Think pink: photosynthesis, plasmids and the Roseobacter clade
Article first published online: 26 JUN 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Thematic issue: Sulfur Metabolism
Volume 14, Issue 10, pages 2661–2672, October 2012
How to Cite
Petersen, J., Brinkmann, H., Bunk, B., Michael, V., Päuker, O. and Pradella, S. (2012), Think pink: photosynthesis, plasmids and the Roseobacter clade. Environmental Microbiology, 14: 2661–2672. doi: 10.1111/j.1462-2920.2012.02806.x
- Issue published online: 3 OCT 2012
- Article first published online: 26 JUN 2012
- Received 14 February, 2012; revised 15 May, 2012; accepted 17 May, 2012.
Fig. S1. Genetic organization of plasmid replication modules inserted within the photosynthesis gene clusters (PGC) of Roseobacter litoralis and Sulfitobacter guttiformis. Genes are coloured according to Fig. 3: light blue, parAB partitioning genes; yellow, dnaA-like replicase; pink, repB-III type replicase; white, genes specifically found in plasmid PGCs. Adjacent conserved genes of the PGC are shaded in grey. The origin of replication (ori) is indicated by a red circle and triangles represent palindromic sequences (inverted repeats) that may reflect cis-acting anchors for plasmid partitioning.
Fig. S2. Phylogenetic Maximum Likelihood tree of the plasmid partitioning protein ParB from Rhodobacterales based on 40 sequences and 216 amino acid positions, inferred by RAxML under an LG+F+Γ4 model. Sequences from Sulfitobacter guttiformis and Roseobacter litoralis are shown in bold. Coloured boxes reflect distinct plasmid compatibility groups of Rhodobacterales (yellow: DnaA-like I, orange: RepABC, blue: RepB-III). The statistical support for the internal nodes was determined by 100 bootstrap replicates and only values > 50% are shown. Accession numbers of all sequences are summarized in Table S1.
Fig. S3. Comparison between the conserved photosynthesis gene cluster (PGC) region of Roseobacter denitrificans and R. litoralis. Homology is indicated by vertical grey shaded areas; conserved genes of the PGC are coloured in pink, others in white. Plasmid-specific genes of the DnaA-like replication module and genes adjacent to the PGC are shown in yellow and red respectively. Adjacent chromosomal genes are indicated with grey lines. A pseudogene is coloured in grey and the origin of plasmid replication (ori) is indicated by a red circle.
Table S1. Accession numbers of replication and partitioning genes used for phylogenetic analyses (Figs 2, 4 and S2).
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