For better or worse: genomic consequences of intracellular mutualism and parasitism

Current Opinion in Genetics & Development - Tập 15 - Trang 572-583 - 2005
Jennifer J Wernegreen1
1Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA

Tài liệu tham khảo

Moran, 2002, The ubiquitous and varied role of infection in the lives of animals and plants, Am Nat, 60, S1, 10.1086/342113 Andersson, 1998, Reductive evolution of resident genomes, Trends Microbiol, 6, 263, 10.1016/S0966-842X(98)01312-2 Moran, 1996, Accelerated evolution and Muller's rachet in endosymbiotic bacteria, Proc Natl Acad Sci USA, 93, 2873, 10.1073/pnas.93.7.2873 Mira, 2001, Deletional bias and the evolution of bacterial genomes, Trends Genet, 17, 589, 10.1016/S0168-9525(01)02447-7 Frank, 2002, Genome deterioration: loss of repeated sequences and accumulation of junk DNA, Genetica, 115, 1, 10.1023/A:1016064511533 Mira, 2002, Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria, Microb Ecol, 44, 137, 10.1007/s00248-002-0012-9 Ohta, 1973, Slightly deleterious mutant substitutions in evolution, Nature, 246, 96, 10.1038/246096a0 Muller, 1964, The relation of recombination to mutational advance, Mutat Res, 106, 2, 10.1016/0027-5107(64)90047-8 Moran, 2004, Genomic changes following host restriction in bacteria, Curr Opin Genet Dev, 14, 627, 10.1016/j.gde.2004.09.003 Subtil, 2004, Chlamydia: five years A.G. (after genome), Curr Opin Microbiol, 7, 85, 10.1016/j.mib.2003.12.012 Gil, 2004, Bacterial endosymbionts of insects: insights from comparative genomics, Environ Microbiol, 6, 1109, 10.1111/j.1462-2920.2004.00691.x Klasson, 2004, Evolution of minimal-gene-sets in host-dependent bacteria, Trends Microbiol, 12, 37, 10.1016/j.tim.2003.11.006 Renesto, 2005, Some lessons from Rickettsia genomics, FEMS Microbiol Rev, 29, 99, 10.1016/j.femsre.2004.09.002 Batut, 2004, The evolution of chronic infection strategies in the alpha-proteobacteria, Nat Rev Microbiol, 2, 933, 10.1038/nrmicro1044 Zientz, 2004, Metabolic interdependence of obligate intracellular bacteria and their insect hosts, Microbiol Mol Biol Rev, 68, 745, 10.1128/MMBR.68.4.745-770.2004 Moran, 2001, The process of genome shrinkage in the obligate symbiont Buchnera aphidicola, Genome Biol, 2, 10.1186/gb-2001-2-12-research0054 Belda, 2005, Genome rearrangement distances and gene order phylogeny in γ-Proteobacteria, Mol Biol Evol, 22, 1456, 10.1093/molbev/msi134 Seshadri, 2003, Complete genome sequence of the Q-fever pathogen Coxiella burnetii, Proc Natl Acad Sci USA, 100, 5455, 10.1073/pnas.0931379100 Cole, 2001, Massive gene decay in the leprosy bacillus, Nature, 409, 1007, 10.1038/35059006 Dale, 2005, Degenerative evolution and functional diversification of type-III secretion systems in the insect endosymbiont Sodalis glossinidius, Mol Biol Evol, 22, 758, 10.1093/molbev/msi061 Gomez-Valero, 2004, The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola, Mol Biol Evol, 21, 2172, 10.1093/molbev/msh232 Perez-Brocal, 2005, Comparative analysis of two genomic regions among four strains of Buchnera aphidicola, primary endosymbiont of aphids, Gene, 345, 73, 10.1016/j.gene.2004.11.021 Foster, 2005, The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode, PLoS Biol, 3, e121, 10.1371/journal.pbio.0030121 Ghedin, 2004, First sequenced genome of a parasitic nematode, Trends Parasitol, 20, 151, 10.1016/j.pt.2004.01.011 Hacker, 2003, Prokaryotic chromosomes and disease, Science, 301, 790, 10.1126/science.1086802 Goebel, 2001, Intracellular survival strategies of mutualistic and parasitic prokaryotes, Trends Microbiol, 9, 267, 10.1016/S0966-842X(01)02040-6 Palmer, 2002, The highest priority: what microbial genomes are telling us about immunity, Vet Immunol Immunopathol, 85, 1, 10.1016/S0165-2427(01)00415-9 Horn, 2004, Illuminating the evolutionary history of chlamydiae, Science, 304, 728, 10.1126/science.1096330 Dale, 2002, Type III secretion systems and the evolution of mutualistic endosymbiosis, Proc Natl Acad Sci U S A, 99, 12397, 10.1073/pnas.182213299 Corsaro, 2004, Emerging chlamydial infections, Crit Rev Microbiol, 30, 75, 10.1080/10408410490435106 Everett, 2005, Novel chlamydiae in whiteflies and scale insects: endosymbionts ‘Candidatus Fritschea bemisiae’ strain Falk and ‘Candidatus Fritschea eriococci’ strain Elm, Int J Syst Evol Microbiol, 55, 1581, 10.1099/ijs.0.63454-0 Schmitz-Esser, 2004, ATP/ADP translocases: a common feature of obligate intracellular amoebal symbionts related to Chlamydiae and Rickettsiae, J Bacteriol, 186, 683, 10.1128/JB.186.3.683-691.2004 McGraw, 2004, Wolbachia pipientis: intracellular infection and pathogenesis in Drosophila, Curr Opin Microbiol, 7, 67, 10.1016/j.mib.2003.12.003 Brownlie, 2005, Wolbachia genomes: insights into an intracellular lifestyle, Curr Biol, 15, R507, 10.1016/j.cub.2005.06.029 Burne, 2000, Bacterial ureases in infectious diseases, Microbes Infect, 2, 533, 10.1016/S1286-4579(00)00312-9 Gil, 2003, The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes, Proc Natl Acad Sci USA, 100, 9388, 10.1073/pnas.1533499100 Degnan, 2005, Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects, Genome Res, 15, 1023, 10.1101/gr.3771305 Fares, 2004, GroEL and the maintenance of bacterial endosymbiosis, Trends Genet, 20, 413, 10.1016/j.tig.2004.07.001 Bencina, 2005, Antibody response to GroEL varies in patients with acute Mycoplasma pneumoniae infection, FEMS Immunol Med Microbiol, 43, 399, 10.1016/j.femsim.2004.10.009 Renesto, 2005, Proteome analysis of Rickettsia conorii by two-dimensional gel electrophoresis coupled with mass spectrometry, FEMS Microbiol Lett, 245, 231, 10.1016/j.femsle.2005.03.004 Hechard, 2004, Molecular cloning of the Chlamydophila abortus groEL gene and evaluation of its protective efficacy in a murine model by genetic vaccination, J Med Microbiol, 53, 861, 10.1099/jmm.0.05442-0 Fares, 2002, Endosymbiotic bacteria: GroEL buffers against deleterious mutations, Nature, 417, 398, 10.1038/417398a Morin, 1999, A GroEL homologue from endosymbiotic bacteria of the whitefly Bemisia tabaci is implicated in the circulative transmission of tomato yellow leaf curl virus, Virology, 256, 75, 10.1006/viro.1999.9631 Fredriksson, 2005, Defense against protein carbonylation by DnaK/DnaJ and proteases of the heat shock regulon, J Bacteriol, 187, 4207, 10.1128/JB.187.12.4207-4213.2005 Akman, 2002, Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia, Nat Genet, 32, 402, 10.1038/ng986 Rocha, 2002, Base composition bias might result from competition for metabolic resources, Trends Genet, 18, 291, 10.1016/S0168-9525(02)02690-2 Ochman, 2001, Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis, Science, 292, 1096, 10.1126/science.1058543 Tamas, 2002, 50 million years of genomic stasis in endosymbiotic bacteria, Science, 296, 2376, 10.1126/science.1071278 Van Ham, 2003, Reductive genome evolution in Buchnera aphidicola, Proc Natl Acad Sci USA, 100, 581, 10.1073/pnas.0235981100 Van Ham, 2000, Postsymbiotic plasmid acquisition and evolution of the repA1-replicon in Buchnera aphidicola, Proc Natl Acad Sci USA, 97, 10855, 10.1073/pnas.180310197 Sabater-Munoz, 2004, Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster, J Bacteriol, 186, 2646, 10.1128/JB.186.9.2646-2654.2004 McLeod, 2004, Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae, J Bacteriol, 186, 5842, 10.1128/JB.186.17.5842-5855.2004 Mira, 2002, Microbial genome evolution: sources of variability, Curr Opin Microbiol, 5, 506, 10.1016/S1369-5274(02)00358-2 Ogata, 2005, The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite, PLoS Biol, 3, e248, 10.1371/journal.pbio.0030248 Greub, 2004, A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system, BMC Microbiol, 4, 48, 10.1186/1471-2180-4-48 Horn, 2004, Bacterial endosymbionts of free-living amoebae, J Eukaryot Microbiol, 51, 509, 10.1111/j.1550-7408.2004.tb00278.x Bordenstein, 2005, Mobile DNA in obligate intracellular bacteria, Nat Rev Microbiol, 3, 688, 10.1038/nrmicro1233 Wu, 2004, Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: A streamlined genome overrun by mobile genetic elements, PLoS Biol, 2, E69, 10.1371/journal.pbio.0020069 Oshima, 2004, Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma, Nat Genet, 36, 27, 10.1038/ng1277 Lee, 2005, Novel insertion sequence-like elements in phytoplasma strains of the aster yellows group are putative new members of the IS3 family, FEMS Microbiol Lett, 242, 353, 10.1016/j.femsle.2004.11.036 Salzberg, 2005, Serendipitous discovery of Wolbachia genomes in multiple Drosophila species, Genome Biol, 6, R23, 10.1186/gb-2005-6-3-r23 Ortutay, 2003, Speciation in Chlamydia: genomewide phylogenetic analyses identified a reliable set of acquired genes, J Mol Evol, 57, 672, 10.1007/s00239-003-2517-3 Gomes, 2004, Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer, J Bacteriol, 186, 4295, 10.1128/JB.186.13.4295-4306.2004 Read, 2003, Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae, Nucleic Acids Res, 31, 2134, 10.1093/nar/gkg321 Brayton, 2005, Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins, Proc Natl Acad Sci USA, 102, 844, 10.1073/pnas.0406656102 Collins, 2005, The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number, Proc Natl Acad Sci USA, 102, 838, 10.1073/pnas.0406633102 Moran, 2005, Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola, J Bacteriol, 187, 4229, 10.1128/JB.187.12.4229-4237.2005 Qin, 2004, Transposon mutagenesis of the obligate intracellular pathogen Rickettsia prowazekii, Appl Environ Microbiol, 70, 2816, 10.1128/AEM.70.5.2816-2822.2004 Buchner, 1965 Baumann, 2000, Bacteriocyte-associated endosymbionts of insects Moran, 1998, Bacteriocyte-associated symbionts of insects, Bioscience, 48, 295, 10.2307/1313356 Aksoy, 2005, Interactions among multiple genomes: tsetse, its symbionts and trypanosomes, Insect Biochem Mol Biol, 35, 691, 10.1016/j.ibmb.2005.02.012 Moran, 2005, Evolutionary relationships of three new species of enterobacteriaceae living as symbionts of aphids and other insects, Appl Environ Microbiol, 71, 3302, 10.1128/AEM.71.6.3302-3310.2005 Brownstein, 2003, The potential of virulent Wolbachia to modulate disease transmission by insects, J Invertebr Pathol, 84, 24, 10.1016/S0022-2011(03)00082-X Rio, 2004, Strategies of the home-team: symbioses exploited for vector-borne disease control, Trends Microbiol, 12, 325, 10.1016/j.tim.2004.05.001 Sinkins, 2004, Use of Wolbachia to drive nuclear transgenes through insect populations, Proc Biol Sci, 271, 1421, 10.1098/rspb.2004.2740 Moran, 2002, Microbial minimalism: genome reduction in bacterial pathogens, Cell, 108, 583, 10.1016/S0092-8674(02)00665-7 Peterson, 2001, The Comprehensive Microbial Resource, Nucleic Acids Res, 29, 123, 10.1093/nar/29.1.123 Hallin, 2004, CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data, Bioinformatics, 20, 3682, 10.1093/bioinformatics/bth423 Ussery, 2004, Genome update: DNA repeats in bacterial genomes, Microbiology, 150, 3519, 10.1099/mic.0.27628-0 Skovgaard, 2002, The atlas visualisation of genome-wide information, Methods Microbiol, 33, 49, 10.1016/S0580-9517(02)33004-6 Jensen, 1999, Three views of microbial genomes, Res Microbiol, 150, 773, 10.1016/S0923-2508(99)00116-3 Frank, 2005, Functional divergence and horizontal transfer of type IV secretion systems, Mol Biol Evol, 22, 1325, 10.1093/molbev/msi124 Gil, 2002, Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life, Proc Natl Acad Sci USA, 99, 4454, 10.1073/pnas.062067299 Moran, 2003, Intracellular symbionts of sharpshooters (Insecta: Hemiptera: Cicadellinae) form a distinct clade with a small genome, Environ Microbiol, 5, 116, 10.1046/j.1462-2920.2003.00391.x Zabalou, 2004, Wolbachia-induced cytoplasmic incompatibility as a means for insect pest population control, Proc Nat Acad Sci USA, 101, 15042, 10.1073/pnas.0403853101 Nilsson, 2005, Bacterial genome size reduction by experimental evolution, Proc Natl Acad Sci USA, 102, 12112, 10.1073/pnas.0503654102 Darby, 2005, Extrachromosomal DNA of the symbiont Sodalis glossinidius, J Bacteriol, 187, 5003, 10.1128/JB.187.14.5003-5007.2005 Sallstrom, 2005, Genome reduction in the α-Proteobacteria, Curr Opin Microbiol, 8, 579, 10.1016/j.mib.2005.08.002 Iturbe-Ormaetxe, 2005, Distribution, expression, and motif variability of ankyrin domain genes in Wolbachia pipientis, J Bacteriol, 187, 5136, 10.1128/JB.187.15.5136-5145.2005 Riegler, 2005, Evidence for a global Wolbachia replacement in Drosophila melanogaster, Curr Biol, 15, 1428, 10.1016/j.cub.2005.06.069