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Genome Evolution and Host Adaptation in Bartonella

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Genome Evolution and Host Adaptation in Bartonella !! ""#$"% ! &'#&"#%#"#' ()*))) #"+', ! " #$%%&%&' () ) ) * +, - + +$%%&+. / 0 +0 + #1(+#! + +23&1!4& 4((541# #4!+ ) ) ) - ) - - 46 +0 ) +2 - 6 - ) - ) 7 ) + 0 ) ) ) 3- - -7 +0 4- 4 - - ) 4 +0 )6 - ) ) ) ) 8 ) - 7 )+ 2 ) ) 9.,0: 4 4 )) ) - ) ) + 0 7 - .,0 ) 4 )) + , - ) 4 ) .,0 )7 ) 4 ) ) 8 ) - + )7 4 )) ) ; 8 ) +, ) 6 - 0 0 )) ) ) - + ) ! " # ! " $% &'" " !()*+,- " < $%%& 233 #( 4#$ 5 23&1!4& 4((541# #4! ' ''' 4 %!=1#9 ';; +6+; > ? ' ''' 4 %!=1#: List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Berglund, E.C., Frank, A.C., Calteau, A., Vinnere Pettersson, O., Granberg, F., Eriksson, A-S., Näslund, K., Holmberg, M., Lindroos, H., Andersson, S.G.E. (2009) Run-Off Replication of Host-Adaptability Genes is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii. PLoS Genetics 5:e1000546 II Berglund, E.C., Ehrenborg, C., Vinnere Pettersson, O., Gran- berg, F., Näslund, K., Holmberg, M., Andersson, S.G.E. (2009) Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents. Submitted III Berglund, E.C., Granberg, F., Zhoupeng, X., Ellegaard, K., Kosoy, M.Y., Birtles, R., Andersson, S.G.E. (2009) Diversifica- tion by recombination in Bartonella grahamii from wild rodents in Asia contrasts with a clonal population structure in Northern Europe and America. Submitted IV Nystedt, B., Guy, L., Berglund, E.C.*, Bjursell, M.K.*, Gran- berg, F.*, Toft, C.*, Zaremba, K.*, Näslund, K., Eriksson, A-S., Andersson, S.G.E. Evolution of host adaptation systems in the mammalian blood specialist Bartonella. Manuscript V Guy, L., Nystedt, B., Sun, Y., Berglund, E.C., Graf, A., Zhou- peng, X., Näslund, K., Andersson, S.G.E. Low-coverage py- rosequencing reveals recombination and run-off replication in Bartonella henselae strains. Manuscript Reprints were made with permission from the respective publishers. * These authors have been listed in alphabetical order Papers by the author not included in this thesis 1. Berglund, E.C., Nystedt, B., Andersson, S.G.E. (2009) Computational Resources in Infectious Disease: Limitations and Challenges. PLoS Comput Biol. 5:e1000481 2. Frank, A.C., Berglund, E.C., Andersson, S.G.E. (2006) The Genomes of Pathogenic Bartonella species. In Pathogenomics: Genome Analysis of Pathogenic Microbes (edited by J. Hacker and U. Dobrindt). WILEY- VCH Verlag GmbH & Co. KgaA, Weinheim Contents Introduction.....................................................................................................9 Bacterial genomes ....................................................................................10 Genes and gene families ......................................................................11 Bacteriophages .........................................................................................11 Importance of phages for bacterial evolution ......................................12 Run-off replication...............................................................................13 Bacterial genome evolution......................................................................14 Replication errors and genome rearrangements...................................14 Horizontal gene transfer ......................................................................15 Selection and drift – the forces that rule evolution..............................16 Features and evolution of intracellular bacteria .......................................21 Infection strategies...............................................................................21 Genome evolution after host adaptation ..............................................23 Genomic diversity within a species..........................................................24 What is a bacterial species? .................................................................25 The genus Bartonella ...............................................................................26 Bartonella infection.............................................................................27 Hosts and vectors.................................................................................27 Bartonella as a human pathogen..........................................................30 Host-interaction factors .......................................................................31 Bartonella genomes.............................................................................32 Bartonella phages ................................................................................33 Prevalence and distribution of Bartonella ...........................................33 Genomic diversity in Bartonella .........................................................34 Methods for comparative genomics..............................................................35 Multi locus sequence typing.....................................................................35 Microarray comparative genome hybridizations......................................36 Pulsed-field gel electrophoresis................................................................36 Re-sequencing ..........................................................................................36 Results and discussion ..................................................................................37 Genus wide comparison of Bartonella genomes......................................37 Features of the Bartonella genomes ....................................................37 Acquisition and evolution of host-adaptability genes..........................38 Prophages and the gene transfer agent .....................................................42 Bartonella prophages...........................................................................42 Identification of the gene transfer agent ..............................................43 Are the GTA and the run-off replication beneficial?...........................44 What are the effects of the GTA? ........................................................46 Intra-species diversity of B. grahamii ......................................................47 Geographic variations in sequence diversity of B. grahamii...............48 How does sequence diversity correlate to gene content?.....................49 Why is B. grahamii so different from B. henselae?.............................49 Conclusions and perspectives .......................................................................51 Svensk sammanfattning ................................................................................53 Acknowledgements.......................................................................................55 References.....................................................................................................57 Abbreviations MLST Multi Locus Sequence Typing MST Multi Spacer Typing ST Sequence Type CGH Comparative Genome Hybridization PFGE Pulsed-Field Gel Electrophoresis bp base pair kb kilo base pair Mb Mega base pair Indel Insertion or deletion HGT Horizontal Gene Transfer T4SS Type IV secretion system T5SS Type V secretion system GTA Gene Transfer Agent Introduction There are three main domains of life: bacteria, eukarya and archaea (Woese and Fox 1977). Bacteria are most abundant of the three, with an estimated number of 1030 cells. They exhibit a tremendous range of different lifestyles and inhabit virtually all environments on Earth, ranging from soil and water to extreme environments like deep in the Antarctic ice, kilometers below the surface of Earth and in nearly saturated salt brines (Horner-Devine et al. 2004). Many bacteria live inside another larger organism, and sometimes even within the cells of the host. Obligate intracellular bacteria are strictly de- pendent on their host to be able to survive and reproduce, while facultative intracellular bacteria can multiply also outside the host cell. The relationship between a bacterium and its host ranges from mutualism that both parts profit from, to parasitism where the bacterium causes disease or even kill the host. Infectious diseases are mostly caused by bacteria or viruses, and kill mil- lions of people annually. One of the most important infectious diseases is tuberculosis, which affects one third of the world’s population (Gordon et al. 2009) and is caused by the bacterium Mycobacterium tuberculosis. While tuberculosis has affected mankind for a very long time, every now and then a new infectious disease appears and spreads in the world, such as most re- cently the swine flue. Such disease is called an emerging infectious disease, and a majority of these are caused by bacteria (Jones et al. 2008). Many bac- terial infectious agents are zoonotic, which means that they normally live in another host, a reservoir host, in which they do not cause disease. The major reservoirs of infectious diseases are ungulates, carnivores and rodents (Woolhouse and Gowtage-Sequeria 2005). The subject of this thesis, Bartonella, is a genus of host-adapted bacteria that infect the red blood cells of mammals and are transmitted between hosts by blood-sucking insects, e.g. fleas and lice.
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