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

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 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