The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin

BACKGROUND: The hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. The hydrogenase permits direct reoxidation of NADH because it consists of a [FeFe] hydrogenase module that is fused to two modules, which are homologous to the 24 kDa and the 51 kDa subunits of a mitochondrial complex I. RESULTS: The [FeFe] hydrogenase belongs to a clade of hydrogenases that are different from well-known eukaryotic hydrogenases. The 24 kDa and the 51 kDa modules are most closely related to homologous modules that function in bacterial [NiFe] hydrogenases. Paralogous, mitochondrial 24 kDa and 51 kDa modules function in the mitochondrial complex I in N. ovalis. The different hydrogenase modules have been fused to form a polyprotein that is targeted into the hydrogenosome. CONCLUSION: The hydrogenase and their associated modules have most likely been acquired by independent lateral gene transfer from different sources. This scenario for a concerted lateral gene transfer is in agreement with the evolution of the hydrogenosome from a genuine ciliate mitochondrion by evolutionary tinkering

Antibiotic susceptibility of members of the Lactobacillus acidophilus group using broth microdilution and molecular identification of their resistance determinants

The range of antibiotic susceptibility to 13 antibiotics in 101 strains of the Lactobacillus acidophilus group was examined using the lactic acid bacteria susceptibility test medium (LSM) and broth microdilution. Additionally, microarray analysis and PCR were applied to identify resistance genes responsible for the displayed resistant phenotypes in a selection of strains. In general, narrow as well as broad unimodal and bimodal MIC distributions were observed for the Lactobacillus acidophilus group and the tested antimicrobial agents. Atypically resistant strains could be determined by visual inspection of the obtained MIC ranges for ampicillin, chloramphenicol, clindamycin, erythromycin, quinupristin/dalfopristin, streptomycin and tetracycline. For most of these atypically resistant strains underlying resistance determinants were found. To our knowledge erm(A) was detected in lactobacilli for the first time within this study. Data derived from this study can be used as a basis for reviewing present microbiological breakpoints for categorization of susceptible and resistant strains within the Lactobacillus acidophilus group to assess the safety of microorganisms intended for use in food and feed application

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