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Näslund, Kristina
Alternative names
Publications (8 of 8) Show all publications
Neuvonen, M. M., Tamarit, D., Näslund, K., Liebig, J., Feldhaar, H., Moran, N. A., . . . Andersson, S. G. .. (2016). The genome of Rhizobiales bacteria in predatory ants indicates a role for urease in lifestyle switches.
Open this publication in new window or tab >>The genome of Rhizobiales bacteria in predatory ants indicates a role for urease in lifestyle switches
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2016 (English)Article in journal (Refereed) Submitted
Abstract [en]

Bacterial symbionts provide amino acids to herbivorous ants, but their role in carnivores is a puzzle. The most prevalent bacterial lineage in ants belongs to the order Rhizobiales. Sequence reads with similarity to Bartonella, a member of the Rhizobiales, were identified in the data collected in a genome project of the carnivorous ant Harpegnatos saltator. Here, we present an analysis of the closed 1.86 Mb genome of the Bartonella-like bacterium, here abbreviated Bhsal. A phylogenetic study showed that Bhsal diverged prior to the radiation of the Bartonella species. Uniquely present in the Bhsal genome is a gene for a giant protein of 6,177 amino acids with a repeated domain structure. We also identified genes for a multi- subunit urease protein complex, potentially involved in the hydrolysis of urea into ammonium. We hypothesize that the urease function protects Bhsal from the acidic environment of the ant gut. The urease genes are also present in Brucella, which has a fecal-oral transmission pathway, but they have been lost in Bartonella species, which use blood-borne transmission pathways. Taken together, the results suggest that the urease function has served an important role for transmission strategies and lifestyle changes in the host-associated members of the Rhizobiales.

Keywords
symbiosis, genomics, Bartonella
National Category
Evolutionary Biology
Research subject
Biology with specialization in Molecular Evolution
Identifiers
urn:nbn:se:uu:diva-301778 (URN)
Available from: 2016-08-25 Created: 2016-08-25 Last updated: 2017-01-13Bibliographically approved
Neuvonen, M. M., Tamarit, D., Näslund, K., Liebig, J., Feldhaar, H., Moran, N. A., . . . Andersson, S. G. E. (2016). The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation. Scientific Reports, 6, 1-11, Article ID 39197.
Open this publication in new window or tab >>The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation
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2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, p. 1-11, article id 39197Article in journal (Refereed) Published
Abstract [en]

Gut-associated microbiota of ants include Rhizobiales bacteria with affiliation to the genus Bartonella. These bacteria may enable the ants to fix atmospheric nitrogen, but no genomes have been sequenced yet to test the hypothesis. Sequence reads from a member of the Rhizobiales were identified in the data collected in a genome project of the ant Harpegnathos saltator. We present an analysis of the closed 1.86 Mb genome of the ant-associated bacterium, for which we suggest the species name Candidatus Tokpelaia hoelldoblerii. A phylogenetic analysis reveals a relationship to Bartonella and Brucella, which infect mammals. Novel gene acquisitions include a gene for a putative extracellular protein of more than 6,000 amino acids secreted by the type I secretion system, which may be involved in attachment to the gut epithelium. No genes for nitrogen fixation could be identified, but genes for a multi-subunit urease protein complex are present in the genome. The urease genes are also present in Brucella, which has a fecal-oral transmission pathway, but not in Bartonella, which use blood-borne transmission pathways. We hypothesize that the gain and loss of the urease function is related to transmission strategies and lifestyle changes in the host-associated members of the Rhizobiales.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-312599 (URN)10.1038/srep39197 (DOI)000392093200001 ()27976703 (PubMedID)
Funder
Swedish Research Council, 349-2007-8732 621-2014-4460Knut and Alice Wallenberg Foundation, 2011.0148 2012.0075
Available from: 2017-01-12 Created: 2017-01-12 Last updated: 2017-11-29Bibliographically approved
Guy, L., Nystedt, B., Toft, C., Zaremba-Niedzwiedzka, K., Berglund, E. C., Granberg, F., . . . Andersson, S. G. E. (2013). A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella. PLOS Genetics, 9(3), e1003393
Open this publication in new window or tab >>A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella
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2013 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 9, no 3, p. e1003393-Article in journal (Refereed) Published
Abstract [en]

Gene transfer agents (GTAs) randomly transfer short fragments of a bacterial genome. A novel putative GTA was recently discovered in the mouse-infecting bacterium Bartonella grahamii. Although GTAs are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. Here, we present a comparative analysis of 16 Bartonella genomes ranging from 1.4 to 2.6 Mb in size, including six novel genomes from Bartonella isolated from a cow, two moose, two dogs, and a kangaroo. A phylogenetic tree inferred from 428 orthologous core genes indicates that the deadly human pathogen B. bacilliformis is related to the ruminant-adapted clade, rather than being the earliest diverging species in the genus as previously thought. A gene flux analysis identified 12 genes for a GTA and a phage-derived origin of replication as the most conserved innovations. These are located in a region of a few hundred kb that also contains 8 insertions of gene clusters for type III, IV, and V secretion systems, and genes for putatively secreted molecules such as cholera-like toxins. The phylogenies indicate a recent transfer of seven genes in the virB gene cluster for a type IV secretion system from a catadapted B. henselae to a dog-adapted B. vinsonii strain. We show that the B. henselae GTA is functional and can transfer genes in vitro. We suggest that the maintenance of the GTA is driven by selection to increase the likelihood of horizontal gene transfer and argue that this process is beneficial at the population level, by facilitating adaptive evolution of the host-adaptation systems and thereby expansion of the host range size. The process counters gene loss and forces all cells to contribute to the production of the GTA and the secreted molecules. The results advance our understanding of the role that GTAs play for the evolution of bacterial genomes.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-199485 (URN)10.1371/journal.pgen.1003393 (DOI)000316866700064 ()
Available from: 2013-05-07 Created: 2013-05-06 Last updated: 2017-12-06Bibliographically approved
Ellegaard, K. M., Klasson, L., Näslund, K., Bourtzis, K. & Andersson, S. G. E. (2013). Comparative Genomics of Wolbachia and the Bacterial Species Concept. PLOS Genetics, 9(4), e1003381
Open this publication in new window or tab >>Comparative Genomics of Wolbachia and the Bacterial Species Concept
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2013 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 9, no 4, p. e1003381-Article in journal (Refereed) Published
Abstract [en]

The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-200821 (URN)10.1371/journal.pgen.1003381 (DOI)000318073300004 ()
Available from: 2013-06-04 Created: 2013-06-04 Last updated: 2017-12-06Bibliographically approved
Guy, L., Nystedt, B., Sun, Y., Näslund, K., Berglund, E. C. & Andersson, S. G. E. (2012). A genome-wide study of recombination rate variation in Bartonella henselae. BMC Evolutionary Biology, 12, 65
Open this publication in new window or tab >>A genome-wide study of recombination rate variation in Bartonella henselae
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2012 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 12, p. 65-Article in journal (Refereed) Published
Abstract [en]

Background: Rates of recombination vary by three orders of magnitude in bacteria but the reasons for this variation is unclear. We performed a genome-wide study of recombination rate variation among genes in the intracellular bacterium Bartonella henselae, which has among the lowest estimated ratio of recombination relative to mutation in prokaryotes. Results: The 1.9 Mb genomes of B. henselae strains IC11, UGA10 and Houston-1 genomes showed only minor gene content variation. Nucleotide sequence divergence levels were less than 1% and the relative rate of recombination to mutation was estimated to 1.1 for the genome overall. Four to eight segments per genome presented significantly enhanced divergences, the most pronounced of which were the virB and trw gene clusters for type IV secretion systems that play essential roles in the infection process. Consistently, multiple recombination events were identified inside these gene clusters. High recombination frequencies were also observed for a gene putatively involved in iron metabolism. A phylogenetic study of this gene in 80 strains of Bartonella quintana, B. henselae and B. grahamii indicated different population structures for each species and revealed horizontal gene transfers across Bartonella species with different host preferences. Conclusions: Our analysis has shown little novel gene acquisition in B. henselae, indicative of a closed pan-genome, but higher recombination frequencies within the population than previously estimated. We propose that the dramatically increased fixation rate for recombination events at gene clusters for type IV secretion systems is driven by selection for sequence variability.

Keywords
Type IV Secretion Systems, Recombination, Bartonella
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-185218 (URN)10.1186/1471-2148-12-65 (DOI)000310328700001 ()
Available from: 2012-11-21 Created: 2012-11-21 Last updated: 2017-12-07Bibliographically approved
Lindroos, H., Vinnere, O., Mira, A., Repsilber, D., Näslund, K. & Andersson, S. (2006). Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae. Journal of Bacteriology, 188(21), 7426-7439
Open this publication in new window or tab >>Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae
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2006 (English)In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 188, no 21, p. 7426-7439Article in journal (Refereed) Published
Abstract [en]

Cats are the natural host for Bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. Here, we have analyzed the natural variation in gene content and genome structure of 38 Bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (PFGE) blots. The variation in gene content was modest and confined to the prophage and the genomic islands, whereas the PFGE analyses indicated extensive rearrangements across the terminus of replication with breakpoints in areas of the genomic islands. We observed no difference in gene content or structure between feline and human strains. Rather, the results suggest multiple sources of human infection from feline B. henselae strains of diverse genotypes. Additionally, the microarray hybridizations revealed DNA amplification in some strains in the so-called chromosome II-like region. The amplified segments were centered at a position corresponding to a putative phage replication initiation site and increased in size with the duration of cultivation. We hypothesize that the variable gene pool in the B. henselae population plays an important role in the establishment of long-term persistent infection in the natural host by promoting antigenic variation and escape from the host immune response.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-96009 (URN)10.1128/JB.00472-06 (DOI)000241471600013 ()16936024 (PubMedID)
Available from: 2007-05-11 Created: 2007-05-11 Last updated: 2017-12-14Bibliographically approved
Lindroos, H., Mira, A., Repsilber, D., Vinnere, O., Näslund, K., Dehio, M., . . . Andersson, S. (2005). Characterization of the genome composition of Bartonella koehlerae by microarray comparative genomic hybridization profiling. Journal of Bacteriology, 187(17), 6155-6165
Open this publication in new window or tab >>Characterization of the genome composition of Bartonella koehlerae by microarray comparative genomic hybridization profiling
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2005 (English)In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 187, no 17, p. 6155-6165Article in journal (Refereed) Published
Abstract [en]

Bartonella henselae is present in a wide range of wild and domestic feline hosts and causes cat-scratch disease and bacillary angiomatosis in humans. We have estimated here the gene content of Bartonella koehlerae, a novel species isolated from cats that was recently identified as an agent of human endocarditis. The investigation was accomplished by comparative genomic hybridization (CGH) to a microarray constructed from the sequenced 1.93-Mb genome of B. henselae. Control hybridizations of labeled DNA from the human pathogen Bartonella quintana with a reduced genome of 1.58 Mb were performed to evaluate the accuracy of the array for genes with known levels of sequence divergence. Genome size estimates of B. koehlerae by pulsed-field gel electrophoresis matched that calculated by the CGH, indicating a genome of 1.7 to 1.8 Mb with few unique genes. As in B. quintana, sequences in the prophage and the genomic islands were reported absent in B. koehlerae. In addition, sequence variability was recorded in the chromosome II-like region, where B. koehlerae showed an intermediate retention pattern of both coding and noncoding sequences. Although most of the genes missing in B. koehlerae are also absent from B. quintana, its phylogenetic placement near B. henselae suggests independent deletion events, indicating that host specificity is not solely attributed to genes in the genomic islands. Rather, the results underscore the instability of the genomic islands even within bacterial populations adapted to the same host-vector system, as in the case of B. henselae and B. koehlerae.

Keywords
Bartonella/*genetics, DNA; Bacterial/genetics, Electrophoresis; Gel; Pulsed-Field, Gene Expression Profiling, Genome; Bacterial, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Polymorphism; Restriction Fragment Length, Research Support; Non-U.S. Gov't, Restriction Mapping
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-77160 (URN)10.1128/JB.187.17.6155-6165.2005 (DOI)16109957 (PubMedID)
Available from: 2006-03-13 Created: 2006-03-13 Last updated: 2017-12-14Bibliographically approved
Andersson, S. G., Zomorodipour, A., Andersson, J. O., Sicheritz-Ponten, T., Alsmark, U., Podowski, R., . . . Kurland, C. G. (1998). The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature, 396(6707), 133-140
Open this publication in new window or tab >>The genome sequence of Rickettsia prowazekii and the origin of mitochondria
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1998 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 396, no 6707, p. 133-140Article in journal (Refereed) Published
Abstract [en]

We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-79106 (URN)000077013300041 ()9823893 (PubMedID)
Note

Addresses: Kurland CG, Univ Uppsala, Dept Mol Biol, S-75124 Uppsala, Sweden. Univ Uppsala, Dept Mol Biol, S-75124 Uppsala, Sweden. Univ S Alabama, Dept Microbiol & Immunol, Mobile, AL 36688 USA.

Available from: 2008-10-17 Created: 2008-10-17 Last updated: 2017-12-14Bibliographically approved
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