Bordetella pertussis is the causative agent of whooping cough, a respiratory disease still considered as a major public health threat and for which recent re-emergence has been observed. Constant reshuffling of Bordetella pertussis genome organization was observed during evolution. These rearrangements are essentially mediated by Insertion Sequences (IS), a mobile genetic elements present in more than 230 copies in the genome, which are supposed to be one of the driving forces enabling the pathogen to escape from vaccine-induced immunity. Here we use high-throughput sequencing approaches (RNA-seq and differential RNA-seq), to decipher Bordetella pertussis transcriptome characteristics and to evaluate the impact of IS elements on transcriptome architecture. Transcriptional organization was determined by identification of transcription start sites and revealed also a large variety of non-coding RNAs including sRNAs, leaderless mRNAs or long 3' and 5'UTR including seven riboswitches. Unusual topological organizations, such as overlapping 5'- or 3'-extremities between oppositely orientated mRNA were also unveiled. The pivotal role of IS elements in the transcriptome architecture and their effect on the transcription of neighboring genes was examined. This effect is mediated by the introduction of IS harbored promoters or by emergence of hybrid promoters. This study revealed that in addition to their impact on genome rearrangements, most of the IS also impact on the expression of their flanking genes. Furthermore, the transcripts produced by IS are strain-specific due to the strain to strain variation in IS copy number and genomic context.

b Univ Lille CNRS Inserm CHU Lille Institut Pasteur de Lille U1019 UMR8204 CIIL Center for Infection and Immunity of Lille Lille France

c Institute of Microbiology of the ASCR; Laboratory of post transcriptional control of gene expression Prague Czech Republic

University of Vienna Theoretical Biochemistry Group Institute for Theoretical Chemistry Vienna Austria

Zobrazit více v PubMed

Crowcroft NS, Stein C, Duclos P, et al.. How best to estimate the global burden of pertussis? Lancet Infect Dis. 2003;3:413–418. PubMed

Paddock CD, Sanden GN, Cherry JD, et al.. Pathology and Pathogenesis of Fatal Bordetella pertussis Infection in Infants. Clin Infect Dis. 2008;47:328–338. PubMed

World Health Organization Pertussis vaccines: WHO position paper - August 2015. Weely Epidemiol Rec. 2015;90:433–460.

Sealey KL, Belcher T, Preston A. Bordetella pertussis epidemiology and evolution in the light of pertussis resurgence. Infect Genet Evol. 2016;40:136–143. PubMed

Kline JM, Lewis WD, Smith EA, et al.. Pertussis: a reemerging infection. Am Fam Physician. 2013;88:507–514. PubMed

Wadman M, You J. The vaccine wars. Science. (80-. ) 2017;356:364–365. PubMed

Witt MA, Katz PH, Witt DJ. Unexpectedly limited durability of immunity following acellular pertussis vaccination in preadolescents in a north American outbreak. Clin Infect Dis. 2012;54:1730–1735. PubMed

Smits K, Pottier G, Smet J, et al.. Different T cell memory in preadolescents after whole-cell or acellular pertussis vaccination. Vaccine. 2013;32:111–118. PubMed

Warfel JM, Edwards KM. Pertussis vaccines and the challenge of inducing durable immunity. Curr Opin Immunol. 2015;35:48–54. PubMed

Edwards KM, Berbers GAM. Immune responses to pertussis vaccines and disease. J Infect Dis. 2014;209:S10–S15. PubMed

Althouse BM, Scarpino S V. Asymptomatic transmission and the resurgence of Bordetella pertussis. BMC Med. 2015;13:146. PubMed PMC

Martin SW, Pawloski L, Williams M, et al.. Pertactin-negative Bordetella pertussis strains: evidence for a possible selective advantage. Clin Infect Dis. 2015;60:223–227. PubMed

Queenan AM, Cassiday PK, Evangelista A. Pertactin-Negative Variants of Bordetella pertussis in the United States. N Engl J Med. 2013;368:583–584. PubMed PMC

Otsuka N, Han H-J, Toyoizumi-Ajisaka H, et al.. Prevalence and genetic characterization of pertactin-deficient bordetella pertussis in Japan. Miyaji EN, editor. PLoS One. 2012;7:e31985. PubMed PMC

Williams MM, Sen K, Weigand MR, et al.. Bordetella pertussis strain lacking pertactin and Pertussis Toxin. Emerg Infect Dis. 2016;22:319–322. PubMed PMC

Parkhill J, Sebaihia M, Preston A, et al.. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet. 2003;35:32–40. PubMed

Park J, Zhang Y, Buboltz AM, et al.. Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens. BMC Genomics. 2012;13:545. PubMed PMC

Cummings CA, Brinig MM, Lepp PW, et al.. Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J Bacteriol. 2004;186:1484–1492. PubMed PMC

Diavatopoulos DA, Cummings CA, Schouls LM, et al.. Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica. PLoS Pathog. 2005;1:e45. PubMed PMC

Xu Y, Liu B, Gröndahl-Yli-Hannuksila K, et al.. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis. Sci Rep. 2015;5:12888. PubMed PMC

Siguier P, Gourbeyre E, Varani A, et al.. Everyman's guide to bacterial insertion sequences. Microbiol Spectr. 2015;3:MDNA3-0030-2014. PubMed

Chain PSG, Hu P, Malfatti SA, et al.. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol. 2006;188:4453–4463. PubMed PMC

Siguier P, Gourbeyre E, Chandler M. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev. 2014;38:865–891. PubMed PMC

Depardieu F, Podglajen I, Leclercq R, et al.. Modes and modulations of antibiotic resistance gene expression. Clin Microbiol Rev. 2007;20:79–114. PubMed PMC

Humayun MZ, Zhang Z, Butcher AM, et al.. Hopping into a hot seat: Role of DNA structural features on IS5-mediated gene activation and inactivation under stress. Kalendar R, editor. PLoS One. 2017;12:e0180156. PubMed PMC

Safi H, Barnes PF, Lakey DL, et al.. IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis. Mol Microbiol. 2004;52:999–1012. PubMed

Schneider D, Lenski RE. Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol. 2004;155:319–327. PubMed

Weigand MR, Peng Y, Loparev V, et al.. The history of Bordetella pertussis genome evolution includes structural rearrangement. Becker A, editor. J Bacteriol. 2017;199:e00806–16. PubMed PMC

Prentki P, Teter B, Chandler M, et al.. Functional promoters created by the insertion of transposable element IS1. J Mol Biol. 1986;191:383–393. PubMed

Wang A, Roth JR. Activation of silent genes by transposons Tn5 and Tn10. Genetics. 1988;120:875–885. PubMed PMC

DeShazer D, Wood GE, Friedman RL. Molecular characterization of catalase from Bordetella pertussis: identification of the katA promoter in an upstream insertion sequence. Mol Microbiol. 1994;14:123–130. PubMed

Han H-J, Kuwae A, Abe A, et al.. Differential expression of type III effector BteA protein due to IS481 insertion in Bordetella pertussis. Neyrolles O, editor. PLoS One. 2011;6:e17797. PubMed PMC

Antoine R, Locht C. Roles of the disulfide bond and the carboxy-terminal region of the S1 subunit in the assembly and biosynthesis of pertussis toxin. Infect Immun. 1990;58:1518–1526. PubMed PMC

Amman F, Wolfinger MT, Lorenz R, et al.. TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics. 2014;15:89. PubMed PMC

Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings Int Conf Intell Syst Mol Biol. 1994;2:28–36. PubMed

Dambach M, Sandoval M, Updegrove TB, et al.. The Ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol Cell. 2015;57:1099–1109. PubMed PMC

Grundy FJ, Henkin TM. tRNA as a positive regulator of transcription antitermination in B. Subtilis. Cell. 1993;74:475–482. PubMed

Condon C, Putzer H, Grunberg-Manago M. Processing of the leader mRNA plays a major role in the induction of thrS expression following threonine starvation in Bacillus subtilis. Proc Natl Acad Sci U S A. 1996;93:6992–6997. PubMed PMC

Mclafferty MA, Harcus DR, Hewlett EL. Nucleotide sequence and characterization of a repetitive DNA element from the genome of bordetella pertussis with characteristics of an insertion sequence. Microbiology. 1988;134:2297–2306. PubMed

Ma C, Simons RW. The IS10 antisense RNA blocks ribosome binding at the transposase translation initiation site. EMBO J. 1990;9:1267–1274. PubMed PMC

Simons RW, Kleckner N. Translational control of IS10 transposition. Cell. 1983;34:683–691. PubMed

Boinett CJ, Harris SR, Langridge GC, et al.. Complete Genome Sequence of Bordetella pertussis D420. Genome Announc. 2015;3:e00657–15. PubMed PMC

Sharma CM, Hoffmann S, Darfeuille F, et al.. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010;464:250–255. PubMed

Stazic D, Voß B. The complexity of bacterial transcriptomes. J Biotechnol. 2016;232:69–78. PubMed

Shine J, Dalgarno L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974;71:1342–1346. PubMed PMC

Seo J-H, Hong JS-J, Kim D, et al.. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics. 2012;13:679. PubMed PMC

Kroger C, Dillon SC, Cameron ADS, et al.. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci. 2012;109:E1277–E1286. PubMed PMC

Cortes T, Schubert OT, Rose G, et al.. Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis. Cell Rep. 2013;5:1121–1131. PubMed PMC

Georg J, Hess WR. cis-Antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev. 2011;75:286–300. PubMed PMC

Wurtzel O, Sesto N, Mellin JR, et al.. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol. 2012;8:583. PubMed PMC

Locht C, Antoine R, Jacob-Dubuisson F. Bordetella pertussis, molecular pathogenesis under multiple aspects. Curr Opin Microbiol. 2001;4:82–89. PubMed

Hot D, Antoine R, Renauld-Mongénie G, et al.. Differential modulation of Bordetella pertussis virulence genes as evidenced by DNA microarray analysis. Mol Genet Genomics. 2003;269:475–486. PubMed

Toledo-Arana A, Dussurget O, Nikitas G, et al.. The Listeria transcriptional landscape from saprophytism to virulence. Nature. 2009;459:950–956. PubMed

Ren G-X, Guo X-P, Sun Y-C. Regulatory 3′ Untranslated Regions of Bacterial mRNAs. Front Microbiol. 2017;8:1276. PubMed PMC

Lasa I, Toledo-Arana A, Gingeras TR. An effort to make sense of antisense transcription in bacteria. RNA Biol. 2012;9:1039–1044. PubMed PMC

Lasa I, Toledo-Arana A, Dobin A, et al.. Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A. 2011;108:20172–20177. PubMed PMC

Svensson SL, Sharma CM. Small RNAs in bacterial virulence and communication. Virulence Mech Bact Pathog Fifth Ed American Society of Microbiology. 2016;4:169–212. PubMed

Brinig MM, Cummings CA, Sanden GN, et al.. Significant gene order and expression differences in Bordetella pertussis despite limited gene content variation. J Bacteriol. 2006;188:2375–2382. PubMed PMC

Zaghloul L, Tang C, Chin HY, et al.. The distribution of insertion sequences in the genome of Shigella flexneri strain 2457T. FEMS Microbiol Lett. 2007;277:197–204. PubMed

Parkhill J, Wren BW, Thomson NR, et al.. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001;413:523–527. PubMed

Kalendar R, Lee D, Schulman AH. FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods Mol Biol. 2014;1116:271–302. PubMed

Altschul SF, Gish W, Miller W, et al.. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. PubMed

Hoffmann S, Otto C, Kurtz S, et al.. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. Searls DB, editor. PLoS Comput Biol. 2009;5:e1000502. PubMed PMC

Fisher RA. Statistical Methods for Research Workers. Springer, New York, NY; 1992. p. 66–70. DOI:10.1007/978-1-4612-4380-9_6 DOI

Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289–300.

Beauregard A, Smith E, Petrone B, et al.. Identification and characterization of small RNAs in Yersinia pestis. RNA Biol. 2013;10:397–405. PubMed PMC

Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842. PubMed PMC

Levin JZ, Yassour M, Adiconis X, et al.. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 2010;7:709–715. PubMed PMC

An IS element-driven antisense RNA attenuates the expression of serotype 2 fimbriae and the cytotoxicity of Bordetella pertussis

Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment

A Unique Reverse Adaptation Mechanism Assists Bordetella pertussis in Resistance to Both Scarcity and Toxicity of Manganese

Omics Analysis of Blood-Responsive Regulon in Bordetella pertussis Identifies a Novel Essential T3SS Substrate

Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution

A Mutation Upstream of the rplN-rpsD Ribosomal Operon Downregulates Bordetella pertussis Virulence Factor Production without Compromising Bacterial Survival within Human Macrophages

Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis

Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis

A Bordetella pertussis MgtC homolog plays a role in the intracellular survival