 30526451 DOI: 10.2174/0929866526666181208170027] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/18/2022]
Abstract
Mutations in the genes encoding Leucine Rich Repeat (LRR) containing proteins are associated with over sixty human diseases; these include high myopia, mitochondrial encephalomyopathy, and Crohn's disease. These mutations occur frequently within the LRR domains and within the regions that shield the hydrophobic core of the LRR domain. The amino acid sequences of fifty-five LRR proteins have been published. They include Nod-Like Receptors (NLRs) such as NLRP1, NLRP3, NLRP14, and Nod-2, Small Leucine Rich Repeat Proteoglycans (SLRPs) such as keratocan, lumican, fibromodulin, PRELP, biglycan, and nyctalopin, and F-box/LRR-repeat proteins such as FBXL2, FBXL4, and FBXL12. For example, 363 missense mutations have been identified. Replacement of arginine, proline, or cysteine by another amino acid, or the reverse, is frequently observed. The diverse effects of the mutations are discussed based on the known structures of LRR proteins. These mutations influence protein folding, aggregation, oligomerization, stability, protein-ligand interactions, disulfide bond formation, and glycosylation. Most of the mutations cause loss of function and a few, gain of function.
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Affiliation(s)
- Norio Matsushima
- Center for Medical Education, Sapporo Medical University, Sapporo 060-8556, Japan.,Institute of Tandem Repeats, Noboribetsu 059-0464, Japan
| | - Shintaro Takatsuka
- Center for Medical Education, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Hiroki Miyashita
- Institute of Tandem Repeats, Noboribetsu 059-0464, Japan.,Hokubu Rinsho Co., Ltd, Sapporo 060-0061, Japan
| | - Robert H Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, United States
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17
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Eshghi A, Gaultney RA, England P, Brûlé S, Miras I, Sato H, Coburn J, Bellalou J, Moriarty TJ, Haouz A, Picardeau M. An extracellular Leptospira interrogans leucine-rich repeat protein binds human E- and VE-cadherins. Cell Microbiol 2018; 21:e12949. [PMID: 30171791 DOI: 10.1111/cmi.12949] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/20/2018] [Accepted: 08/24/2018] [Indexed: 01/07/2023]
Abstract
Pathogenic Leptospira bacteria are the causative agents of leptospirosis, a zoonotic disease affecting animals and humans worldwide. These pathogenic species have the ability to rapidly cross host tissue barriers by a yet unknown mechanism. A comparative analysis of pathogens and saprophytes revealed a higher abundance of genes encoding proteins with leucine-rich repeat (LRR) domains in the genomes of pathogens. In other bacterial pathogens, proteins with LRR domains have been shown to be involved in mediating host cell attachment and invasion. One protein from the pathogenic species Leptospira interrogans, LIC10831, has been previously analysed via X-ray crystallography, with findings suggesting it may be an important bacterial adhesin. Herein we show that LIC10831 elicits an antibody response in infected animals, is actively secreted by the bacterium, and binds human E- and VE-cadherins. These results provide biochemical and cellular evidences of LRR protein-mediated host-pathogen interactions and identify a new multireceptor binding protein from this infectious Leptospira species.
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Affiliation(s)
- Azad Eshghi
- Unité de Biologie des Spirochètes, Institut Pasteur, Paris, France.,University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | | | - Patrick England
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Sébastien Brûlé
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Isabelle Miras
- Plate-forme de Cristallographie, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Hiromi Sato
- Center for Infectious Disease Research, Department of Medicine (Division of Infectious Diseases), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jenifer Coburn
- Center for Infectious Disease Research, Department of Medicine (Division of Infectious Diseases), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jacques Bellalou
- Plate-forme de Protéines Recombinantes, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Tara J Moriarty
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Faculty of Medicine (Department of Laboratory Medicine and Pathobiology), University of Toronto, Toronto, Ontario, Canada
| | - Ahmed Haouz
- Plate-forme de Cristallographie, Institut Pasteur, CNRS-UMR 3528, Paris, France
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18
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Adhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Front Cell Infect Microbiol 2018; 8:45. [PMID: 29600195 PMCID: PMC5863495 DOI: 10.3389/fcimb.2018.00045] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/08/2018] [Indexed: 11/17/2022] Open
Abstract
Leptospirosis is an emerging zoonotic disease with more than 1 million cases annually. Currently there is lack of evidence for signaling pathways involved during the infection process of Leptospira. In our comprehensive genomic analysis of 20 Leptospira spp. we identified seven pathogen-specific Two-Component System (TCS) proteins. Disruption of two these TCS genes in pathogenic Leptospira strain resulted in loss-of-virulence in a hamster model of leptospirosis. Corresponding genes lvrA and lvrB (leptospira virulence regulator) are juxtaposed in an operon and are predicted to encode a hybrid histidine kinase and a hybrid response regulator, respectively. Transcriptome analysis of lvr mutant strains with disruption of one (lvrB) or both genes (lvrA/B) revealed global transcriptional regulation of 850 differentially expressed genes. Phosphotransfer assays demonstrated that LvrA phosphorylates LvrB and predicted further signaling downstream to one or more DNA-binding response regulators, suggesting that it is a branched pathway. Phylogenetic analyses indicated that lvrA and lvrB evolved independently within different ecological lineages in Leptospira via gene duplication. This study uncovers a novel-signaling pathway that regulates virulence in pathogenic Leptospira (Lvr), providing a framework to understand the molecular bases of regulation in this life-threatening bacterium.
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Affiliation(s)
- Haritha Adhikarla
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Ariel E Mechaly
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Sameet Mehta
- Yale Centre for Genome Analysis, West Haven, CT, United States
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Luciane Santos
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.,Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, Brazil
| | - Vimla Bisht
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Peter Diggle
- Lancaster Medical School, Lancaster, United Kingdom
| | - Gerald Murray
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ben Adler
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, VIC, Australia
| | - Francesc Lopez
- Yale Centre for Genome Analysis, West Haven, CT, United States
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Eduardo Groisman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, United States
| | | | - Alejandro Buschiazzo
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Department of Microbiology, Institut Pasteur, Paris, France
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.,Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, Brazil
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19
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Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G. DIALS: implementation and evaluation of a new integration package. Acta Crystallogr D Struct Biol 2018; 74:85-97. [PMID: 29533234 PMCID: PMC5947772 DOI: 10.1107/s2059798317017235] [Citation(s) in RCA: 686] [Impact Index Per Article: 114.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/30/2017] [Indexed: 01/07/2023] Open
Abstract
The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.
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Affiliation(s)
- Graeme Winter
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - David G. Waterman
- STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - James M. Parkhurst
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Aaron S. Brewster
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Richard J. Gildea
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Markus Gerstel
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Luis Fuentes-Montero
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Melanie Vollmar
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tara Michels-Clark
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Iris D. Young
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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20
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Ghazaei C. Pathogenic Leptospira: Advances in understanding the molecular pathogenesis and virulence. Open Vet J 2018; 8:13-24. [PMID: 29445617 PMCID: PMC5806663 DOI: 10.4314/ovj.v8i1.4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/08/2018] [Indexed: 12/16/2022] Open
Abstract
Leptospirosis is a common zoonotic disease has emerged as a major public health problem, with developing countries bearing disproportionate burdens. Although the diverse range of clinical manifestations of the leptospirosis in humans is widely documented, the mechanisms through which the pathogen causes disease remain undetermined. In addition, leptospirosis is a much-neglected life-threatening disease although it is one of the most important zoonoses occurring in a diverse range of epidemiological distribution. Recent advances in molecular profiling of pathogenic species of the genus Leptospira have improved our understanding of the evolutionary factors that determine virulence and mechanisms that the bacteria employ to survive. However, a major impediment to the formulation of intervention strategies has been the limited understanding of the disease determinants. Consequently, the association of the biological mechanisms to the pathogenesis of Leptospira, as well as the functions of numerous essential virulence factors still remain implicit. This review examines recent advances in genetic screening technologies, the underlying microbiological processes, the virulence factors and associated molecular mechanisms driving pathogenesis of Leptospira species.
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Affiliation(s)
- Ciamak Ghazaei
- Department of Microbiology, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil, Iran
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