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Batarseh TN, Batarseh SN, Morales-Cruz A, Gaut BS. Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history. Front Microbiol 2023; 14:1206094. [PMID: 37434713 PMCID: PMC10330825 DOI: 10.3389/fmicb.2023.1206094] [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: 04/14/2023] [Accepted: 06/09/2023] [Indexed: 07/13/2023] Open
Abstract
'Candidatus Liberibacter' is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the 'Ca. Liberibacter solanacearum' species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the 'Ca. L. capsica' species based on high values of dN.
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Affiliation(s)
| | - Sarah N. Batarseh
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, United States
| | - Abraham Morales-Cruz
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, United States
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2
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Martin M, Newton ILG. The Wolbachia WalE1 effector alters Drosophila endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530160. [PMID: 36909520 PMCID: PMC10002650 DOI: 10.1101/2023.02.26.530160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most common intracellular bacterial infection is Wolbachia pipientis, a microbe that manipulates host reproduction and is used in control of insect vectors. Phenotypes induced by Wolbachia have been studied for decades and range from sperm-egg incompatibility to male killing. How Wolbachia alters host biology is less well understood. Previously, we characterized the first Wolbachia effector - WalE1, which encodes a synuclein domain at the N terminus. Purified WalE1 sediments with and bundles actin and when heterologously expressed in flies, increases Wolbachia titer in the developing oocyte. In this work, we first identify the native expression WalE1 by Wolbachia infecting both fly cells and whole animals. WalE1 appears as aggregates, separate from Wolbachia cells. We next show that WalE1 co-immunoprecipitates with the host protein Past1 and that WalE1 manipulates host endocytosis. Yeast expressing WalE1 show deficiency in uptake of FM4-64 dye, and flies harboring mutations in Past1 or overexpressing WalE1 are sensitive to AgNO3, a hallmark of endocytosis defects. Finally, we also show that Past1 null flies harbor more Wolbachia overall and in late egg chambers. Our results identify interactions between a Wolbachia secreted effector and a host protein and point to yet another important host cell process impinged upon by Wolbachia.
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Affiliation(s)
- MaryAnn Martin
- Department of Biology, Indiana University, Bloomington, IN USA
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3
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Kong F, Yang L. Pathogen-triggered changes in plant development: Virulence strategies or host defense mechanism? Front Microbiol 2023; 14:1122947. [PMID: 36876088 PMCID: PMC9975269 DOI: 10.3389/fmicb.2023.1122947] [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: 12/13/2022] [Accepted: 01/25/2023] [Indexed: 02/17/2023] Open
Abstract
Plants, as sessile organisms, are constantly exposed to pathogens in nature. Plants rely on physical barriers, constitutive chemical defenses, and sophisticated inducible immunity to fight against pathogens. The output of these defense strategies is highly associated with host development and morphology. Successful pathogens utilize various virulence strategies to colonize, retrieve nutrients, and cause disease. In addition to the overall defense-growth balance, the host-pathogen interactions often lead to changes in the development of specific tissues/organs. In this review, we focus on recent advances in understanding the molecular mechanisms of pathogen-induced changes in plants' development. We discuss that changes in host development could be a target of pathogen virulence strategies or an active defense strategy of plants. Current and ongoing research about how pathogens shape plant development to increase their virulence and causes diseases could give us novel views on plant disease control.
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Affiliation(s)
- Feng Kong
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Li Yang
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
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4
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CrkII/Abl phosphorylation cascade is critical for NLRC4 inflammasome activity and is blocked by Pseudomonas aeruginosa ExoT. Nat Commun 2022; 13:1295. [PMID: 35277504 PMCID: PMC8917168 DOI: 10.1038/s41467-022-28967-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
Type 3 Secretion System (T3SS) is a highly conserved virulence structure that plays an essential role in the pathogenesis of many Gram-negative pathogenic bacteria, including Pseudomonas aeruginosa. Exotoxin T (ExoT) is the only T3SS effector protein that is expressed in all T3SS-expressing P. aeruginosa strains. Here we show that T3SS recognition leads to a rapid phosphorylation cascade involving Abl / PKCδ / NLRC4, which results in NLRC4 inflammasome activation, culminating in inflammatory responses that limit P. aeruginosa infection in wounds. We further show that ExoT functions as the main anti-inflammatory agent for P. aeruginosa in that it blocks the phosphorylation cascade through Abl / PKCδ / NLRC4 by targeting CrkII, which we further demonstrate to be important for Abl transactivation and NLRC4 inflammasome activation in response to T3SS and P. aeruginosa infection. Pseudomonas aeruginosa secretes the toxin ExoT, which is important for pathogenesis. Here, the authors show that ExoT inhibits NLRC4-dependent inflammatory responses during wound infection.
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5
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Zhang J, Zhou M, Liu W, Nie J, Huang L. Pseudomonas syringae pv. actinidiae Effector HopAU1 Interacts with Calcium-Sensing Receptor to Activate Plant Immunity. Int J Mol Sci 2022; 23:508. [PMID: 35008934 PMCID: PMC8745740 DOI: 10.3390/ijms23010508] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/01/2023] Open
Abstract
Kiwifruit canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is a destructive pathogen that globally threatens the kiwifruit industry. Understanding the molecular mechanism of plant-pathogen interaction can accelerate applying resistance breeding and controlling plant diseases. All known effectors secreted by pathogens play an important role in plant-pathogen interaction. However, the effectors in Psa and their function mechanism remain largely unclear. Here, we successfully identified a T3SS effector HopAU1 which had no virulence contribution to Psa, but could, however, induce cell death and activate a series of immune responses by agroinfiltration in Nicotiana benthamiana, including elevated transcripts of immune-related genes, accumulation of reactive oxygen species (ROS), and callose deposition. We found that HopAU1 interacted with a calcium sensing receptor in N. benthamiana (NbCaS) as well as its close homologue in kiwifruit (AcCaS). More importantly, silencing CaS by RNAi in N. benthamiana greatly attenuated HopAU1-triggered cell death, suggesting CaS is a crucial component for HopAU1 detection. Further researches showed that overexpression of NbCaS in N. benthamiana significantly enhanced plant resistance against Sclerotinia sclerotiorum and Phytophthora capsici, indicating that CaS serves as a promising resistance-related gene for disease resistance breeding. We concluded that HopAU1 is an immune elicitor that targets CaS to trigger plant immunity.
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Affiliation(s)
| | | | | | | | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (J.Z.); (M.Z.); (W.L.); (J.N.)
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6
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Abstract
Despite the maintenance of YopP/J alleles throughout the human-pathogenic Yersinia lineage, the benefit of YopP/J-induced phagocyte death for Yersinia pathogenesis in animals is not obvious. To determine how the sequence divergence of YopP/J has impacted Yersinia virulence, we examined protein polymorphisms in this type III secreted effector protein across 17 Yersinia species and tested the consequences of polymorphism in a murine model of subacute systemic yersiniosis. Our evolutionary analysis revealed that codon 177 has been subjected to positive selection; the Yersinia enterocolitica residue had been altered from a leucine to a phenylalanine in nearly all Yersinia pseudotuberculosis and Yersinia pestis strains examined. Despite this change being minor, as both leucine and phenylalanine have hydrophobic side chains, reversion of YopJF177 to the ancestral YopJL177 variant yielded a Y. pseudotuberculosis strain with enhanced cytotoxicity toward macrophages, consistent with previous findings. Surprisingly, expression of YopJF177L in the mildly attenuated ksgA- background rendered the strain completely avirulent in mice. Consistent with this hypothesis that YopJ activity relates indirectly to Yersinia pathogenesis in vivo, ksgA- strains lacking functional YopJ failed to kill macrophages but actually regained virulence in animals. Also, treatment with the antiapoptosis drug suramin prevented YopJ-mediated macrophage cytotoxicity and enhanced Y. pseudotuberculosis virulence in vivo. Our results demonstrate that Yersinia-induced cell death is detrimental for bacterial pathogenesis in this animal model of illness and indicate that positive selection has driven YopJ/P and Yersinia evolution toward diminished cytotoxicity and increased virulence, respectively.
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7
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" Candidatus Liberibacter asiaticus" Secretes Nonclassically Secreted Proteins That Suppress Host Hypersensitive Cell Death and Induce Expression of Plant Pathogenesis-Related Proteins. Appl Environ Microbiol 2021; 87:AEM.00019-21. [PMID: 33579681 PMCID: PMC8091116 DOI: 10.1128/aem.00019-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although emerging evidence indicates that bacteria extracellularly export many cytoplasmic proteins referred to as non-classically secreted proteins (ncSecPs) for their own benefit, the mechanisms and functional significance of the ncSecPs in extracellular milieu remain elusive. "Candidatus Liberibacter asiaticus" (CLas) is a fastidious Gram-negative bacterium that causes Huanglongbing (HLB), the most globally devastating citrus disease. In this study, using the SecretomeP program coupled with an Escherichia coli alkaline phosphatase assay, we identified 27 ncSecPs from the CLas genome. Further, we demonstrated that 10 of these exhibited significantly higher levels of gene expression in citrus than in psyllid hosts, and particularly suppressed hypersensitive response (HR)-based cell death and H2O2 overaccumulation in Nicotiana benthamiana, indicating their opposing effects on early plant defenses. However, these proteins also dramatically enhanced the gene expression of pathogenesis-related 1 protein (PR-1), PR-2, and PR-5, essential components of plant defense mechanisms. Additional experiments disclosed that the increased expression of these PR genes, in particular PR-1 and PR-5, could negatively regulate HR-based cell death development and H2O2 accumulation. Remarkably, CLas infection clearly induced gene expression of PR-1, PR-2, and PR-5 in both HLB-tolerant and HLB-susceptible species of citrus plants. Taken together, we hypothesized that CLas has evolved an arsenal of ncSecPs that function cooperatively to overwhelm the early plant defenses by inducing host PR genes.IMPORTANCE In this study, we present a combined computational and experimental methodology that allows a rapid and efficient identification of the ncSecPs from bacteria, in particular the unculturable bacteria like CLas. Meanwhile, the study determined that a number of CLas ncSecPs suppressed HR-based cell death, and thus indicated a novel role for the bacterial ncSecPs in extracellular milieu. More importantly, these ncSecPs were found to suppress cell death presumably by utilizing host PR proteins. The data overall provide a novel clue to understand the CLas pathogenesis and also suggest a new way by which phytopathogens manipulate host cellular machinery to establish infection.
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8
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Zhang WB, Yan HL, Zhu ZC, Zhang C, Du PX, Zhao WJ, Li WM. Genome-wide identification of the Sec-dependent secretory protease genes in Erwinia amylovora and analysis of their expression during infection of immature pear fruit. J Zhejiang Univ Sci B 2020; 21:716-726. [PMID: 32893528 DOI: 10.1631/jzus.b2000281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The general secretory (Sec) pathway represents a common mechanism by which bacteria secrete proteins, including virulence factors, into the extracytoplasmic milieu. However, there is little information about this system, as well as its associated secretory proteins, in relation to the fire blight pathogen Erwinia amylovora. In this study, data mining revealed that E. amylovora harbors all of the essential components of the Sec system. Based on this information, we identified putative Sec-dependent secretory proteases in E. amylovora on a genome-wide scale. Using the programs SignalP, LipoP, and Phobius, a total of 15 putative proteases were predicted to contain the N-terminal signal peptides (SPs) that might link them to the Sec-dependent pathway. The activities of the predicted SPs were further validated using an Escherichia coli-based alkaline phosphatase (PhoA) gene fusion system that confirmed their extracytoplasmic property. Transcriptional analyses showed that the expression of 11 of the 15 extracytoplasmic protease genes increased significantly when E. amylovora was used to inoculate immature pears, suggesting their potential roles in plant infection. The results of this study support the suggestion that E. amylovora might employ the Sec system to secrete a suite of proteases to enable successful infection of plants, and shed new light on the interaction of E. amylovora with host plants.
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Affiliation(s)
- Wang-Bin Zhang
- College of Plant Science, Tarim University, Alar 843300, China.,Southern Xinjiang Key Laboratory of Integrated Pest Management, Tarim University, Alar 843300, China
| | - Hai-Lin Yan
- College of Plant Science, Tarim University, Alar 843300, China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zong-Cai Zhu
- College of Plant Science, Tarim University, Alar 843300, China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pei-Xiu Du
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen-Jun Zhao
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Wei-Min Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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9
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Ali A, Ahmad S, Wadood A, Rehman AU, Zahid H, Qayash Khan M, Nawab J, Rahman ZU, Alouffi AS. Modeling Novel Putative Drugs and Vaccine Candidates against Tick-Borne Pathogens: A Subtractive Proteomics Approach. Vet Sci 2020; 7:E129. [PMID: 32906620 PMCID: PMC7557734 DOI: 10.3390/vetsci7030129] [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: 08/18/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Ticks and tick-borne pathogens (TBPs) continuously causing substantial losses to the public and veterinary health sectors. The identification of putative drug targets and vaccine candidates is crucial to control TBPs. No information has been recorded on designing novel drug targets and vaccine candidates based on proteins. Subtractive proteomics is an in silico approach that utilizes extensive screening for the identification of novel drug targets or vaccine candidates based on the determination of potential target proteins available in a pathogen proteome that may be used effectively to control diseases caused by these infectious agents. The present study aimed to investigate novel drug targets and vaccine candidates by utilizing subtractive proteomics to scan the available proteomes of TBPs and predict essential and non-host homologous proteins required for the survival of these diseases causing agents. Subtractive proteome analysis revealed a list of fifteen essential, non-host homologous, and unique metabolic proteins in the complete proteome of selected pathogens. Among these therapeutic target proteins, three were excluded due to the presence in host gut metagenome, eleven were found to be highly potential drug targets, while only one was found as a potential vaccine candidate against TBPs. The present study may provide a foundation to design potential drug targets and vaccine candidates for the effective control of infections caused by TBPs.
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Affiliation(s)
- Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Shabir Ahmad
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.W.); (A.U.R.)
| | - Ashfaq U. Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.W.); (A.U.R.)
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hafsa Zahid
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Muhammad Qayash Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Javed Nawab
- Department of Environmental Sciences, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan;
| | - Zia Ur Rahman
- Department of Microbiology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan;
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10
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Zhang C, Wang X, Liu X, Fan Y, Zhang Y, Zhou X, Li W. A Novel ' Candidatus Liberibacter asiaticus'-Encoded Sec-Dependent Secretory Protein Suppresses Programmed Cell Death in Nicotiana benthamiana. Int J Mol Sci 2019; 20:E5802. [PMID: 31752214 PMCID: PMC6888338 DOI: 10.3390/ijms20225802] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 12/28/2022] Open
Abstract
'Candidatus Liberibacter asiaticus' (CLas) is one of the causal agents of citrus Huanglongbing (HLB), a bacterial disease of citrus trees that greatly reduces fruit yield and quality. CLas strains produce an array of currently uncharacterized Sec-dependent secretory proteins. In this study, the conserved chromosomally encoded protein CLIBASIA_03875 was identified as a novel Sec-dependent secreted protein. We show that CLIBASIA_03875 contains a putative Sec- secretion signal peptide (SP), a 29 amino acid residue located at the N-terminus, with a mature protein (m3875) of 22 amino acids found to localize in multiple subcellular components of the leaf epidermal cells of Nicotiana benthamiana. When overexpressed via a Potato virus X (PVX)-based expression vector in N. benthamiana, m3875 suppressed programmed cell death (PCD) and the H2O2 accumulation triggered by the pro-apoptotic mouse protein BAX and the Phytophthora infestans elicitin INF1. Overexpression also resulted in a phenotype of dwarfing, leaf deformation and mosaics, suggesting that m3875 has roles in plant immune response, growth, and development. Substitution mutagenesis of the charged amino acid (D7, R9, R11, and K22) with alanine within m3875 did not recover the phenotypes for PCD and normal growth. In addition, the transiently overexpressed m3875 regulated the transcriptional levels of N. benthamiana orthologs of CNGCs (cyclic nucleotide-gated channels), BI-1 (Bax-inhibitor 1), and WRKY33 that are involved in plant defense mechanisms. To our knowledge, m3875 is the first PCD suppressor identified from CLas. Studying the function of this protein provides insight as to how CLas attenuates the host immune responses to proliferate and cause Huanglongbing disease in citrus plants.
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Affiliation(s)
- Chao Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100094, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
| | - Xuefeng Wang
- Citrus Research Institute, Southwest University, Chongqing 400712, China;
| | - Xuelu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
- Citrus Research Institute, Southwest University, Chongqing 400712, China;
| | - Yanyan Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
- College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Yongqiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
| | - Xueping Zhou
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100094, China;
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
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11
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Bugalhão JN, Mota LJ. The multiple functions of the numerous Chlamydia trachomatis secreted proteins: the tip of the iceberg. MICROBIAL CELL 2019; 6:414-449. [PMID: 31528632 PMCID: PMC6717882 DOI: 10.15698/mic2019.09.691] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chlamydia trachomatis serovars are obligate intracellular bacterial pathogens mainly causing ocular and urogenital infections that affect millions of people worldwide and which can lead to blindness or sterility. They reside and multiply intracellularly within a membrane-bound vacuolar compartment, known as inclusion, and are characterized by a developmental cycle involving two morphologically and physiologically distinct chlamydial forms. Completion of the developmental cycle involves the secretion of > 70 C. trachomatis proteins that function in the host cell cytoplasm and nucleus, in the inclusion membrane and lumen, and in the extracellular milieu. These proteins can, for example, interfere with the host cell cytoskeleton, vesicular and non-vesicular transport, metabolism, and immune signalling. Generally, this promotes C. trachomatis invasion into, and escape from, host cells, the acquisition of nutrients by the chlamydiae, and evasion of cell-autonomous, humoral and cellular innate immunity. Here, we present an in-depth review on the current knowledge and outstanding questions about these C. trachomatis secreted proteins.
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Affiliation(s)
- Joana N Bugalhão
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Luís Jaime Mota
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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12
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Liu X, Fan Y, Zhang C, Dai M, Wang X, Li W. Nuclear Import of a Secreted " Candidatus Liberibacter asiaticus" Protein is Temperature Dependent and Contributes to Pathogenicity in Nicotiana benthamiana. Front Microbiol 2019; 10:1684. [PMID: 31396191 PMCID: PMC6668550 DOI: 10.3389/fmicb.2019.01684] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/08/2019] [Indexed: 01/14/2023] Open
Abstract
“Candidatus Liberibacter asiaticus” (CLas), one of the causal agents of citrus Huanglongbing (HLB), secretes proteins with functions that are largely unknown. In this study, we demonstrated that CLIBASIA_00460, one of the CLas-encoded Sec-dependent presecretory proteins, might contribute to the phytopathogenicity of CLas. CLIBASIA_00460 was conserved in CLas strains and expressed at a significantly higher level in citrus than in Asian citrus psyllid. Agrobacteria-mediated transient expression in Nicotiana benthamiana epidermal cells showed that the mature CLIBASIA_00460 (m460) without the putative Sec-dependent signal peptide was localized in multiple cellular compartments including nucleus at 25°C, but that nuclear accumulation was greatly decreased as the temperature rose to 32°C. When overexpressed via a Potato virus X (PVX)-based expression vector in N. benthamiana, m460 induced no local symptoms, but tiny necrotic spots were scattered on the systemic leaves. However, NLS-m460, which contains the SV40 nuclear localization sequence (NLS) at the N-terminus to promote nuclear import of m460, caused chlorosis and necrosis in the local leaves and severe necrosis in the systemic leaves. Taken together, these data suggest that CLIBASIA_00460 represented a novel virulence factor of CLas, and that nuclear localization of this protein was temperature dependent and positively correlated with its pathogenicity in planta.
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Affiliation(s)
- Xuelu Liu
- Citrus Research Institute, Southwest University, Chongqing, China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanyan Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Science, Shandong Normal University, Jinan, China
| | - Chao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meixue Dai
- College of Life Science, Shandong Normal University, Jinan, China
| | - Xuefeng Wang
- Citrus Research Institute, Southwest University, Chongqing, China
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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Park BC, Reese M, Tagliabracci VS. Thinking outside of the cell: Secreted protein kinases in bacteria, parasites, and mammals. IUBMB Life 2019; 71:749-759. [PMID: 30941842 DOI: 10.1002/iub.2040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 01/02/2023]
Abstract
Previous decades have seen an explosion in our understanding of protein kinase function in human health and disease. Hundreds of unique kinase structures have been solved, allowing us to create generalized rules for catalysis, assign roles of communities within the catalytic core, and develop specific drugs for targeting various pathways. Although our understanding of intracellular kinases has developed at a fast rate, our exploration into extracellular kinases has just begun. In this review, we will cover the secreted protein kinase families found in humans, bacteria, and parasites. © 2019 IUBMB Life, 71(6):749-759, 2019.
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Affiliation(s)
- Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Reese
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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14
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Dhroso A, Eidson S, Korkin D. Genome-wide prediction of bacterial effector candidates across six secretion system types using a feature-based statistical framework. Sci Rep 2018; 8:17209. [PMID: 30464223 PMCID: PMC6249201 DOI: 10.1038/s41598-018-33874-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/06/2018] [Indexed: 01/12/2023] Open
Abstract
Gram-negative bacteria are responsible for hundreds of millions infections worldwide, including the emerging hospital-acquired infections and neglected tropical diseases in the third-world countries. Finding a fast and cheap way to understand the molecular mechanisms behind the bacterial infections is critical for efficient diagnostics and treatment. An important step towards understanding these mechanisms is the discovery of bacterial effectors, the proteins secreted into the host through one of the six common secretion system types. Unfortunately, current prediction methods are designed to specifically target one of three secretion systems, and no accurate "secretion system-agnostic" method is available. Here, we present PREFFECTOR, a computational feature-based approach to discover effector candidates in Gram-negative bacteria, without prior knowledge on bacterial secretion system(s) or cryptic secretion signals. Our approach was first evaluated using several assessment protocols on a manually curated, balanced dataset of experimentally determined effectors across all six secretion systems, as well as non-effector proteins. The evaluation revealed high accuracy of the top performing classifiers in PREFFECTOR, with the small false positive discovery rate across all six secretion systems. Our method was also applied to six bacteria that had limited knowledge on virulence factors or secreted effectors. PREFFECTOR web-server is freely available at: http://korkinlab.org/preffector .
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Affiliation(s)
- Andi Dhroso
- Department of Computer Science, and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Samantha Eidson
- Mathematics and Computer Science Department, Fontbonne University, St. Louis, MO, USA
| | - Dmitry Korkin
- Department of Computer Science, and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA.
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15
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Kaminski A, Gupta KH, Goldufsky JW, Lee HW, Gupta V, Shafikhani SH. Pseudomonas aeruginosa ExoS Induces Intrinsic Apoptosis in Target Host Cells in a Manner That is Dependent on its GAP Domain Activity. Sci Rep 2018; 8:14047. [PMID: 30232373 PMCID: PMC6145893 DOI: 10.1038/s41598-018-32491-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/03/2018] [Indexed: 11/08/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes serious infections in immunocompromised individuals and cystic fibrosis patients. ExoS and ExoT are two homologous bifunctional Type III Secretion System (T3SS) virulence factors that induce apoptosis in target host cells. They possess a GTPase Activating Protein (GAP) domain at their N-termini, which share ~76% homology, and an ADP-ribosyltransferase (ADPRT) domain at their C-termini, which target non-overlapping substrates. Both the GAP and the ADPRT domains contribute to ExoT's cytotoxicity in target epithelial cells, whereas, ExoS-induced apoptosis is reported to be primarily due to its ADPRT domain. In this report, we demonstrate that ExoS/GAP domain is both necessary and sufficient to induce mitochondrial apoptosis. Our data demonstrate that intoxication with ExoS/GAP domain leads to enrichment of Bax and Bim into the mitochondrial outer-membrane, disruption of mitochondrial membrane and release of and cytochrome c into the cytosol, which activates initiator caspase-9 and effector caspase-3, that executes cellular death. We posit that the contribution of the GAP domain in ExoS-induced apoptosis was overlooked in prior studies due to its slower kinetics of cytotoxicity as compared to ADPRT. Our data clarify the field and reveal a novel virulence function for ExoS/GAP as an inducer of apoptosis.
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Affiliation(s)
- Amber Kaminski
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Kajal H Gupta
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Josef W Goldufsky
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Ha Won Lee
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Vineet Gupta
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sasha H Shafikhani
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA.
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA.
- Cancer Center, Rush University Medical Center, Chicago, IL, USA.
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16
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Small Molecules That Sabotage Bacterial Virulence. Trends Pharmacol Sci 2017; 38:339-362. [PMID: 28209403 DOI: 10.1016/j.tips.2017.01.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/01/2017] [Accepted: 01/06/2017] [Indexed: 02/08/2023]
Abstract
The continued rise of antibiotic-resistant bacterial infections has motivated alternative strategies for target discovery and treatment of infections. Antivirulence therapies function through inhibition of in vivo required virulence factors to disarm the pathogen instead of directly targeting viability or growth. This approach to treating bacteria-mediated diseases may have advantages over traditional antibiotics because it targets factors specific for pathogenesis, potentially reducing selection for resistance and limiting collateral damage to the resident microbiota. This review examines vulnerable molecular mechanisms used by bacteria to cause disease and the antivirulence compounds that sabotage these virulence pathways. By expanding the study of antimicrobial targets beyond those that are essential for growth, antivirulence strategies offer new and innovative opportunities to combat infectious diseases.
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17
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Yasuda M, Miwa H, Masuda S, Takebayashi Y, Sakakibara H, Okazaki S. Effector-Triggered Immunity Determines Host Genotype-Specific Incompatibility in Legume-Rhizobium Symbiosis. PLANT & CELL PHYSIOLOGY 2016; 57:1791-800. [PMID: 27373538 DOI: 10.1093/pcp/pcw104] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/16/2016] [Indexed: 05/06/2023]
Abstract
Symbiosis between legumes and rhizobia leads to the formation of N2-fixing root nodules. In soybean, several host genes, referred to as Rj genes, control nodulation. Soybean cultivars carrying the Rj4 gene restrict nodulation by specific rhizobia such as Bradyrhizobium elkanii We previously reported that the restriction of nodulation was caused by B. elkanii possessing a functional type III secretion system (T3SS), which is known for its delivery of virulence factors by pathogenic bacteria. In the present study, we investigated the molecular basis for the T3SS-dependent nodulation restriction in Rj4 soybean. Inoculation tests revealed that soybean cultivar BARC-2 (Rj4/Rj4) restricted nodulation by B. elkanii USDA61, whereas its nearly isogenic line BARC-3 (rj4/rj4) formed nitrogen-fixing nodules with the same strain. Root-hair curling and infection threads were not observed in the roots of BARC-2 inoculated with USDA61, indicating that Rj4 blocked B. elkanii infection in the early stages. Accumulation of H2O2 and salicylic acid (SA) was observed in the roots of BARC-2 inoculated with USDA61. Transcriptome analyses revealed that inoculation of USDA61, but not its T3SS mutant in BARC-2, induced defense-related genes, including those coding for hypersensitive-induced responsive protein, which act in effector-triggered immunity (ETI) in Arabidopsis. These findings suggest that B. elkanii T3SS triggers the SA-mediated ETI-type response in Rj4 soybean, which consequently blocks symbiotic interactions. This study revealed a common molecular mechanism underlying both plant-pathogen and plant-symbiont interactions, and suggests that establishment of a root nodule symbiosis requires the evasion or suppression of plant immune responses triggered by rhizobial effectors.
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Affiliation(s)
- Michiko Yasuda
- International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509 Japan
| | - Hiroki Miwa
- International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509 Japan
| | - Sachiko Masuda
- International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509 Japan
| | - Yumiko Takebayashi
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource Science 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Hitoshi Sakakibara
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource Science 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Shin Okazaki
- International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509 Japan
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18
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Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016; 80:1-43. [PMID: 26609051 PMCID: PMC4711186 DOI: 10.1128/mmbr.00019-15] [Citation(s) in RCA: 896] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
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Affiliation(s)
- Essaid Ait Barka
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Parul Vatsa
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Nathalie Gaveau-Vaillant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Cedric Jacquard
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christophe Clément
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Yder Ouhdouch
- Faculté de Sciences Semlalia, Université Cadi Ayyad, Laboratoire de Biologie et de Biotechnologie des Microorganismes, Marrakesh, Morocco
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Sylvius Laboratories, Leiden University, Leiden, The Netherlands
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19
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Sarris PF, Cevik V, Dagdas G, Jones JDG, Krasileva KV. Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens. BMC Biol 2016; 14:8. [PMID: 26891798 PMCID: PMC4759884 DOI: 10.1186/s12915-016-0228-7] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/11/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Plants deploy immune receptors to detect pathogen-derived molecules and initiate defense responses. Intracellular plant immune receptors called nucleotide-binding leucine-rich repeat (NLR) proteins contain a central nucleotide-binding (NB) domain followed by a series of leucine-rich repeats (LRRs), and are key initiators of plant defense responses. However, recent studies demonstrated that NLRs with non-canonical domain architectures play an important role in plant immunity. These composite immune receptors are thought to arise from fusions between NLRs and additional domains that serve as "baits" for the pathogen-derived effector proteins, thus enabling pathogen recognition. Several names have been proposed to describe these proteins, including "integrated decoys" and "integrated sensors". We adopt and argue for "integrated domains" or NLR-IDs, which describes the product of the fusion without assigning a universal mode of action. RESULTS We have scanned available plant genome sequences for the full spectrum of NLR-IDs to evaluate the diversity of integrations of potential sensor/decoy domains across flowering plants, including 19 crop species. We manually curated wheat and brassicas and experimentally validated a subset of NLR-IDs in wild and cultivated wheat varieties. We have examined NLR fusions that occur in multiple plant families and identified that some domains show re-occurring integration across lineages. Domains fused to NLRs overlap with previously identified pathogen targets confirming that they act as baits for the pathogen. While some of the integrated domains have been previously implicated in disease resistance, others provide new targets for engineering durable resistance to plant pathogens. CONCLUSIONS We have built a robust reproducible pipeline for detecting variable domain architectures in plant immune receptors across species. We hypothesize that NLR-IDs that we revealed provide clues to the host proteins targeted by pathogens, and that this information can be deployed to discover new sources of disease resistance.
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Affiliation(s)
- Panagiotis F Sarris
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,Division of Plant and Microbial Sciences, School of Biosciences, University of Exeter, Exeter, UK
| | - Volkan Cevik
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Gulay Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Ksenia V Krasileva
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK. .,The Genome Analysis Centre, Norwich Research Park, Norwich, UK.
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20
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Jamshidi N, Raghunathan A. Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Front Microbiol 2015; 6:1032. [PMID: 26500611 PMCID: PMC4594423 DOI: 10.3389/fmicb.2015.01032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/11/2015] [Indexed: 12/12/2022] Open
Abstract
Constraint-based models have become popular methods for systems biology as they enable the integration of complex, disparate datasets in a biologically cohesive framework that also supports the description of biological processes in terms of basic physicochemical constraints and relationships. The scope, scale, and application of genome scale models have grown from single cell bacteria to multi-cellular interaction modeling; host-pathogen modeling represents one of these examples at the current horizon of constraint-based methods. There are now a small number of examples of host-pathogen constraint-based models in the literature, however there has not yet been a definitive description of the methodology required for the functional integration of genome scale models in order to generate simulation capable host-pathogen models. Herein we outline a systematic procedure to produce functional host-pathogen models, highlighting steps which require debugging and iterative revisions in order to successfully build a functional model. The construction of such models will enable the exploration of host-pathogen interactions by leveraging the growing wealth of omic data in order to better understand mechanism of infection and identify novel therapeutic strategies.
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Affiliation(s)
- Neema Jamshidi
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA ; Department of Radiological Sciences, University of California, Los Angeles Los Angeles, CA, USA
| | - Anu Raghunathan
- Chemical Engineering Division, National Chemical Laboratory Pune, India
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21
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Goldufsky J, Wood SJ, Jayaraman V, Majdobeh O, Chen L, Qin S, Zhang C, DiPietro LA, Shafikhani SH. Pseudomonas aeruginosa uses T3SS to inhibit diabetic wound healing. Wound Repair Regen 2015; 23:557-64. [PMID: 25912785 DOI: 10.1111/wrr.12310] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 04/22/2015] [Indexed: 12/16/2022]
Abstract
Diabetic foot ulcers are responsible for more hospitalizations than any other complication of diabetes. Bacterial infection is recognized as an important factor associated with impaired healing in diabetic ulcers. Pseudomonas aeruginosa is the most frequently detected Gram-negative pathogen in diabetic ulcers. P. aeruginosa infection has been shown to impair healing in diabetic wounds in a manner that correlates with its ability to form biofilm. While the majority of infections in diabetic ulcers are biofilm associated, 33% of infections are nonbiofilm in nature. P. aeruginosa is the most prevalent Gram-negative pathogen in all diabetic wound types, which suggests that the deleterious impact of P. aeruginosa on healing in diabetic wounds goes beyond its ability to form biofilm and likely involves other factors. The Type III Secretion System (T3SS) virulence structure is required for the pathogenesis of all P. aeruginosa clinical isolates, suggesting that it may also play a role in the inhibition of wound repair in diabetic skin ulcers. We evaluated the role of T3SS in mediating P. aeruginosa-induced tissue damage in the wounds of diabetic mice. Our data demonstrate that P. aeruginosa establishes a robust and persistent infection in diabetic wounds independent of its ability to form biofilm and causes severe wound damage in a manner that primarily depends on its T3SS.
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Affiliation(s)
- Josef Goldufsky
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois
| | - Stephen J Wood
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois
| | - Vijayakumar Jayaraman
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois
| | - Omar Majdobeh
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois
| | - Lin Chen
- Center for Wound Healing and Tissue Regeneration, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois
| | - Shanshan Qin
- Department of Pharmacology, Rush University Medical Center, Chicago, Illinois
| | - Chunxiang Zhang
- Department of Pharmacology, Rush University Medical Center, Chicago, Illinois
| | - Luisa A DiPietro
- Center for Wound Healing and Tissue Regeneration, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois
| | - Sasha H Shafikhani
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois.,Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois.,Cancer Center, Rush University Medical Center Chicago, Illinois
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22
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Wood S, Goldufsky J, Shafikhani SH. Pseudomonas aeruginosa ExoT Induces Atypical Anoikis Apoptosis in Target Host Cells by Transforming Crk Adaptor Protein into a Cytotoxin. PLoS Pathog 2015; 11:e1004934. [PMID: 26020630 PMCID: PMC4447348 DOI: 10.1371/journal.ppat.1004934] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 05/04/2015] [Indexed: 11/19/2022] Open
Abstract
Previously, we demonstrated that Pseudomonas aeruginosa ExoT induces potent apoptosis in host epithelial cells in a manner that primarily depends on its ADP-ribosyltransferase domain (ADPRT) activity. However, the mechanism underlying ExoT/ADPRT-induced apoptosis remains undetermined. We now report that ExoT/ADPRT disrupts focal adhesion sites, activates p38β and JNK, and interferes with integrin-mediated survival signaling; causing atypical anoikis. We show that ExoT/ADPRT-induced anoikis is mediated by the Crk adaptor protein. We found that Crk-/- knockout cells are significantly more resistant to ExoT-induced apoptosis, while Crk-/- cells complemented with Crk are rendered sensitive to ExoT-induced apoptosis. Moreover, a dominant negative (DN) mutant form of Crk phenocopies ExoT-induced apoptosis both kinetically and mechanistically. Crk is generally believed to be a component of focal adhesion (FA) and its role in cellular survival remains controversial in that it has been found to be either pro-survival or pro-apoptosis. Our data demonstrate that although Crk is recruited to FA sites, its function is likely not required for FA assembly or for survival per se. However, when modified by ExoT or by mutagenesis, it can be transformed into a cytotoxin that induces anoikis by disrupting FA sites and interfering with integrin survival signaling. To our knowledge, this is the first example whereby a bacterial toxin exerts its cytotoxicity by subverting the function of an innocuous host cellular protein and turning it against the host cell.
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Affiliation(s)
- Stephen Wood
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Josef Goldufsky
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Sasha H. Shafikhani
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
- Cancer Center, Rush University Medical Center, Chicago, Illinois, United States of America
- * E-mail:
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23
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Barbosa EGV, Aburjaile FF, Ramos RTJ, Carneiro AR, Le Loir Y, Baumbach J, Miyoshi A, Silva A, Azevedo V. Value of a newly sequenced bacterial genome. World J Biol Chem 2014; 5:161-168. [PMID: 24921006 PMCID: PMC4050110 DOI: 10.4331/wjbc.v5.i2.161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 04/03/2014] [Indexed: 02/05/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the “scientific value” of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.
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24
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Mucyn TS, Yourstone S, Lind AL, Biswas S, Nishimura MT, Baltrus DA, Cumbie JS, Chang JH, Jones CD, Dangl JL, Grant SR. Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny. PLoS Pathog 2014; 10:e1003807. [PMID: 24391493 PMCID: PMC3879358 DOI: 10.1371/journal.ppat.1003807] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/17/2013] [Indexed: 01/12/2023] Open
Abstract
Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system (T3SS) and the type three secreted effector proteins (T3E) that are collectively essential for virulence. HrpL also regulates expression of an under-explored suite of non-type III effector genes (non-T3E), including toxin production systems and operons not previously associated with virulence. We implemented and refined genome-wide transcriptional analysis methods using cDNA-derived high-throughput sequencing (RNA-seq) data to characterize the HrpL regulon from six isolates of P. syringae spanning the diversity of the species. Our transcriptomes, mapped onto both complete and draft genomes, significantly extend earlier studies. We confirmed HrpL-regulation for a majority of previously defined T3E genes in these six strains. We identified two new T3E families from P. syringae pv. oryzae 1_6, a strain within the relatively underexplored phylogenetic Multi-Locus Sequence Typing (MLST) group IV. The HrpL regulons varied among strains in gene number and content across both their T3E and non-T3E gene suites. Strains within MLST group II consistently express the lowest number of HrpL-regulated genes. We identified events leading to recruitment into, and loss from, the HrpL regulon. These included gene gain and loss, and loss of HrpL regulation caused by group-specific cis element mutations in otherwise conserved genes. Novel non-T3E HrpL-regulated genes include an operon that we show is required for full virulence of P. syringae pv. phaseolicola 1448A on French bean. We highlight the power of integrating genomic, transcriptomic, and phylogenetic information to drive concise functional experimentation and to derive better insight into the evolution of virulence across an evolutionarily diverse pathogen species.
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Affiliation(s)
- Tatiana S Mucyn
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Scott Yourstone
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Abigail L Lind
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Surojit Biswas
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Marc T Nishimura
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David A Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Jason S Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America ; Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America ; Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America ; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sarah R Grant
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Santos AR, Pereira VB, Barbosa E, Baumbach J, Pauling J, Röttger R, Turk MZ, Silva A, Miyoshi A, Azevedo V. Mature Epitope Density--a strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC Genomics 2013; 14 Suppl 6:S4. [PMID: 24564223 PMCID: PMC3908659 DOI: 10.1186/1471-2164-14-s6-s4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Current immunological bioinformatic approaches focus on the prediction of allele-specific epitopes capable of triggering immunogenic activity. The prediction of major histocompatibility complex (MHC) class I epitopes is well studied, and various software solutions exist for this purpose. However, currently available tools do not account for the concentration of epitope products in the mature protein product and its relation to the reliability of target selection. Results We developed a computational strategy based on measuring the epitope's concentration in the mature protein, called Mature Epitope Density (MED). Our method, though simple, is capable of identifying promising vaccine targets. Our online software implementation provides a computationally light and reliable analysis of bacterial exoproteins and their potential for vaccines or diagnosis projects against pathogenic organisms. We evaluated our computational approach by using the Mycobacterium tuberculosis (Mtb) H37Rv exoproteome as a gold standard model. A literature search was carried out on 60 out of 553 Mtb's predicted exoproteins, looking for previous experimental evidence concerning their possible antigenicity. Half of the 60 proteins were classified as highest scored by the MED statistic, while the other half were classified as lowest scored. Among the lowest scored proteins, ~13% were confirmed as not related to antigenicity or not contributing to the bacterial pathogenicity, and 70% of the highest scored proteins were confirmed as related. There was no experimental evidence of antigenic or pathogenic contributions for three of the highest MED-scored Mtb proteins. Hence, these three proteins could represent novel putative vaccine and drug targets for Mtb. A web version of MED is publicly available online at http://med.mmci.uni-saarland.de/. Conclusions The software presented here offers a practical and accurate method to identify potential vaccine and diagnosis candidates against pathogenic bacteria by "reading" results from well-established reverse vaccinology software in a novel way, considering the epitope's concentration in the mature portion of the protein.
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Sadarangani V, Datta S, Arunachalam M. New players in the same old game: a system level in silico study to predict type III secretion system and effector proteins in bacterial genomes reveals common themes in T3SS mediated pathogenesis. BMC Res Notes 2013; 6:297. [PMID: 23890184 PMCID: PMC3734048 DOI: 10.1186/1756-0500-6-297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 07/10/2013] [Indexed: 11/10/2022] Open
Abstract
Background Type III secretion system (T3SS) plays an important role in virulence or symbiosis of many pathogenic or symbiotic bacteria [CHM 2:291–294, 2007; Physiology (Bethesda) 20:326–339, 2005]. T3SS acts like a tunnel between a bacterium and its host through which the bacterium injects ‘effector’ proteins into the latter [Nature 444:567–573, 2006; COSB 18:258–266, 2008]. The effectors spatially and temporally modify the host signalling pathways [FEMS Microbiol Rev 35:1100–1125, 2011; Cell Host Microbe5:571–579, 2009]. In spite its crucial role in host-pathogen interaction, the study of T3SS and the associated effectors has been limited to a few bacteria [Cell Microbiol 13:1858–1869, 2011; Nat Rev Microbiol 6:11–16, 2008; Mol Microbiol 80:1420–1438, 2011]. Before one set out to perform systematic experimental studies on an unknown set of bacteria it would be beneficial to identify the potential candidates by developing an in silico screening algorithm. A system level study would also be advantageous over traditional laboratory methods to extract an overriding theme for host-pathogen interaction, if any, from the vast resources of data generated by sequencing multiple bacterial genomes. Results We have developed an in silico protocol in which the most conserved set of T3SS proteins was used as the query against the entire bacterial database with increasingly stringent search parameters. It enabled us to identify several uncharacterized T3SS positive bacteria. We adopted a similar strategy to predict the presence of the already known effectors in the newly identified T3SS positive bacteria. The huge resources of biochemical data [FEMS Microbiol Rev 35:1100–1125, 2011; Cell Host Microbe 5:571–579, 2009; BMC Bioinformatics 7(11):S4, 2010] on the T3SS effectors enabled us to search for the common theme in T3SS mediated pathogenesis. We identified few cellular signalling networks in the host, which are manipulated by most of the T3SS containing pathogens. We went on to look for correlation, if any, between the biological quirks of a particular class of bacteria with the effectors they harbour. We could pin point few effectors, which were enriched in certain classes of bacteria. Conclusion The current study would open up new avenues to explore many uncharacterized T3SS positive bacteria. The experimental validation of the predictions from this study will unravel a generalized mechanism for T3SS positive bacterial infection into host cell.
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Affiliation(s)
- Vineet Sadarangani
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Dahan J, Mireau H. The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes. RNA Biol 2013; 10:1469-76. [PMID: 23872480 DOI: 10.4161/rna.25568] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In the last years, a number of nuclear genes restoring cytoplasmic male sterility (CMS) have been cloned in various crop species. The majority of these genes have been shown to encode pentatricopeptide repeat proteins (PPR) that act by specifically suppressing the expression of sterility-causing mitochondrial transcripts. Functional analysis of these proteins has indicated that the inhibitory effects of restoring PPR (Rf-PPR) proteins involve various mechanisms, including RNA cleavage, RNA destabilization, or translation inhibition. Cross-species sequence comparison of PPR protein complements revealed that most plant genomes encode 10-30 Rf-like (RFL) proteins sharing high-sequence similarity with the identified Rf-PPRs from crops. Evolutionary analyses further showed that they constitute a monophyletic group apart in the PPR family, with peculiar evolution dynamic and constraints. Here we review recent data on RF-PPRs and present the latest discoveries on the RFL family, with prospects on the functionality and evolution of this peculiar subclass of PPR.
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Affiliation(s)
- Jennifer Dahan
- INRA; UMR1318; Institut Jean-Pierre Bourgin; RD10; Versailles, France; AgroParisTech; Institut Jean-Pierre Bourgin; RD10; Versailles, France
| | - Hakim Mireau
- INRA; UMR1318; Institut Jean-Pierre Bourgin; RD10; Versailles, France; AgroParisTech; Institut Jean-Pierre Bourgin; RD10; Versailles, France
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Rosenblum EB, Poorten TJ, Joneson S, Settles M. Substrate-specific gene expression in Batrachochytrium dendrobatidis, the chytrid pathogen of amphibians. PLoS One 2012. [PMID: 23185485 PMCID: PMC3502224 DOI: 10.1371/journal.pone.0049924] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Determining the mechanisms of host-pathogen interaction is critical for understanding and mitigating infectious disease. Mechanisms of fungal pathogenicity are of particular interest given the recent outbreaks of fungal diseases in wildlife populations. Our study focuses on Batrachochytrium dendrobatidis (Bd), the chytrid pathogen responsible for amphibian declines around the world. Previous studies have hypothesized a role for several specific families of secreted proteases as pathogenicity factors in Bd, but the expression of these genes has only been evaluated in laboratory growth conditions. Here we conduct a genome-wide study of Bd gene expression under two different nutrient conditions. We compare Bd gene expression profiles in standard laboratory growth media and in pulverized host tissue (i.e., frog skin). A large proportion of genes in the Bd genome show increased expression when grown in host tissue, indicating the importance of studying pathogens on host substrate. A number of gene classes show particularly high levels of expression in host tissue, including three families of secreted proteases (metallo-, serine- and aspartyl-proteases), adhesion genes, lipase-3 encoding genes, and a group of phylogenetically unusual crinkler-like effectors. We discuss the roles of these different genes as putative pathogenicity factors and discuss what they can teach us about Bd’s metabolic targets, host invasion, and pathogenesis.
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Affiliation(s)
- Erica Bree Rosenblum
- Department of Environmental Science Policy and Management, University of California, Berkeley, California, United States of America.
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Decker JE, Vasco DA, McKay SD, McClure MC, Rolf MM, Kim J, Northcutt SL, Bauck S, Woodward BW, Schnabel RD, Taylor JF. A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits. BMC Genomics 2012; 13:606. [PMID: 23140540 PMCID: PMC3532096 DOI: 10.1186/1471-2164-13-606] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection. RESULTS We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCπ analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis. CONCLUSIONS We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.
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Affiliation(s)
- Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
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Santos AR, Carneiro A, Gala-García A, Pinto A, Barh D, Barbosa E, Aburjaile F, Dorella F, Rocha F, Guimarães L, Zurita-Turk M, Ramos R, Almeida S, Soares S, Pereira U, Abreu VC, Silva A, Miyoshi A, Azevedo V. The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome. BMC Genomics 2012; 13 Suppl 5:S6. [PMID: 23095951 PMCID: PMC3476999 DOI: 10.1186/1471-2164-13-s5-s6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Pan-genomic studies aim, for instance, at defining the core, dispensable and unique genes within a species. A pan-genomics study for vaccine design tries to assess the best candidates for a vaccine against a specific pathogen. In this context, rather than studying genes predicted to be exported in a single genome, with pan-genomics it is possible to study genes present in different strains within the same species, such as virulence factors. The target organism of this pan-genomic work here presented is Corynebacterium pseudotuberculosis, the etiologic agent of caseous lymphadenitis (CLA) in goat and sheep, which causes significant economic losses in those herds around the world. Currently, only a few antigens against CLA are known as being the basis of commercial and still ineffective vaccines. In this regard, the here presented work analyses, in silico, five C. pseudotuberculosis genomes and gathers data to predict common exported proteins in all five genomes. These candidates were also compared to two recent C. pseudotuberculosis in vitro exoproteome results. Results The complete genome of five C. pseudotuberculosis strains (1002, C231, I19, FRC41 and PAT10) were submitted to pan-genomics analysis, yielding 306, 59 and 12 gene sets, respectively, representing the core, dispensable and unique in silico predicted exported pan-genomes. These sets bear 150 genes classified as secreted (SEC) and 227 as potentially surface exposed (PSE). Our findings suggest that the main C. pseudotuberculosis in vitro exoproteome could be greater, appended by a fraction of the 35 proteins formerly predicted as making part of the variant in vitro exoproteome. These genomes were manually curated for correct methionine initiation and redeposited with a total of 1885 homogenized genes. Conclusions The in silico prediction of exported proteins has allowed to define a list of putative vaccine candidate genes present in all five complete C. pseudotuberculosis genomes. Moreover, it has also been possible to define the in silico predicted dispensable and unique C. pseudotuberculosis exported proteins. These results provide in silico evidence to further guide experiments in the areas of vaccines, diagnosis and drugs. The work here presented is the first whole C. pseudotuberculosis in silico predicted pan-exoproteome completed till today.
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Affiliation(s)
- Anderson R Santos
- Molecular and Celular Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Correa VR, Majerczak DR, Ammar ED, Merighi M, Pratt RC, Hogenhout SA, Coplin DL, Redinbaugh MG. The bacterium Pantoea stewartii uses two different type III secretion systems to colonize its plant host and insect vector. Appl Environ Microbiol 2012; 78:6327-36. [PMID: 22773631 PMCID: PMC3416588 DOI: 10.1128/aem.00892-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/26/2012] [Indexed: 12/30/2022] Open
Abstract
Plant- and animal-pathogenic bacteria utilize phylogenetically distinct type III secretion systems (T3SS) that produce needle-like injectisomes or pili for the delivery of effector proteins into host cells. Pantoea stewartii subsp. stewartii (herein referred to as P. stewartii), the causative agent of Stewart's bacterial wilt and leaf blight of maize, carries phylogenetically distinct T3SSs. In addition to an Hrc-Hrp T3SS, known to be essential for maize pathogenesis, P. stewartii has a second T3SS (Pantoea secretion island 2 [PSI-2]) that is required for persistence in its flea beetle vector, Chaetocnema pulicaria (Melsh). PSI-2 belongs to the Inv-Mxi-Spa T3SS family, typically found in animal pathogens. Mutagenesis of the PSI-2 psaN gene, which encodes an ATPase essential for secretion of T3SS effectors by the injectisome, greatly reduces both the persistence of P. stewartii in flea beetle guts and the beetle's ability to transmit P. stewartii to maize. Ectopic expression of the psaN gene complements these phenotypes. In addition, the PSI-2 psaN gene is not required for P. stewartii pathogenesis of maize and is transcriptionally upregulated in insects compared to maize tissues. Thus, the Hrp and PSI-2 T3SSs play different roles in the life cycle of P. stewartii as it alternates between its insect vector and plant host.
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Affiliation(s)
- Valdir R. Correa
- Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio, USA
| | - Doris R. Majerczak
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - El-Desouky Ammar
- Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio, USA
| | - Massimo Merighi
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Richard C. Pratt
- Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio, USA
| | - Saskia A. Hogenhout
- Department of Disease and Stress Biology, John Innes Centre, Norwich, United Kingdom
| | - David L. Coplin
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Margaret G. Redinbaugh
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- USDA, ARS, Corn and Soybean Research Unit, Wooster, Ohio, USA
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Type three effector gene distribution and sequence analysis provide new insights into the pathogenicity of plant-pathogenic Xanthomonas arboricola. Appl Environ Microbiol 2011; 78:371-84. [PMID: 22101042 DOI: 10.1128/aem.06119-11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas arboricola is a complex bacterial species which mainly attacks fruit trees and is responsible for emerging diseases in Europe. It comprises seven pathovars (X. arboricola pv. pruni, X. arboricola pv. corylina, X. arboricola pv. juglandis, X. arboricola pv. populi, X. arboricola pv. poinsettiicola, X. arboricola pv. celebensis, and X. arboricola pv. fragariae), each exhibiting characteristic disease symptoms and distinct host specificities. To better understand the factors underlying this ecological trait, we first assessed the phylogenetic relationships among a worldwide collection of X. arboricola strains by sequencing the housekeeping gene rpoD. This analysis revealed that strains of X. arboricola pathovar populi are divergent from the main X. arboricola cluster formed by all other strains. Then, we investigated the distribution of 53 type III effector (T3E) genes in a collection of 57 X. arboricola strains that are representative of the main X. arboricola cluster. Our results showed that T3E repertoires vary greatly between X. arboricola pathovars in terms of size. Indeed, X. arboricola pathovars pruni, corylina, and juglandis, which are responsible for economically important stone fruit and nut diseases in Europe, harbored the largest T3E repertoires, whereas pathovars poinsettiicola, celebensis, and fragariae harbored the smallest. We also identified several differences in T3E gene content between X. arboricola pathovars pruni, corylina, and juglandis which may account for their differing host specificities. Further, we examined the allelic diversity of eight T3E genes from X. arboricola pathovars. This analysis revealed very limited allelic variations at the different loci. Altogether, the data presented here provide new insights into the evolution of pathogenicity and host range of X. arboricola and are discussed in terms of emergence of new diseases within this bacterial species.
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Abstract
Miniature inverted terminal repeat elements (MITEs) are nonautonomous mobile elements that have a significant impact on bacterial evolution. Here we characterize E622, a 611-bp virulence-associated MITE from Pseudomonas syringae, which contains no coding region but has almost perfect 168-bp inverted repeats. Using an antibiotic coupling assay, we show that E622 is transposable and can mobilize an antibiotic resistance gene contained between its borders. Its predicted parent element, designated TnE622, has a typical transposon structure with a three-gene operon, consisting of resolvase, integrase, and exeA-like genes, which is bounded by the same terminal inverted repeats as E622. A broader genome level survey of the E622/TnE622 inverted repeats identified homologs in Pseudomonas, Salmonella, Shewanella, Erwinia, Pantoea, and the cyanobacteria Nostoc and Cyanothece, many of which appear to encompass known virulence genes, including genes encoding toxins, enzymes, and type III secreted effectors. Its association with niche-specific genetic determinants, along with its persistence and evolutionary diversification, indicates that this mobile element family has played a prominent role in the evolution of many agriculturally and clinically relevant pathogenic bacteria.
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A combined approach for comparative exoproteome analysis of Corynebacterium pseudotuberculosis. BMC Microbiol 2011; 11:12. [PMID: 21241507 PMCID: PMC3025830 DOI: 10.1186/1471-2180-11-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 01/17/2011] [Indexed: 11/17/2022] Open
Abstract
Background Bacterial exported proteins represent key components of the host-pathogen interplay. Hence, we sought to implement a combined approach for characterizing the entire exoproteome of the pathogenic bacterium Corynebacterium pseudotuberculosis, the etiological agent of caseous lymphadenitis (CLA) in sheep and goats. Results An optimized protocol of three-phase partitioning (TPP) was used to obtain the C. pseudotuberculosis exoproteins, and a newly introduced method of data-independent MS acquisition (LC-MSE) was employed for protein identification and label-free quantification. Additionally, the recently developed tool SurfG+ was used for in silico prediction of sub-cellular localization of the identified proteins. In total, 93 different extracellular proteins of C. pseudotuberculosis were identified with high confidence by this strategy; 44 proteins were commonly identified in two different strains, isolated from distinct hosts, then composing a core C. pseudotuberculosis exoproteome. Analysis with the SurfG+ tool showed that more than 75% (70/93) of the identified proteins could be predicted as containing signals for active exportation. Moreover, evidence could be found for probable non-classical export of most of the remaining proteins. Conclusions Comparative analyses of the exoproteomes of two C. pseudotuberculosis strains, in addition to comparison with other experimentally determined corynebacterial exoproteomes, were helpful to gain novel insights into the contribution of the exported proteins in the virulence of this bacterium. The results presented here compose the most comprehensive coverage of the exoproteome of a corynebacterial species so far.
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Xu S, Zhang C, Miao Y, Gao J, Xu D. Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif. BMC Genomics 2010; 11 Suppl 3:S1. [PMID: 21143776 PMCID: PMC2999339 DOI: 10.1186/1471-2164-11-s3-s1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Effector secretion is a common strategy of pathogen in mediating host-pathogen interaction. Eight EPIYA-motif containing effectors have recently been discovered in six pathogens. Once these effectors enter host cells through type III/IV secretion systems (T3SS/T4SS), tyrosine in the EPIYA motif is phosphorylated, which triggers effectors binding other proteins to manipulate host-cell functions. The objectives of this study are to evaluate the distribution pattern of EPIYA motif in broad biological species, to predict potential effectors with EPIYA motif, and to suggest roles and biological functions of potential effectors in host-pathogen interactions. Results A hidden Markov model (HMM) of five amino acids was built for the EPIYA-motif based on the eight known effectors. Using this HMM to search the non-redundant protein database containing 9,216,047 sequences, we obtained 107,231 sequences with at least one EPIYA motif occurrence and 3115 sequences with multiple repeats of the EPIYA motif. Although the EPIYA motif exists among broad species, it is significantly over-represented in some particular groups of species. For those proteins containing at least four copies of EPIYA motif, most of them are from intracellular bacteria, extracellular bacteria with T3SS or T4SS or intracellular protozoan parasites. By combining the EPIYA motif and the adjacent SH2 binding motifs (KK, R4, Tarp and Tir), we built HMMs of nine amino acids and predicted many potential effectors in bacteria and protista by the HMMs. Some potential effectors for pathogens (such as Lawsonia intracellularis, Plasmodium falciparum and Leishmania major) are suggested. Conclusions Our study indicates that the EPIYA motif may be a ubiquitous functional site for effectors that play an important pathogenicity role in mediating host-pathogen interactions. We suggest that some intracellular protozoan parasites could secrete EPIYA-motif containing effectors through secretion systems similar to the T3SS/T4SS in bacteria. Our predicted effectors provide useful hypotheses for further studies.
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Affiliation(s)
- Shunfu Xu
- Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu 210029, China.
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Terauchi R, Yoshida K. Towards population genomics of effector-effector target interactions. THE NEW PHYTOLOGIST 2010; 187:929-39. [PMID: 20707855 DOI: 10.1111/j.1469-8137.2010.03408.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pathogen-plant host coevolutionary interactions exert strong natural selection on both organisms, specifically on the genes coding for effectors (pathogens), as well as on those coding for effector targets and R proteins (plant hosts). Natural selection leaves behind DNA sequence signatures on such genes and on linked genomic regions. These signatures can readily be detected by studying the patterns of intraspecies polymorphisms and interspecies divergence of the DNA sequences. Recent developments in DNA sequencing technology have made whole-genome studies on patterns of DNA polymorphisms : divergence possible. This type of analysis, called 'population genomics', appears to be powerful enough to identify novel effector-effector target genes. Here, we provide an overview of the statistical tools used for population genomics and their applications. This is followed by a brief review of evolutionary studies on plant genes involved in host-pathogen interactions. Finally we provide an example from our study on Magnaporthe oryzae.
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Affiliation(s)
- Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan.
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DebRoy S, Keenan AB, Ueno N, Jeronimo SMB, Donelson JE, Wilson ME. Leishmania infantum chagasi: a genome-based approach to identification of excreted/secreted proteins. Exp Parasitol 2010; 126:582-91. [PMID: 20542033 DOI: 10.1016/j.exppara.2010.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 05/17/2010] [Accepted: 06/06/2010] [Indexed: 12/24/2022]
Abstract
The parasitic protozoan, Leishmania, survives in harsh environments within its mammalian and sand fly hosts. Secreted proteins likely play critical roles in the parasite's interactions with its environment. As a preliminary identification of the spectrum of potential excreted/secreted (ES) proteins of Leishmania infantum chagasi (Lic), a causative agent of visceral leishmaniasis, we used standard algorithms to screen the annotated L. infantum genome for genes whose predicted protein products have an N-terminal signal peptide and lack transmembrane domains and membrane anchors. A suite of 181 candidate ES proteins were identified. These included several that were documented in the literature to be released by other Leishmania spp. Six candidate ES proteins were selected for further validation of their expression and release by different parasite stages. We found both amastigote-specific and promastigote-specific released proteins. The ES proteins of Lic are candidates for future studies of parasite virulence determinants and host protective immunity.
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Affiliation(s)
- Sruti DebRoy
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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Weflen AW, Alto NM, Viswanathan VK, Hecht G. E. coli secreted protein F promotes EPEC invasion of intestinal epithelial cells via an SNX9-dependent mechanism. Cell Microbiol 2010; 12:919-29. [PMID: 20088948 DOI: 10.1111/j.1462-5822.2010.01440.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enteropathogenic Escherichia coli (EPEC) infection requires the injection of effector proteins into intestinal epithelial cells (IECs) via type 3 secretion. Type 3-secreted effectors can interfere with IEC signalling pathways via specific protein-protein interactions. For example, E. coli secreted protein F (EspF) binds sorting nexin 9 (SNX9), an endocytic regulator, resulting in tubulation of the plasma membrane. Our aim was to determine the mechanism of EspF/SNX9-induced membrane tubulation. Point mutation of the SNX9 lipid binding domains or truncation of the EspF SNX9 binding domains significantly inhibited tubulation, as did inhibition of clathrin coated pit (CCP) assembly. Although characterized as non-invasive, EPEC are known to invade IECs in vitro and in vivo. Indeed, we found significant invasion of Caco-2 cells by EPEC, which, like tubulation, was blocked by pharmacological inhibition of CCPs. Interestingly, however, inhibition of dynamin activity did not prevent tubulation or EPEC invasion, which is in contrast to Salmonella invasion, which requires dynamin activity. Our data also indicate that EPEC invasion is dependent on EspF and its interaction with SNX9. Together, these findings suggest that EspF promotes EPEC invasion of IECs by harnessing the membrane-deforming activity of SNX9.
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Affiliation(s)
- Andrew W Weflen
- Department of Medicine, Section of Digestive Disease and Nutrition, University of Illinois at Chicago, Chicago, IL 60612, USA
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Abstract
Antibiotic resistance is one of the greatest challenges of the twenty-first century. However, the increasing understanding of bacterial pathogenesis and intercellular communication has revealed many potential strategies to develop novel drugs to treat bacteria-mediated disease. Interference with bacterial virulence and/or cell-to-cell signalling pathways is an especially compelling approach, as it is thought to apply less selective pressure for the development of bacterial resistance than traditional strategies, which are aimed at killing bacteria or preventing their growth. Here, we discuss the mechanisms of bacterial virulence and present promising anti-virulence strategies and compounds for the future treatment of bacterial infections.
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Bernal-Bayard J, Ramos-Morales F. Salmonella type III secretion effector SlrP is an E3 ubiquitin ligase for mammalian thioredoxin. J Biol Chem 2009; 284:27587-95. [PMID: 19690162 DOI: 10.1074/jbc.m109.010363] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Salmonella enterica encodes two virulence-related type III secretion systems in Salmonella pathogenicity islands 1 and 2, respectively. These systems mediate the translocation of protein effectors into the eukaryotic host cell, where they alter cell signaling and manipulate host cell functions. However, the precise role of most effectors remains unknown. Using a genetic screen, we identified the small, reduction/oxidation-regulatory protein thioredoxin as a mammalian binding partner of the Salmonella effector SlrP. The interaction was confirmed by affinity chromatography and coimmunoprecipitation. In vitro, SlrP was able to mediate ubiquitination of ubiquitin and thioredoxin. A Cys residue conserved in other effectors of the same family that also possess E3 ubiquitin ligase activity was essential for this catalytic function. Stable expression of SlrP in HeLa cells resulted in a significant decrease of thioredoxin activity and in an increase of cell death. The physiological significance of these results was strengthened by the finding that Salmonella was able to trigger cell death and inhibit thioredoxin activity in HeLa cells several hours post-infection. This study assigns a functional role to the Salmonella effector SlrP as a binding partner and an E3 ubiquitin ligase for mammalian thioredoxin.
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Affiliation(s)
- Joaquín Bernal-Bayard
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41080 Sevilla, Spain
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Hajri A, Brin C, Hunault G, Lardeux F, Lemaire C, Manceau C, Boureau T, Poussier S. A "repertoire for repertoire" hypothesis: repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas. PLoS One 2009; 4:e6632. [PMID: 19680562 PMCID: PMC2722093 DOI: 10.1371/journal.pone.0006632] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 07/09/2009] [Indexed: 11/21/2022] Open
Abstract
Background The genetic basis of host specificity for animal and plant pathogenic bacteria remains poorly understood. For plant pathogenic bacteria, host range is restricted to one or a few host plant species reflecting a tight adaptation to specific hosts. Methodology/Principal Findings Two hypotheses can be formulated to explain host specificity: either it can be explained by the phylogenetic position of the strains, or by the association of virulence genes enabling a pathological convergence of phylogenically distant strains. In this latter hypothesis, host specificity would result from the interaction between repertoires of bacterial virulence genes and repertoires of genes involved in host defences. To challenge these two hypotheses, we selected 132 Xanthomonas axonopodis strains representative of 18 different pathovars which display different host range. First, the phylogenetic position of each strain was determined by sequencing the housekeeping gene rpoD. This study showed that many pathovars of Xanthomonas axonopodis are polyphyletic. Second, we investigated the distribution of 35 type III effector genes (T3Es) in these strains by both PCR and hybridization methods. Indeed, for pathogenic bacteria T3Es were shown to trigger and to subvert host defences. Our study revealed that T3E repertoires comprise core and variable gene suites that likely have distinct roles in pathogenicity and different evolutionary histories. Our results showed a correspondence between composition of T3E repertoires and pathovars of Xanthomonas axonopodis. For polyphyletic pathovars, this suggests that T3E genes might explain a pathological convergence of phylogenetically distant strains. We also identified several DNA rearrangements within T3E genes, some of which correlate with host specificity of strains. Conclusions/Significance These data provide insight into the potential role played by T3E genes for pathogenic bacteria and support a “repertoire for repertoire” hypothesis that may explain host specificity. Our work provides resources for functional and evolutionary studies aiming at understanding host specificity of pathogenic bacteria, functional redundancy between T3Es and the driving forces shaping T3E repertoires.
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Affiliation(s)
- Ahmed Hajri
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique (INRA), Beaucouzé, France
| | - Chrystelle Brin
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique (INRA), Beaucouzé, France
| | - Gilles Hunault
- Département d'Informatique, Université d'Angers, Angers, France
| | | | | | - Charles Manceau
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique (INRA), Beaucouzé, France
| | - Tristan Boureau
- Département de Biologie, Université d'Angers, Angers, Beaucouzé, France
- * E-mail: (TB); (SP)
| | - Stéphane Poussier
- Département de Sciences Biologiques, Agrocampus Ouest centre d'Angers, Institut National d'Horticulture et de Paysage (INHP), Beaucouzé, France
- * E-mail: (TB); (SP)
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Samudrala R, Heffron F, McDermott JE. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog 2009; 5:e1000375. [PMID: 19390620 PMCID: PMC2668754 DOI: 10.1371/journal.ppat.1000375] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 03/11/2009] [Indexed: 11/18/2022] Open
Abstract
The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the secretion system apparatus are conserved, its substrates--effector proteins--are not. We have used a novel computational approach to confidently identify new secreted effectors by integrating protein sequence-based features, including evolutionary measures such as the pattern of homologs in a range of other organisms, G+C content, amino acid composition, and the N-terminal 30 residues of the protein sequence. The method was trained on known effectors from the plant pathogen Pseudomonas syringae and validated on a set of effectors from the animal pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) after eliminating effectors with detectable sequence similarity. We show that this approach can predict known secreted effectors with high specificity and sensitivity. Furthermore, by considering a large set of effectors from multiple organisms, we computationally identify a common putative secretion signal in the N-terminal 20 residues of secreted effectors. This signal can be used to discriminate 46 out of 68 total known effectors from both organisms, suggesting that it is a real, shared signal applicable to many type III secreted effectors. We use the method to make novel predictions of secreted effectors in S. Typhimurium, some of which have been experimentally validated. We also apply the method to predict secreted effectors in the genetically intractable human pathogen Chlamydia trachomatis, identifying the majority of known secreted proteins in addition to providing a number of novel predictions. This approach provides a new way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal.
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Affiliation(s)
- Ram Samudrala
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Jason E. McDermott
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
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Salmonella enterica serovar typhimurium pathogenicity island 1-encoded type III secretion system translocases mediate intimate attachment to nonphagocytic cells. Infect Immun 2009; 77:2635-42. [PMID: 19364837 DOI: 10.1128/iai.00077-09] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Delivery of bacterial proteins into mammalian cells by type III secretion systems (TTSS) is thought to require the intimate association of bacteria with target cells. The molecular bases of this intimate association appear to be different in different bacteria involving TTSS components, as well as surface determinants not associated with TTSS. We show here that the protein translocases SipB, SipC, and SipD of the Salmonella enterica serovar Typhimurium pathogenicity island 1 (SPI-1)-encoded TTSS are required for the intimate association of these bacteria with mammalian cells. S. Typhimurium mutant strains lacking any of the translocases were defective for intimate attachment. Immunofluorescence microscopy showed that SipD is present on the bacterial surface prior to bacterial contact with host cells. In contrast, SipB and SipC were detected on the bacterial surface only subsequent to bacterial contact with the target cell. We conclude that the coordinated deployment and interaction between the protein translocases mediate the SPI-1 TTSS-dependent intimate association of S. Typhimurium with host cells.
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Brain damage in newborn rat model of meningitis by Enterobacter sakazakii: a role for outer membrane protein A. J Transl Med 2009; 89:263-77. [PMID: 19139724 PMCID: PMC3256236 DOI: 10.1038/labinvest.2008.164] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Enterobacter sakazakii (ES) is an emerging pathogen that causes sepsis, meningitis, and necrotizing enterocolitis in neonates. Very limited information is available regarding the pathogenesis of these diseases and the specific virulence factors of ES. Here, we demonstrate, for the first time using a newborn rat model, that outer membrane protein A (OmpA) expression is important for the onset of meningitis by ES. Orally administered OmpA(+) ES traverses the intestinal barrier, multiplies in blood, and subsequently penetrates the blood-brain barrier. OmpA(+) ES were present in high numbers in the brains of infected animals along with associated neutrophil infiltration, hemorrhage, and gliosis. In contrast, OmpA(-) ES could not bind to the intestinal epithelial cells in vitro and in vivo efficiently. The bound OmpA(+) ES also caused apoptosis of enterocytes in the intestinal segments of infected animals; OmpA(-) ES did not. Furthermore, OmpA(-) ES are very susceptible to blood and serum killing, whereas OmpA(+) ES are resistant. Of note, 100% mortality rates were observed in OmpA(+) ES-infected newborn rats, whereas OmpA(-) ES-infected rats survived without any pathological manifestations. The inability of OmpA(-) ES to cause disease was restored by complementation with the ompA gene. These results suggest that OmpA expression in ES is necessary for the colonization of the gastrointestinal tract and for subsequent survival in blood to cause meningitis.
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Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 2008; 19:294-305. [PMID: 19015323 DOI: 10.1101/gr.083311.108] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. By combining data generated from 454 Life Sciences (Roche) and Illumina (formerly known as Solexa sequencing) sequencing platforms, we reliably assembled genomes into large scaffolds at a fraction of the traditional cost and without use of a reference sequence. We applied this method to two isolates of the phytopathogenic bacteria Pseudomonas syringae. Sequencing and reassembly of the well-studied tomato and Arabidopsis pathogen, Pto(DC3000), facilitated development and testing of our method. Sequencing of a distantly related rice pathogen, Por(1_)(6), demonstrated our method's efficacy for de novo assembly of novel genomes. Our assembly of Por(1_6) yielded an N50 scaffold size of 531,821 bp with >75% of the predicted genome covered by scaffolds over 100,000 bp. One of the critical phenotypic differences between strains of P. syringae is the range of plant hosts they infect. This is largely determined by their complement of type III effector proteins. The genome of Por(1_6) is the first sequenced for a P. syringae isolate that is a pathogen of monocots, and, as might be predicted, its complement of type III effectors differs substantially from the previously sequenced isolates of this species. The genome of Por(1_6) helps to define an expansion of the P. syringae pan-genome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species.
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Affiliation(s)
- Josephine A Reinhardt
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Soanes DM, Alam I, Cornell M, Wong HM, Hedeler C, Paton NW, Rattray M, Hubbard SJ, Oliver SG, Talbot NJ. Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS One 2008; 3:e2300. [PMID: 18523684 PMCID: PMC2409186 DOI: 10.1371/journal.pone.0002300] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 04/15/2008] [Indexed: 12/30/2022] Open
Abstract
Fungi and oomycetes are the causal agents of many of the most serious diseases of plants. Here we report a detailed comparative analysis of the genome sequences of thirty-six species of fungi and oomycetes, including seven plant pathogenic species, that aims to explore the common genetic features associated with plant disease-causing species. The predicted translational products of each genome have been clustered into groups of potential orthologues using Markov Chain Clustering and the data integrated into the e-Fungi object-oriented data warehouse (http://www.e-fungi.org.uk/). Analysis of the species distribution of members of these clusters has identified proteins that are specific to filamentous fungal species and a group of proteins found only in plant pathogens. By comparing the gene inventories of filamentous, ascomycetous phytopathogenic and free-living species of fungi, we have identified a set of gene families that appear to have expanded during the evolution of phytopathogens and may therefore serve important roles in plant disease. We have also characterised the predicted set of secreted proteins encoded by each genome and identified a set of protein families which are significantly over-represented in the secretomes of plant pathogenic fungi, including putative effector proteins that might perturb host cell biology during plant infection. The results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis.
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Affiliation(s)
- Darren M. Soanes
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Intikhab Alam
- School of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Mike Cornell
- School of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Han Min Wong
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Cornelia Hedeler
- School of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Norman W. Paton
- School of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- School of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Simon J. Hubbard
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, United Kingdom
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, Cambridge, United Kingdom
| | - Nicholas J. Talbot
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
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