Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment-2

<p><b>Copyright information:</b></p><p>Taken from "Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment"</p><p>BMC Genomics 2006;7():22-22.</p><p>Published online 10 Feb 2006</p><p>PMCID:PMC1413528.</p><p>Copyright © 2006 Ricard et al; licensee BioMed Central Ltd.</p>ndidate, an algorithm examines the presence or absence of Bacteria, Archaea and Eukaryotes in the second smaller partition containing the target sequence. In the example, the smallest second partition containing the target sequence contains also the sequences from , , and , which are all Bacteria. AM054010 was therefore retained as a HGT candidate

Schematic representation of the minichromosomes encoding the hydrogenase (a) and the "mitochondrial" 24 and 51 kDa genes (b)

<p><b>Copyright information:</b></p><p>Taken from "The [FeFe] hydrogenase of has a chimeric origin"</p><p>http://www.biomedcentral.com/1471-2148/7/230</p><p>BMC Evolutionary Biology 2007;7():230-230.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2216082.</p><p></p> The macronuclear minichromosomes are capped by telomeres (T) and contain non-coding DNA sequences (N) at the N- and C-terminal parts of the chromosome. A mitochondrial targeting signal (M) is found at the N terminal part of the coding sequence. 1. a. The hydrogenase is chimeric, i.e. it consists of a long-type [FeFe] hydrogenase with 4 FeS clusters (black bars in HDG), a 24 kDa (hoxF) module ("24") with an N1a type FeS cluster, and a 51 kDa (hoxU) ("51") module with a N3-type [4Fe-4S] cluster plus a FMN and a NAD binding site. 1. b. The subunits of the "mitochondrial" complex I are localized on individual minichromosomes. They each possess a mitochondrial targeting signal (M) and upstream and downstream non-coding DNA (N). The "mitochondrial" 51 kDa module possesses two small introns (arrows) that are absent from the correspondent hydrogenase module

Phylogenetic tree of the 24 kDa-like module of the hydrogenase of , mitochondrial complex I 24 kDa subunits, bacterial NuoE, and bacterial hydrogenase subunits

<p><b>Copyright information:</b></p><p>Taken from "The [FeFe] hydrogenase of has a chimeric origin"</p><p>http://www.biomedcentral.com/1471-2148/7/230</p><p>BMC Evolutionary Biology 2007;7():230-230.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2216082.</p><p></p> See methods for the Accession Numbers and how the tree was calculated. H: hydrogenase, M: ciliate mitochondrial. Bootstraps are only indicated in the tree if they are ≥ 50. Box 1 marks 24 kDa modules that are fused with their corresponding 51 kDa modules (with the exception of ). All bacteria in this box (with the exception of ) have a [NiFe] hydrogenase. The mitochondrial/alpha-proteobacterial 24 kDa modules are not fused with their 51 kDa counterparts (Box 2)

Principal component analysis of the codon-usage of the hydrogenase and mitochondrial 24/51 kDa modules

<p><b>Copyright information:</b></p><p>Taken from "The [FeFe] hydrogenase of has a chimeric origin"</p><p>http://www.biomedcentral.com/1471-2148/7/230</p><p>BMC Evolutionary Biology 2007;7():230-230.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2216082.</p><p></p> While most of the strains exhibit only slight differences in codon-preference, the isolate from the host cockroach strain Amsterdam has a substantially different codon-usage. In both cases, the bacterial-derived 24 and 51 kDa modules acquired the typical ciliate codon-usage that is not significantly different from the one used for the (nuclear-encoded) mitochondrial modules. Even the top-down distribution shows a complete ameliorisation of the modules

Phylogenetic tree of the 51 kDa-like module of the hydrogenase of , mitochondrial complex I 51 kDa subunits, bacterial NuoF, and bacterial hydrogenase subunits

<p><b>Copyright information:</b></p><p>Taken from "The [FeFe] hydrogenase of has a chimeric origin"</p><p>http://www.biomedcentral.com/1471-2148/7/230</p><p>BMC Evolutionary Biology 2007;7():230-230.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2216082.</p><p></p> See methods for how the tree was calculated. H: hydrogenase, M: ciliate mitochondrial. Only bootstraps ≥ 50 are indicated in the tree. Box 1 marks the fused modules (with the exception of ), Box 2 the non-fused modules of mitochondrial and alpha-proteobacterial origin. All bacteria in Box 1 (with the exception of ) have a [NiFe] hydrogenase

Phylogenetic tree of the H-cluster of FeFe-hydrogenases and NARs or NARs-like proteins

<p><b>Copyright information:</b></p><p>Taken from "The [FeFe] hydrogenase of has a chimeric origin"</p><p>http://www.biomedcentral.com/1471-2148/7/230</p><p>BMC Evolutionary Biology 2007;7():230-230.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2216082.</p><p></p> Accession numbers of sequences are indicated when more than one sequence from a species is included. The numbers at the nodes represent the posterior probability resulting from a Bayesian inference. : H-clusters recovered from a metagenomic approach using DNA from total ciliate population in the rumen of a cow. The H1 block marks the "classical " [FeFe] hydrogenases and NAR's. Block 1 is characterized by the clade of (long and short – type) hydrogenases. It hosts also the majority of the rumen sequences plus the hydrogenases from the type-strain rumen ciliates , and . Block 2 marks the long-type hydrogenases from the anaerobic chytridiomycetes and and the (short) plastidic hydrogenases from the algae and . Block 3 marks H-clusters from rumen ciliates that are likely to lack hydrogenosomes. Block H2 marks a well supported clade of Fe hydrogenases dominated by . Besides and its close relatives, this clade consists of hydrogenases from the amoeboflagellate , the rumen ciliate , the free-living ciliate . and the rumen (meta) sequences . A fusion of the H-cluster with the 24 and 51 kDa modules has so far only been observed for the clade. The hydrogenase has no fused 24/51 kDa modules