Rhizobium‐induced root nodules are specialized organs for symbiotic nitrogen fixation. Indeterminate‐type nodules are formed from an apical meristem and exhibit a spatial zonation which corresponds ...to successive developmental stages. To get a dynamic and integrated view of plant and bacterial gene expression associated with nodule development, we used a sensitive and comprehensive approach based upon oriented high‐depth RNA sequencing coupled to laser microdissection of nodule regions. This study, focused on the association between the model legume Medicago truncatula and its symbiont Sinorhizobium meliloti, led to the production of 942 million sequencing read pairs that were unambiguously mapped on plant and bacterial genomes. Bioinformatic and statistical analyses enabled in‐depth comparison, at a whole‐genome level, of gene expression in specific nodule zones. Previously characterized symbiotic genes displayed the expected spatial pattern of expression, thus validating the robustness of our approach. We illustrate the use of this resource by examining gene expression associated with three essential elements of nodule development, namely meristem activity, cell differentiation and selected signaling processes related to bacterial Nod factors and redox status. We found that transcription factor genes essential for the control of the root apical meristem were also expressed in the nodule meristem, while the plant mRNAs most enriched in nodules compared with roots were mostly associated with zones comprising both plant and bacterial partners. The data, accessible on a dedicated website, represent a rich resource for microbiologists and plant biologists to address a variety of questions of both fundamental and applied interest.
Paleogenomics seeks to reconstruct ancestral genomes from the genes of today's species. The characterization of paleo-duplications represented by 11,737 orthologs and 4,382 paralogs identified in ...five species belonging to three of the agronomically most important subfamilies of grasses, that is, Ehrhartoideae (rice) Panicoideae (sorghum, maize), and Pooideae (wheat, barley), permitted us to propose a model for an ancestral genome with a minimal size of 33.6 Mb structured in five proto-chromosomes containing at least 9,138 predicted proto-genes. It appears that only four major evolutionary shuffling events (α, β, γ, and δ) explain the divergence of these five cereal genomes during their evolution from a common paleo-ancestor. Comparative analysis of ancestral gene function with rice as a reference indicated that five categories of genes were preferentially modified during evolution. Furthermore, alignments between the five grass proto-chromosomes and the recently identified seven eudicot proto-chromosomes indicated that additional very active episodes of genome rearrangements and gene mobility occurred during angiosperm evolution. If one compares the pace of primate evolution of 90 million years (233 species) to 60 million years of the Poaceae (10,000 species), change in chromosome structure through speciation has accelerated significantly in plants.
New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to ...the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr.
ENDscript is a web server grouping popular programs such as BLAST, Multalin and DSSP. It uses as query the co-ordinates file of a protein in Protein Data Bank format and generates PostScript and png ...figures showing: residues conserved after a multiple alignment against homologous sequences, secondary structure elements, accessibility, hydropathy and intermolecular contacts. Thus, the user can relate quickly 1D, 2D and 3D information of a protein of known structure. Availability: http://genopole.toulouse.inra.fr/ENDscript Contact: p.gouet@ibcp.fr * To whom correspondence should be addressed.
The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ...ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Cα trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript.
Background: Leucocidins and
γ-hemolysins are bi-component toxins secreted by
Staphylococcus aureus. These toxins activate responses of specific cells and form lethal transmembrane pores. Their ...leucotoxic and hemolytic activities involve the sequential binding and the synergistic association of a class S and a class F component, which form hetero-oligomeric complexes. The components of each protein class are produced as non-associated, water-soluble proteins that undergo conformational changes and oligomerization after recognition of their cell targets.
Results: The crystal structure of the monomeric water-soluble form of the F component of Panton–Valentine leucocidin (LukF-PV) has been solved by the multiwavelength anomalous dispersion (MAD) method and refined at 2.0 Å resolution. The core of this three-domain protein is similar to that of
α-hemolysin, but significant differences occur in regions that may be involved in the mechanism of pore formation. The glycine-rich stem, which undergoes a major rearrangement in this process, forms an additional domain in LukF-PV. The fold of this domain is similar to that of the neurotoxins and cardiotoxins from snake venom.
Conclusions: The structure analysis and a multiple sequence alignment of all toxic components, suggest that LukF-PV represents the fold of any water-soluble secreted protein in this family of transmembrane pore-forming toxins. The comparison of the structures of LukF-PV and
α-hemolysin provides some insights into the mechanism of transmembrane pore formation for the bi-component toxins, which may diverge from that of the
α-hemolysin heptamer.
The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP. It can read ...secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information.
ESPript can be run via a command file or a friendly html-based user interface. The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences. It offers a palette of markers to highlight important regions in the alignment. ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program.
ESPript can be accessed on its Web site at http://www.ipbs.fr/ESPript. Sources and helpfiles can be downloaded via anonymous ftp from ftp.ipbs.fr. A tar file is held in the directory pub/ESPript.
ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) ...information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics.
New developments in the InterPro database Mulder, Nicola J.; Apweiler, Rolf; Attwood, Teresa K. ...
Nucleic acids research,
01/2007, Letnik:
35, Številka:
suppl-1
Journal Article
Recenzirano
Odprti dostop
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, ...PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (), and for download by anonymous FTP (). The InterProScan search tool is now also available via a web service at .
InterPro, progress and status in 2005 Mulder, Nicola J.; Apweiler, Rolf; Attwood, Teresa K. ...
Nucleic acids research,
01/2005, Letnik:
33, Številka:
suppl-1
Journal Article
Recenzirano
Odprti dostop
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, ...PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).
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