The Pathogenicity of Pseudomonas syringae MB03 against Caenorhabditis elegans and the Transcriptional Response of Nematicidal Genes upon Different Nutritional Conditions

Knowledge of how anthelmintics are metabolized and excreted in nematodes is an integral part of understanding the factors that determine their potency, spectrum of activity and for investigating mechanisms of resistance. Although there is remarkably little information on these processes in nematodes, it is often suggested that they are of minimal importance for the major anthelmintic drugs. Consequently, we have investigated how the model nematode Caenorhabditis elegans responds to and metabolizes albendazole, one of the most important anthelmintic drugs for human and animal use. Using a mutant strain lacking the β-tubulin drug target to minimize generalized stress responses, we show that the transcriptional response is dominated by genes encoding XMEs (xenobiotic-metabolizing enzymes), particularly cytochrome P450s and UGTs (UDP-glucuronosyl transferases). The most highly induced genes are predominantly expressed in the worm intestine, supporting their role in drug metabolism. HPLC-MS/MS revealed the production of two novel glucoside metabolites in C. elegans identifying a major difference in the biotransformation of this drug between nematodes and mammals. This is the first demonstration of metabolism of a therapeutic anthelmintic in C. elegans and provides a framework for its use to functionally investigate nematode anthelmintic metabolism.

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The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions

Frontiers in Plant Science ◽

10.3389/fpls.2021.637595 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jun Liu ◽

Menghao Yu ◽

Yixin Ge ◽

Yanli Tian ◽

Baishi Hu ◽

...

Keyword(s):

Gene Expression ◽

Pseudomonas Syringae ◽

Stress Responses ◽

Capsular Polysaccharide ◽

Rna Binding ◽

Rna Binding Proteins ◽

Expression Profiles ◽

Transcriptomic Analysis ◽

Phosphate Metabolism ◽

Nutritional Conditions

The post-transcriptional regulator RsmA globally controls gene expression in bacteria. Previous studies showed that RsmA2 and RsmA3 played critical roles in regulating type III secretion system (T3SS), motility, syringafactin, and alginate productions in Pseudomonas syringae pv. tomato strain DC3000 (PstDC3000). In this study, we investigated global gene expression profiles of the wild-type PstDC3000, the rsmA3 mutant, and the rsmA2/A3 double mutant in the hrp-inducing minimum medium (HMM) and King’s B (KB) medium. By comparing the rsmA2/A3 and rsmA3 mutants to PstDC3000, a total of 1358 and 1074 differentially expressed genes (DEGs) in HMM, and 870 and 1463 DEGs in KB were uncovered, respectively. When comparing the rsmA2/A3 mutant with the rsmA3 mutant, 277 and 741 DEGs in HMM and KB, respectively, were revealed. Transcriptomic analysis revealed that the rsmY, rsmZ, and rsmX1-5 non-coding small RNAs (ncsRNAs) were positively affected by RsmA2 and RsmA3, while RsmA3 positively regulates the expression of the rsmA2 gene and negatively regulates both rsmA1 and rsmA5 gene expression. Comparative transcriptomic analysis showed that RsmA2 and RsmA3 synergistically influenced the expression of genes involved in T3SS and alginate biosynthesis in HMM and chemotaxis in KB. RsmA2 and RsmA3 inversely affected genes involved in syringafactin production in HMM and ribosomal protein biosynthesis in KB. In addition, RsmA2 played a major role in influencing genes involved in sarcosine and thiamine biosynthesis in HMM and in mannitol and phosphate metabolism in KB. On the other hand, genes involved in fatty acid metabolism, cellulose biosynthesis, signal transduction, and stress responses were mainly impacted by RsmA3 in both HMM and KB; whereas RsmA3 played a major role in controlling genes involved in c-di-GMP, phosphate metabolism, chemotaxis, and capsular polysaccharide in HMM. Furthermore, regulation of syringafactin production and oxidative stress by RsmA2 and RsmA3 was experimentally verified. Our results suggested the potential interplay among the RsmA proteins, which exhibit distinct and overlapping roles in modulating virulence and survival in P. syringae under different nutritional conditions.

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Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock

Nucleic Acids Research ◽

10.1093/nar/gkz693 ◽

2019 ◽

Vol 47 (18) ◽

pp. 9829-9841 ◽

Cited By ~ 6

Author(s):

William P Schreiner ◽

Delaney C Pagliuso ◽

Jacob M Garrigues ◽

Jerry S Chen ◽

Antti P Aalto ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Heat Shock ◽

Elevated Temperatures ◽

Transcriptional Response ◽

Heat Shock Factor 1 ◽

Protein Coding ◽

Repeat Elements ◽

Cellular Survival ◽

Non Coding Rna ◽

Shock Proteins

Abstract Elevated temperatures activate a heat shock response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor heat shock factor 1 (HSF-1), which binds heat shock elements (HSEs) in the promoters of genes induced by heat shock (HS). The upregulation of protein-coding genes (PCGs), such as heat shock proteins and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to HS has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and downregulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.

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HIF-1 and SKN-1 Coordinate the Transcriptional Response to Hydrogen Sulfide in Caenorhabditis elegans

PLoS ONE ◽

10.1371/journal.pone.0025476 ◽

2011 ◽

Vol 6 (9) ◽

pp. e25476 ◽

Cited By ~ 26

Author(s):

Dana L. Miller ◽

Mark W. Budde ◽

Mark B. Roth

Keyword(s):

Hydrogen Sulfide ◽

Caenorhabditis Elegans ◽

Transcriptional Response

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The Cuticle Mutant eca2 Modifies Plant Defense Responses to Biotrophic and Necrotrophic Pathogens and Herbivory Insects

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-07-17-0181-r ◽

2018 ◽

Vol 31 (3) ◽

pp. 344-355 ◽

Cited By ~ 7

Author(s):

Catherine Blanc ◽

Fania Coluccia ◽

Floriane L’Haridon ◽

Martha Torres ◽

Marlene Ortiz-Berrocal ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Defense Mechanism ◽

Induced Defense ◽

Constitutive Expression ◽

Bacterial Pathogen ◽

Transcriptional Response ◽

Chemical Characterization ◽

Biotic Interactions ◽

Defense Responses ◽

Herbivorous Insect

We isolated previously several Arabidopsis thaliana mutants with constitutive expression of the early microbe-associated molecular pattern–induced gene ATL2, named eca (expresión constitutiva de ATL2). Here, we further explored the interaction of eca mutants with pest and pathogens. Of all eca mutants, eca2 was more resistant to a fungal pathogen (Botrytis cinerea) and a bacterial pathogen (Pseudomonas syringae) as well as to a generalist herbivorous insect (Spodoptera littoralis). Permeability of the cuticle is increased in eca2; chemical characterization shows that eca2 has a significant reduction of both cuticular wax and cutin. Additionally, we determined that eca2 did not display a similar compensatory transcriptional response, compared with a previously characterized cuticular mutant, and that resistance to B. cinerea is mediated by the priming of the early and late induced defense responses, including salicylic acid– and jasmonic acid–induced genes. These results suggest that ECA2-dependent responses are involved in the nonhost defense mechanism against biotrophic and necrotrophic pathogens and against a generalist insect by modulation and priming of innate immunity and late defense responses. Making eca2 an interesting model to characterize the molecular basis for plant defenses against different biotic interactions and to study the initial events that take place in the cuticle surface of the aerial organs.

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Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression

Genetics ◽

10.1534/genetics.120.302923 ◽

2020 ◽

Vol 215 (4) ◽

pp. 1039-1054

Author(s):

Sophie J. Walton ◽

Han Wang ◽

Porfirio Quintero-Cadena ◽

Alex Bateman ◽

Paul W. Sternberg

Keyword(s):

Gene Expression ◽

Heat Stress ◽

Caenorhabditis Elegans ◽

Heat Shock ◽

Heat Shock Response ◽

Genetic Locus ◽

Transcriptional Response ◽

Transcriptional Elongation ◽

Link Type ◽

Shock Response

To mitigate the deleterious effects of temperature increases on cellular organization and proteotoxicity, organisms have developed mechanisms to respond to heat stress. In eukaryotes, HSF1 is the master regulator of the heat shock transcriptional response, but the heat shock response pathway is not yet fully understood. From a forward genetic screen for suppressors of heat-shock-induced gene expression in Caenorhabditis elegans, we found a new allele of hsf-1 that alters its DNA-binding domain, and we found three additional alleles of sup-45, a previously molecularly uncharacterized genetic locus. We identified sup-45 as one of the two hitherto unknown C. elegans orthologs of the human AF4/FMR2 family proteins, which are involved in regulation of transcriptional elongation rate. We thus renamed sup-45 as affl-2 (AF4/FMR2-Like). Through RNA-seq, we demonstrated that affl-2 mutants are deficient in heat-shock-induced transcription. Additionally, affl-2 mutants have herniated intestines, while worms lacking its sole paralog (affl-1) appear wild type. AFFL-2 is a broadly expressed nuclear protein, and nuclear localization of AFFL-2 is necessary for its role in heat shock response. affl-2 and its paralog are not essential for proper HSF-1 expression and localization after heat shock, which suggests that affl-2 may function downstream of, or parallel to, hsf-1. Our characterization of affl-2 provides insights into the regulation of heat-shock-induced gene expression to protect against heat stress.

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Transcriptional response of Caenorhabditis elegans when exposed to Shigella flexneri

Genomics ◽

10.1016/j.ygeno.2019.05.016 ◽

2020 ◽

Vol 112 (1) ◽

pp. 774-781 ◽

Cited By ~ 2

Author(s):

Pamodha Somasiri ◽

Carolyn A. Behm ◽

Marcin Adamski ◽

Jiayu Wen ◽

Naresh K. Verma

Keyword(s):

Caenorhabditis Elegans ◽

Shigella Flexneri ◽

Transcriptional Response

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Pseudomonas syringae pv. tomato DC3000 Uses Constitutive and Apoplast-Induced Nutrient Assimilation Pathways to Catabolize Nutrients That Are Abundant in the Tomato Apoplast

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-21-2-0269 ◽

2008 ◽

Vol 21 (2) ◽

pp. 269-282 ◽

Cited By ~ 139

Author(s):

Arantza Rico ◽

Gail M. Preston

Keyword(s):

Pseudomonas Syringae ◽

Stress Responses ◽

Nutrient Utilization ◽

Plant Colonization ◽

Tomato Dc3000 ◽

Secretion Pathway ◽

Physiological Processes ◽

Nutritional Conditions ◽

Apoplastic Fluid ◽

Type Iii Protein Secretion

The plant apoplast is the intercellular space that surrounds plant cells, in which metabolic and physiological processes relating to cell wall biosynthesis, nutrient transport, and stress responses occur. The apoplast is also the primary site of infection for hemibiotrophic pathogens such as P. syringae, which obtain nutrients directly from apoplastic fluid. We have used apoplastic fluid extracted from healthy tomato leaves as a growth medium for Pseudomonas spp. in order to investigate the role of apoplastic nutrients in plant colonization by Pseudomonas syringae. We have confirmed that apoplast extracts mimic some of the environmental and nutritional conditions that bacteria encounter during apoplast colonization by demonstrating that expression of the plant-induced type III protein secretion pathway is upregulated during bacterial growth in apoplast extracts. We used a modified phenoarray technique to show that apoplast-adapted P. syringae pv. tomato DC3000 expresses nutrient utilization pathways that allow it to use sugars, organic acids, and amino acids that are highly abundant in the tomato apoplast. Comparative analyses of the nutrient utilization profiles of the genome-sequenced strains P. syringae pv. tomato DC3000, P. syringae pv. syringae B728a, P. syringae pv. phaseolicola 1448A, and the unsequenced strain P. syringae pv. tabaci 11528 with nine other genome-sequenced strains of Pseudomonas provide further evidence that P. syringae strains are adapted to use nutrients that are abundant in the leaf apoplast. Interestingly, P. syringae pv. phaseolicola 1448A lacks many of the nutrient utilization abilities that are present in three other P. syringae strains tested, which can be directly linked to differences in the P. syringae pv. phaseolicola 1448A genome.

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