Progress 01/15/06 to 01/14/09
Outputs
OUTPUTS: The project aims to sequence the genome of the entomopathogenic nematode Heterorhabditis bacteriophora strain TTO1 as a representative of 45 other species that are used as biological control agents for insect pests worldwide. H. bacteriophora possesses unique attributes including an obligate mutualistic association with the insect pathogenic bacterium, Photorhabdus luminescens. The EST sequencing yielded 31,485 ESTs, which represent 10,886 distinct ESTs after assembly. By comparing the 10,886 disctinct ESTs generated so far with the ESTs and proteins of free-living, animal- and human-parasitic, and plant-parasitic nematodes, we have identified 554 ESTs that are specific to parasitic nematodes. Further characterization identified 142 transcripts having matches to proteins from various organisms. Noticeably, most of matches (68%) are to proteins from human-parasitic nematode Brugia malayi, whose complete genome is published recently. The parasitic nematode-specific genes include those encoding theromacin (an antimicrobial peptide against Gram-positive bacteria), Bax-mediated apoptosis inhibitor, an F-box-like/WD-repeat protein, and a PAZ domain containing protein. Such genes may be involved in parasitic nematode-specific functions such as symbiosis with bacteria and parasitism towards hosts. We have identified 171 distinct ESTs encoding 69 aging and stress-related genes that include components in insulin/IGF-1, JNK, and TOR signaling pathways, which shed lights on the aging mechanisms of H. bacteriophora. We have also identified 22 ESTs corresponding to 14 genes potentially involved in dauer-related processes and 54 ESTs corresponding to 27 genes involved in defense and stress responses. We have identified an EST encoding a macrophage migration inhibitory factor (MMIF). MMIF homolog in Brugia malayi showed the ability to inhibit the random migration of human macrophage. H. bacteriophora MMIF may have role in modifying host immune response to promote its survival. We have identified only 12 genes in RNA interference pathways, two of which are missing in the draft genome of Brugia malayi. However, as demonstrated in recently published work by two co-PDs, RNAi pathway seems to be functional. We expect to identify more components as more ESTs and the complete genome sequence are revealed. We have identified 168 microsatellite loci from 157 H. bacteriophora ESTs. The polymorphism in these EST-derived microsatellite loci and microsatellite loci enriched from genomic DNA was assessed by PCR reactions. From these, we have identified 8 microsatellite loci that are polymorphic within a northeast Ohio population of H. bacteriophora. We started investigating the differential gene expression of H. bacteriophora under different conditions using Illumina sequencing platform. The complete genome has just been sequenced and is undergoing assembly at this time. We will describe the genome in next few months. PARTICIPANTS: Dr. Parwinder S. Grewal/ The Ohio State University - OARDC (PD) Dr. Byron J. Adams/ Brigham Young University (co-PD) Dr. Todd A. Ciche/ Michigan State University (co-PD) Dr. Randy Gaugler/ Rutgers University (co-PD) Dr. Paul W. Sternberg/ California Institute of Technology (co-PD) Dr. Saskia A. Hogenhout/ The John Innes Centre (collaborator) Dr. Sandra Cliffton/ Washington University at St. Louis (collaborator) Dr. John Spieth/ Washington University at St. Louis (collaborator) Dr. Xiaodong Bai/The Ohio State University (Post-doctoral Research Associate) TARGET AUDIENCES: Scientific community at large Scientists working on molecular mechanisms of pathogenicity, symbiosis, and parasitism Researchers working on entomopathogenic nematodes worldwide Farmers, Ranchers, nursery managers, homeowners, urban landscapers and lawnscare companies using entomopathogenic nematodes for biological pest control. PROJECT MODIFICATIONS: Genome sequence of H. bacteriophora has been in the pipeline for two years. It was delayed due to other NIH priorities. But it has now been sequenced and assesbly is underway.
Impacts
The complete genome of P. luminescens will provide unique insights into genes associated with pathogenicity and mutualism. Aside from the significance to biological control, the intellectual merit of the project lies in the comparison between the genomes of H. bacteriophora and C. elegans and C. briggsae which will enhance our understanding of the evolutionary and biological processes in animal involved in mutualism and parasitism. Further, the genome sequence of H. bacteriophora will provide a new view of the patterns and processes that shape the genomes in response to mutualism and parasitism, and will identify novel genome and regulatory sequences involved in infection, parasitism, pathogenicity, and mutualism. Specific broader impacts will be: (i) Revolutionization of research in over 100 academic and industrial laboratories developing entomopathogenic nematode and their symbiotic bacteria as biological control agents worldwide; (ii) Facilitation of functional genomic research geared towards the enhancement of infective juvenile longevity, stress tolerance, and virulence that will result in improved efficacy and wider use of nematode in biocontrol, leading to reduced reliance on chemical insecticides; (iii) Establishment of H. bacteriophora as a tractable model for the study of parasitism, mutualism, and pathogenicity; (iv) Provision of avenues for investigating the obligate tripartite interactions among H. bacteriophora, P. luminescens and insect larvae, including recognition and signaling, leading to immediate and direct applications in agriculture (e.g., targets for pharmacological intervention and genetic manipulation); (v) Training of undergraduate, graduate, and post-graduate students including minorities and women in genome annotation; (vi) Enhanced awareness of the value of genome sequencing among extension personnel, farmers, and general public.
Publications
- Bai, X., Hogenhout, S. A., Adams, B. J., Ciche, T. A., Clifton, S., Gaugler, R. Hogenhout, S., Spieth, J., Sternberg, P. W. & Grewal, P. S. 2009. Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1. BMC Genomics, in press
- Bai, X., Saeb, A. T. M., Michel, A. & Grewal, P. S. 2009. Isolation and characterization of microsatellite loci in the entomopathogenic nematode Heterorhabditis bacteriophora. Mol. Ecol. Res. 9, 207-209.
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Progress 01/15/07 to 01/14/08
Outputs
OUTPUTS: We have obtained and compared Heterorhabditis bacteriophora TTO1 expressed sequence tags (ESTs) to the ESTs and proteins of animal-parasitic, human-parasitic, plant-parasitic, and free-living nematodes using BLAST algorithms. A total of 27,380 ESTs have been generated and analyzed. This analysis has identified 718 ESTs that are specific to parasitic nematodes. Assembly of the 718 ESTs returned 56 contigs and 475 singletons. Further characterization identified 121 transcripts having matches to proteins from various organisms. Noticeably, most of matches (65%) are to proteins from human-parasitic nematode Brugia malayi, whose complete genome is published recently. The parasitic nematode-specific genes include those encoding theromacin (an antimicrobial peptide against Gram-positive bacteria), Bax-mediated apoptosis inhibitor, PNAS-107 related to apoptosis/differentiation, and an F-box containing protein. Such genes may be involved in parasitic nematode-specific functions such
as symbiosis with bacteria and parasitism towards hosts. We have identified an EST encoding a macrophage migration inhibitory factor (MMIF). MMIF homolog in Brugia malayi showed the ability to inhibit the random migration of human macrophage. H. bacteriophora MMIF may have the potential to modify host immune response to promote parasite survival. We have identified 334 ESTs encoding 29 aging and stress-related genes that include components in insulin/IGF-1, JNK, and TOR signaling pathways, which shed lights on the aging mechanisms of H. bacteriophora. We have identified 7 genes in RNA interference pathways, two of which are missing in the draft genome of Brugia malayi. So far, we failed to identify dicer- or Argonaut-encoding ESTs. However, as demonstrated in recently published work by two co-PDs, RNAi pathway seems to be functional in H. bacteriophora. We expect to identify more components as more ESTs and the complete genome sequence are revealed.
PARTICIPANTS: Parwinder Grewal, Department of Entomology, Ohio State University, Wooster, Ohio Byron Adams, Brigham Young University, Salt Lake City, Utah Todd Ciche, Department of Microbiology, Michigan State University, East Lancing, Michigan Randy Gaugler, Department of Entomology, Rutgers University, New Brunswick, New Jersey Paul Sternberg, California Institute of Technology, Pasadena, California Sandra Clifton, Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri John Spieth, Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri Saskia Hogenhout, Department of Entomology, Ohio State University, Wooster, Ohio Xiaodong Bai, Department of Entomology, Ohio State University, Wooster, Ohio
TARGET AUDIENCES: Scientific community, specifically scientists working on entomopathogenic nematodes and their symbiotic bacteria in over 100 laboratories worldwide Broader scientific community, specifically scientists working on symbiosis, pathogenesis, virulence, and phylogeny of living organisms and more. Farmers, landscape managers, nursery managers, etc.
PROJECT MODIFICATIONS: None
Impacts
This project will revolutionize research on entomopathogenic nematode and bacteria (EPNs-EPBs) in over 100 laboratories worldwide. There have been three international meetings (1990, 1994, and 2003) and many regional meetings in Europe, North and South America, Australia, and Asia. Over 100 researchers from 14 countries attended the 2003 International meeting in Wooster, Ohio (www.oardc.ohio-state.edu/nematodes) in which it was decided to hold the international meeting every two years. Over 1000 papers were published on EPNs and their symbiotic bacteria during the past 10 years. With a large contingent of academic, government and industrial labs researching EPNs and EPBs, the genome sequence of H. bacteriophora will have a large impact on society and agriculture. Many students are now trained in the biology of EPNs and symbiotic bacteria. Apart from its significance to biological control and agriculture, H. bacteriophora genome sequence will have a large impact on
biological sciences and the society particularly due to the following: 1. H. bacteriophora is a unique model for the study of parasitism and pathogenicity 2. H. bacteriophora serves as a tractable model for the study of mutualism 3. H. bacteriophora genome sequence will serve as a bridge between C. elegans and more distantly related nematode parasites
Publications
- Bai, X., Grewal, P. S., Hogenhout, S. A., Adams, B. J., Ciche, T. A., Gaugler, R. & Sternberg, P. W. 2007. Expressed sequence tag analysis of gene representation in insect parasitic nematode Heterorhabditis bacteriophora. J. Parasitol. 93, 1343-1349.
- Bai, X. & Grewal, P. S. 2007. Identification of two down-regulated genes in entomopathogenic nematode Heterorhabditis bacteriophora infective juveniles upon contact with insect hemolymph. Mol. Biochem. Parasitol, 156, 162-166.
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Progress 01/15/06 to 01/15/07
Outputs
This project is on schedule and the high through put sequencing will begin in March, 2007. In anticipation of the availability of the full genome sequence, we compared Heterorhabditis bacteriophora GPS11 expressed sequence tags (ESTs) to the ESTs of animal-parasitic, human-parasitic, plant-parasitic, and free-living nematodes using BLAST algorithm. We identified 135 previously non-described ESTs of which 127 had homologs in ESTs and 8 had homologs in proteins of free-living nematodes. Among the ESTs assigned putative functions were those encoding transcription proteins, proteins involved in signal transduction, cell cycle control, metabolism and information processing, and cellular processes. These newly identified ESTs provided new insights into the housekeeping functions of H. bacteriophora, such as metabolism, sex determination, and signal transduction. We also identified 39 H. bacteriophora ESTs that had no homologs in ESTs or proteins of free-living nematodes,
but had homologs in ESTs of parasitic nematodes. These ESTs potentially play roles in parasitism. Some interesting ESTs encode centrin, ankyrin-repeat containing protein, protein phosphatase 2C containing protein, and nuclear hormone receptor. Our analysis also revealed that H. bacteriophora parasitic nematode-specific ESTs had more homologs in animal-parasitic nematodes than those parasitizing humans and plants. This finding is consistent with the close phylogenetic relationship between these two groups based on the nucleotide sequence of ubiquitin conjugating enzyme 2 (ubc-2) encoding EST.
Impacts
This project will revolutionize research on entomopathogenic nematode and bacteria (EPNs-EPBs) in over 100 laboratories worldwide. There have been three international meetings (1990, 1994, and 2003) and many regional meetings in Europe, North and South America, Australia, and Asia. Over 100 researchers from 14 countries attended the 2003 International meeting in Wooster, Ohio (www.oardc.ohio-state.edu/nematodes) in which it was decided to hold the international meeting every two years. Over 1000 papers were published on EPNs and their symbiotic bacteria during the past 10 years. With a large contingent of academic, government and industrial labs researching EPNs and EPBs, the genome sequence of H. bacteriophora will have a large impact on society and agriculture. Many students are now trained in the biology of EPNs and symbiotic bacteria. Apart from its significance to biological control and agriculture, H. bacteriophora genome sequence will have a large impact on
biological sciences and the society particularly due to the following: 1. H. bacteriophora is a unique model for the study of parasitism and pathogenicity 2. H. bacteriophora serves as a tractable model for the study of mutualism 3. H. bacteriophora genome sequence will serve as a bridge between C. elegans and more distantly related nematode parasites
Publications
- No publications reported this period
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