scholarly journals Time-resolved dual root-microbe transcriptomics reveals early induced Nicotiana benthamiana genes and conserved infection-promoting Phytophthora palmivora effectors

2017 ◽  
Author(s):  
Edouard Evangelisti ◽  
Anna Gogleva ◽  
Thomas Hainaux ◽  
Mehdi Doumane ◽  
Frej Tulin ◽  
...  
Keyword(s):  
De Novo ◽  
Resistance Breeding ◽  
Black Pepper ◽  
Effector Proteins ◽  
Phytophthora Palmivora ◽  
Broad Host Range ◽  
Major Advance ◽  
Root Tips ◽  
Time Resolved ◽  
Molecular Features

AbstractBackgroundPlant-pathogenic oomycetes are responsible for economically important losses on crops worldwide. Phytophthora palmivora, a broad-host-range tropical relative of the potato late blight pathogen, causes rotting diseases in many important tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus.Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped understanding of how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce.ResultsWe employed the model plant N. benthamiana to study the P. palmivora root infections at the cellular and molecular level. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features.ConclusionsThese results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.

scholarly journals In silico identification of effector proteins from generalist herbivore Spodoptera litura

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Vinod Kumar Prajapati ◽  
Mahendra Varma ◽  
Jyothilakshmi Vadassery
Keyword(s):  
Salivary Gland ◽  
Plant Defense ◽  
Salivary Glands ◽  
Spodoptera Litura ◽  
De Novo ◽  
Effector Proteins ◽  
Secretory Proteins ◽  
Broad Host Range ◽  
Generalist Herbivore ◽  
Common Cutworm

Abstract Background The common cutworm, Spodoptera litura Fabricius is a leaf and fruit feeding generalist insect of the order Lepidoptera and a destructive agriculture pest. The broad host range of the herbivore is due to its ability to downregulate plant defense across different plants. The identity of Spodoptera litura released effectors that downregulate plant defense are largely unknown. The current study aims to identify genes encoding effector proteins from salivary glands of S. litura (Fab.). Results Head and salivary glands of Spodoptera litura were used for de-novo transcriptome analysis and effector prediction. Eight hundred ninety-nine proteins from the head and 330 from salivary gland were identified as secretory proteins. Eight hundred eight proteins from the head and 267 from salivary gland proteins were predicted to be potential effector proteins. Conclusions This study is the first report on identification of potential effectors from Spodoptera litura salivary glands.

scholarly journals Increase of Tospoviral Diversity in Brazil with the Identification of Two New Tospovirus Species, One from Chrysanthemum and One from Zucchini

1999 ◽  
Vol 89 (9) ◽  
pp. 823-830 ◽  
Author(s):  
I. C. Bezerra ◽  
R. de O. Resende ◽  
L. Pozzer ◽  
T. Nagata ◽  
R. Kormelink ◽  
...  
Keyword(s):  
Yellow Spot ◽  
Enzyme Linked Immunosorbent Assay ◽  
Broad Host Range ◽  
Spot Virus ◽  
Chlorotic Spot ◽  
Molecular Features ◽  
Tomato Spotted Wilt ◽  
Tospovirus Species ◽  
Stem Necrosis ◽  
Wilt Virus

During a survey conducted in several different regions of Brazil, two unique tospoviruses were isolated and characterized, one from chrysanthemum and the other from zucchini. The chrysanthemum virus displayed a broad host range, whereas the virus from zucchini was restricted mainly to the family Cucurbitaceae. Double-antibody sandwich-enzyme-linked immunosorbent assay and western immunoblot analyses demonstrated that both viruses were serologically distinct from all reported tospovirus species including the recently proposed peanut yellow spot virus and iris yellow spot virus (IYSV) species. The nucleotide sequences of the nucleocapsid (N) genes of both viruses contain 780 nucleotides encoding for deduced proteins of 260 amino acids. The N proteins of these two viruses displayed amino acid sequence similarities with the previously described tospovirus species ranging from 20 to 75%, but they were more closely related to each other (80%). Based on the biological and molecular features, these viruses are proposed as two new tospovirus species, designated chrysanthemum stem necrosis virus (CSNV) and zucchini lethal chlorosis virus (ZLCV). With the identification of CSNV and ZLCV, in addition to tomato spotted wilt virus, groundnut ring spot virus, tomato chlorotic spot virus, and IYSV, Brazil harbors the broadest spectrum of tospovirus species reported.

scholarly journals A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions

2020 ◽  
Vol 33 (10) ◽  
pp. 1177-1188
Author(s):  
Manuel I. Villalobos Solis ◽  
Suresh Poudel ◽  
Clemence Bonnot ◽  
Him K. Shrestha ◽  
Robert L. Hettich ◽  
...  
Keyword(s):  
Performance Metrics ◽  
De Novo ◽  
Hybrid Poplar ◽  
Cell Communication ◽  
Proteolytic Cleavage ◽  
Peptide Sequencing ◽  
Root Tips ◽  
Extramatrical Mycelium ◽  
Biologically Relevant ◽  
Selective Enrichment

Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry–based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo–assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar Populus × canescens 717-1B4 in interaction with the ectomycorrhizal basidiomycete Laccaria bicolor. In total, we identified 1,660 and 2,870 Populus and L. bicolor unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of L. bicolor. These PCPs mapped to 64 Populus proteins and 69 L. bicolor proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.

scholarly journals Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens

2020 ◽  
Vol 117 (33) ◽  
pp. 19720-19730 ◽  
Author(s):  
Yifan Wang ◽  
Kathy Fange Liu ◽  
Yu Yang ◽  
Ian Davis ◽  
Aimin Liu
Keyword(s):  
Conformational Changes ◽  
Quinolinic Acid ◽  
De Novo ◽  
Crystalline Lens ◽  
Paramagnetic Resonance ◽  
Time Resolved ◽  
X Ray Crystallography ◽  
Protein Conformational Changes ◽  
Catalytic Intermediates ◽  
Electron Paramagnetic

The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolvedin crystalloreactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.

scholarly journals Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Lulu Deng ◽  
Long Li ◽  
Cheng Zou ◽  
Chengchi Fang ◽  
Changchun Li
Keyword(s):  
Single Molecule ◽  
Posttranscriptional Regulation ◽  
Muscle Development ◽  
Target Genes ◽  
Rna Binding ◽  
De Novo ◽  
Rna Binding Proteins ◽  
Fast And Slow Muscles ◽  
Molecular Features ◽  
Polyadenylation Sites

Many increasing documents have proved that alternative polyadenylation (APA) events with different polyadenylation sites (PAS) contribute to posttranscriptional regulation. However, little is known about the detailed molecular features of PASs and its role in porcine fast and slow skeletal muscles through microRNAs (miRNAs) and RNA binding proteins (RBPs). In this study, we combined single-molecule real-time sequencing and Illumina RNA-seq datasets to comprehensively analyze polyadenylation in pigs. We identified a total of 10,334 PASs, of which 8734 were characterized by reference genome annotation. 32.86% of PAS-associated genes were determined to have more than one PAS. Further analysis demonstrated that tissue-specific PASs between fast and slow muscles were enriched in skeletal muscle development pathways. In addition, we obtained 1407 target genes regulated by APA events through potential binding 69 miRNAs and 28 RBPs in variable 3′ UTR regions and some are involved in myofiber transformation. Furthermore, the de novo motif search confirmed that the most common usage of canonical motif AAUAAA and three types of PASs may be related to the strength of motifs. In summary, our results provide a useful annotation of PASs for pig transcriptome and suggest that APA may serve as a role in fast and slow muscle development under the regulation of miRNAs and RBPs.

scholarly journals Leukemia secondary to myeloproliferative neoplasms

Blood ◽  
2020 ◽  
Vol 136 (1) ◽  
pp. 61-70 ◽  
Author(s):  
Andrew J. Dunbar ◽  
Raajit K. Rampal ◽  
Ross Levine
Keyword(s):  
Cancer Genomics ◽  
De Novo ◽  
Myeloproliferative Neoplasms ◽  
Myeloproliferative Neoplasm ◽  
Unmet Need ◽  
Chemotherapeutic Agents ◽  
Cell Transplant ◽  
Leukemic Transformation ◽  
Long Term Outcome ◽  
Molecular Features

Abstract Secondary acute myeloid leukemias (AMLs) evolving from an antecedent myeloproliferative neoplasm (MPN) are characterized by a unique set of cytogenetic and molecular features distinct from de novo AML. Given the high frequency of poor-risk cytogenetic and molecular features, malignant clones are frequently insensitive to traditional AML chemotherapeutic agents. Allogeneic stem cell transplant, the only treatment modality shown to have any beneficial long-term outcome, is often not possible given the advanced age of patients at time of diagnosis and frequent presence of competing comorbidities. Even in this setting, relapse rates remain high. As a result, outcomes are generally poor and there remains a significant unmet need for novel therapeutic strategies. Although advances in cancer genomics have dramatically enhanced our understanding of the molecular events governing clonal evolution in MPNs, the cell-intrinsic and -extrinsic mechanisms driving leukemic transformation at this level remain poorly understood. Here, we review known risk factors for the development of leukemic transformation in MPNs, recent progress made in our understanding of the molecular features associated with leukemic transformation, current treatment strategies, and emerging therapeutic options for this high-risk myeloid malignancy.

Disease Resistance Against a Broad-Host-Range Pathogen

2013 ◽  
Vol 14 (1) ◽  
pp. 32
Author(s):  
Jonathan M. Jacobs ◽  
Caitilyn Allen
Keyword(s):  
Disease Resistance ◽  
Host Range ◽  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Pathogenic Bacteria ◽  
Resistance Breeding ◽  
Wilt Disease ◽  
Family Type ◽  
Broad Host Range ◽  
Bacterial Wilt Disease

The bacterial wilt pathogen Ralstonia solanacearum causes major agricultural losses on many crop hosts worldwide. Resistance breeding is the best way to control bacterial wilt disease, but the biological basis for bacterial wilt resistance is unknown. We found that R. solanacearum uses an AvrE-family, Type III-secreted effector called PopS to overcome plant defenses and cause disease on tomato. Orthologs of PopS are widely conserved across distinct classes of plant pathogenic bacteria and could provide novel, durable targets for resistance. Accepted for publication 25 September 2013. Published 25 November 2013.

scholarly journals Biochemical and Localization Analyses of Putative Type III Secretion Translocator Proteins CopB and CopB2 of Chlamydia trachomatis Reveal Significant Distinctions

2011 ◽  
Vol 79 (8) ◽  
pp. 3036-3045 ◽  
Author(s):  
B. Chellas-Géry ◽  
K. Wolf ◽  
J. Tisoncik ◽  
T. Hackstadt ◽  
K. A. Fields
Keyword(s):  
Type Iii Secretion ◽  
De Novo ◽  
Ectopic Expression ◽  
Effector Proteins ◽  
Developmental Cycle ◽  
Inclusion Membrane ◽  
Content Type ◽  
Type Iii ◽  
Intracellular Parasites ◽  
The Many

ABSTRACTChlamydiaspp. are among the many pathogenic Gram-negative bacteria that employ a type III secretion system (T3SS) to overcome host defenses and exploit available resources. Significant progress has been made in elucidating contributions of T3S to the pathogenesis of these medically important, obligate intracellular parasites, yet important questions remain. Chief among these is how secreted effector proteins traverse eukaryotic membranes to gain access to the host cytosol. Due to a complex developmental cycle, it is possible that chlamydiae utilize a different complement of proteins to accomplish translocation at different stages of development. We investigated this possibility by extending the characterization ofC. trachomatisCopB and CopB2. CopB is detected early during infection but is depleted and not detected again until about 20 h postinfection. In contrast, CopB2 was detectible throughout development. CopB is associated with the inclusion membrane. Biochemical and ectopic expression analyses were consistent with peripheral association of CopB2 with inclusion membranes. This interaction correlated with development and required both chlamydialde novoprotein synthesis and T3SS activity. Collectively, our data indicate that it is unlikely that CopB serves as the sole chlamydial translocation pore and that CopB2 is capable of association with the inclusion membrane.

scholarly journals Extracellular Proteins Involved in Soybean Cultivar-Specific Nodulation Are Associated with Pilus-Like Surface Appendages and Exported by a Type III Protein Secretion System in Sinorhizobium fredii USDA257

2003 ◽  
Vol 16 (7) ◽  
pp. 617-625 ◽  
Author(s):  
Hari B. Krishnan ◽  
Julio Lorio ◽  
Won Seok Kim ◽  
Guoqiao Jiang ◽  
Kil Yong Kim ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Symbiotic Bacterium ◽  
Secretion System ◽  
Extracellular Proteins ◽  
Effector Proteins ◽  
Broad Host Range ◽  
Sinorhizobium Fredii ◽  
Type Iii ◽  
Conserved Genes ◽  
Type Iii Protein Secretion

Several gram-negative plant and animal pathogenic bacteria have evolved a type III secretion system (TTSS) to deliver effector proteins directly into the host cell cytosol. Sinorhizobium fredii USDA257, a symbiont of soybean and many other legumes, secretes proteins called Nops (nodulation outer proteins) into the extracellular environment upon flavonoid induction. Mutation analysis and the nucleotide sequence of a 31.2-kb symbiosis (sym) plasmid DNA region of USDA257 revealed the existence of a TTSS locus in this symbiotic bacterium. This locus includes rhc (rhizobia conserved) genes that encode components of a TTSS and proteins that are secreted into the environment (Nops). The genomic organization of the TTSS locus of USDA257 is remarkably similar to that of another broad-host range symbiont, Rhizobium sp. strain NGR234. Flavonoids that activate the transcription of the nod genes of USDA257 also stimulate the production of novel filamentous appendages known as pili. Electron microscope examination of isolated pili reveals needle-like filaments of 6 to 8 nm in diameter. The production of the pili is dependent on a functional nodD1 and the presence of a nod gene-inducing compound. Mutations in several of the TTSS genes negate the ability of USDA257 to elaborate pili. Western blot analysis using antibodies raised against purified NopX, Nop38, and Nop7 reveals that these proteins were associated with the pili. Mutations in rhcN, rhcJ, rhcC, and ttsI alter the ability of USDA257 to form nodules on Glycine max and Macroptilium atropurpureum.

Sign in / Sign up

Export Citation Format

Share Document