scholarly journals The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Stéphane Hacquard ◽  
Benjamin Petre ◽  
Pascal Frey ◽  
Arnaud Hecker ◽  
Nicolas Rouhier ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Rust Fungus ◽  
Gene Families ◽  
Genetic Determinants ◽  
Plant Host ◽  
Recombinant Protein Purification ◽  
Functional Studies ◽  
Regulated Expression ◽  
Genes Encoding ◽  
Host Tissues

Poplars are extensively cultivated worldwide, and their susceptibility to the leaf rust fungusMelampsora larici-populinaleads to considerable damages in plantations. Despite a good knowledge of the poplar rust life cycle, and particularly the epidemics on poplar, the perennial status of the plant host and the obligate biotrophic lifestyle of the rust fungus are bottlenecks for molecular investigations. Following the completion of bothM. larici-populinaandPopulus trichocarpagenome sequences, gene families involved in poplar resistance or in rust fungus virulence were investigated, allowing the identification of key genetic determinants likely controlling the outcome of the interaction. Specific expansions of resistance and defense-related genes in poplar indicate probable innovations in perennial species in relation with host-pathogen interactions. The genome ofM. Larici-populinacontains a strikingly high number of genes encoding small secreted proteins (SSPs) representing hundreds of candidate effectors. Transcriptome analyses of interacting partners in compatible and incompatible interactions revealed conserved set of genes involved in poplar defense reactions as well as timely regulated expression of SSP transcripts during host tissues colonisation. Ongoing functional studies of selected candidate effectors will be achieved mainly on the basis of recombinant protein purification and subsequent characterisation.

scholarly journals Gene families and evolution of trehalose metabolism in plants

2007 ◽  
Vol 34 (6) ◽  
pp. 550 ◽  
Author(s):  
John E. Lunn
Keyword(s):  
Physcomitrella Patens ◽  
Oryza Sativa L ◽  
Populus Trichocarpa ◽  
Gene Families ◽  
Class I ◽  
Trehalose Metabolism ◽  
Genes Encoding ◽  
Catalytically Active ◽  
Large Families ◽  
Selaginella Moellendorffii

The genomes of Arabidopsis thaliana L., rice (Oryza sativa L.) and poplar (Populus trichocarpa Torr. & A.Gray) contain large families of genes encoding trehalose-phosphate synthase (TPS) and trehalose-phosphatase (TPP). The class I subfamily of TPS genes encodes catalytically active TPS enzymes, and is represented by only one or two genes in most species. A. thaliana is atypical in having four class I TPS genes, three of which (AtTPS2–4) encode unusual short isoforms of TPS that appear to be found only in members of the Brassicaceae family. The class II TPS genes encode TPS-like proteins with a C-terminal TPP-like domain, but there is no experimental evidence that they have any enzymatic activity and their function is unknown. Both classes of TPS gene are represented in the genomes of chlorophyte algae (Ostreococcus species) and non-flowering plants [Physcomitrella patens (Hedw.) Bruch & Schimp.(B.S.G.) and Selaginella moellendorffii (Hieron. in Engl. & Prantl.)]. This survey shows that the gene families encoding the enzymes of trehalose metabolism are very ancient, pre-dating the divergence of the streptophyte and chlorophyte lineages. It also provides a frame of reference for future studies to elucidate the function of trehalose metabolism in plants.

Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene familiesThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

2007 ◽  
Vol 85 (12) ◽  
pp. 1182-1201 ◽  
Author(s):  
Björn Hamberger ◽  
Margaret Ellis ◽  
Michael Friedmann ◽  
Clarice de Azevedo Souza ◽  
Brad Barbazuk ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Populus Trichocarpa ◽  
Rice Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Comparative Approach ◽  
Expression Data ◽  
Poplar Genome ◽  
Genes Encoding ◽  
Bona Fide

The completion of the Populus trichocarpa (Torr. & A. Gray) (poplar) genome sequence offers an opportunity to study complete genome families in a third fully sequenced angiosperm (after Arabidopsis and rice) and to conduct comparative genomics studies of angiosperm gene family evolution. We focussed on gene families encoding phenylpropanoid and phenylpropanoid-like enzymes, and identified and annotated the full set of genes encoding these and related enzymes in the poplar genome. We used a similar approach to identify an analogous set of genes from the rice genome and generated phylogenetic trees for nine phenylpropanoid gene families from aligned poplar, Arabidopsis, and rice predicted protein sequences. This enabled us to identify the likely full set of bona fide poplar lignin-related phenylpropanoid genes (poplar “lignification toolbox”) apparent within well-defined clades in all phylogenetic trees. Analysis of expression data for poplar genes confirmed and refined annotations of lignin-related genes, which generally showed high expression in wood-forming tissues. Expression data from both poplar and Arabidopsis were used to make inferences regarding biochemical and biological functions of phenylpropanoid-like genes with unknown functions. The comparative approach also provided insights into the evolution of angiosperm phenylpropanoid-like gene families, illustrating lineage-specific clades as well as ancient clades containing genes with apparent conserved function.

scholarly journals A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors in Melampsora larici-populina (Poplar Leaf Rust)

2012 ◽  
Vol 25 (3) ◽  
pp. 279-293 ◽  
Author(s):  
Stéphane Hacquard ◽  
David L. Joly ◽  
Yao-Cheng Lin ◽  
Emilie Tisserant ◽  
Nicolas Feau ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Rust Fungus ◽  
Secreted Proteins ◽  
Recent Analysis ◽  
Functional Studies ◽  
Genes Encoding ◽  
Coordinated Expression ◽  
Encoding Genes ◽  
Poplar Leaf ◽  
Small Secreted Proteins

The obligate biotrophic rust fungus Melampsora larici-populina is the most devastating and widespread pathogen of poplars. Studies over recent years have identified various small secreted proteins (SSP) from plant biotrophic filamentous pathogens and have highlighted their role as effectors in host–pathogen interactions. The recent analysis of the M. larici-populina genome sequence has revealed the presence of 1,184 SSP-encoding genes in this rust fungus. In the present study, the expression and evolutionary dynamics of these SSP were investigated to pinpoint the arsenal of putative effectors that could be involved in the interaction between the rust fungus and poplar. Similarity with effectors previously described in Melampsora spp., richness in cysteines, and organization in large families were extensively detailed and discussed. Positive selection analyses conducted over clusters of paralogous genes revealed fast-evolving candidate effectors. Transcript profiling of selected M. laricipopulina SSP showed a timely coordinated expression during leaf infection, and the accumulation of four candidate effectors in distinct rust infection structures was demonstrated by immunolocalization. This integrated and multifaceted approach helps to prioritize candidate effector genes for functional studies.

scholarly journals Genetic determinants of endophytism in the Arabidopsis root mycobiome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fantin Mesny ◽  
Shingo Miyauchi ◽  
Thorsten Thiergart ◽  
Brigitte Pickel ◽  
Lea Atanasova ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Gene Families ◽  
Plant Health ◽  
Transcriptional Program ◽  
Genetic Determinants ◽  
Cell Wall Degrading Enzymes ◽  
Arabidopsis Root ◽  
Disease States ◽  
Genes Encoding ◽  
Health And Disease

AbstractThe roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.

scholarly journals A peroxisomal β-oxidative pathway contributes to the formation of C6–C1 aromatic volatiles in poplar

2021 ◽  
Author(s):  
Nathalie D Lackus ◽  
Axel Schmidt ◽  
Jonathan Gershenzon ◽  
Tobias G Köllner
Keyword(s):  
Cinnamic Acid ◽  
Aromatic Compounds ◽  
Populus Trichocarpa ◽  
Alternative Pathway ◽  
Gene Families ◽  
Defense Responses ◽  
In Planta ◽  
Black Cottonwood ◽  
Oxidative Pathway

AbstractBenzenoids (C6–C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6–C3). The biosynthesis of C6–C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6–C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors

2014 ◽  
Vol 5 ◽  
Author(s):  
Jana Sperschneider ◽  
Hua Ying ◽  
Peter N. Dodds ◽  
Donald M. Gardiner ◽  
Narayana M. Upadhyaya ◽  
...  
Keyword(s):  
Stem Rust ◽  
Rust Fungus ◽  
Gene Families ◽  
Wheat Stem Rust ◽  
Diversifying Selection

scholarly journals Genetic determinants of Pseudomonas aeruginosa biofilm establishment

Microbiology ◽  
2010 ◽  
Vol 156 (2) ◽  
pp. 431-441 ◽  
Author(s):  
Mathias Müsken ◽  
Stefano Di Fiore ◽  
Andreas Dötsch ◽  
Rainer Fischer ◽  
Susanne Häussler
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Laser Scanning ◽  
Growth Conditions ◽  
Confocal Laser Scanning Microscope ◽  
Confocal Laser ◽  
Repair System ◽  
Ph Homeostasis ◽  
Genetic Determinants ◽  
Complex Process ◽  
Genes Encoding

The establishment of bacterial biofilms on surfaces is a complex process that requires various factors for each consecutive developmental step. Here we report the screening of the comprehensive Harvard Pseudomonas aeruginosa PA14 mutant library for mutants exhibiting an altered biofilm phenotype. We analysed the capability of all mutants to form biofilms at the bottom of a 96-well plate by the use of an automated confocal laser-scanning microscope and found 394 and 285 genetic determinants of reduced and enhanced biofilm production, respectively. Overall, 67 % of the identified mutants were affected within genes encoding hypothetical proteins, indicating that novel developmental pathways are likely to be dissected in the future. Nevertheless, a common theme that emerged from the analysis of the genes with a predicted function is that the establishment of a biofilm requires regulatory components that are involved in survival under microaerophilic growth conditions, arginine metabolism, alkyl-quinolone signalling, pH homeostasis and the DNA repair system.

scholarly journals Comparative Analysis of Genetic Determinants Encoding Cadmium, Arsenic, and Benzalkonium Chloride Resistance in Listeria monocytogenes of Human, Food, and Environmental Origin

2021 ◽  
Vol 11 ◽  
Author(s):  
Tereza Gelbicova ◽  
Martina Florianova ◽  
Lucie Hluchanova ◽  
Alžběta Kalova ◽  
Kristýna Korena ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Benzalkonium Chloride ◽  
Extensive Study ◽  
Whole Genome Sequencing Data ◽  
Production Environment ◽  
Sequencing Data ◽  
Genetic Determinants ◽  
Cadmium Resistance ◽  
Chloride Resistance ◽  
Genes Encoding

Environmental adaptation of Listeria monocytogenes is a complex process involving various mechanisms that can contribute to their survival in the environment, further spreading throughout the food chain and the development of listeriosis. The aim of this study was to analyze whole-genome sequencing data in a set of 270 strains of L. monocytogenes derived from human listeriosis cases and food and environmental sources in order to compare the prevalence and type of genetic determinants encoding cadmium, arsenic, and benzalkonium chloride resistance. Most of the detected genes of cadmium (27.8%), arsenic (15.6%), and benzalkonium chloride (7.0%) resistance were located on mobile genetic elements, even in phylogenetically distant lineages I and II, which indicates the possibility of their horizontal spread. Although no differences were found in the prevalence of these genes between human and food strains, they have been detected sporadically in strains from the environment. Regarding cadmium resistance genes, cadA1C1_Tn5422 predominated, especially in clonal complexes (CCs) 121, 8, and 3 strains. At the same time, qacH_Tn6188-encoding benzalkonium chloride resistance was most frequently detected in the genome of CC121 strains. Genes encoding arsenic resistance were detected mainly in strains CC2 (located on the chromosomal island LGI2) and CC9 (carried on Tn554). The results indicated a relationship between the spread of genes encoding resistance to cadmium, arsenic, and benzalkonium chloride in certain serotypes and CCs and showed the need for a more extensive study of L. monocytogenes strains to better understand their ability to adapt to the food production environment.

scholarly journals Growth-regulated expression of rhoG, a new member of the ras homolog gene family.

1992 ◽  
Vol 12 (7) ◽  
pp. 3138-3148 ◽  
Author(s):  
S Vincent ◽  
P Jeanteur ◽  
P Fort
Keyword(s):  
Gene Family ◽  
Transcriptional Activation ◽  
Small Gtpase ◽  
Lung Fibroblasts ◽  
Human Organs ◽  
Regulated Expression ◽  
Genes Encoding ◽  
Rna Stabilization ◽  
Rna Accumulation ◽  
High Level

Cellular transition from the resting state to DNA synthesis involves master switches genes encoding transcriptional factors (e.g., fos, jun, and egr genes), whose targets remain to be fully characterized. To isolate coding sequences specifically accumulated in late G1, a differential screening was performed on a cDNA library prepared from hamster lung fibroblasts stimulated for 5 h with serum. One of the positive clones which displayed a sevenfold induction, turned out to code for a protein sharing homology to Ras-like products. Cloning and sequence analysis of the human homolog revealed that this putative new small GTPase, referred to as rhoG, is more closely related to the rac, CDC42, and TC10 members of the rho (ras homolog) gene family and might have diverged very early during evolution. rhoG mRNA accumulates in proportion to the mitogenic strength of various purified growth factors used for the stimulation, as a consequence of transcriptional activation. G1-specific RNA accumulation is impaired upon addition of antimitogenic cyclic AMP and is enhanced when protein synthesis is inhibited, mainly as a result of RNA stabilization. rhoG mRNA expression is observed in a wide variety of human organs but reaches a particularly high level in lung and placental tissues.

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