MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

Abstract

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest.

Figure 1.

Curation status of MicroScope genomes with at least one gene manually curated. Status is defined by dividing the number of manually annotated genes (at least once) by the total number of genes in the genome: (i) expertly curated genomes: between 80 and 100%; (ii) adequately curated genomes: between 30 and 80%; (iii) crudely curated genomes: between 5 and 30%; and (iv) genomes with curation of specific functions: <5%.

Figure 2.

MicroScope usage trend and types of managed projects.

Figure 3.

GUI for exploring evolution data stored in MicroScope. The ‘comparative mode’ allows the user to compare the mutation content of several clones/organisms. It is shown here using public data from the long-term evolution experiment of E. coli B (26). (A) The query interface allows the user to compare the mutational events (SNPs/InDels) between several clones of the Ara-1 lineage. The mutation content of the selected clones is retrieved using the parameters indicated in the ‘With these restrictions’ part of the query interface. (B) The outcome of the analysis is presented in a table reporting all the genomic objects of the reference genome which contains mutations (blue frame) and the mutations found in intergenic regions (pink frame). In the example shown here, the pcnB gene of E. coli B REL606 has undergone a T→G transversion (H302N) at position 904, which appeared at the 15 k generation; it seems to have been subsequently fixed in the population, as it is still present at 20 k generation. In the query interface shown in panel A, the ‘parallelism mode’ allows the user to analyse the dynamics of mutations found in clones/lineages over time. The ‘graphical mode’ enables the visualization of mutations along the chromosome of the reference organism and eases the detection of mutation hot spots. All these tools provide links to the main MicroScope database, enabling exploration and analyses of results in a broader context.

Figure 4.

Metabolic data curation strategy in MicroScope platform applied to CDP-3,6-dideoxyhexose biosynthesis in S. typhimurium LT2. (A) CanOE results for the single global orphan reaction identified in S. typhimurium LT2 corresponding to CDP-4-dehydro-6-deoxyglucose reductase activity (1.17.1.1-RXN). This reaction is not linked to any gene but is located in a conserved genomic and metabolic context (genomic Metabolon) with other genes of the CDP-3,6-dideoxyhexose biosynthesis pathway. The CanOE strategy proposes a potential association between this global orphan reaction (yellow box) and STM2090, a metabolic gene with no associated reaction (blue box). (B) Pathway curation interface displaying the CDP-3,6-dideoxyhexose biosynthesis pathway. The pathway is incomplete in the initial pathway projection process. By clicking on the pathway identifier (PWY-5833), the reaction table of the CDP-3,6-dideoxyhexose biosynthesis pathway is displayed, showing a single pathway hole that corresponds to the global orphan reaction 1.17.1.1-RXN identified by CanOE (C). The same interface also allows the user to display the list of co-evolved genes with other genes of the pathway. In this table, the STM2090 gene proposed by CanOE as possibly associated with 1.17.1.1-RXN is associated to the third best average co-evolution score after the STM2092 and STM2091 genes (which are associated to the other steps of the pathway).

Figure 5.

Metabolic data curation strategy in MicroScope platform applied to CDP-3,6-dideoxyhexose biosynthesis in S. typhimurium LT2. (A) Gene annotation interface of STM2090 in MicroScope. Curation includes the update of the Product and EC number annotation fields and also the manual validation of the corresponding reactions in MetaCyc (1.17.1.1-RXN) and RhEA (RHEA: 19653 and RHEA: 19657) repositories, which can be retrieved automatically from the EC number annotation or using keyword searches. (B) Display of the pathway curation interface of MicroScope for CDP-3,6-dideoxyhexose biosynthesis pathway after the curation process. The pathway appears complete (Completion = 1), and it has been assigned to the ‘validated’ status. (C) Display of the complete S. typhimurium LT2 CDP-3,6-dideoxyhexose biosynthesis pathway in the specific MicroCyc pathway interface of MicroScope.