Publications by authors named "Jonathan Hodgkin"

62 Publications

Allele-specific suppression in C. elegans reveals details of EMS mutagenesis and a possible moonlighting interaction between the vesicular acetylcholine transporter and ERD2 receptors.

Genetics 2021 Apr 29. Epub 2021 Apr 29.

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

A missense mutant, unc-17(e245), which affects the Caenorhabditis elegans vesicular acetylcholine transporter UNC-17, has a severe uncoordinated phenotype, allowing efficient selection of dominant suppressors that revert this phenotype to wild-type. Such selections permitted isolation of numerous suppressors after EMS (ethyl methanesulfonate) mutagenesis, leading to demonstration of delays in mutation fixation after initial EMS treatment, as has been shown in T4 bacteriophage but not previously in eukaryotes. Three strong dominant extragenic suppressor loci have been defined, all of which act specifically on allele e245, which causes a G347R mutation in UNC-17. Two of the suppressors (sup-1 and sup-8/snb-1) have previously been shown to encode synaptic proteins able to interact directly with UNC-17. We found that the remaining suppressor, sup-2, corresponds to a mutation in erd-2.1, which encodes an endoplasmic reticulum retention protein; sup-2 causes a V186E missense mutation in transmembrane helix 7 of ERD-2.1. The same missense change introduced into the redundant paralogous gene erd-2.2 also suppressed unc-17(e245). Suppression presumably occurred by compensatory charge interactions between transmembrane helices of UNC-17 and ERD-2.1 or ERD-2.2, as previously proposed in work on suppression by SUP-1(G84E) or SUP-8(I97D)/synaptobrevin. erd-2.1(V186E) homozygotes were fully viable, but erd-2.1(V186E); erd-2.2(RNAi) exhibited synthetic lethality (like erd-2.1(RNAi); erd-2.2(RNAi)), indicating that the missense change in ERD-2.1 impairs its normal function in the secretory pathway but may allow it to adopt a novel moonlighting function as an unc-17 suppressor.
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http://dx.doi.org/10.1093/genetics/iyab065DOI Listing
April 2021

From pathogen to a commensal: modification of the interaction during chronic infection by the absence of host insulin signalling.

Biol Open 2020 10 7;9(10). Epub 2020 Oct 7.

Laboratory of Cell Biology, Development and Genetics, Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK

The nematode worm depends on microbes in decaying vegetation as its food source. To survive in an environment rich in opportunistic pathogens, has evolved an epithelial defence system where surface-exposed tissues such as epidermis, pharynx, intestine, vulva and hindgut have the capacity of eliciting appropriate immune defences to acute gut infection. However, it is unclear how the worm responds to chronic intestinal infections. To this end, we have surveyed mutants that are involved in inflammation, immunity and longevity to find their phenotypes during chronic infection. Worms that grew in a monoculture of the natural pathogen (CBX102 strain) had a reduced lifespan and vigour. This was independent of intestinal colonisation as both CBX102 and the derived avirulent strain UV336 were early persistent colonisers. In contrast, the long-lived mutant was resistant to chronic infection, showing reduced colonisation and higher vigour. In fact, UV336 interaction with resulted in a host lifespan extension beyond OP50, the strain used for laboratory culture. Longevity and vigour of mutants growing on CBX102 was dependent on the FOXO orthologue DAF-16. Our results indicate that the interaction between host genotype and strain-specific bacteria determines longevity and health for .
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http://dx.doi.org/10.1242/bio.053504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7561485PMC
October 2020

Nematode Autotomy Requires Molting and Entails Tissue Healing without Obvious Regeneration.

Authors:
Jonathan Hodgkin

J Dev Biol 2019 Nov 23;7(4). Epub 2019 Nov 23.

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Autotomy in , which results in the severing of the body into two fragments, has been observed as a response to late larval worm-star formation after exposure to a bacterial surface pathogen. It was found that autotomy can occur in both hermaphroditic and gonochoristic nematode species, and during either the L3 or the L4 molt. Severing was hypothesized to be driven by a 'balloon-twisting' mechanism during molting but was found to be independent of lethargus-associated flipping. Extensive healing and apparent tissue fusion were seen at the site of scission. No obvious regeneration of lost body parts was seen in either L4 or adult truncated worms. A variety of mutants defective in processes of cell death, healing, regeneration, responses to damage, stress or pathogens were found to be competent to autotomize. Mutants specifically defective in autotomy have yet to be found. Autotomy may represent a modification of the essential normal process of molting.
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http://dx.doi.org/10.3390/jdb7040021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955759PMC
November 2019

The model organism diaspora.

Authors:
Jonathan Hodgkin

Heredity (Edinb) 2019 07 12;123(1):14-17. Epub 2019 Jun 12.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.

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http://dx.doi.org/10.1038/s41437-019-0191-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781165PMC
July 2019

Lipodisqs for eukaryote lipidomics with retention of viability: Sensitivity and resistance to Leucobacter infection linked to C.elegans cuticle composition.

Chem Phys Lipids 2019 08 15;222:51-58. Epub 2019 May 15.

Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, United Kingdom. Electronic address:

Lipodisq™ nanoparticles have been used to extract surface lipids from the cuticle of two strains (wild type, N2 and the bacteria-resistant strain, agmo-1) of the C. elegans nematode without loss of viability. The extracted lipids were characterized by thin layer chromatography and MALDI-TOF-MS. The lipid profiles differed between the two strains. The extracted lipids from the bacteria-resistant strain, agmo-1, contained ether-linked (O-alkyl chain) lipids, in contrast to the wild-type strain which contained exclusively ester- linked (O-acyl) lipids. This observation is consistent with the loss of a functional alkylglycerol monooxygenase (AGMO) in the bacterial resistant strain agmo-1. The presence and abundance of other lipid species also differs between the wild-type N2 and agmo-1 nematodes, suggesting that the agmo-1 mutant strain attempts to compensate for the increase in ether-linked lipids by modulating other lipid-synthesis pathways. Together these differences not only affect the fragility of the cuticle and the buoyancy of the worm in aqueous buffer, but also interactions with surface-adhering bacteria. The much greater chemical stability of O-alkyl, non-hydrolysable linked lipids compared with hydrolysable O-acyl linked lipids, may be the origin of the resistance of the agmo-1 strain to bacterial infection, providing a more resilient cuticle for the nematode. Additionally, we show that lipid extraction with a polymer of styrene and maleic acid (SMA) provides a viable route to lipidomics studies with minimal perturbation of the organism.
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http://dx.doi.org/10.1016/j.chemphyslip.2019.02.005DOI Listing
August 2019

The heme auxotroph Caenorhabditis elegans can cleave the thioether bonds of c-type cytochromes.

FEBS Lett 2018 03 1;592(6):928-938. Epub 2018 Mar 1.

Department of Biochemistry, University of Oxford, UK.

Heme is essential and synthesized via highly regulated processes. For this reason, most organisms strive to recycle it or acquire it from their environment. When heme is bound to proteins noncovalently, degradation of the polypeptide is sufficient to release it. However, in some hemoproteins, such as c-type cytochromes, heme is covalently bound to the protein backbone. We use the heme auxotroph Caenorhabditis elegans to investigate if cytochromes c can be a heme source, and we show that this organism must encode a novel system which specifically cleaves the thioether bonds of c-type cytochromes. We also find that at limiting heme concentrations, while somatic tissues develop normally the germline fails to proliferate, suggesting the presence of a heme-sensing checkpoint in C. elegans.
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http://dx.doi.org/10.1002/1873-3468.13006DOI Listing
March 2018

Frontiers of Knowledge: An Interview with 2017 Edward Novitski Prize Recipient Jonathan Hodgkin.

Authors:
Jonathan Hodgkin

Genetics 2017 12;207(4):1219-1220

Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom.

The Genetics Society of America's Edward Novitski Prize recognizes a single experimental accomplishment or a body of work in which an exceptional level of creativity and intellectual ingenuity has been used to design and execute scientific experiments to solve a difficult problem in genetics. The 2017 winner, Jonathan Hodgkin, used elegant genetic studies to unravel the sex determination pathway in He inferred the order of genes in the pathway and their modes of regulation using epistasis analyses-a powerful tool that was quickly adopted by other researchers. He expanded the number and use of informational suppressor mutants in that are able to act on many genes. He also introduced the use of collections of wild to study naturally occurring genetic variation, paving the way for SNP mapping and QTL analysis, as well as studies of hybrid incompatibilities between worm species. His current work focuses on nematode-bacterial interactions and innate immunity.
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http://dx.doi.org/10.1534/genetics.117.300400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714439PMC
December 2017

The Invertebrate Lysozyme Effector ILYS-3 Is Systemically Activated in Response to Danger Signals and Confers Antimicrobial Protection in C. elegans.

PLoS Pathog 2016 08 15;12(8):e1005826. Epub 2016 Aug 15.

Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

Little is known about the relative contributions and importance of antibacterial effectors in the nematode C. elegans, despite extensive work on the innate immune responses in this organism. We report an investigation of the expression, function and regulation of the six ilys (invertebrate-type lysozyme) genes of C. elegans. These genes exhibited a surprising variety of tissue-specific expression patterns and responses to starvation or bacterial infection. The most strongly expressed, ilys-3, was investigated in detail. ILYS-3 protein was expressed constitutively in the pharynx and coelomocytes, and dynamically in the intestine. Analysis of mutants showed that ILYS-3 was required for pharyngeal grinding (disruption of bacterial cells) during normal growth and consequently it contributes to longevity, as well as being protective against bacterial pathogens. Both starvation and challenge with Gram-positive pathogens resulted in ERK-MAPK-dependent up-regulation of ilys-3 in the intestine. The intestinal induction by pathogens, but not starvation, was found to be dependent on MPK-1 activity in the pharynx rather than in the intestine, demonstrating unexpected communication between these two tissues. The coelomocyte expression appeared to contribute little to normal growth or immunity. Recombinant ILYS-3 protein was found to exhibit appropriate lytic activity against Gram-positive cell wall material.
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http://dx.doi.org/10.1371/journal.ppat.1005826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985157PMC
August 2016

Caenorhabditis microbiota: worm guts get populated.

BMC Biol 2016 05 9;14:37. Epub 2016 May 9.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.

Until recently, almost nothing has been known about the natural microbiota of the model nematode Caenorhabditis elegans. Reporting their research in BMC Biology, Dirksen and colleagues describe the first sequencing effort to characterize the gut microbiota of environmentally isolated C. elegans and the related taxa Caenorhabditis briggsae and Caenorhabditis remanei In contrast to the monoxenic, microbiota-free cultures that are studied in hundreds of laboratories, it appears that natural populations of Caenorhabditis harbor distinct microbiotas.
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http://dx.doi.org/10.1186/s12915-016-0260-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860763PMC
May 2016

Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis.

Curr Biol 2015 Dec 10;25(24):3232-8. Epub 2015 Dec 10.

Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA. Electronic address:

Cilia and extracellular vesicles (EVs) are signaling organelles [1]. Cilia act as cellular sensory antennae, with defects resulting in human ciliopathies. Cilia both release and bind to EVs [1]. EVs are sub-micron-sized particles released by cells and function in both short- and long-range intercellular communication. In C. elegans and mammals, the autosomal dominant polycystic kidney disease (ADPKD) gene products polycystin-1 and polycystin-2 localize to both cilia and EVs, act in the same genetic pathway, and function in a sensory capacity, suggesting ancient conservation [2]. A fundamental understanding of EV biology and the relationship between the polycystins, cilia, and EVs is lacking. To define properties of a ciliated EV-releasing cell, we performed RNA-seq on 27 GFP-labeled EV-releasing neurons (EVNs) isolated from adult C. elegans. We identified 335 significantly overrepresented genes, of which 61 were validated by GFP reporters. The EVN transcriptional profile uncovered new pathways controlling EV biogenesis and polycystin signaling and also identified EV cargo, which included an antimicrobial peptide and ASIC channel. Tumor-necrosis-associated factor (TRAF) homologs trf-1 and trf-2 and the p38 mitogen-activated protein kinase (MAPK) pmk-1 acted in polycystin-signaling pathways controlling male mating behaviors. pmk-1 was also required for EV biogenesis, independent of the innate immunity MAPK signaling cascade. This first high-resolution transcriptome profile of a subtype of ciliated sensory neurons isolated from adult animals reveals the functional components of an EVN.
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http://dx.doi.org/10.1016/j.cub.2015.10.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4698341PMC
December 2015

Caenorhabditis elegans star formation and negative chemotaxis induced by infection with corynebacteria.

Microbiology (Reading) 2016 Jan 19;162(1):84-93. Epub 2015 Oct 19.

Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.

Caenorhabditis elegans is one of the major model systems in biology based on advantageous properties such as short life span, transparency, genetic tractability and ease of culture using an Escherichia coli diet. In its natural habitat, compost and rotting plant material, this nematode lives on bacteria. However, C. elegans is a predator of bacteria, but can also be infected by nematopathogenic coryneform bacteria such Microbacterium and Leucobacter species, which display intriguing and diverse modes of pathogenicity. Depending on the nematode pathogen, aggregates of worms, termed worm-stars, can be formed, or severe rectal swelling, so-called Dar formation, can be induced. Using the human and animal pathogens Corynebacterium diphtheriae and Corynebacterium ulcerans as well as the non-pathogenic species Corynebacterium glutamicum, we show that these coryneform bacteria can also induce star formation slowly in worms, as well as a severe tail-swelling phenotype. While C. glutamicum had a significant, but minor influence on survival of C. elegans, nematodes were killed after infection with C. diphtheriae and C. ulcerans. The two pathogenic species were avoided by the nematodes and induced aversive learning in C. elegans.
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http://dx.doi.org/10.1099/mic.0.000201DOI Listing
January 2016

Leucobacter musarum subsp. musarum sp. nov., subsp. nov., Leucobacter musarum subsp. japonicus subsp. nov., and Leucobacter celer subsp. astrifaciens subsp. nov., three nematopathogenic bacteria isolated from Caenorhabditis, with an emended description of Leucobacter celer.

Int J Syst Evol Microbiol 2015 Nov 13;65(11):3977-3984. Epub 2015 Aug 13.

Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

Three Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151T, CBX152T) and Kakegawa, Japan (CBX130T). Based on 16S rRNA gene sequence similarity, strains CBX130T, CBX151T and CBX152T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0). Strains CBX130T and CBX152T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130T = DSM 27158T = CIP 110719T). The third novel strain, CBX151T, showed genetic similarities with Leucobacter celer NAL101T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101T = KACC 14220T = JCM 16465T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151T = DSM 27159T = CIP 110720T), and to emend the description of Leucobacter celerShin et al. 2011.
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http://dx.doi.org/10.1099/ijsem.0.000523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804768PMC
November 2015

Cuticle integrity and biogenic amine synthesis in Caenorhabditis elegans require the cofactor tetrahydrobiopterin (BH4).

Genetics 2015 May 24;200(1):237-53. Epub 2015 Mar 24.

Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.

Tetrahydrobiopterin (BH4) is the natural cofactor of several enzymes widely distributed among eukaryotes, including aromatic amino acid hydroxylases (AAAHs), nitric oxide synthases (NOSs), and alkylglycerol monooxygenase (AGMO). We show here that the nematode Caenorhabditis elegans, which has three AAAH genes and one AGMO gene, contains BH4 and has genes that function in BH4 synthesis and regeneration. Knockout mutants for putative BH4 synthetic enzyme genes lack the predicted enzymatic activities, synthesize no BH4, and have indistinguishable behavioral and neurotransmitter phenotypes, including serotonin and dopamine deficiency. The BH4 regeneration enzymes are not required for steady-state levels of biogenic amines, but become rate limiting in conditions of reduced BH4 synthesis. BH4-deficient mutants also have a fragile cuticle and are generally hypersensitive to exogenous agents, a phenotype that is not due to AAAH deficiency, but rather to dysfunction in the lipid metabolic enzyme AGMO, which is expressed in the epidermis. Loss of AGMO or BH4 synthesis also specifically alters the sensitivity of C. elegans to bacterial pathogens, revealing a cuticular function for AGMO-dependent lipid metabolism in host-pathogen interactions.
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http://dx.doi.org/10.1534/genetics.114.174110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423366PMC
May 2015

Caenorhabditis elegans bacterial pathogen resistant bus-4 mutants produce altered mucins.

PLoS One 2014 8;9(10):e107250. Epub 2014 Oct 8.

Food and Drug Administration, Center for Biologics Evaluation and Research, Bethesda, Maryland, United States of America.

Caenorabditis elegans bus-4 glycosyltransferase mutants are resistant to infection by Microbacterium nematophilum, Yersinia pestis and Yersinia pseudotuberculosis and have altered susceptibility to two Leucobacter species Verde1 and Verde2. Our objective in this study was to define the glycosylation changes leading to this phenotype to better understand how these changes lead to pathogen resistance. We performed MALDI-TOF MS, tandem MS and GC/MS experiments to reveal fine structural detail for the bus-4 N- and O-glycan pools. We observed dramatic changes in O-glycans and moderate ones in N-glycan pools compared to the parent strain. Ce core-I glycans, the nematode's mucin glycan equivalent, were doubled in abundance, halved in charge and bore shifts in terminal substitutions. The fucosyl O-glycans, Ce core-II and neutral fucosyl forms, were also increased in abundance as were fucosyl N-glycans. Quantitative expression analysis revealed that two mucins, let-653 and osm-8, were upregulated nearly 40 fold and also revealed was a dramatic increase in GDP-Man 4,6 dehydratease expression. We performed detailed lectin binding studies that showed changes in glycoconjugates in the surface coat, cuticle surface and intestine. The combined changes in cell surface glycoconjugate distribution, increased abundance and altered properties of mucin provide an environment where likely the above pathogens are not exposed to normal glycoconjugate dependent cues leading to barriers to these bacterial infections.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107250PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189790PMC
June 2015

Worm-stars and half-worms: Novel dangers and novel defense.

Worm 2014 31;3:e27939. Epub 2014 Jan 31.

Department of Biochemistry; University of Oxford; Oxford, UK.

In a recent paper, we reported the isolation and surprising effects of two new bacterial pathogens for Caenorhabditis and related nematodes. These two pathogens belong to the genus Leucobacter and were discovered co-infecting a wild isolate of Caenorhabditis that had been collected in Cape Verde. The interactions of these bacteria with C. elegans revealed both unusual mechanisms of pathogenic attack, and an unexpected defense mechanism on the part of the worm. One pathogen, known as Verde1, is able to trap swimming nematodes by sticking their tails together, resulting in the formation of "worm-star" aggregates, within which worms are killed and degraded. Trapped larval worms, but not adults, can sometimes escape by undergoing whole-body autotomy into half-worms. The other pathogen, Verde2, kills worms by a different mechanism associated with rectal infection. Many C. elegans mutants with alterations in surface glycosylation are resistant to Verde2 infection, but hypersensitive to Verde1, being rapidly killed without worm-star formation. Conversely, surface infection of wild-type worms with Verde1 is mildly protective against Verde2. Thus, there are trade-offs in susceptibility to the two bacteria. The Leucobacter pathogens reveal novel nematode biology and provide powerful tools for exploring nematode surface properties and bacterial susceptibility.
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http://dx.doi.org/10.4161/worm.27939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165538PMC
September 2014

Serotonergic chemosensory neurons modify the C. elegans immune response by regulating G-protein signaling in epithelial cells.

PLoS Pathog 2013 12;9(12):e1003787. Epub 2013 Dec 12.

Department of Life Sciences, Imperial College London, South Kensington Campus, London, United Kingdom.

The nervous and immune systems influence each other, allowing animals to rapidly protect themselves from changes in their internal and external environment. However, the complex nature of these systems in mammals makes it difficult to determine how neuronal signaling influences the immune response. Here we show that serotonin, synthesized in Caenorhabditis elegans chemosensory neurons, modulates the immune response. Serotonin released from these cells acts, directly or indirectly, to regulate G-protein signaling in epithelial cells. Signaling in these cells is required for the immune response to infection by the natural pathogen Microbacterium nematophilum. Here we show that serotonin signaling suppresses the innate immune response and limits the rate of pathogen clearance. We show that C. elegans uses classical neurotransmitters to alter the immune response. Serotonin released from sensory neurons may function to modify the immune system in response to changes in the animal's external environment such as the availability, or quality, of food.
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http://dx.doi.org/10.1371/journal.ppat.1003787DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861540PMC
September 2014

Two Leucobacter strains exert complementary virulence on Caenorhabditis including death by worm-star formation.

Curr Biol 2013 Nov 24;23(21):2157-61. Epub 2013 Oct 24.

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. Electronic address:

The nematode Caenorhabditis elegans has been much studied as a host for microbial infection. Some pathogens can infect its intestine, while others attack via its external surface. Cultures of Caenorhabditis isolated from natural environments have yielded new nematode pathogens, such as microsporidia and viruses. We report here a novel mechanism for bacterial attack on worms, discovered during investigation of a diseased and coinfected natural isolate of Caenorhabditis from Cape Verde. Two related coryneform pathogens (genus Leucobacter) were obtained from this isolate, which had complementary effects on C. elegans and related nematodes. One pathogen, Verde1, was able to cause swimming worms to stick together irreversibly by their tails, leading to the rapid formation of aggregated "worm-stars." Adult worms trapped in these aggregates were immobilized and subsequently died, with concomitant growth of bacteria. Trapped larval worms were sometimes able to escape from worm-stars by undergoing autotomy, separating their bodies into two parts. The other pathogen, Verde2, killed worms after rectal invasion, in a more virulent version of a previously studied infection. Resistance to killing by Verde2, by means of alterations in host surface glycosylation, resulted in hypersensitivity to Verde1, revealing a trade-off in bacterial susceptibility. Conversely, a sublethal surface infection of worms with Verde1 conferred partial protection against Verde2. The formation of worm-stars by Verde1 occurred only when worms were swimming in liquid but provides a striking example of asymmetric warfare as well as a bacterial equivalent to the trapping strategies used by nematophagous fungi.
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http://dx.doi.org/10.1016/j.cub.2013.08.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898767PMC
November 2013

WormBase 2014: new views of curated biology.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D789-93. Epub 2013 Nov 4.

Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, Genome Sequencing Center, Washington University, School of Medicine, St Louis, MO 63108, USA, Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, CA 91125, USA, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Genetics Campus, Washington University School of Medicine, St. Louis, MO 63110, USA, Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.

WormBase (http://www.wormbase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest.
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http://dx.doi.org/10.1093/nar/gkt1063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965043PMC
January 2014

Commensals, probiotics and pathogens in the Caenorhabditis elegans model.

Cell Microbiol 2014 Jan 15;16(1):27-38. Epub 2013 Nov 15.

Department of Biochemistry, University of Oxford, Oxford, UK.

Caenorhabditis elegans is a useful model host for a wide variety of microorganisms that have implications for human health. Recent surveys of mammalian and metazoan microbiota demonstrate the often profound effects of gut commensal bacteria on host lifespan, health and development. Work using C. elegans has revealed the surprising extent to which bacterial metabolism can interact with host pathways with examples from Escherichia coli folate metabolism and Bacillus subtilis nitric oxide synthesis. The C. elegans model has also shed light on the mechanisms by which probiotic bacteria influence lifespan.
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http://dx.doi.org/10.1111/cmi.12234DOI Listing
January 2014

Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator.

ISME J 2013 Jun 21;7(6):1126-38. Epub 2013 Feb 21.

Department of Plant Sciences, University of Oxford, Oxford, UK.

The bacteriovorous nematode Caenorhabditis elegans has been used to investigate many aspects of animal biology, including interactions with pathogenic bacteria. However, studies examining C. elegans interactions with bacteria isolated from environments in which it is found naturally are relatively scarce. C. elegans is frequently associated with cultivation of the edible mushroom Agaricus bisporus, and has been reported to increase the severity of bacterial blotch of mushrooms, a disease caused by bacteria from the Pseudomonas fluorescens complex. We observed that pseudomonads isolated from mushroom farms showed differential resistance to nematode predation. Under nutrient poor conditions, in which most pseudomonads were consumed, the mushroom pathogenic isolate P. fluorescens NZI7 was able to repel C. elegans without causing nematode death. A draft genome sequence of NZI7 showed it to be related to the biocontrol strain P. protegens Pf-5. To identify the genetic basis of nematode repellence in NZI7, we developed a grid-based screen for mutants that lacked the ability to repel C. elegans. The mutants isolated in this screen included strains with insertions in the global regulator GacS and in a previously undescribed GacS-regulated gene cluster, 'EDB' ('edible'). Our results suggest that the product of the EDB cluster is a poorly diffusible or cell-associated factor that acts together with other features of NZI7 to provide a novel mechanism to deter nematode grazing. As nematodes interact with NZI7 colonies before being repelled, the EDB factor may enable NZI7 to come into contact with and be disseminated by C. elegans without being subject to intensive predation.
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http://dx.doi.org/10.1038/ismej.2013.9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660686PMC
June 2013

Genetic interactions between UNC-17/VAChT and a novel transmembrane protein in Caenorhabditis elegans.

Genetics 2012 Dec 10;192(4):1315-25. Epub 2012 Oct 10.

Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.

The unc-17 gene encodes the vesicular acetylcholine transporter (VAChT) in Caenorhabditis elegans. unc-17 reduction-of-function mutants are small, slow growing, and uncoordinated. Several independent unc-17 alleles are associated with a glycine-to-arginine substitution (G347R), which introduces a positive charge in the ninth transmembrane domain (TMD) of UNC-17. To identify proteins that interact with UNC-17/VAChT, we screened for mutations that suppress the uncoordinated phenotype of UNC-17(G347R) mutants. We identified several dominant allele-specific suppressors, including mutations in the sup-1 locus. The sup-1 gene encodes a single-pass transmembrane protein that is expressed in a subset of neurons and in body muscles. Two independent suppressor alleles of sup-1 are associated with a glycine-to-glutamic acid substitution (G84E), resulting in a negative charge in the SUP-1 TMD. A sup-1 null mutant has no obvious deficits in cholinergic neurotransmission and does not suppress unc-17 mutant phenotypes. Bimolecular fluorescence complementation (BiFC) analysis demonstrated close association of SUP-1 and UNC-17 in synapse-rich regions of the cholinergic nervous system, including the nerve ring and dorsal nerve cords. These observations suggest that UNC-17 and SUP-1 are in close proximity at synapses. We propose that electrostatic interactions between the UNC-17(G347R) and SUP-1(G84E) TMDs alter the conformation of the mutant UNC-17 protein, thereby restoring UNC-17 function; this is similar to the interaction between UNC-17/VAChT and synaptobrevin.
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http://dx.doi.org/10.1534/genetics.112.145771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512141PMC
December 2012

WormBase 2012: more genomes, more data, new website.

Nucleic Acids Res 2012 Jan 8;40(Database issue):D735-41. Epub 2011 Nov 8.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community.
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http://dx.doi.org/10.1093/nar/gkr954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245152PMC
January 2012

Glycosylation genes expressed in seam cells determine complex surface properties and bacterial adhesion to the cuticle of Caenorhabditis elegans.

Genetics 2011 Jan 26;187(1):141-55. Epub 2010 Oct 26.

Department of Cell and Tissue Biology, University of California, San Francisco, California 94143, USA.

The surface of the nematode Caenorhabditis elegans is poorly understood but critical for its interactions with the environment and with pathogens. We show here that six genes (bus-2, bus-4, and bus-12, together with the previously cloned srf-3, bus-8, and bus-17) encode proteins predicted to act in surface glycosylation, thereby affecting disease susceptibility, locomotory competence, and sexual recognition. Mutations in all six genes cause resistance to the bacterial pathogen Microbacterium nematophilum, and most of these mutations also affect bacterial adhesion and biofilm formation by Yersinia species, demonstrating that both infection and biofilm formation depend on interaction with complex surface carbohydrates. A new bacterial interaction, involving locomotory inhibition by a strain of Bacillus pumilus, reveals diversity in the surface properties of these mutants. Another biological property--contact recognition of hermaphrodites by males during mating--was also found to be impaired in mutants of all six genes. An important common feature is that all are expressed most strongly in seam cells, rather than in the main hypodermal syncytium, indicating that seam cells play the major role in secreting surface coat and consequently in determining environmental interactions. To test for possible redundancies in gene action, the 15 double mutants for this set of genes were constructed and examined, but no synthetic phenotypes were observed. Comparison of the six genes shows that each has distinctive properties, suggesting that they do not act in a linear pathway.
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http://dx.doi.org/10.1534/genetics.110.122002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018313PMC
January 2011

The Caenorhabditis elegans bus-2 mutant reveals a new class of O-glycans affecting bacterial resistance.

J Biol Chem 2010 Jun 12;285(23):17662-72. Epub 2010 Apr 12.

Department of Biochemistry and Molecular Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA.

Microbacterium nematophilum causes a deleterious infection of the C. elegans hindgut initiated by adhesion to rectal and anal cuticle. C. elegans bus-2 mutants, which are resistant to M. nematophilum and also to the formation of surface biofilms by Yersinia sp., carry genetic lesions in a putative glycosyltransferase containing conserved domains of core-1 beta1,3-galactosyltransferases. bus-2 is predicted to act in the synthesis of core-1 type O-glycans. This observation implies that the infection requires the presence of host core-1 O-glycoconjugates and is therefore carbohydrate-dependent. Chemical analysis reported here reveals that bus-2 is indeed deficient in core-1 O-glycans. These mutants also exhibit a new subclass of O-glycans whose structures were determined by high performance tandem mass spectrometry; these are highly fucosylated and have a novel core that contains internally linked GlcA. Lectin studies showed that core-1 glycans and this novel class of O-glycans are both expressed in the tissue that is infected in the wild type worms. In worms having the bus-2 genetic background, core-1 glycans are decreased, whereas the novel fucosyl O-glycans are increased in abundance in this region. Expression analysis using a red fluorescent protein marker showed that bus-2 is expressed in the posterior gut, cuticle seam cells, and spermatheca, the first two of which are likely to be involved in secreting the carbohydrate-rich surface coat of the cuticle. Therefore, in the bus-2 background of reduced core-1 O-glycans, the novel fucosyl glycans likely replace or mask remaining core-1 ligands, leading to the resistance phenotype. There are more than 35 Microbacterium species, some of which are pathogenic in man. This study is the first to analyze the biochemistry of adhesion to a host tissue by a Microbacterium species.
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http://dx.doi.org/10.1074/jbc.M109.065433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878530PMC
June 2010

Signal transduction pathways that function in both development and innate immunity.

Dev Dyn 2010 May;239(5):1330-6

Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

C. elegans is developing in importance as a model for innate immunity. Several signaling pathways are known to be required for immune responses to a diverse range of pathogens, including the insulin signaling, p38 MAP kinase and transforming growth factor-beta pathways. These pathways also have roles during development, which can complicate the analysis of their functions in immunity. Recent studies have suggested that immunity in C. elegans is integrated across the organism by both paracrine and neuronal communication, showing the complexity of the immune system in this organism.
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http://dx.doi.org/10.1002/dvdy.22232DOI Listing
May 2010

Characterization of the Caenorhabditis elegans UDP-galactopyranose mutase homolog glf-1 reveals an essential role for galactofuranose metabolism in nematode surface coat synthesis.

Dev Biol 2009 Nov 12;335(2):340-55. Epub 2009 Sep 12.

New England Biolabs, Inc., Ipswich, MA 01938, USA.

Galactofuranose (Gal(f)), the furanoic form of d-galactose produced by UDP-galactopyranose mutases (UGMs), is present in surface glycans of some prokaryotes and lower eukaryotes. Absence of the Gal(f) biosynthetic pathway in vertebrates and its importance in several pathogens make UGMs attractive drug targets. Since the existence of Gal(f) in nematodes has not been established, we investigated the role of the Caenorhabditis elegans UGM homolog glf-1 in worm development. glf-1 mutants display significant late embryonic and larval lethality, and other phenotypes indicative of defective surface coat synthesis, the glycan-rich outermost layer of the nematode cuticle. The glf homolog from the protozoan Leishmania major partially complements C. elegans glf-1. glf-1 mutants rescued by L. major glf, which behave as glf-1 hypomorphs, display resistance to infection by Microbacterium nematophilum, a pathogen of rhabditid nematodes thought to bind to surface coat glycans. To confirm the presence of Gal(f) in C. elegans, we analyzed C. elegans nucleotide sugar pools using online electrospray ionization-mass spectrometry (ESI-MS). UDP-Gal(f) was detected in wild-type animals while absent in glf-1 deletion mutants. Our data indicate that Gal(f) likely has a pivotal role in maintenance of surface integrity in nematodes, supporting investigation of UGM as a drug target in parasitic species.
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http://dx.doi.org/10.1016/j.ydbio.2009.09.010DOI Listing
November 2009

Regulation of transcription termination in the nematode Caenorhabditis elegans.

Nucleic Acids Res 2009 Nov 9;37(20):6723-36. Epub 2009 Sep 9.

Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

The current predicted mechanisms that describe RNA polymerase II (pol II) transcription termination downstream of protein expressing genes fail to adequately explain, how premature termination is prevented in eukaryotes that possess operon-like structures. Here we address this issue by analysing transcription termination at the end of single protein expressing genes and genes located within operons in the nematode Caenorhabditis elegans. By using a combination of RT-PCR and ChIP analysis we found that pol II generally transcribes up to 1 kb past the poly(A) sites into the 3' flanking regions of the nematode genes before it terminates. We also show that pol II does not terminate after transcription of internal poly(A) sites in operons. We provide experimental evidence that five randomly chosen C. elegans operons are transcribed as polycistronic pre-mRNAs. Furthermore, we show that cis-splicing of the first intron located in downstream positioned genes in these polycistronic pre-mRNAs is critical for their expression and may play a role in preventing premature pol II transcription termination.
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http://dx.doi.org/10.1093/nar/gkp744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777434PMC
November 2009

The C. elegans Hox gene egl-5 is required for correct development of the hermaphrodite hindgut and for the response to rectal infection by Microbacterium nematophilum.

Dev Biol 2009 May 13;329(1):16-24. Epub 2009 Feb 13.

School of Molecular and Microbial Biosciences, University of Sydney, NSW, Australia.

Members of the Hox gene family encode transcription factors that specify positional identity along the anterior-posterior axis of nearly all metazoans. One among the Caenorhabditis elegans Hox genes is egl-5. A deletion allele of egl-5 was isolated in a screen for animals which fail to develop swollen tails when exposed to the bacterial pathogen Microbacterium nematophilum. We show that compromised rectal development, which occurs as a result of loss of egl-5 function, results in a failure of rectal epithelial cells to express the ERK MAP kinase mpk-1, which was previously shown to mediate tail-swelling in response to bacterial infection. Tissue-specific rescue experiments demonstrated that egl-5 and mpk-1 act autonomously in rectal cells in the morphological response. The weak egl-5 allele (n1439), which does not compromise rectal development, fails to affect tail-swelling. We find that this allele carries an inserted repeat element approximately 13.8 kb upstream of the egl-5 open reading frame, which specifically disrupts the cell-specific expression of this gene in HSN egg-laying neurons. Together these findings extend the complexity of regulation and function of Hox genes in C. elegans and demonstrate the importance of their tissue-specific expression for correct development and response to infection.
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http://dx.doi.org/10.1016/j.ydbio.2009.01.044DOI Listing
May 2009

Caenorhabditis elegans meets microsporidia: the nematode killers from Paris.

PLoS Biol 2008 Dec;6(12):2634-7

Department of Biochemistry,University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1371/journal.pbio.1000005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605933PMC
December 2008