Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan Jellyfish Craspedacusta sowerbyi

Formation of all metazoan bodies is controlled by a group of selector genes including homeobox genes, highly conserved across the entire animal kingdom. The homeobox genes from Pou and Six classes are key members of the regulation cascades determining development of sensory organs, nervous system, gonads and muscles. Besides using common bilaterian models, more attention has recently been targeted at the identification and characterization of these genes within the basal metazoan phyla. Cnidaria as a diploblastic sister group to bilateria with simple and yet specialized organs are suitable models for studies on the sensory organ origin and the associated role of homeobox genes. In this work, Pou and Six homeobox genes, together with a broad range of other sensory-specific transcription factors, were identified in the transcriptome of hydrozoan jellyfish Craspedacusta sowerbyi. Phylogenetic analyses of Pou and Six proteins revealed cnidarian-specific sequence motifs and contributed to the classification of individual factors. The majority of the Craspedacusta sowerbyi Pou and Six homeobox genes are predominantly expressed in statocysts, manubrium and nerve ring, the tissues with sensory and nervous activities. The described diversity and expression patterns of Pou and Six factors in hydrozoan jellyfish highlight their evolutionarily conserved functions. This study extends the knowledge of the cnidarian genome complexity and shows that the transcriptome of hydrozoan jellyfish is generally rich in homeodomain transcription factors employed in the regulation of sensory and nervous functions

Complete Genome Sequence of the Haloaromatic Acid-Degrading Bacterium Achromobacter xylosoxidans A8 ▿

Achromobacter xylosoxidans strain A8 was isolated from soil contaminated with polychlorinated biphenyls. It can use 2-chlorobenzoate and 2,5-dichlorobenzoate as sole sources of carbon and energy. This property makes it a good starting microorganism for further development toward a bioremediation tool. The genome of A. xylosoxidans consists of a 7-Mb chromosome and two large plasmids (98 kb and 248 kb). Besides genes for the utilization of xenobiotic organic substrates, it contains genes associated with pathogenesis, toxin production, and resistance. Here, we report the complete genome sequence

Complete Genome Sequence of the Photosynthetic Purple Nonsulfur Bacterium Rhodobacter capsulatus SB 1003▿

Rhodobacter capsulatus SB 1003 belongs to the group of purple nonsulfur bacteria. Its genome consists of a 3.7-Mb chromosome and a 133-kb plasmid. The genome encodes genes for photosynthesis, nitrogen fixation, utilization of xenobiotic organic substrates, and synthesis of polyhydroxyalkanoates. These features made it a favorite research tool for studying these processes. Here we report its complete genome sequence

Comparison of phylogenetic trees of HD (A) and SD (B) regions of Six class transcription factors.

<p>The phylogenetic trees were calculated by the maximum likelihood method (WAG protein substitution model, bootstrap 1000) and processed by NJ Plot software. Phylogenetically representative sequences from the following metazoan animals were selected for comparison: sponges (<i>Chalinula loosanoffi, Ephydatia fluviatilis, Sycon calcaravis</i>), cnidarians (<i>Nematostella vectensis</i>, <i>Anthopleura japonica</i>, <i>Podocoryne carnea</i>, <i>Hydra magnipapillata</i>, <i>Cladonema radiatum</i>, <i>Aurelia aurita</i>), invertebrates (<i>Saccoglossus kowalevskii</i>, <i>Drosophila melanogaster</i>, <i>Branchistoma floridae</i>) and vertebrates (<i>Danio rerio</i> and <i>Homo sapiens</i>). For the list of ID numbers of reference sequences see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036420#pone.0036420.s011" target="_blank">Text S1</a>.</p

<i>Craspedacusta sowerbyi</i> body plan scheme.

<p>Radial symmetric body plan of <i>Craspedacusta sowerbyi</i> is divided in subumbrella and exumbrella regions from the side projection. The most distinct features are four gonads and the presence of up to two hundreds of tentacles. Particular organs are described in the scheme. Body size is up to 2.5 cm in diameter.</p

Biphenyl-Metabolizing Bacteria in the Rhizosphere of Horseradish and Bulk Soil Contaminated by Polychlorinated Biphenyls as Revealed by Stable Isotope Probing▿ †

DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [13C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase α subunits (BphA) from bacteria that incorporated [13C]into DNA in 3-day incubations of the soils with [13C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl

Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in Rhodobacter capsulatus▿ †

The purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in Caulobacter crescentus has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in R. capsulatus shares a high degree of sequence similarity with the C. crescentus protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and ctrA mutant cultures to identify the genes dysregulated by the loss of CtrA in R. capsulatus. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of ∼6% of genes in the R. capsulatus genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral ctrA gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages

Assembly of the cnidarian camera-type eye from vertebrate-like components

Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of dark shielding pigment. Cnidaria as the likely sister group to the Bilateria are the earliest branching phylum with a well developed visual system. Here, we show that camera-type eyes of the cubozoan jellyfish, Tripedalia cystophora, use genetic building blocks typical of vertebrate eyes, namely, a ciliary phototransduction cascade and melanogenic pathway. Our findings indicative of parallelism provide an insight into eye evolution. Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution

Mg, Ca and Sr isotope dynamics in a small forested catchment underlain by paragneiss: The role of geogenic, atmospheric, and biogenic sources of base cations

Knowledge of the origin of magnesium (Mg) and calcium (Ca) in soil solutions and catchment runoff helps to predict forest ecosystems’ vulnerability to deficiencies in essential nutrients in an era of climate change, environmental pollution and bark-beetle calamities. Here we discuss isotope aspects of Mg, Ca and strontium (Sr) cycling in a spruce-forested headwater catchment in a relatively unpolluted part of Central Europe. We investigated to what extent Mg and Ca isotope signatures of runoff reflect the isotope compositions of specific Mg- and Ca-rich minerals that easily dissolve during the weathering of paragneiss, and compared the isotope variability of Mg and Ca in fresh bedrock minerals, soils and other ecosystem reservoirs. We also compared conclusions from Mg and Ca isotope systematics with inferences from catchment input–output mass budgets. Long-term input–output monitoring in the studied catchment situated near the Czech–German border (Central Europe) revealed 3.5–7 times higher outputs of Mg, Ca, and Sr via surface runoff relative to their present-day atmospheric inputs. It follows that hydrological exports of recent atmospheric Mg, Ca and Sr are minor. Release of geogenic base cations into the runoff results from the interplay between mineral abundances, concentrations of the studied elements in the minerals, and their dissolution rates. Chemical depletion fractions for the studied elements from bedrock to the soil were 50–70 %, and the losses of dominant soluble minerals in the soil were 30–80 %. Exports of residual Mg, Ca and Sr following partial incorporation of these elements into secondary phyllosilicates are probably low because newly-formed clay minerals are not abundant in the soil. Residual Ca following preferential incorporation of isotopically light Ca into growing tree biomass may contribute to the isotopically heavy runoff Ca. Isotope ratios of base cations were obtained for six minerals (plagioclase, orthoclase, biotite, muscovite, apatite, and ilmenite). Mineral fractions differ greatly in δ²⁶Mg and δ⁴⁴Ca values and ⁸⁷Sr/⁸⁶Sr ratios. 80–97 % of each of the three studied base cations are present in the bedrock in a single relatively easily dissolvable mineral: Mg in biotite, and Ca and Sr in plagioclase. The isotope composition of Mg in biotite was similar to the isotope composition of Mg in runoff. The isotope compositions of Ca and Sr in plagioclase were also similar to Ca and Sr isotope compositions in runoff. Thus, the dominant geogenic source of each of the studied elements (Mg, Ca and Sr) in the investigated paragneiss catchment can be represented by one relatively soluble mineral.ISSN:0016-7061ISSN:1872-625