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Rapid Virulence Annotation (RVA): Identification of Virulence Factors Using a Bacterial Genome Library and Multiple Invertebrate Hosts

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Rapid Virulence Annotation (RVA): Identification of Virulence Factors Using a Bacterial Genome Library and Multiple Invertebrate Hosts Corrections MICROBIOLOGY GENETICS Correction for ‘‘Rapid Virulence Annotation (RVA): Identifi- Correction for ‘‘Linear-After-The-Exponential (LATE)–PCR: cation of virulence factors using a bacterial genome library and An advanced method of asymmetric PCR and its uses in multiple invertebrate hosts,’’ by Nicholas R. Waterfield, Maria quantitative real-time analysis,’’ by J. Aquiles Sanchez, Kenneth Sanchez-Contreras, Ioannis Eleftherianos, Andrea Dowling, E. Pierce, John E. Rice, and Lawrence J. Wangh, which appeared Paul Wilkinson, Julian Parkhill, Nicholas Thomson, Stuart E. in issue 7, February 17, 2004, of Proc Natl Acad Sci USA Reynolds, Helge B. Bode, Steven Dorus, and Richard H. (101:1933–1938; first published February 9, 2004; 10.1073͞ ffrench-Constant, which appeared in issue 41, October 14, 2008, pnas.0305476101). of Proc Natl Acad Sci USA (105:15967–15972; first published The authors note that on page 1934, left column, line 12, ‘‘70 October 6, 2008; 10.1073͞pnas.0711114105). nM’’ should instead appear as ‘‘70 mM.’’ This error does not The authors request that Guowei Yang, Department of Biol- affect the conclusions of the article. ogy and Biochemistry, University of Bath, Bath BA2 7AY, ͞ ͞ ͞ ͞ United Kingdom, be added to the author list, between Andrea www.pnas.org cgi doi 10.1073 pnas.0811993106 Dowling and Paul Wilkinson, and be credited with performing research. The author line has been corrected online. The cor- rected author and affiliation lines, and related footnotes, appear below. Nicholas R. Waterfield*†‡, Maria Sanchez-Contreras*†, Ioannis Eleftherianos*, Andrea Dowling§, Guowei Yang*, Paul Wilkinson*, Julian Parkhill¶, Nicholas Thomson¶, Stuart E. Reynolds*, Helge B. Bodeʈ, Steven Dorus*, and Richard H. ffrench-Constant§ *Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom; §Department of Biological Sciences, University of Exeter in Cornwall, Penryn TR10 9EZ, United Kingdom; ¶Pathogen Sequencing Group, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom; and ʈDepartment of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbru¨cken, Germany Author contributions: N.R.W. and R.H.f.-C. designed research; M.S.-C., I.E., A.D., and G.Y. performed research; N.R.W., P.W., J.P., N.T., S.E.R., H.B.B., and S.D. analyzed data; and N.R.W., M.S.-C., and R.H.f.-C. wrote the paper. †N.R.W and M.S.-C. contributed equally to this work. ‡To whom correspondence should be addressed. E-mail: [email protected]. www.pnas.org͞cgi͞doi͞10.1073͞pnas.0811896106 CORRECTIONS www.pnas.org PNAS ͉ February 10, 2009 ͉ vol. 106 ͉ no. 6 ͉ 2083 Downloaded by guest on September 30, 2021 Rapid Virulence Annotation (RVA): Identification of virulence factors using a bacterial genome library and multiple invertebrate hosts Nicholas R. Waterfield*†‡, Maria Sanchez-Contreras*†, Ioannis Eleftherianos*, Andrea Dowling§, Guowei Yang*, Paul Wilkinson*, Julian Parkhill¶, Nicholas Thomson¶, Stuart E. Reynolds*, Helge B. Bodeʈ, Steven Dorus*, and Richard H. ffrench-Constant§ *Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom; §Department of Biological Sciences, University of Exeter in Cornwall, Penryn TR10 9EZ, United Kingdom ; ¶Pathogen sequencing group, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom; and ʈDepartment of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbru¨ cken, Germany Edited by Frederick M. Ausubel, Harvard Medical School, Boston, MA, and approved July 25, 2008 (received for review November 23, 2007) Current sequence databases now contain numerous whole genome bacteria. The worm feeds off the bacteria and reproduces until sequences of pathogenic bacteria. However, many of the predicted the insect resource is exhausted, whereupon they repackage the genes lack any functional annotation. We describe an assumption- bacteria and leave in search of new prey (7). The requirement to free approach, Rapid Virulence Annotation (RVA), for the high- overcome the insect immune system and to keep the insect throughput parallel screening of genomic libraries against four dif- cadaver free of saprophytic organisms in the soil means that all ferent taxa: insects, nematodes, amoeba, and mammalian Photorhabdus produce a range of bioactive molecules including macrophages. These hosts represent different aspects of both the immune inhibitors, toxins, and powerful antimicrobials. The vertebrate and invertebrate immune system. Here, we apply RVA to fully annotated genome sequence of the insect-only pathogen the emerging human pathogen Photorhabdus asymbiotica using Photorhabdus luminescens strain TT01 is available (8) and the ‘‘gain of toxicity’’ assays of recombinant Escherichia coli clones. We genome sequence of the clinical isolate Photorhabdus asymbi- describe a wealth of potential virulence loci and attribute biological otica ATCC43949 is almost completed (http://www.sanger.ac.uk/ function to several putative genomic islands, which may then be Projects/P࿝asymbiotica/). The availability of the two genomes further characterized using conventional molecular techniques. The allows us to correlate the RVA data with regions unique to the application of RVA to other pathogen genomes promises to ascribe human pathogenic P. asymbiotica. biological function to otherwise uncharacterized virulence genes. For RVA analysis we sheared the P. asymbiotica ATCC43949 genome and cloned it into recombinant Escherichia coli. The bacteria ͉ pathogenomics ͉ screening ͉ toxins ͉ entomopathogenic library, covering 91.4% of the estimated 5.0 Mb genome with an average insert size of 37 kb, was arrayed into 16 96-well plates. he growing speed with which the genomes of bacteria can be All 1,536 clones were sequenced at both ends and end-sequences MICROBIOLOGY Tsequenced is producing an ever expanding knowledge gap were assembled onto the genomic scaffold. This cosmid library between sequence data and its functional annotation. In the case was screened for gain of toxicity (GOT) assays against the of bacterial pathogens, the identification of virulence factors has nematode Caenorhabditis elegans (nGOT), serving as an oral typically relied on genetic knock-out and demonstration that route model; the single-cell protozoa Acanthamoeba polyphaga virulence is attenuated in a suitable animal model. This ap- (aGOT), used as a phagocytosis model; and two caterpillar proach is not only time consuming and expensive but also, in the models (iGOT), the Tobacco hornworm Manduca sexta and the case of the use of vertebrate models, ethically debatable. Here, Waxmoth Galleria mellonella, both of which represent the more we demonstrate the power of using parallel screens for the complex insect immune systems. Numerous examples of the use identification of virulence genes using three invertebrate infec- of invertebrates as model hosts can be found in the literature (1, tion models and mammalian macrophages in tissue culture, 9–12). Finally, we used the mouse BALB/c macrophage cell line collectively termed Rapid Virulence Annotation (RVA). RVA J774–2 (mGOT) to represent the phagocytic component of the utility relies upon similarities between the immune responses of vertebrate immune system. The use of GOT studies in E. coli,in vertebrates and invertebrates. The innate immune systems of which the model host is challenged with individual clones, has insects and mammals share many common features, both mech- the advantage over chromosomal mutagenesis of ‘‘unmasking’’ anistically and genetically (1, 2). In addition, much of the basic any virulence factors that would otherwise be hidden due to cellular machinery and pathways that bacterial pathogens can toxin redundancy or the presence of potent dominant toxins. To subvert during infection is also well conserved among eu- define the virulence-related regions (RVA regions), the end karyotes, presenting common targets. This suggests that viru- sequences of cosmids showing an effect were assembled onto a lence mechanisms used by pathogens of mammals may work against invertebrates and vice versa. Indeed, we suggest many virulence strategies evolved initially to combat invertebrates Author contributions: N.R.W. and R.f.-C. designed research; M.S.-C., I.E., A.D., and G.Y. have subsequently been redeployed against vertebrates (3). To performed research; N.R.W., P.W., J.P., N.T., S.E.R., H.B.B., and S.D. analyzed data; and test these predictions, we conducted an RVA-based screen on a N.R.W., M.S.-C., and R.f.-C. wrote the paper. recently emerging pathogen, Photorhabdus asymbiotica, which is The authors declare no conflict of interest. a pathogen of both insects and man (4) and causes invasive soft This article is a PNAS Direct Submission. tissue and disseminated bacteraemic infections (5, 6). Photorh- Data deposition: The sequences reported in this paper have been deposited in the EMBL abdus are members of the Enterobacteriaceae that live in database (accession nos. FM211043–FM211060). association with soil dwelling entomopathogenic Heterorhabditid †These authors contributed equally. nematodes and that invade and kill insects. Infective juvenile ‡To whom correspondence should be addressed. E-mail: [email protected]. nematodes seek out and penetrate the insect prey, regurgitating This article contains supporting information online at www.pnas.org/cgi/content/full/ a small number of Photorhabdus cells that evade the immune 0711114105/DCSupplemental. system, kill the insect, and then bio-convert the tissues into more © 2008 by The National
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