The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like γ-proteobacterium

<p>Abstract</p> <p>Background</p> <p><it>Paulinella chromatophora </it>is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living <it>Prochlorococcus </it>and <it>Synechococcus </it>species (PS-clade). Members of the PS-clade of cyanobacteria contain a proteobacterial form 1A RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (HGT) of a carboxysomal operon. In rDNA-phylogenies, the <it>Paulinella </it>chromatophore diverged basal to the PS-clade, raising the question whether the HGT occurred before or after the split of the chromatophore ancestor.</p> <p>Results</p> <p>Phylogenetic analyses of the almost complete rDNA operon with an improved taxon sampling containing most known cyanobacterial lineages recovered the <it>Paulinella </it>chromatophore as sister to the complete PS-clade. The sequence of the complete carboxysomal operon of <it>Paulinella </it>was determined. Analysis of RubisCO large subunit (<it>rbcL</it>) sequences revealed that <it>Paulinella </it>shares the proteobacterial form 1A RubisCO with the PS-clade. The γ-proteobacterium <it>Nitrococcus mobilis </it>was identified as sister of the <it>Paulinella </it>chromatophore and the PS-clade in the RubisCO phylogeny. Gene content and order in the carboxysomal operon correlates well with the RubisCO phylogeny demonstrating that the complete carboxysomal operon was acquired by the common ancestor of the <it>Paulinella </it>chromatophore and the PS-clade through HGT. The carboxysomal operon shows a significantly elevated AT content in <it>Paulinella</it>, which in the <it>rbcL </it>gene is confined to third codon positions. Combined phylogenies using <it>rbcL </it>and the rDNA-operon resulted in a nearly fully resolved tree of the PS-clade.</p> <p>Conclusion</p> <p>The HGT of the carboxysomal operon predated the divergence of the chromatophore ancestor from the PS-clade. Following HGT and divergence of the chromatophore ancestor, diversification of the PS-clade into at least three subclades occurred. The γ-proteobacterium <it>Nitrococcus mobilis </it>represents the closest known relative to the donor of the carboxysomal operon. The isolated position of the <it>Paulinella </it>chromatophore in molecular phylogenies as well as its elevated AT content suggests that the <it>Paulinella </it>chromatophore has already undergone typical steps in the reductive evolution of an endosymbiont.</p

The genome of <i>Prasinoderma coloniale</i> unveils the existence of a third phylum within green plants

Genome analysis of the pico-eukaryotic marine green algaPrasinoderma colonialeCCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of theP. colonialegenome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations ofP. colonialeto its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C(4)photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B-1, B(7)and B(12)auxotrophy. TheP. colonialegenome provides first insights into the dawn of green plant evolution. Genome analysis of the pico-eukaryotic marine green algaPrasinoderma colonialeCCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta

The chromatin insulator CTCF and the emergence of metazoan diversity

The great majority of metazoans belong to bilaterian phyla. They diversified during a short interval in Earth's history known as the Cambrian explosion, similar to 540 million years ago. However, the genetic basis of these events is poorly understood. Here we argue that the vertebrate genome organizer CTCF (CCCTC-binding factor) played an important role for the evolution of bilaterian animals. We provide evidence that the CTCF protein and a genome-wide abundance of CTCF-specific binding motifs are unique to bilaterian phyla, but absent in other eukaryotes. We demonstrate that CTCF-binding sites within vertebrate and Drosophila Hox gene clusters have been maintained for several hundred million years, suggesting an ancient origin of the previously known interaction between Hox gene regulation and CTCF. In addition, a close correlation between the presence of CTCF and Hox gene clusters throughout the animal kingdom suggests conservation of the Hox-CTCF link across the Bilateria. On the basis of these findings, we propose the existence of a Hox-CTCF kernel as principal organizer of bilaterian body plans. Such a kernel could explain (i) the formation of Hox clusters in Bilateria, (ii) the diversity of bilaterian body plans, and (iii) the uniqueness and time of onset of the Cambrian explosion

The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium-3

<p><b>Copyright information:</b></p><p>Taken from "The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium"</p><p>http://www.biomedcentral.com/1471-2148/7/85</p><p>BMC Evolutionary Biology 2007;7():85-85.</p><p>Published online 5 Jun 2007</p><p>PMCID:PMC1904183.</p><p></p>onsensus tree). Three synapomorphies shared by and α-cyanobacteria are shown in red colour (positions 36, 59, 64); Histidine 399 and Serine 405 (blue) are unique for and free-living α-cyanobacteria to the exclusion of all proteobacterial ancestors and β-cyanobacteria

The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium-5

<p><b>Copyright information:</b></p><p>Taken from "The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium"</p><p>http://www.biomedcentral.com/1471-2148/7/85</p><p>BMC Evolutionary Biology 2007;7():85-85.</p><p>Published online 5 Jun 2007</p><p>PMCID:PMC1904183.</p><p></p>gure 1 (4317 vs. 4126 characters). . Phylogeny inferred from concatenated and rDNA sequences. Tree topologies resulted from ML analyses using a GTR+I+Γ model; significance values shown as in Figure 1

The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium-6

<p><b>Copyright information:</b></p><p>Taken from "The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium"</p><p>http://www.biomedcentral.com/1471-2148/7/85</p><p>BMC Evolutionary Biology 2007;7():85-85.</p><p>Published online 5 Jun 2007</p><p>PMCID:PMC1904183.</p><p></p>ird codon position displays a sharply elevated AT-content in as well as strains (). The AT-content integrated over the complete carboxysomal operon (from to ) including intergenic spacer regions shows a similar bias, although less pronounced ()

The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium-4

<p><b>Copyright information:</b></p><p>Taken from "The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium"</p><p>http://www.biomedcentral.com/1471-2148/7/85</p><p>BMC Evolutionary Biology 2007;7():85-85.</p><p>Published online 5 Jun 2007</p><p>PMCID:PMC1904183.</p><p></p> amino acid sequences. Four major types of gene arrangements can be distinguished (for details, see text). The operon of is member of the α-cyano-cso-type, which is derived from the ancestral cso-type present in proteobacteria, providing evidence for a HGT of the complete operon. Homologous genes share the same colour. Abbreviations: Carboxysomal shell proteins 1, 2, 3 (csoS1, 2, 3); RubisCO large and small subunit (, = , ); carboxysomal peptides A, B (, ); bacterioferritin (); LysR-type transcriptional activator (); putative RubisCO activation proteins (, ); hypothetical proteins (hypo). Dotted lines indicate that no data are available

The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium-2

<p><b>Copyright information:</b></p><p>Taken from "The ancestor of the chromatophore obtained a carboxysomal operon by horizontal gene transfer from a -like γ-proteobacterium"</p><p>http://www.biomedcentral.com/1471-2148/7/85</p><p>BMC Evolutionary Biology 2007;7():85-85.</p><p>Published online 5 Jun 2007</p><p>PMCID:PMC1904183.</p><p></p>, plastids and proteobacteria under the RtREV+I+Γ model of amino acid substitution. Numbers at branches are ML bootstrap values ≥ 50%. Strain designations (when available) and NCBI accession numbers are indicated after the species name. Newly determined sequences are given in bold. Greek letters in grey indicate α-, β-, or γ- proteobacteria. Arrowheads highlight strains for which the gene arrangement of the carboxysomal operon is shown in Figure 5