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Andersson, Siv
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Publications (10 of 66) Show all publications
Mahajan, M., Yee, B., Hägglund, E., Guy, L., Fuerst, J. & Andersson, S. (2019). Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.. Molecular biology and evolution, Article ID msz287.
Open this publication in new window or tab >>Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.
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2019 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, article id msz287Article in journal (Refereed) Epub ahead of print
Abstract [en]

Bacteria of the phylum Planctomycetes have a unique cell plan with an elaborate intracellular membrane system, thereby resembling eukaryotic cells. The origin and evolution of these remarkable features is debated. To study the evolutionary genomics of bacteria with complex cell architectures, we have re-sequenced the 9.2 Mb genome of the model organism Gemmata obscuriglobus and sequenced the 10 Mb genome of Gemmata massiliana Soil9, the 7.9 Mb genome of Cjuql4 and the 6.7 Mb genome of Tuwongella immobilis, all of which belong to the family Gemmataceae. A gene flux analysis of the Planctomycetes revealed a massive emergence of novel protein families at multiple nodes within the Gemmataceae. The expanded protein families have unique multi-domain architectures composed of domains that are characteristic of prokaryotes, such as the sigma factor domain of extracytoplasmic sigma factors, and domains that have proliferated in eukaryotes, such as the WD40, LRR, TPR and Ser/Thr kinase domains. Proteins with identifiable domains in the Gemmataceae have longer lengths and linkers than proteins in most other bacteria, and the analyses suggest that these traits were ancestrally present in the Planctomycetales. A broad comparison of protein length distribution profiles revealed an overlap between the longest proteins in prokaryotes and the shortest proteins in eukaryotes. We conclude that the many similarities between proteins in the Planctomycetales and the eukaryotes are due to convergent evolution and that there is no strict boundary between prokaryotes and eukaryotes with regard to features such as gene paralogy, protein length and protein domain composition patterns.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-401483 (URN)10.1093/molbev/msz287 (DOI)31808939 (PubMedID)
Available from: 2020-01-08 Created: 2020-01-08 Last updated: 2020-01-08
Garcia, S. L., Stevens, S. L., Crary, B., Martinez-Garcia, M., Stepanauskas, R., Woyke, T., . . . McMahon, K. D. (2018). Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. The ISME Journal, 12(3), 742-755
Open this publication in new window or tab >>Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
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2018 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 3, p. 742-755Article in journal (Refereed) Published
Abstract [en]

To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.

National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-350143 (URN)10.1038/s41396-017-0001-0 (DOI)000427226100010 ()29222442 (PubMedID)
Funder
Wenner-Gren FoundationsSwedish Research Council
Available from: 2018-05-04 Created: 2018-05-04 Last updated: 2018-05-28Bibliographically approved
Bisch, G., Neuvonen, M. M., Pierce, N. E., Russell, J. A., Koga, R., Sanders, J. G., . . . Andersson, S. G. E. (2018). Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale. Genome Biology and Evolution, 10(7), 1687-1704
Open this publication in new window or tab >>Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale
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2018 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 7, p. 1687-1704Article in journal (Refereed) Published
Abstract [en]

Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota-and conversely, the importance of the microbiota for the nutrition of hosts.

Place, publisher, year, edition, pages
Oxford University Press, 2018
Keywords
ants, bacteria, genomics, molecular evolution, nutritional symbionts
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-364009 (URN)10.1093/gbe/evy126 (DOI)000442378100006 ()29982531 (PubMedID)
Funder
Swedish Research Council, 349-2007-8732 621-2014-4460Knut and Alice Wallenberg Foundation, 2011.0148 2012.0075
Available from: 2018-10-30 Created: 2018-10-30 Last updated: 2018-10-30Bibliographically approved
Tamarit, D., Neuvonen, M. M., Engel, P., Guy, L. & Andersson, S. G. E. (2018). Origin and evolution of the Bartonella Gene Transfer Agent. Molecular biology and evolution, 35(2), 451-464
Open this publication in new window or tab >>Origin and evolution of the Bartonella Gene Transfer Agent
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2018 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, no 2, p. 451-464Article in journal (Refereed) Published
Abstract [en]

Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transferof bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forcesthat drive the emergence of GTAs are still poorly understood. Two GTAs have been identifiedintheAlphaproteobacteria:the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range thatincludes vector-borne intracellular bacteria of the genusBartonella. The RcGTA packages chromosomal DNA randomly,whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplifiedfrom a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bac-teriophage genes identified in the genomes ofBartonellaspecies and close relatives. Unlike the BaGTA, the prophagegenes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and sub-stitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integra-tion and recombination events in the prophages. Furthermore, the organizationof segments flanking the BaGTA differsfrom that of the prophages by a few rearrangement events,which have abolished the normal coordination betweenphage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose amodel for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.

Keywords
mobile elements, Phage domestication, GTA
National Category
Evolutionary Biology
Research subject
Biology with specialization in Molecular Evolution
Identifiers
urn:nbn:se:uu:diva-301779 (URN)10.1093/molbev/msx299 (DOI)000423713100014 ()29161442 (PubMedID)
Funder
Swedish Research Council, 349-2007-8732, 621-2014-4460Knut and Alice Wallenberg Foundation, 2011.0148, 2012.0075
Available from: 2016-08-25 Created: 2016-08-25 Last updated: 2018-10-23
Urbina, H., Breed, M. F., Zhao, W., Gurrala, K. L., Andersson, S. G. .., Ågren, J., . . . Rosling, A. (2018). Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere. Fungal Biology, 122(4), 231-240
Open this publication in new window or tab >>Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere
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2018 (English)In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 122, no 4, p. 231-240Article in journal (Refereed) Published
Abstract [en]

Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endo-sphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.

Keywords
Arabidopsis, Archaeorhizomcyetes, Brassicaceae, Ion Torrent, ITS metabarcoding, Rhizosphere
National Category
Botany
Identifiers
urn:nbn:se:uu:diva-354246 (URN)10.1016/j.funbio.2017.12.013 (DOI)000430773300005 ()29551197 (PubMedID)
Funder
Swedish Research Council, 349-2007-8731Swedish Research Council, 2012-3950Australian Research Council, DE150100542Australian Research Council, DP150103414
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2018-06-19 Created: 2018-06-19 Last updated: 2019-08-28Bibliographically approved
Hagström, E. & Andersson, S. G. E. (2018). The challenges of integrating two genomes in one cell. Current Opinion in Microbiology, 41, 89-94
Open this publication in new window or tab >>The challenges of integrating two genomes in one cell
2018 (English)In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 41, p. 89-94Article, review/survey (Refereed) Published
Abstract [en]

Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single genome. Functional gene transfers to the host nuclear genome is uncommon in mutualistic bacteria and lost gene functions are rather rescued by co-symbiotic bacteria. Recent findings suggest that the mitochondria! genome is retained to avoid conflicting signals between protein targeting pathways in the cell. However, if the selective pressure for oxygenic respiration is lost, the mitochondrial genome will start to deteriorate and soon be lost.

Place, publisher, year, edition, pages
CURRENT BIOLOGY LTD, 2018
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-357190 (URN)10.1016/j.mib.2017.12.003 (DOI)000429514300014 ()29277086 (PubMedID)
Funder
Swedish Research Council, 349-2007-8732Swedish Research Council, 621-2014-4460Knut and Alice Wallenberg Foundation, 2011.0148Knut and Alice Wallenberg Foundation, 2012.0075
Available from: 2018-08-13 Created: 2018-08-13 Last updated: 2018-08-13Bibliographically approved
Sun, Y., Tamarit, D. & Andersson, S. (2017). Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites. Genome Biology and Evolution, 9(10), 2560-2579
Open this publication in new window or tab >>Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites
2017 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 10, p. 2560-2579Article in journal (Refereed) Published
Abstract [en]

The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bacterial genomes with extreme nucleotide composition biases provide informative model systems. Switches in the background substitution biases from GC to AT have occurred in Gardnerella vaginalis (GC = 32%), and from AT to GC in Lactobacillus delbrueckii (GC=62%) and Lactobacillus fermentum (GC = 63%). We show that despite the large effects on codon usage patterns by these switches, all three species evolve under selection on synonymous sites. In G. vaginalis, the dramatic codon frequency changes coincide with shifts of optimal codons. In contrast, the optimal codons have not shifted in the two Lactobacillus genomes despite an increased fraction of GC-ending codons. We suggest that all three species are in different phases of an on-going shift of optimal codons, and attribute the difference to a stronger background substitution bias and/or longer time since the switch in G. vaginalis. We show that comparative and correlative methods for optimal codon identification yield conflicting results for genomes in flux and discuss possible reasons for the mispredictions. We conclude that switches in the direction of the background substitution biases can drive major shifts in codon preference patterns even under sustained selection on synonymous codon sites.

Keywords
Codon Usage, Lactobacillus, Bifidobacterium, GC content
National Category
Evolutionary Biology
Research subject
Biology with specialization in Molecular Evolution
Identifiers
urn:nbn:se:uu:diva-300909 (URN)10.1093/gbe/evw201 (DOI)000414778600006 ()27540085 (PubMedID)
Funder
Swedish Research Council, 349-2007-8732 621-2014-4460Knut and Alice Wallenberg Foundation, 2011.0148 2012.0075
Available from: 2016-08-15 Created: 2016-08-15 Last updated: 2018-02-14Bibliographically approved
Seeger, C., Butler, M. K., Yee, B., Mahajan, M., Fuerst, J. A. & Andersson, S. (2017). Tuwongella immobilis gen. nov., sp nov., a novel non-motile bacterium within the phylum Planctomycetes. International Journal of Systematic and Evolutionary Microbiology, 67(12), 4923-4929
Open this publication in new window or tab >>Tuwongella immobilis gen. nov., sp nov., a novel non-motile bacterium within the phylum Planctomycetes
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2017 (English)In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 67, no 12, p. 4923-4929Article in journal (Refereed) Published
Abstract [en]

A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1(T)) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1(T) displays modest salt tolerance and grows optimally at pH values of 7.5-8.0 and at temperatures of 32-36 degrees C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 omega 5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1(T) should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1(T) (=CCUG 69661(T) =DSM 105045(T)).

Place, publisher, year, edition, pages
MICROBIOLOGY SOC, 2017
Keywords
Planctomycetes, freshwater bacteria, nucleoid, phylogeny, fatty acids
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-340273 (URN)10.1099/ijsem.0.002271 (DOI)000417933700007 ()
Funder
Swedish Research Council, 349-2007-8732, 621-2014-4460Knut and Alice Wallenberg Foundation, 2011.0148, 2012.0075Australian Research Council
Available from: 2018-01-31 Created: 2018-01-31 Last updated: 2018-01-31Bibliographically approved
Björkholm, P., Ernst, A. M., Hagström, E. & Andersson, S. G. E. (2017). Why mitochondria need a genome revisited. FEBS Letters, 591(1), 65-75
Open this publication in new window or tab >>Why mitochondria need a genome revisited
2017 (English)In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 591, no 1, p. 65-75Article in journal (Refereed) Published
Abstract [en]

In this paper, we experimentally address the debate about why functional transfer of mitochondrial genes to the nucleus has been halted in some organismal groups and why cytosolic expression of mitochondrial proteins has proven remarkably difficult. By expressing all 13 human mitochondrial-encoded genes with strong mitochondrial-targeting sequences in the cytosol of human cells, we show that all proteins, except ATP8, are transported to the endoplasmic reticulum (ER). These results confirm and extend previous findings based on three mitochondrial genes lacking mitochondrial-targeting sequences that also were relocated to the ER during cytosolic expression. We conclude that subcellular protein targeting constitutes a major barrier to functional transfer of mitochondrial genes to the nuclear genome.

Place, publisher, year, edition, pages
WILEY-BLACKWELL, 2017
Keywords
endoplasmic reticulum, hydrophobicity, mitochondria, signal recognition particle, transmembrane domain
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-319810 (URN)10.1002/1873-3468.12510 (DOI)000393957400008 ()27928819 (PubMedID)
Funder
Swedish Research Council, 349-2007-8732 621-2014-4460Knut and Alice Wallenberg Foundation, 2011.0148 2012.0075German Research Foundation (DFG)
Available from: 2017-04-10 Created: 2017-04-10 Last updated: 2017-11-29Bibliographically approved
Andersson, S. G. E. (2016). Stress management strategies in single bacterial cells. Proceedings of the National Academy of Sciences of the United States of America, 113(15), 3921-3923
Open this publication in new window or tab >>Stress management strategies in single bacterial cells
2016 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 15, p. 3921-3923Article in journal, Editorial material (Other academic) Published
National Category
Biochemistry and Molecular Biology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-299105 (URN)10.1073/pnas.1603151113 (DOI)000373762400025 ()27036005 (PubMedID)
Available from: 2016-07-15 Created: 2016-07-14 Last updated: 2017-11-28Bibliographically approved
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