scholarly journals Escherichia coli Metabolite Profiling Leads to the Development of an RNA Interference Strain for Caenorhabditis elegans

2019 ◽  
Vol 10 (1) ◽  
pp. 189-198 ◽  
Author(s):  
Isaiah A. A. Neve ◽  
Jessica N. Sowa ◽  
Chih-Chun J. Lin ◽  
Priya Sivaramakrishnan ◽  
Christophe Herman ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Mitochondrial Morphology ◽  
Bacterial Strains ◽  
Hybrid Strain ◽  
Fat Storage ◽  
C Elegans ◽  
Interference Response ◽  
K 12

The relationship of genotypes to phenotypes can be modified by environmental inputs. Such crucial environmental inputs include metabolic cues derived from microbes living together with animals. Thus, the analysis of genetic effects on animals’ physiology can be confounded by variations in the metabolic profile of microbes. Caenorhabditis elegans exposed to distinct bacterial strains and species exhibit phenotypes different at cellular, developmental, and behavioral levels. Here we reported metabolomic profiles of three Escherichia coli strains, B strain OP50, K-12 strain MG1655, and B-K-12 hybrid strain HB101, as well as different mitochondrial and fat storage phenotypes of C. elegans exposed to MG1655 and HB101 vs. OP50. We found that these metabolic phenotypes of C. elegans are not correlated with overall metabolic patterning of bacterial strains, but their specific metabolites. In particular, the fat storage phenotype is traced to the betaine level in different bacterial strains. HT115 is another K-12 E. coli strain that is commonly utilized to elicit an RNA interference response, and we showed that C. elegans exposed to OP50 and HT115 exhibit differences in mitochondrial morphology and fat storage levels. We thus generated an RNA interference competent OP50 (iOP50) strain that can robustly and consistently knockdown endogenous C. elegans genes in different tissues. Together, these studies suggest the importance of specific bacterial metabolites in regulating the host’s physiology and provide a tool to prevent confounding effects when analyzing genotype-phenotype interactions under different bacterial backgrounds.

scholarly journals Escherichia coli Metabolite Profiling Leads to the Development of an RNA Interference Strain for Caenorhabditis elegans

2019 ◽  
Author(s):  
Isaiah A. A. Neve ◽  
Jessica N. Sowa ◽  
Chih-Chun J. Lin ◽  
Priya Sivaramakrishnan ◽  
Christophe Herman ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Mitochondrial Morphology ◽  
Bacterial Strains ◽  
Hybrid Strain ◽  
Fat Storage ◽  
C Elegans ◽  
Interference Response ◽  
K 12

AbstractThe relationship of genotypes to phenotypes can be modified by environmental inputs. Such crucial environmental inputs include metabolic cues derived from microbes living together with animals. Thus the analysis of genetic effects on animals’ physiology can be confounded by variations in the metabolic profile of microbes. Caenorhabditis elegans exposed to distinct bacterial strains and species exhibit phenotypes different at cellular, developmental and behavioral levels. Here we reported metabolomic profiles of three Escherichia coli strains, B strain OP50, K-12 strain MG1655, and B-K-12 hybrid strain HB101, and also different mitochondrial and fat storage phenotypes of C. elegans exposed to MG1655 and HB101 versus OP50. We found that these metabolic phenotypes of C. elegans are not correlated with overall metabolic patterning of bacterial strains, but their specific metabolites. In particular, the fat storage phenotype is traced to the betaine level in different bacterial strains. HT115 is another K-12 E. coli strain that is commonly utilized to elicit an RNA interference response, and we showed that C. elegans exposed to OP50 and HT115 exhibit differences in mitochondrial morphology and fat storage levels. We thus generated an RNA interference competent OP50 (iOP50) strain that can robustly and consistently knockdown endogenous C. elegans genes in different tissues. Together, these studies suggest the importance of specific bacterial metabolites in regulating the host’s physiology, and provide a tool to prevent confounding effects when analyzing genotype-phenotype interactions under different bacterial backgrounds.

scholarly journals Iron Acquisition of Urinary Tract Infection Escherichia coli Involves Pathogenicity in Caenorhabditis elegans

2021 ◽  
Vol 9 (2) ◽  
pp. 310
Author(s):  
Masayuki Hashimoto ◽  
Yi-Fen Ma ◽  
Sin-Tian Wang ◽  
Chang-Shi Chen ◽  
Ching-Hao Teng
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Caenorhabditis Elegans ◽  
Large Scale ◽  
Iron Acquisition ◽  
Infection Model ◽  
High Throughput Analysis ◽  
E Coli ◽  
C Elegans ◽  
Tract Infections

Uropathogenic Escherichia coli (UPEC) is a major bacterial pathogen that causes urinary tract infections (UTIs). The mouse is an available UTI model for studying the pathogenicity; however, Caenorhabditis elegans represents as an alternative surrogate host with the capacity for high-throughput analysis. Then, we established a simple assay for a UPEC infection model with C. elegans for large-scale screening. A total of 133 clinically isolated E. coli strains, which included UTI-associated and fecal isolates, were applied to demonstrate the simple pathogenicity assay. From the screening, several virulence factors (VFs) involved with iron acquisition (chuA, fyuA, and irp2) were significantly associated with high pathogenicity. We then evaluated whether the VFs in UPEC were involved in the pathogenicity. Mutants of E. coli UTI89 with defective iron acquisition systems were applied to a solid killing assay with C. elegans. As a result, the survival rate of C. elegans fed with the mutants significantly increased compared to when fed with the parent strain. The results demonstrated, the simple assay with C. elegans was useful as a UPEC infectious model. To our knowledge, this is the first report of the involvement of iron acquisition in the pathogenicity of UPEC in a C. elegans model.

scholarly journals A Pathoadaptive Deletion in an Enteroaggregative Escherichia coli Outbreak Strain Enhances Virulence in a Caenorhabditis elegans Model

2010 ◽  
Vol 78 (9) ◽  
pp. 4068-4076 ◽  
Author(s):  
Jennifer Hwang ◽  
Lisa M. Mattei ◽  
Laura G. VanArendonk ◽  
Philip M. Meneely ◽  
Iruka N. Okeke
Keyword(s):  
Escherichia Coli ◽  
Caenorhabditis Elegans ◽  
Epithelial Cells ◽  
Genetic Material ◽  
Decarboxylase Activity ◽  
Multicopy Plasmid ◽  
Lysine Decarboxylase ◽  
Outbreak Strain ◽  
E Coli ◽  
C Elegans

ABSTRACT Enteroaggregative Escherichia coli (EAEC) strains are important diarrheal pathogens. EAEC strains are defined by their characteristic stacked-brick pattern of adherence to epithelial cells but show heterogeneous virulence and have different combinations of adhesin and toxin genes. Pathoadaptive deletions in the lysine decarboxylase (cad) genes have been noted among hypervirulent E. coli subtypes of Shigella and enterohemorrhagic E. coli. To test the hypothesis that cad deletions might account for heterogeneity in EAEC virulence, we developed a Caenorhabditis elegans pathogenesis model. Well-characterized EAEC strains were shown to colonize and kill C. elegans, and differences in virulence could be measured quantitatively. Of 49 EAEC strains screened for lysine decarboxylase activity, 3 tested negative. Most notable is isolate 101-1, which was recovered in Japan, from the largest documented EAEC outbreak. EAEC strain 101-1 was unable to decarboxylate lysine in vitro due to deletions in cadA and cadC, which, respectively, encode lysine decarboxylase and a transcriptional activator of the cadAB genes. Strain 101-1 was significantly more lethal to C. elegans than control strain OP50. Lethality was attenuated when the lysine decarboxylase defect was complemented from a multicopy plasmid and in single copy. In addition, restoring lysine decarboxylase function produced derivatives of 101-1 deficient in aggregative adherence to cultured human epithelial cells. Lysine decarboxylase inactivation is pathoadapative in an important EAEC outbreak strain, and deletion of cad genes could produce hypervirulent EAEC lineages in the future. These results suggest that loss, as well as gain, of genetic material can account for heterogeneous virulence among EAEC strains.

scholarly journals Temporal Transcriptomics of Gut Escherichia coli in Caenorhabditis elegans Models of Aging

2021 ◽  
Author(s):  
Joshua D. Brycki ◽  
Jeremy R. Chen See ◽  
Gillian R. Letson ◽  
Cade S. Emlet ◽  
Lavinia V. Unverdorben ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Caenorhabditis Elegans ◽  
Life Span ◽  
Wild Type ◽  
Health Span ◽  
Content Type ◽  
C Elegans ◽  
Evolutionarily Conserved

Previous research has reported effects of the microbiome on health span and life span of Caenorhabditis elegans , including interactions with evolutionarily conserved pathways in humans. We build on this literature by reporting the gene expression of Escherichia coli OP50 in wild-type (N2) and three long-lived mutants of C. elegans .

scholarly journals HCP-4/CENP-C Promotes the Prophase Timing of Centromere Resolution by Enabling the Centromere Association of HCP-6 in Caenorhabditis elegans

2005 ◽  
Vol 25 (7) ◽  
pp. 2583-2592 ◽  
Author(s):  
Landon L. Moore ◽  
Gerald Stanvitch ◽  
Mark B. Roth ◽  
David Rosen
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Holocentric Chromosomes ◽  
Kinetochore Protein ◽  
C Elegans ◽  
Kinetochore Assembly ◽  
Centromere Protein ◽  
Sister Centromere ◽  
Microtubule Capture

ABSTRACT Prior to microtubule capture, sister centromeres resolve from one another, coming to rest on opposite surfaces of the condensing chromosome. Subsequent assembly of sister kinetochores at each sister centromere generates a geometry favorable for equal levels of segregation of chromatids. The holocentric chromosomes of Caenorhabditis elegans are uniquely suited for the study of centromere resolution and subsequent kinetochore assembly. In C. elegans, only two proteins have been identified as being necessary for centromere resolution, the kinase AIR-2 (prophase only) and the centromere protein HCP-4/CENP-C. Here we found that the loss of proteins involved in chromosome cohesion bypassed the requirement for HCP-4/CENP-C but not for AIR-2. Interestingly, the loss of cohesin proteins also restored the localization of HCP-6 to the kinetochore. The loss of the condensin II protein HCP-6 or MIX-1/SMC2 impaired centromere resolution. Furthermore, the loss of HCP-6 or MIX-1/SMC2 resulted in no centromere resolution when either nocodazole or RNA interference (RNAi) of the kinetochore protein KNL-1 perturbed spindle-kinetochore interactions. This result suggests that normal prophase centromere resolution is mediated by condensin II proteins, which are actively recruited to sister centromeres to mediate the process of resolution.

scholarly journals Inducible Systemic RNA Silencing in Caenorhabditis elegans

2003 ◽  
Vol 14 (7) ◽  
pp. 2972-2983 ◽  
Author(s):  
Lisa Timmons ◽  
Hiroaki Tabara ◽  
Craig C. Mello ◽  
Andrew Z. Fire
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Rna Silencing ◽  
Molecular Mechanisms ◽  
Normal Animal ◽  
Cell Types ◽  
Animal Cells ◽  
Tissue Specific ◽  
C Elegans ◽  
Systemic Rna

Introduction of double-stranded RNA (dsRNA) can elicit a gene-specific RNA interference response in a variety of organisms and cell types. In many cases, this response has a systemic character in that silencing of gene expression is observed in cells distal from the site of dsRNA delivery. The molecular mechanisms underlying the mobile nature of RNA silencing are unknown. For example, although cellular entry of dsRNA is possible, cellular exit of dsRNA from normal animal cells has not been directly observed. We provide evidence that transgenic strains of Caenorhabditis elegans transcribing dsRNA from a tissue-specific promoter do not exhibit comprehensive systemic RNA interference phenotypes. In these same animals, modifications of environmental conditions can result in more robust systemic RNA silencing. Additionally, we find that genetic mutations can influence the systemic character of RNA silencing in C. elegans and can separate mechanisms underlying systemic RNA silencing into tissue-specific components. These data suggest that trafficking of RNA silencing signals in C. elegans is regulated by specific physiological and genetic factors.

scholarly journals ATP-binding Cassette Transporters Are Required for Efficient RNA Interference in Caenorhabditis elegans

2006 ◽  
Vol 17 (8) ◽  
pp. 3678-3688 ◽  
Author(s):  
Prema Sundaram ◽  
Benjamin Echalier ◽  
Wang Han ◽  
Dawn Hull ◽  
Lisa Timmons
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Abc Transporters ◽  
Transport Systems ◽  
Atp Binding ◽  
C Elegans ◽  
Steep Concentration Gradient ◽  
Conserved Gene ◽  
Membrane Transport Systems ◽  
Atp Binding Cassette

RNA interference (RNAi) is a conserved gene-silencing phenomenon that can be triggered by delivery of double-stranded RNA (dsRNA) to cells and is a widely exploited technology in analyses of gene function. Although a number of proteins that facilitate RNAi have been identified, current descriptions of RNAi and interrelated mechanisms are far from complete. Here, we report that the Caenorhabditis elegans gene haf-6 is required for efficient RNAi. HAF-6 is a member of the ATP-binding cassette (ABC) transporter gene superfamily. ABC transporters use ATP to translocate small molecule substrates across the membranes in which they reside, often against a steep concentration gradient. Collectively, ABC transporters are involved in a variety of activities, including protective or barrier mechanisms that export drugs or toxins from cells, organellar biogenesis, and mechanisms that protect against viral infection. HAF-6 is expressed predominantly in the intestine and germline and is localized to intracellular reticular organelles. We further demonstrate that eight additional ABC genes from diverse subfamilies are each required for efficient RNAi in C. elegans. Thus, the ability to mount a robust RNAi response to dsRNA depends upon the deployment of two ancient systems that respond to environmental assaults: RNAi mechanisms and membrane transport systems that use ABC proteins.

scholarly journals Feeding behaviour of Caenorhabditis elegans is an indicator of Pseudomonas aeruginosa PAO1 virulence

2014 ◽  
Author(s):  
Shawn Lewenza ◽  
Laetitia Charron-Mazenod ◽  
Lauriane Giroux ◽  
Alexandra D Zamponi
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Caenorhabditis Elegans ◽  
Feeding Behaviour ◽  
Food Sources ◽  
Infection Model ◽  
Bacterial Strains ◽  
Type Iii Effectors ◽  
Type Iii ◽  
C Elegans ◽  
Transposon Mutants

Caenorhabditis elegans is commonly used as an infection model for pathogenesis studies in Pseudomonas aeruginosa. While the standard virulence assays rely on the slow and fast killing or paralysis of nematodes, here we developed a behaviour assay to monitor the preferred bacterial food sources of C. elegans. The type III secretion system is a well-conserved virulence trait that is not required for slow or fast killing of C. elegans. However, ΔexsE mutants that are competent for hypersecretion of ExoS, ExoT and ExoY effectors were avoided as food sources in binary assays. Conversely, mutants lacking the secretion machinery or type III effectors were preferred food sources for PAO1. In binary feeding assays, both food sources were ingested and observed in the gastrointestinal tract, but non-preferred food sources were ultimately avoided. Next we developed a high throughput feeding behaviour assay to test a library of 2370 transposon mutants in order to identify preferred food sources. After primary and secondary screens, 37 mutants were identified as preferred food sources, which included mutations in many known virulence genes and that showed reduced virulence in the slow killing assay. We propose that C. elegans feeding behaviour can be used as a sensitive indicator of virulence for bacterial strains that have moderate worm killing activity.

scholarly journals Feeding behaviour of Caenorhabditis elegans is an indicator of Pseudomonas aeruginosa PAO1 virulence

2014 ◽  
Author(s):  
Shawn Lewenza ◽  
Laetitia Charron-Mazenod ◽  
Lauriane Giroux ◽  
Alexandra D Zamponi
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Caenorhabditis Elegans ◽  
Feeding Behaviour ◽  
Food Sources ◽  
Infection Model ◽  
Bacterial Strains ◽  
Type Iii Effectors ◽  
Type Iii ◽  
C Elegans ◽  
Transposon Mutants

Caenorhabditis elegans is commonly used as an infection model for pathogenesis studies in Pseudomonas aeruginosa. While the standard virulence assays rely on the slow and fast killing or paralysis of nematodes, here we developed a behaviour assay to monitor the preferred bacterial food sources of C. elegans. The type III secretion system is a well-conserved virulence trait that is not required for slow or fast killing of C. elegans. However, ΔexsE mutants that are competent for hypersecretion of ExoS, ExoT and ExoY effectors were avoided as food sources in binary assays. Conversely, mutants lacking the secretion machinery or type III effectors were preferred food sources for PAO1. In binary feeding assays, both food sources were ingested and observed in the gastrointestinal tract, but non-preferred food sources were ultimately avoided. Next we developed a high throughput feeding behaviour assay to test a library of 2370 transposon mutants in order to identify preferred food sources. After primary and secondary screens, 37 mutants were identified as preferred food sources, which included mutations in many known virulence genes and that showed reduced virulence in the slow killing assay. We propose that C. elegans feeding behaviour can be used as a sensitive indicator of virulence for bacterial strains that have moderate worm killing activity.

Uncover Genetic Interactions in Caenorhabditis elegans by RNA Interference

2005 ◽  
Vol 25 (5-6) ◽  
pp. 299-307 ◽  
Author(s):  
Angelo Fortunato ◽  
Andrew G. Fraser
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Gene Function ◽  
Genetic Interactions ◽  
Loss Of Function ◽  
Future Directions ◽  
C Elegans ◽  
Genomics Tools ◽  
Almost All ◽  
Nematode Worm

RNA-mediated interference (RNAi) has emerged recently as one of the most powerful functional genomics tools. RNAi has been particularly effective in the nematode worm C. elegans where RNAi has been used to analyse the loss-of-function phenotypes of almost all predicted genes. In this review, we illustrate how RNAi has been used to analyse gene function in C. elegans as well as pointing to some future directions for using RNAi to examine genetic interactions in a systematic manner.

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