Epsilonproteobacterial hydroxylamine oxidoreductase (εHao): characterization of a ‘missing link’ in the multihaem cytochrome c family

Members of the multihaem cytochrome c family such as pentahaem cytochrome c nitrite reductase (NrfA) or octahaem hydroxylamine oxidoreductase (Hao) are involved in various microbial respiratory electron transport chains. Some members of the Hao subfamily, here called εHao proteins, have been predicted from the genomes of nitrate/nitrite‐ammonifying bacteria that usually lack NrfA. Here, εHao proteins from the host‐associated Epsilonproteobacteria Campylobacter fetus and Campylobacter curvus and the deep‐sea hydrothermal vent bacteria Caminibacter mediatlanticus and Nautilia profundicola were purified as εHao‐maltose binding protein fusions produced in Wolinella succinogenes. All four proteins were able to catalyze reduction of nitrite (yielding ammonium) and hydroxylamine whereas hydroxylamine oxidation was negligible. The introduction of a tyrosine residue at a position known to cause covalent trimerization of Hao proteins did neither stimulate hydroxylamine oxidation nor generate the Hao‐typical absorbance maximum at 460 nm. In most cases, the εHao‐encoding gene haoA was situated downstream of haoC, which predicts a tetrahaem cytochrome c of the NapC/NrfH family. This suggested the formation of a membrane‐bound HaoCA assembly reminiscent of the menaquinol‐oxidizing NrfHA complex. The results indicate that εHao proteins form a subfamily of ammonifying cytochrome c nitrite reductases that represents a ‘missing link’ in the evolution of NrfA and Hao enzymes.     

Genomic prediction ability for yield-related traits in German winter barley elite material

Key message

Genomic prediction was evaluated in German winter barley breeding lines. In this material, prediction ability is strongly influenced by population structure and main determinant of prediction ability is the close genetic relatedness of the breeding material.

Abstract

To ensure breeding progress under changing environmental conditions the implementation and evaluation of new breeding methods is of crucial importance. Modern breeding approaches like genomic selection may significantly accelerate breeding progress. We assessed the potential of genomic prediction in a training population of 750 genotypes, consisting of multiple six-rowed winter barley (Hordeum vulgare L.) elite material families and old cultivars, which reflect the breeding history of barley in Germany. Crosses of parents selected from the training set were used to create a set of double-haploid families consisting of 750 genotypes. Those were used to confirm prediction ability estimates based on a cross-validation with the training set material using 11 different genomic prediction models. Population structure was inferred with dimensionality reduction methods like discriminant analysis of principle components and the influence of population structure on prediction ability was investigated. In addition to the size of the training set, marker density is of crucial importance for genomic prediction. We used genome-wide linkage disequilibrium and persistence of linkage phase as indicators to estimate that 11,203 evenly spaced markers are required to capture all QTL effects. Although a 9k SNP array does not contain a sufficient number of polymorphic markers for long-term genomic selection, we obtained fairly high prediction accuracies ranging from 0.31 to 0.71 for the traits earing, hectoliter weight, spikes per square meter, thousand kernel weight and yield and show that they result from the close genetic relatedness of the material. Our work contributes to designing long-term genetic prediction programs for barley breeding.

     

Biological control of snow mould (Microdochium nivale) in winter cereals by Pseudomonas brassicacearum, MA250

Seed lots of winter wheat and rye, naturally infested with Microdochium nivale and Fusarium spp., were treated with an isolate of Pseudomonas, which was recovered from roots of Brassica napus. Seeds were treated with bacterial fermentate and dried before sowing or they were directly sprayed in the furrow-opener at the moment of sowing. Besides field experiments, parallel climate chamber bioassays were performed to assess the effect of bacterial treatment on snow mould caused by seed-borne M. nivale and Fusarium spp. The biocontrol effect was assessed by plant density counts and by measuring yield. Significant biocontrol activity, measured by plant density counts, was detected both in field and climate chamber experiments sown with wheat. Biocontrol effect after spray application at sowing was less pronounced, although a slight increase in plant density was observed. The cell concentration required to obtain adequate biocontrol effect was 10⁹ CFU per ml for the dose used. The bacterial isolate was identified by 16S rDNA sequencing and biochemical tests as a Pseudomonas brassicacearum strain.     

Comparative analysis of high-affinity ligand binding and G protein coupling of the human CXCR1 chemokine receptor and of a CXCR1-Galpha fusion protein after heterologous production in baculovirus-infected insect cells.

In order to perform biochemical and pharmacological characterization of CXCR1, we designed several CXCR1 constructs. All constructs, including a CXCR1-G(i2)alpha fusion protein, were produced in insect cells after infection with recombinant baculovirus. The recombinant receptors exhibited specific high-affinity binding of (125)I-labelled interleukin-8, and Scatchard transformation of the binding data indicated the presence of a population of single homogenous binding sites. Furthermore, the pharmacological profiles for the different CXCR1 constructs produced in the baculovirus-infected insect cells were almost identical to those reported for CXCR1 on human neutrophils. Interestingly, when the CXCR1 constructs were coproduced with G(i2) protein as a result of coinfection with baculoviruses encoding the G(i2)alpha-, the beta- and the gamma- subunits, the B(max) values were significantly increased. Hence, the level of FlagCXCR1Bio, after coproduction with G(i2) protein, was found to be almost 10 times higher than that of the FlagCXCR1Bio alone. However, no differences in the K(i) values were observed of the receptor constructs produced either after single infection or coinfection of insect cells. The addition of guanyl-5'-yl imidodiphosphate resulted in a dramatic reduction of the number of binding sites; however, the K(i) values remained unchanged, indicating coupling of the receptor to the guanine nucleotide-binding protein.     

Molecular characterization and SNP development for the porcine IL6 and IL10 genes

Different cytokines are secreted in response to specific microbial molecules referred to as pathogen associated molecular patterns (PAMPs). Interleukin 6 (IL6) and interleukin 10 (IL10), both secreted by macrophages and lymphocytes, play a central role in the immunological response. In this work we obtained the genomic structure and complete DNA sequence of the porcine IL6 and IL10 genes and identified polymorphisms in the genomic sequences of these genes on a panel of ten different pig breeds. Comparative intra- and interbreed sequence analysis revealed a total of eight polymorphisms in the porcine IL6 gene and 21 in the porcine IL10 gene, which include single nucleotide polymorphisms (SNPs) and insertion deletion polymorphisms (indels). Additionally, the chromosomal localization of the IL10 gene was determined by FISH and RH mapping.     

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

The BioMoby project was initiated in 2001 from within the modelorganism database community. It aimed to standardize methodologiesto facilitate information exchange and access to analyticalresources, using a consensus driven approach. Six years later,the BioMoby development community is pleased to announce therelease of the 1.0 version of the interoperability framework,registry Application Programming Interface and supporting Perland Java code-bases. Together, these provide interoperable accessto over 1400 bioinformatics resources worldwide through theBioMoby platform, and this number continues to grow. Here wehighlight and discuss the features of BioMoby that make it distinctfrom other Semantic Web Service and interoperability initiatives,and that have been instrumental to its deployment and use bya wide community of bioinformatics service providers. The standard,client software, and supporting code libraries are all freelyavailable at http://www.biomoby.org/.      

Yeast sphingolipid metabolism: clues and connections.

This review of sphingolipid metabolism in the budding yeast Saccharomyces cerevisiae contains information on the enzymes and the genes that encode them, as well as connections to other metabolic pathways. Particular attention is given to yeast homologs, domains, and motifs in the sequence, cellular localization of enzymes, and possible protein-protein interactions. Also included are genetic interactions of special interest that provide clues to the cellular biological roles of particular sphingolipid metabolic pathways and specific sphingolipids.     

Moss and liverwort xyloglucans contain galacturonic acid and are structurally distinct from the xyloglucans synthesized by hornworts and vascular plants

Xyloglucan is a well-characterized hemicellulosic polysaccharide that is present in the cell walls of all seed-bearing plants. The cell walls of avascular and seedless vascular plants are also believed to contain xyloglucan. However, these xyloglucans have not been structurally characterized. This lack of information is an impediment to understanding changes in xyloglucan structure that occurred during land plant evolution. In this study, xyloglucans were isolated from the walls of avascular (liverworts, mosses, and hornworts) and seedless vascular plants (club and spike mosses and ferns and fern allies). Each xyloglucan was fragmented with a xyloglucan-specific endo-glucanase and the resulting oligosaccharides then structurally characterized using NMR spectroscopy, MALDI-TOF and electrospray mass spectrometry, and glycosyl-linkage and glycosyl residue composition analyses. Our data show that xyloglucan is present in the cell walls of all major divisions of land plants and that these xyloglucans have several common structural motifs. However, these polysaccharides are not identical because specific plant groups synthesize xyloglucans with unique structural motifs. For example, the moss Physcomitrella patens and the liverwort Marchantia polymorpha synthesize XXGGG- and XXGG-type xyloglucans, respectively, with sidechains that contain a beta-D-galactosyluronic acid and a branched xylosyl residue. By contrast, hornworts synthesize XXXG-type xyloglucans that are structurally homologous to the xyloglucans synthesized by many seed-bearing and seedless vascular plants. Our results increase our understanding of the evolution, diversity, and function of structural motifs in land-plant xyloglucans and provide support to the proposal that hornworts are sisters to the vascular plants.