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NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes

Veesenmeyer, Jeff L. and Andersen, Aaron W. and Lu, Xiaojun and Hussa, Elizabeth A. and Murfin, Kristen E. and Chaston, John M. and Dillman, Adler R. and Wassarman, Karen M. and Sternberg, Paul W. and Goodrich-Blair, Heidi (2014) NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes. Molecular Microbiology, 93 (5). pp. 1026-1042. ISSN 0950-382X. PMCID PMC4152777.

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The bacterium Xenorhabdus nematophila is a mutualist of entomopathogenic Steinernema carpocapsae nematodes and facilitates infection of insect hosts. X. nematophila colonizes the intestine of S. carpocapsae which carries it between insects. In the X. nematophila colonization-defective mutant nilD6::Tn5, the transposon is inserted in a region lacking obvious coding potential. We demonstrate that the transposon disrupts expression of a single CRISPR RNA, NilD RNA. A variant NilD RNA also is expressed by X. nematophila strains from S. anatoliense and S. websteri nematodes. Only nilD from the S. carpocapsae strain of X. nematophila rescued the colonization defect of the nilD6::Tn5 mutant, and this mutant was defective in colonizing all three nematode host species. NilD expression depends on the presence of the associated Cas6e but not Cas3, components of the Type I-E CRISPR-associated machinery. While cas6e deletion in the complemented strain abolished nematode colonization, its disruption in the wild-type parent did not. Likewise, nilD deletion in the parental strain did not impact colonization of the nematode, revealing that the requirement for NilD is evident only in certain genetic backgrounds. Our data demonstrate that NilD RNA is conditionally necessary for mutualistic host colonization and suggest that it functions to regulate endogenous gene expression.

Item Type:Article
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URLURL TypeDescription CentralArticle
Dillman, Adler R.0000-0001-7171-4332
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© 2014 John Wiley & Sons Ltd. Issue published online: 29 AUG 2014; Article first published online: 6 AUG 2014; Accepted manuscript online: 14 JUL 2014 02:49AM EST; Manuscript Accepted: 10 JUL 2014. We wish to thank Amy Cavanagh (UW-Madison) for technical support on Northerns and RPAs, and Jonathan Klassen (UConn-Storrs) and the Magnifying Genome team for their assistance in genome analysis and annotation. We gratefully acknowledge former and current members of the Goodrich- Blair lab: Dr Kurt Heungens for preliminary data on the nilD locus, James Weger and Nick Feirer for contributions to cas mutant phenotypic analyses, and Ángel Casanova-Torres for quantitative reverse transcriptase PCR analysis of putative target genes. We thank Dr Brian Tjaden (Wellesley College) for providing the Target RNA program for X. nematophila, S. Patricia Stock and S. Forst for collaborative work on S. anatoliense and S. websteri, and Caitilyn Allen and Katrina Forest (UW-Madison) for helpful discussions. Work in the Goodrich-Blair lab was funded by a grant from the National Science Foundation IOS-0950873. X.L. was supported by the UW-Madison Graduate School research funds. J.M.C. and K.E.M. were supported by a National Institutes of Health (NIH) National Research Service Award T32 (AI55397) ‘Microbes in Health and Disease’. J.M.C. was also supported by a National Science Foundation (NSF) Graduate Research Fellowship. E.A.H. was supported by the National Institutes of Health grant 1F32AI084441. A.R.D. was supported by a United States Public Health Service Training Grant (T32GM07616), and the Howard Hughes Medical Institute, with which P.W.S. is an investigator. The authors have no conflict of interest to declare.
Funding AgencyGrant Number
NIH Predoctoral FellowshipT32 (AI55397)
NSF Graduate Research FellowshipUNSPECIFIED
NIH Postdoctoral Fellowship1F32AI084441
NIH Predoctoral FellowshipT32GM07616
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Issue or Number:5
PubMed Central ID:PMC4152777
Record Number:CaltechAUTHORS:20141009-141146108
Persistent URL:
Official Citation:Veesenmeyer, J. L., Andersen, A. W., Lu, X., Hussa, E. A., Murfin, K. E., Chaston, J. M., Dillman, A. R., Wassarman, K. M., Sternberg, P. W. and Goodrich-Blair, H. (2014), NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes. Molecular Microbiology, 93: 1026–1042. doi: 10.1111/mmi.12715
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:50317
Deposited By: Jason Perez
Deposited On:09 Oct 2014 22:19
Last Modified:29 Oct 2019 21:31

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