InterPro: the integrative protein signature database

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/

Complete genome sequences of Trifolium spp. inoculant strains rhizobium leguminosarum sv. trifolii TA1 and CC275e: Resources for genomic study of the Rhizobium-Trifolium symbiosis

Rhizobium leguminosarum symbiovar trifolii strains TA1 and CC275e are nitrogen-fixing microsymbionts of Trifolium spp. and have been used as commercial inoculant strains for clovers in pastoral agriculture in Australia and New Zealand. Here we present the complete genome sequences of both strains, resolving their multipartite genome structures and allowing for future studies using genomic approaches

Trifolium repens and T. subterraneum modify their nodule microbiome in response to soil pH

The influence of soil edaphic factors on recruitment and composition of bacteria in the legume nodule is unknown. Typically, low (acidic) pH soils have a negative effect on the plant‐rhizobia symbiosis and thereby reduce clover growth. However, the specific relationship between soil pH and the ecology of rhizobia is unknown, in either their free‐living or nodule‐inhabiting states. We used New Zealand pasture systems with soils of different pH, and white (WC) and subterranean (SC) clovers, to examine the relationship between soil pH and the diversity of bacteria that inhabit the nodules

Diverse bacterial taxa inhabit root nodules of lucerne (Medicago sativa L.) in New Zealand pastoral soils

Background and aims: Pseudomonas spp. have previously been isolated from lucerne nodules. The aims of this study were to: 1) investigate the microbiome within a lucerne nodule; and 2) assess the ability of two Pseudomonas spp. isolated from lucerne nodules to form nodules. Methods: The microbial community within 27 lucerne nodules, collected from plants inoculated with Sinorhizobium meliloti as a seed coat or peat slurry and an uninoculated control, was identified using 16S rRNA based Illumina sequencing. Lucerne seedlings were inoculated with the two Pseudomonas spp. strains. The plants were grown in sterile conditions for 6 weeks and nodulation was assessed. 16S rRNA, nodC, nodA and nifH genes were amplified. Results: Sinorhizobium was the dominant genus in nodules, comprising 90–99% of all sequences regardless of inoculation treatment. Overall, 9 other genera were identified, with each represented by <3% of the total sequences. Both Pseudomonas strains were able to form nodules with lucerne. From one of these strains, a nodC gene was detected. Conclusion: Lucerne nodules contained a diverse assemblage of bacterial species, some of which were capable of forming nodules in the absence of rhizobia

Dual role for a bacteriophytochrome in the bioenergetic control of Rhodopsdeudomonas palustris : enhancement of photosystem synthesis and limitation of respiration

In the purple photosynthetic bacterium Rhodopseudomonas palustris, far-red illumination induces photosystem synthesis via the action of the bacteriophytochrome RpBphP1. This bacteriophytochrome antagonizes the repressive effect of the transcriptional regulator PpsR2 under aerobic condition. We show here that, in addition to photosystem synthesis, far-red light induces a significant growth rate limitation, compared to cells grown in the dark, linked to a decrease in the respiratory activity. The phenotypes of mutants inactivated in RpBphP1 and PpsR2 show their involvement in this regulation. Based on enzymatic and transcriptional studies, a 30% decrease in the expression of the alpha-ketoglutarate dehydrogenase complex, a central enzyme of the Krebs cycle, is observed under far-red light. We propose that this decrease is responsible for the down-regulation of respiration in this condition. This regulation mechanism at the Krebs cycle level still allows the formation of the photosynthetic apparatus via the synthesis of key biosynthesis precursors but lowers the production of NADH, i.e. the respiratory activity. Overall, the dual action of RpBphP1 on the regulation of both the photosynthesis genes and the Krebs cycle allows a fine adaptation of bacteria to environmental conditions by enhancement of the most favorable bioenergetic process in the light, photosynthesis versus respiration

Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e

Rhizobium leguminosarum bv. trifolii strain CC275e is a highly effective, N₂ fixing microsymbiont of white clover (Trifolium repens L.). The bacterium has been widely used in both Australia and New Zealand as a clover seed inoculant and, as such, has delivered the equivalent of millions of dollars of nitrogen into these pastoral systems. R. leguminosarum strain CC275e is a rod-shaped, motile, Gram-negative, non-spore forming bacterium. The genome was sequenced on an Illumina MiSeq instrument using a 2 × 150 bp paired end library and assembled into 29 scaffolds. The genome size is 7,077,367 nucleotides, with a GC content of 60.9 %. The final, high-quality draft genome contains 6693 protein coding genes, close to 85 % of which were assigned to COG categories. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JRXL00000000. The sequencing of this genome will enable identification of genetic traits associated with host compatibility and high N₂ fixation characteristics in Rhizobium leguminosarum. The sequence will also be useful for development of strain-specific markers to assess factors associated with environmental fitness, competiveness for host nodule occupancy, and survival on legume seeds (New Zealand Ministry of Business, Innovation and Employment program, ‘Improving forage legume rhizobia performance’ contract C10X1308 and DairyNZ Ltd.)

Experience using web services for biological sequence analysis

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed