Allelic Variation and Selection in Effector Genes of Phytophthora infestans (Mont.) de Bary

Phytophthora infestans is a devastating plant pathogen in several crops such as potato (Solanum tuberosum), tomato (Solanum lycopersicum) and Andean fruits such as tree tomato (Solanum betaceum), lulo (Solanum quitoense), uchuva (Physalis peruviana) and wild species in the genus Solanum sp. Despite intense research performed around the world, P. infestans populations from Colombia, South America, are poorly understood. Of particular importance is knowledge about pathogen effector proteins, which are responsible for virulence. The present work was performed with the objective to analyze gene sequences coding for effector proteins of P. infestans from isolates collected from different hosts and geographical regions. Several genetic parameters, phylogenetic analyses and neutrality tests for non-synonymous and synonymous substitutions were calculated. Non-synonymous substitutions were identified for all genes that exhibited polymorphisms at the DNA level. Significant negative selection values were found for two genes (PITG_08994 and PITG_12737) suggesting active coevolution with the corresponding host resistance proteins. Implications for pathogen virulence mechanisms and disease management are discussed.

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Phytophthora infestans Effectors IPI-O1 and IPI-O4 Each Contribute to Pathogen Virulence

Phytopathology ◽

10.1094/phyto-06-16-0240-r ◽

2017 ◽

Vol 107 (5) ◽

pp. 600-606 ◽

Cited By ~ 6

Author(s):

Yu Chen ◽

Dennis A. Halterman

Keyword(s):

Phytophthora Infestans ◽

Potato Production ◽

Plant Diseases ◽

In Planta ◽

Solanum Bulbocastanum ◽

Wild Potato Species ◽

Pathogen Virulence ◽

Pathogen Effector ◽

Oomycete Pathogen ◽

Major Resistance Genes

Potato late blight, caused by the oomycete pathogen Phytophthora infestans, is one of the most destructive plant diseases. Despite decades of intensive breeding efforts, it remains a threat to potato production worldwide, because newly evolved pathogen strains have overcome major resistance genes quickly. The RB protein, from the diploid wild potato species Solanum bulbocastanum, confers partial resistance to most P. infestans strains through its recognition of members of the corresponding pathogen effector protein family IPI-O. IPI-O comprises a multigene family and while some variants are recognized by RB to elicit host resistance (e.g., IPI-O1 and IPI-O2), others are able to elude detection (e.g., IPI-O4). IPI-O1 is almost ubiquitous in global P. infestans strains while IPI-O4 is more rare. No direct experimental evidence has been shown to demonstrate the effect of IPI-O on pathogen virulence in the P. infestans−potato pathosystem. Here, our work has demonstrated that in planta expression of both IPI-O1 and IPI-O4 increases P. infestans aggressiveness resulting in enlarged lesions in potato leaflets. We have previously shown that IPI-O4 has gained the ability to suppress the hypersensitive response induced by IPI-O1 in the presence of RB. In this study, our work has shown that this gain-of-function of IPI-O4 does not compromise its virulence effect, as IPI-O4 overexpression results in larger lesions than IPI-O1. We have also found that higher expression of IPI-O effectors correlates with enlarged lesions, indicating that IPI-O can contribute to virulence quantitatively. In summary, this study has provided accurate and valuable information on IPI-O’s virulence effect on the potato host.

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Fungal Induced Protein Hyperacetylation Identified by Acetylome Profiling

10.1101/057174 ◽

2016 ◽

Author(s):

Justin W Walley ◽

Zhouxin Shen ◽

Maxwell R. McReynolds ◽

Steven P. Briggs

Keyword(s):

Immune Response ◽

Protein Function ◽

Effector Proteins ◽

Protein Acetylation ◽

Post Translational Modification ◽

Cochliobolus Carbonum ◽

Pathogen Virulence ◽

Pathogen Effector ◽

Race 1 ◽

Hc Toxin

ABSTRACTLysine acetylation is a key post-translational modification that regulates diverse proteins involved in a range of biological processes. The role of histone acetylation in plant defense is well established and it is known that pathogen effector proteins encoding acetyltransferses can directly acetylate host proteins to alter immunity. However, it is unclear whether endogenous plant enzymes can modulate protein acetylation during an immune response. Here we investigate how the effector molecule HC-toxin, a histone deacetylase inhibitor, produced by Cochliobolus carbonum race 1 promotes pathogen virulence in maize through altering protein acetylation. Using mass spectrometry we globally quantified the abundance of 3,636 proteins and the levels of acetylation at 2,791 sites in maize plants treated with HC-toxin as well as HC-toxin deficient or producing strains of C. carbonum. Analyses of these data demonstrate that acetylation is a widespread post-translational modification impacting proteins encoded by many intensively studied maize genes. Furthermore, the application of exogenous HC-toxin enabled us to show that the activity of plant-encoded enzymes can be modulated to alter acetylation of non-histone proteins during an immune response. Collectively, these results provide a resource for further mechanistic studies examining the regulation of protein function and offer insight into the complex immune response triggered by virulent C. carbonum.

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Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence

Genes ◽

10.3390/genes12040568 ◽

2021 ◽

Vol 12 (4) ◽

pp. 568

Author(s):

Laura Vilanova ◽

Claudio A. Valero-Jiménez ◽

Jan A.L. van Kan

Keyword(s):

Brown Rot ◽

Biological Properties ◽

Effector Proteins ◽

Stone Fruit ◽

Rna Seq ◽

Sequencing Technology ◽

Pathogen Virulence ◽

Effector Genes ◽

Gene Models ◽

High Quality Genome

Brown rot is the most economically important fungal disease of stone fruits and is primarily caused by Monilinia laxa and Monlinia fructicola. Both species co-occur in European orchards although M. fructicola is considered to cause the most severe yield losses in stone fruit. This study aimed to generate a high-quality genome of M. fructicola and to exploit it to identify genes that may contribute to pathogen virulence. PacBio sequencing technology was used to assemble the genome of M. fructicola. Manual structural curation of gene models, supported by RNA-Seq, and functional annotation of the proteome yielded 10,086 trustworthy gene models. The genome was examined for the presence of genes that encode secreted proteins and more specifically effector proteins. A set of 134 putative effectors was defined. Several effector genes were cloned into Agrobacterium tumefaciens for transient expression in Nicotiana benthamiana plants, and some of them triggered necrotic lesions. Studying effectors and their biological properties will help to better understand the interaction between M. fructicola and its stone fruit host plants.

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Characterization and Establishment of a Novel EBV Strain Simultaneously Associated With Nasopharyngeal Carcinoma and B-Cell Lymphoma

Frontiers in Oncology ◽

10.3389/fonc.2021.626659 ◽

2021 ◽

Vol 11 ◽

Author(s):

Fenggang Yu ◽

Nicholas L. Syn ◽

Yanan Lu ◽

Qing Yun Chong ◽

Junyun Lai ◽

...

Keyword(s):

Nasopharyngeal Carcinoma ◽

Phylogenetic Analyses ◽

Human Tumor ◽

B Cell Lymphoma ◽

Asia Pacific ◽

B Lymphoma ◽

Barr Virus ◽

Molecular Features ◽

Geographical Regions ◽

Epstein Barr

Epstein-Barr virus (EBV)—the prototypical human tumor virus—is responsible for 1–2% of the global cancer burden, but divergent strains seem to exist in different geographical regions with distinct predilections for causing lymphoid or epithelial malignancies. Here we report the establishment and characterization of Yu103, an Asia Pacific EBV strain with a highly remarkable provenance of being derived from nasopharyngeal carcinoma biopsy but subsequently propagated in human B-lymphoma cells and xenograft models. Unlike previously characterized EBV strains which are either predominantly B-lymphotropic or epitheliotropic, Yu103 evinces an uncanny capacity to infect and transform both B-lymphocytes and nasopharyngeal epithelial cells. Genomic and phylogenetic analyses indicated that Yu103 EBV lies midway along the spectrum of EBV strains known to drive lymphomagenesis or carcinogenesis, and harbors molecular features which likely account for its unusual properties. To our knowledge, Yu103 EBV is currently the only EBV isolate shown to drive human nasopharyngeal carcinoma and B-lymphoma, and should therefore provide a powerful novel platform for research on EBV-driven hematological and epithelial malignancies.

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Recognition of Phytophthora infestans in potato (Solanum tuberosum L.): Scr74 gene as an example

Open Agriculture ◽

10.1515/opag-2016-0021 ◽

2016 ◽

Vol 1 (1) ◽

Author(s):

Mulusew Kassa Bitew ◽

Emmanouil Domazakis

Keyword(s):

Amino Acid ◽

Phytophthora Infestans ◽

Solanum Tuberosum L ◽

Effector Proteins ◽

Wild Potato ◽

Detached Leaf ◽

Polymorphic Genes ◽

Cysteine Rich Protein ◽

In The Wild ◽

Polymorphic Gene

AbstractPhytophthora infestans is the causal agent of late blight, the most devastating disease of potato worldwide. The P. infestans genome encodes potentially polymorphic genes that evolve continually to evade the recognition of plant R genes, though it has hundreds of predicted and conserved effector proteins recognised by the plant. The gene Scr74 encodes a predicted 74-amino acid secreted cysteine-rich protein belonging to a highly polymorphic gene family within P. infestans. This study screened the recognition of Scr74 genes in wild potato genotypes from August 2013 to January 2014 in the Plant Breeding Laboratory of Wageningen University, the Netherlands. To identify the recognition of the Scr74 gene, we grew potato genotypes in the green house for PVX assays, detached leaf assays and molecular work. Twenty-seven good-quality sequences of the Scr74 gene variant with a length of 74 amino acids were found and more frequent amino acid variation was detected on the mature protein. Seventeen Scr74 constructs were identified as diversified and two effectors were strongly recognised by wild S. verrucosum genotypes via effectoromics from the PVX assay. A strong plant cell death hypersensitive response (HR) was recorded on wild S. verrucosum and S. tuberosum genotypes from the detached leaf assay. This recognition seems to be a useful indicator for the presence of a resistance gene (s) to the polymorphic effectors of P. infestans (as it has seen on Scr74 gene) in the wild potato genotypes.

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Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties

FEMS Microbiology Letters ◽

10.1093/femsle/fnaa084 ◽

2020 ◽

Vol 367 (11) ◽

Author(s):

Mokhtar Rejili ◽

Mohamed Ali BenAbderrahim ◽

Mohamed Mars ◽

Janine Darla Sherrier

Keyword(s):

Phylogenetic Analysis ◽

Soil Properties ◽

Phylogenetic Analyses ◽

Geographical Regions ◽

Ensifer Meliloti ◽

Rhizobial Species ◽

Nodc Gene

ABSTRACT Phylogenetically diverse rhizobial strains endemic to Tunisia were isolated from symbiotic nodules of Lotus creticus, growing in different arid extremophile geographical regions of Tunisia, and speciated using multiloci-phylogenetic analysis as Neorhizobium huautlense (LCK33, LCK35, LCO42 and LCO49), Ensifer numidicus (LCD22, LCD25, LCK22 and LCK25), Ensifer meliloti (LCK8, LCK9 and LCK12) and Mesorhizobium camelthorni (LCD11, LCD13, LCD31 and LCD33). In addition, phylogenetic analyses revealed eight additional strains with previously undescribed chromosomal lineages within the genera Ensifer (LCF5, LCF6 and LCF8),Rhizobium (LCF11, LCF12 and LCF14) and Mesorhizobium (LCF16 and LCF19). Analysis using the nodC gene identified five symbiovar groups, four of which were already known. The remaining group composed of two strains (LCD11 and LCD33) represented a new symbiovar of Mesorhizobium camelthorni, which we propose designating as sv. hedysari. Interestingly, we report that soil properties drive and structure the symbiosis of L. creticus and its rhizobia.

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Redescription and phylogenetic analyses of Thaparocleidus gomtius and T. sudhakari (Monogenea: Dactylogyridae) from Wallago attu (Siluriformes: Siluridae) in India

Helminthologia ◽

10.1515/helm-2017-0008 ◽

2017 ◽

Vol 54 (1) ◽

pp. 87-96 ◽

Cited By ~ 1

Author(s):

C. Verma ◽

A. Chaudhary ◽

H. S. Singh

Keyword(s):

Phylogenetic Relationships ◽

18S Rrna ◽

Phylogenetic Analyses ◽

Uttar Pradesh ◽

18S Rrna Gene ◽

Morphometric Study ◽

Rrna Gene ◽

Molecular Analyses ◽

Wallago Attu ◽

Geographical Regions

Summary Two species of Thaparocleidus Jain (1952a) were found harboring W. attu from the Ganga River at two localities, Meerut and Farrukhabad, Uttar Pradesh, India, during the period of 2013-2015. Morphology and morphometric study of specimens identified as Thaparocleidus gomtius (Jain, 1952a) Lim, 1996 and T. sudhakari (Gusev, 1976) Lim, 1996. Molecular analyses using the 18S rRNA gene confirmed the validity of T. gomtius and T. sudhakari and demonstrated that both the species clustered with other Thaparocleidus species from different geographical regions. We aim at reassessing the taxonomy and establishing the phylogenetic relationships among these two redescribed species with other representatives of the genus Thaparocleidus.

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Identification of Photobionts from the lichen family Physciaceae using algal-specific ITS rDNA sequencing

The Lichenologist ◽

10.1006/lich.2000.0298 ◽

2001 ◽

Vol 33 (1) ◽

pp. 73-86 ◽

Cited By ~ 116

Author(s):

Gert Helms ◽

Thomas Friedl ◽

Gerhard Rambold ◽

Helmut Mayrhofer

Keyword(s):

Phylogenetic Analyses ◽

Pcr Primers ◽

Its Rdna ◽

Generic Level ◽

Sequence Comparisons ◽

Its Phylogeny ◽

Specific Pcr ◽

Rdna Sequences ◽

Rdna Sequencing ◽

Geographical Regions

AbstractThe identity of photobionts from 20 species of the Physciaceae from different habitats and geographical regions has been determined by ITS rDNA sequence comparisons in order to estimate the diversity of photobionts within that lichen group, to detect patterns of specificity of mycobionts towards their photobionts and as a part of an ongoing study to investigate possible parallel cladogenesis of both symbionts. Algal-specific PCR primers have been used to determine the ITS rDNA sequences from DNA extractions of dried lichens that were up to 5 years old. Direct comparisons and phylogenetic analyses allowed the assignment of Physciaceae photobionts to four distinct clades in the photobiont ITS rDNA phylogeny. The results indicate a diversity within the genus Trebouxia Puymaly and Physciaceae photobionts that is higher than expected on the basis morphology alone. Physciaceae photobionts belonged to 12 different ITS lineages of which nine could unambiguously be assigned to six morphospecies of Trebouxia. The identity of the remaining three sequences was not clarified; they may represent new species. Specificity at the generic level was low as a whole range of photobiont species were found within a genus of Physciaceae and different ranges were detected. The photobionts of Physcia (Schreb.) Michaux were closely related and represented one morphospecies of Trebouxia, whereas the algal partners of Buellia De Not and Rinodina (Ach.) Gray were in distant lineages of the ITS phylogeny and from several Trebouxia morphospecies. Photobiont variation within a genus of Physciaceae may be due to phylogeny, geographical distance or because photobionts from neighbouring lichens were taken (“algal sharing“). At the species level Physciaceae mycobionts seem to be rather selective and contained photobionts that were very closely related within one morphospecies of Trebouxia.

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Manipulation of the host by pathogens to survive the lysosome

Biochemical Society Transactions ◽

10.1042/bst0381417 ◽

2010 ◽

Vol 38 (6) ◽

pp. 1417-1419 ◽

Cited By ~ 2

Author(s):

Paul R. Pryor ◽

Sally A. Raines

Keyword(s):

Innate Immunity ◽

Membrane Trafficking ◽

Molecular Mechanisms ◽

Regulatory Elements ◽

Effector Proteins ◽

Intracellular Pathogens ◽

Intracellular Environment ◽

Pathogen Effector ◽

Form Part ◽

Survival Mechanisms

Lysosomes form part of our innate immunity and are an important line of defence against microbes, viruses and parasites. Although it is more than 50 years since de Duve discovered lysosomes, it is only in more recent years that we are slowly unravelling the molecular mechanisms involved in the delivery of material to the lysosome. However, successful intracellular pathogens often have a better grip on the mechanisms involved in delivery to the lysosome and can manipulate membrane trafficking pathways to create an intracellular environment that is favourable for replication. By studying pathogen effector proteins that are secreted into the host's cytosol, we can learn about both pathogen-survival mechanisms and further regulatory elements involved in trafficking to the lysosome.

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