The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

<p>Abstract</p> <p>Background</p> <p>Bacteria occur in facultative association and intracellular symbiosis with a diversity of eukaryotic hosts. Recently, we have helped to characterise an intracellular nitrogen fixing bacterium, the so-called spheroid body, located within the diatom <it>Rhopalodia gibba</it>. Spheroid bodies are of cyanobacterial origin and exhibit features that suggest physiological adaptation to their intracellular life style. To investigate the genome modifications that have accompanied the process of endosymbiosis, here we compare gene structure, content and organisation in spheroid body and cyanobacterial genomes.</p> <p>Results</p> <p>Comparison of the spheroid body's genome sequence with corresponding regions of near free-living relatives indicates that multiple modifications have occurred in the endosymbiont's genome. These include localised changes that have led to elimination of some genes. This gene loss has been accompanied either by deletion of the respective DNA region or replacement with non-coding DNA that is AT rich in composition. In addition, genome modifications have led to the fusion and truncation of genes. We also report that in the spheroid body's genome there is an accumulation of deleterious mutations in genes for cell wall biosynthesis and processes controlled by transposases. Interestingly, the formation of pseudogenes in the spheroid body has occurred in the presence of intact, and presumably functional, <it>rec</it>A and <it>rec</it>F genes. This is in contrast to the situation in most investigated obligate intracellular bacterium-eukaryote symbioses, where at least either <it>rec</it>A or <it>rec</it>F has been eliminated.</p> <p>Conclusion</p> <p>Our analyses suggest highly specific targeting/loss of individual genes during the process of genome reduction and establishment of a cyanobacterial endosymbiont inside a eukaryotic cell. Our findings confirm, at the genome level, earlier speculation on the obligate intracellular status of the spheroid body in <it>Rhopalodia gibba</it>. This association is the first example of an obligate cyanobacterial symbiosis involving nitrogen fixation for which genomic data are available. It represents a new model system to study molecular adaptations of genome evolution that accompany a switch from free-living to intracellular existence.</p

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-2

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>p. ATVV51142); CyaPCC8801: (sp. ); CyaCCY0110: (sp. ); GloeK068DGA: (sp. ); NostPCC7120: (PCC 7120); AnabATCC29413: (). . Alignment of sp. FdxN protein with the spheroid body fdxN* pseudogene translated in 3 forward reading frames. Evidence of homology, at the level of amino acid similarity, is distributed across all 3 reading frames of the pseudogene, indicating multiple substitutions and single nucleotide deletion events

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-4

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>ns Cyl0018 and Cyl0020. Deletion in the endosymbiont genome of 0019 in the creation of 0010 can be inferred during reductive genome evolution. In Sb10010, homologues of Cyl0018 and Cyl0020 have been conserved in full length and are separated by a 17 amino acid residues. Cyl0018: green, Cyl0020: orange, Sbl0010: black. . Cyl0018 and Cyl0020 are highly conserved in cyanobacteria closely related to the spheroid body. They are aseparated by 1–5 genes when they co-occur at the same locus, but in some cases they are encoded at different loci of the genome (indicated by x)

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-1

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>N, NifS and ABC, HesA, NdhK, ModC, PerM, UvrD, SAM, Sbr0014 of different cyanobacetria (see Materials and Methods). . Supernetwork reconstructed using strict consensus maximum likelihood trees for NifD, NifH, NifK, NifE, and ABC, HesA, NdhK, ModC, PerM, UvrD, SAM, Sbr0014. The networks are outgroup rooted using PCC 6803. A reticulation occurs in the centre of both graphs because of the local instability in the placement of PCC 6803

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-9

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>N, NifS and ABC, HesA, NdhK, ModC, PerM, UvrD, SAM, Sbr0014 of different cyanobacetria (see Materials and Methods). . Supernetwork reconstructed using strict consensus maximum likelihood trees for NifD, NifH, NifK, NifE, and ABC, HesA, NdhK, ModC, PerM, UvrD, SAM, Sbr0014. The networks are outgroup rooted using PCC 6803. A reticulation occurs in the centre of both graphs because of the local instability in the placement of PCC 6803

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-0

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>he locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. N*); B) Gene deletion with DNA loss (e.g. 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. 0019). See text for further description of individual modifications

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-7

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>C51142 (CY) genomes. The spheroid body encodes complete full length A and F

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-3

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>dow size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 92.0. GATAPlotter score settings: Max: 141 bits, expect 9E-38; Min: 28 bits, expect 9E-4. GATAPlotter scores are indicated. . Multiple alignment of predicted amino acid sequences for NifU indicating an N-terminal truncation in the homologue from the endosymbiont. NifU accession numbers: Cya51142: AAW56987.1 (sp. ATCC 51142); Cya0110: ZP_01727764.1 (sp. CCY0110); GloKO68DGA: BAF47150.1 (sp. KO68DGA); Cya8801: AAC33371.1 (sp. PCC 8801); Lyn8106: ZP_01620769.1 (sp. PCC 8106); TriIMS101: AAF82636.1 (sp. IMS101); NdCCY9414: ZP_01628437.1 (CCY9414); Nos73102: ZP_00112317.1 (PCC 73102); SynJA2: YP_476679.1 (sp. JA-2-3B'a(2–13)); sb8: AAW57048.1 (spheroid body); Syn6803: NP_442853.1 (sp. PCC6803); Glo7421: NP_925823.1 (PCC 7421); Cro8501: ZP_00516385.1 (WH 8501)

The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution-8

<p><b>Copyright information:</b></p><p>Taken from "The cyanobacterial endosymbiont of the unicellular algae shows reductive genome evolution"</p><p>http://www.biomedcentral.com/1471-2148/8/30</p><p>BMC Evolutionary Biology 2008;8():30-30.</p><p>Published online 28 Jan 2008</p><p>PMCID:PMC2246100.</p><p></p>he locations of pseudogenes in the spheroid body fragment have been indicated with green bars. Genes have been named either according to homology matches in BLAST analyses or numbered consecutively for each organism (see also additional files and ). A GATA [29] plot is shown and indicates regions of high synteny between both organisms. GATaligner settings were: Window size: 100; Match: 5; MisMatch:-4; Gap Creation:-10; Gap Extension:-4; Raw Score Cut Off: 80. GATAPlotter score settings: Max: 141 bits, expect 1E-33; Min: 46.8 bits, expect 5E-5. GATAPlotter scores have been represented using a greyscale bar. Regions of the spheroid body genome showing modifications of special interest have been indicated. A) Gene inactivation by pseudogenisation (e.g. N*); B) Gene deletion with DNA loss (e.g. 0012); C) Gene deletion without DNA loss resulting in large non-coding regions (e.g. 0016); D) Gene deletion with DNA loss resulting in gene fusion (e.g. 0019). See text for further description of individual modifications