Dissection of Two Complex Clusters of Resistance Genes in Lettuce (Lactuca sativa)

Of the over 50 phenotypic resistance genes mapped in lettuce, 25 colocalize to three major resistance clusters (MRC) on chromosomes 1, 2, and 4. Similarly, the majority of candidate resistance genes encoding nucleotide binding-leucine rich repeat (NLR) proteins genetically colocalize with phenotypic resistance loci. MRC1 and MRC4 span over 66 and 63 Mb containing 84 and 21 NLR-encoding genes, respectively, as well as 765 and 627 genes that are not related to NLR genes. Forward and reverse genetic approaches were applied to dissect MRC1 and MRC4. Transgenic lines exhibiting silencing were selected using silencing of β-glucuronidase as a reporter. Silencing of two of five NLR-encoding gene families resulted in abrogation of nine of 14 tested resistance phenotypes mapping to these two regions. At MRC1, members of the coiled coil-NLR-encoding RGC1 gene family were implicated in host and nonhost resistance through requirement for Dm5/8- and Dm45-mediated resistance to downy mildew caused by Bremia lactucae as well as the hypersensitive response to effectors AvrB, AvrRpm1, and AvrRpt2 of the nonpathogen Pseudomonas syringae. At MRC4, RGC12 family members, which encode toll interleukin receptor-NLR proteins, were implicated in Dm4-, Dm7-, Dm11-, and Dm44-mediated resistance to B. lactucae. Lesions were identified in the sequence of a candidate gene within dm7 loss-of-resistance mutant lines, confirming that RGC12G confers Dm7.

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

Genetics ◽

10.1093/genetics/159.4.1765 ◽

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.

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A DeoR-Type Transcription Regulator Is Required for Sugar-Induced Expression of Type III Secretion-Encoding Genes in Pseudomonas syringae pv. tomato DC3000

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-19-0290-r ◽

2020 ◽

Vol 33 (3) ◽

pp. 509-518 ◽

Cited By ~ 1

Author(s):

Sydney E. Turner ◽

Yin-Yuin Pang ◽

Megan R. O’Malley ◽

Alexandra J. Weisberg ◽

Valerie N. Fraser ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Type Iii Secretion ◽

Molecular Mechanisms ◽

In Planta ◽

Induced Expression ◽

Tn5 Transposon ◽

Type Iii ◽

Genes Encoding ◽

Tn5 Mutant ◽

Encoding Genes

The type III secretion system (T3SS) of plant-pathogenic Pseudomonas syringae is essential for virulence. Genes encoding the T3SS are not constitutively expressed and must be induced upon infection. Plant-derived metabolites, including sugars such as fructose and sucrose, are inducers of T3SS-encoding genes, yet the molecular mechanisms underlying perception of these host signals by P. syringae are unknown. Here, we report that sugar-induced expression of type III secretion A (setA), predicted to encode a DeoR-type transcription factor, is required for maximal sugar-induced expression of T3SS-associated genes in P. syringae DC3000. From a Tn5 transposon mutagenesis screen, we identified two independent mutants with insertions in setA. When both setA::Tn5 mutants were cultured in minimal medium containing fructose, genes encoding the T3SS master regulator HrpL and effector AvrRpm1 were expressed at lower levels relative to that of a wild-type strain. Decreased hrpL and avrRpm1 expression also occurred in a setA::Tn5 mutant in response to glucose, sucrose, galactose, and mannitol, demonstrating that setA is genetically required for T3SS induction by many different sugars. Expression of upstream regulators hrpR/S and rpoN was not altered in setA::Tn5, indicating that SetA positively regulates hrpL expression independently of increased transcription of these genes. In addition to decreased response to defined sugar signals, a setA::Tn5 mutant had decreased T3SS deployment during infection and was compromised in its ability to grow in planta and cause disease. These data suggest that SetA is necessary for P. syringae to effectively respond to T3SS-inducing sugar signals encountered during infection.

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Transcriptional profiling of three Pseudomonas syringae pv. actinidiae biovars reveals different responses to apoplast-like conditions related to strain virulence on host

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-20-0248-r ◽

2020 ◽

Author(s):

Elodie VANDELLE ◽

Teresa Colombo ◽

Alice Regaiolo ◽

Vanessa Maurizio ◽

Tommaso Libardi ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Transcriptional Profiling ◽

Gene Families ◽

Response Regulators ◽

Environmental Signals ◽

Detailed Structural Analysis ◽

Genes Encoding ◽

Whole Genome Microarray ◽

Operon Regulation ◽

Dependent Cell

Pseudomonas syringae pv. actinidiae (Psa) is a phytopathogen that causes devastating bacterial canker in kiwifruit. Among five biovars defined by genetic, biochemical and virulence traits, Psa3 is the most aggressive and is responsible for the most recent reported outbreaks, but the molecular basis of its heightened virulence is unclear. We therefore designed the first P. syringae multi-strain whole-genome microarray, encompassing biovars Psa1, Psa2 and Psa3 and the well-established model P. syringae pv. tomato, and analyzed early bacterial responses to an apoplast-like minimal medium. Transcriptomic profiling revealed (i) the strong activation in Psa3 of all hrp/hrc cluster genes, encoding components of the type III secretion system required for bacterial pathogenicity and involved in responses to environmental signals; (ii) potential repression of the hrp/hrc cluster in Psa2; and (iii) activation of flagellum-dependent cell motility and chemotaxis genes in Psa1. The detailed investigation of three gene families encoding upstream regulatory proteins (histidine kinases, their cognate response regulators, and proteins with diguanylate cyclase and/or phosphodiesterase domains) indicated that c-di-GMP may be a key regulator of virulence in Psa biovars. The gene expression data were supported by the quantification of biofilm formation. Our findings suggest that diverse early responses to the host apoplast, even among bacteria belonging to the same pathovar, can lead to different virulence strategies and may explain the differing outcomes of infections. Based on our detailed structural analysis of hrp operons, we also propose a revision of hrp cluster organization and operon regulation in P. syringae.

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Identification and characterization of genes encoding the nuclear envelope LINC complex in the monocot species Zea mays

10.1101/343939 ◽

2018 ◽

Author(s):

Hardeep K. Gumber ◽

Joseph F. McKenna ◽

Amado L. Estrada ◽

Andrea F. Tolmie ◽

Katja Graumann ◽

...

Keyword(s):

Nuclear Envelope ◽

Nuclear Periphery ◽

Coiled Coil ◽

Gene Families ◽

Grass Species ◽

Linc Complex ◽

Genes Encoding ◽

Model Grass ◽

And Function

ABSTRACTThe LINC (Linker of Nucleoskeleton to Cytoskeleton) complex is an essential multi-protein structure spanning the nuclear envelope. It connects the cytoplasm to the nucleoplasm, functions to maintain nuclear shape and architecture, and regulates chromosome dynamics during cell division. Knowledge of LINC complex composition and function in the plant kingdom is primarily limited to Arabidopsis, but critically missing from the evolutionarily distant monocots which include grasses, the most important agronomic crops worldwide. To fill this knowledge gap, we identified and characterized 22 maize genes, including a new grass-specific KASH gene family. Using bioinformatic, biochemical, and cell biological approaches, we provide evidence that representative KASH candidates localize to the nuclear periphery and interact with ZmSUN2 in vivo. FRAP experiments using domain-deletion constructs verified that this SUN-KASH interaction was dependent on the SUN but not the coiled-coil domain of ZmSUN2. A summary working model is proposed for the entire maize LINC complex encoded by conserved and divergent gene families. These findings expand our knowledge of the plant nuclear envelope in a model grass species, with implications for both basic and applied cellular research.SUMMARY STATEMENTGenes encoding maize candidates for the core LINC and associated complex proteins have been comprehensively identified with functional validation by one or more assays for several of the KASH genes.

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Comparative Mapping of Three Bacterial, Three Fungal, and One Virus Disease-resistance Genes in Common Bean

HortScience ◽

10.21273/hortsci.33.3.547a ◽

1998 ◽

Vol 33 (3) ◽

pp. 547a-547

Author(s):

Geunhwa Jung ◽

James Nienhuis ◽

Dermot P. Coyne ◽

H.M. Ariyarathne

Keyword(s):

Disease Resistance ◽

Common Bean ◽

Pseudomonas Syringae ◽

Resistance Genes ◽

Fungal Pathogens ◽

Xanthomonas Campestris ◽

Virus Disease ◽

Disease Resistance Genes ◽

Brown Spot ◽

Viral Pathogen

Common bacterial blight (CBB), bacterial brown spot (BBS), and halo blight (HB), incited by the bacterial pathogens Xanthomonas campestris pv. phaseoli (Smith) Dye, Pseodomonas syringae pv. syringa, and Pseudomonas syringae pv. phaseolicola, respectively are important diseases of common bean. In addition three fungal pathogens, web blight (WB) Thanatephorus cucumeris, rust Uromyces appendiculatus, and white mold (WM) Sclerotinia sclerotiorum, are also destructive diseases attacking common bean. Bean common mosaic virus is also one of most major virus disease. Resistance genes (QTLs and major genes) to three bacterial (CBB, BBS, and HB), three fungal (WB, rust, and WM), and one viral pathogen (BCMV) were previously mapped in two common bean populations (BAC 6 × HT 7719 and Belneb RR-1 × A55). The objective of this research was to use an integrated RAPD map of the two populations to compare the positions and effect of resistance QTL in common bean. Results indicate that two chromosomal regions associated with QTL for CBB resistance mapped in both populations. The same chromosomal regions associated with QTL for disease resistance to different pathogens or same pathogens were detected in the integrated population.

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Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

European Journal of Clinical Microbiology & Infectious Diseases ◽

10.1007/s10096-021-04185-7 ◽

2021 ◽

Author(s):

Fatma Ben Abid ◽

Clement K. M. Tsui ◽

Yohei Doi ◽

Anand Deshmukh ◽

Christi L. McElheny ◽

...

Keyword(s):

Common Species ◽

Clinical Samples ◽

Whole Genome ◽

E Coli ◽

Carbapenem Resistant ◽

Genes Encoding ◽

Encoding Genes ◽

Sequence Types ◽

Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

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Identification of Three Putative Signal Transduction Genes Involved in R Gene-Specified Disease Resistance in Arabidopsis

Genetics ◽

10.1093/genetics/152.1.401 ◽

1999 ◽

Vol 152 (1) ◽

pp. 401-412 ◽

Cited By ~ 1

Author(s):

Randall F Warren ◽

Peter M Merritt ◽

Eric Holub ◽

Roger W Innes

Keyword(s):

Disease Resistance ◽

Pseudomonas Syringae ◽

Resistance Genes ◽

Virulent Strain ◽

Disease Resistance Genes ◽

Avirulence Gene ◽

Detectable Effect ◽

Disease Resistance Gene ◽

Protein Functions ◽

Signal Transduction Genes

Abstract The RPS5 disease resistance gene of Arabidopsis mediates recognition of Pseudomonas syringae strains that possess the avirulence gene avrPphB. By screening for loss of RPS5-specified resistance, we identified five pbs (avrPphB susceptible) mutants that represent three different genes. Mutations in PBS1 completely blocked RPS5-mediated resistance, but had little to no effect on resistance specified by other disease resistance genes, suggesting that PBS1 facilitates recognition of the avrPphB protein. The pbs2 mutation dramatically reduced resistance mediated by the RPS5 and RPM1 resistance genes, but had no detectable effect on resistance mediated by RPS4 and had an intermediate effect on RPS2-mediated resistance. The pbs2 mutation also had varying effects on resistance mediated by seven different RPP (recognition of Peronospora parasitica) genes. These data indicate that the PBS2 protein functions in a pathway that is important only to a subset of disease-resistance genes. The pbs3 mutation partially suppressed all four P. syringae-resistance genes (RPS5, RPM1, RPS2, and RPS4), and it had weak-to-intermediate effects on the RPP genes. In addition, the pbs3 mutant allowed higher bacterial growth in response to a virulent strain of P. syringae, indicating that the PBS3 gene product functions in a pathway involved in restricting the spread of both virulent and avirulent pathogens. The pbs mutations are recessive and have been mapped to chromosomes I (pbs2) and V (pbs1 and pbs3).

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Transcriptomic and genetic approaches reveal an essential role of the NAC transcription factor SlNAP1 in the growth and defense response of tomato

Horticulture Research ◽

10.1038/s41438-020-00442-6 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Jiao Wang ◽

Chenfei Zheng ◽

Xiangqi Shao ◽

Zhangjian Hu ◽

Jianxin Li ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Defense Response ◽

Global Climate ◽

Plant Responses ◽

Multiple Stresses ◽

Bacterial Diseases ◽

Bacterial Wilt Disease ◽

Transgenic Lines ◽

Breeding Target

AbstractWith global climate change, plants are frequently being exposed to various stresses, such as pathogen attack, drought, and extreme temperatures. Transcription factors (TFs) play crucial roles in numerous plant biological processes; however, the functions of many tomato (Solanum lycopersicum L.) TFs that regulate plant responses to multiple stresses are largely unknown. Here, using an RNA-seq approach, we identified SlNAP1, a NAC TF-encoding gene, which was strongly induced by various stresses. By generating SlNAP1 transgenic lines and evaluating their responses to biotic and abiotic stresses in tomato, we found that SlNAP1-overexpressing plants showed significantly enhanced defense against two widespread bacterial diseases, leaf speck disease, caused by Pseudomonas syringae pv. tomato (Pst) DC3000, and root-borne bacterial wilt disease, caused by Ralstonia solanacearum. In addition, SlNAP1 overexpression dramatically improved drought tolerance in tomato. Although the SlNAP1-overexpressing plants were shorter than the wild-type plants during the early vegetative stage, eventually, their fruit yield increased by 10.7%. Analysis of different hormone contents revealed a reduced level of physiologically active gibberellins (GAs) and an increased level of salicylic acid (SA) and abscisic acid (ABA) in the SlNAP1-overexpressing plants. Moreover, EMSAs and ChIP-qPCR assays showed that SlNAP1 directly activated the transcription of multiple genes involved in GA deactivation and both SA and ABA biosynthesis. Our findings reveal that SlNAP1 is a positive regulator of the tomato defense response against multiple stresses and thus may be a potential breeding target for improving crop yield and stress resistance.

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Preliminary Results on the Prevalence of Salmonella Spp. in Marine Animals Stranded in Sicilian Coasts: Antibiotic Susceptibility Profile and ARGs Detection in the Isolated Strains

Pathogens ◽

10.3390/pathogens10080930 ◽

2021 ◽

Vol 10 (8) ◽

pp. 930

Author(s):

Delia Gambino ◽

Sonia Sciortino ◽

Sergio Migliore ◽

Lucia Galuppo ◽

Roberto Puleio ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Susceptibility ◽

Antibiotic Resistance Genes ◽

Diffusion Method ◽

Salmonella Spp ◽

Marine Animals ◽

Disk Diffusion Method ◽

Phenotypic Resistance ◽

Low Prevalence

The presence of Salmonella spp. in marine animals is a consequence of contamination from terrestrial sources (human activities and animals). Bacteria present in marine environments, including Salmonella spp., can be antibiotic resistant or harbor resistance genes. In this study, Salmonella spp. detection was performed on 176 marine animals stranded in the Sicilian coasts (south Italy). Antibiotic susceptibility, by disk diffusion method and MIC determination, and antibiotic resistance genes, by molecular methods (PCR) of the Salmonella spp. strains, were evaluated. We isolated Salmonella spp. in three animals, though no pathological signs were detected. Our results showed a low prevalence of Salmonella spp. (1.7%) and a low incidence of phenotypic resistance in three Salmonella spp. strains isolated. Indeed, of the three strains, only Salmonella subsp. enterica serovar Typhimurium from S. coeruleoalba and M. mobular showed phenotypic resistance: the first to ampicillin, tetracycline, and sulphamethoxazole, while the latter only to sulphamethoxazole. However, all strains harbored resistance genes (blaTEM, blaOXA, tet(A), tet(D), tet(E), sulI, and sulII). Although the low prevalence of Salmonella spp. found in this study does not represent a relevant health issue, our data contribute to the collection of information on the spread of ARGs, elements involved in antibiotic resistance, now considered a zoonosis in a One Health approach.

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Molecular investigation of an outbreak associated with total parenteral nutrition contaminated with NDM-producing Leclercia adecarboxylata

BMC Infectious Diseases ◽

10.1186/s12879-021-05923-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Elvira Garza-González ◽

Paola Bocanegra-Ibarias ◽

Eduardo Rodríguez-Noriega ◽

Esteban González-Díaz ◽

Jesús Silva-Sanchez ◽

...

Keyword(s):

Comparative Genomics ◽

Carbapenem Resistance ◽

Clonal Diversity ◽

Molecular Characteristics ◽

Molecular Evidence ◽

Carbapenem Resistant ◽

Parental Nutrition ◽

Genes Encoding ◽

Main Lineage ◽

Encoding Genes

Abstract Background This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). Methods For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase–encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary. Results All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for blaNDM-1, blaTEM-1B, and blaSHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The blaNDM-1 gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains. Conclusion We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.

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