Bioinformatics Advance Access originally published online on January 5, 2006
Bioinformatics 2006 22(5):641-642; doi:10.1093/bioinformatics/btk024
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
BuchneraBASE: a post-genomic resource for Buchnera sp. APS
Department of Biology, University of York PO Box 373, York YO10 5YW, UK
*To whom correspondence should be addressed.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
Summary: BuchneraBASE is a bioinformatic research tool for the genome of the symbiotic bacterium Buchnera sp. APS that includes an improved genome annotation, comparative information about related insect symbiont genomes and a complete mapping of metabolic reactions to an Escherichia coli in silico model. The database is designed to accommodate genome-wide post-genomic datasets that are becoming available for this organism.
Availability: BuchneraBASE is available at http://www.buchnera.org/
Contact: ght2{at}york.ac.uk
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
The first symbiotic bacterium of insects for which a full genome sequence was obtained is the
-proteobacterium Buchnera sp. APS in pea aphids (Shigenobu et al., 2000). Buchnera sp. APS has a tiny genome, just 0.64 Mb, and the original annotation identified 583 coding sequences (CDSs), all but four of which had unambiguous sequence similarity to CDSs in the related bacterium Escherichia coli (Shigenobu et al., 2000). In other words, the Buchnera sp. APS genome approximates to a subset of the E.coli genome and, by transfer of annotations from the well-studied E.coli, the function of 
90% of putative gene products of Buchnera sp. APS could be predicted. Subsequently, complete genome sequences have become available for Buchnera sp. in two other aphids, Schizaphis graminum (SG) (Tamas et al., 2002) and Baizongia pistacea (BP) (van Ham et al., 2003), and for two further symbiotic bacteria considered to be closely related to Buchnera sp. by some authorities: Wigglesworthia glossinidia brevipalpis in the tsetse fly Glossina brevipalpis (Akman et al., 2002) and Blochmannia floridanus in the carpenter ant Camponotus floridanus (Gil et al., 2003). The predicted gene contents of these bacteria are subsets of the E.coli genome and overlap with each other and with Buchnera sp. APS. In this paper, we describe a new database for Buchnera sp. and allied symbiotic bacteria based around our successful post-genomic database for E.coli, EchoBASE (Misra et al., 2005). During the creation of this database, we reannotated portions of the Buchnera sp. APS genome and key changes are summarized. |
CREATION AND ORGANIZATION OF BUCHNERABASE |
|---|
|
TOPABSTRACTINTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
The database was constructed with MySQL using the schema developed for EchoBASE and Macromedia Coldfusion to create the WWW interface. It holds information on Buchnera genes and their products originally obtained from the GenBank entry for Buchnera aphidicola str. APS (BA000003 [GenBank] ), and includes the sequences of the two Buchnera sp. APS plasmids, pLeu and pTrp. Each gene can be viewed on a ‘gene page’ that displays basic features and annotation information. Gene pages displaying information on CDSs display the top three BLASTP hits in E.coli, and each CDS has been mapped to its E. coli orthologue and links to the respective gene page in EchoBASE. The gene page provides links to the nucleotide and protein sequence of each gene and to other useful resources. Synonyms for gene names were added from EchoBASE. MultiFun codes have been imported from E. coli and the gene products can be browsed using this protein functional classification scheme (Serres and Riley, 2000). The database has been designed to be flexible and allow the simple addition and integration of additional
-proteobacterial symbiont genomes as they are completed. It also builds on a structure created in EchoBASE that will allow the connection of experimental information to individual gene products as these become available. |
SUMMARY OF ANNOTATION CHANGES TO BUCHNERA SP. APS GENOME SEQUENCE |
|---|
|
TOPABSTRACTINTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
In the first stage of the annotation check, each CDS from Buchnera sp. APS was used as the query sequence in a BLAST search against E.coli K-12 MG1655 genome sequence. The gene name of the most significant match was checked against the name of the gene encoding that CDS in Buchnera sp. APS. There was generally agreement with the original annotation of Shigenobu et al. (2000). However, the few errors in the original annotation noted by us and others (van Ham et al., 2003) are corrected, including the identification of the yba1 gene (originally annotated as unique to Buchnera) as the 5'-region of a truncated fliK gene. We have updated the functions of several gene products, e.g. the gene for the elusive 6-phosphogluconolactonase recently characterized in E.coli as the ybhE gene product (Thomason et al., 2004). Also, gene names have been changed, where appropriate, from the ybXXXX nomenclature to the y gene nomenclature now preferred in E.coli. To facilitate easy querying of genes, a synonym table of gene names taken from our sister database EchoBASE is provided. We have added annotations for obvious pseudogenes, of interest in tracing the recent evolutionary history of Buchnera, e.g. metR, disrupted relatively recently in the history of Buchnera sp. APS. The lengths of some gene have been changed where comparison with E.coli orthologues suggests an incorrect initiator methionine was chosen during the original annotation.
Using our knowledge of the E.coli genome annotation, we have identified two previously unrecognized small RNA-encoding genes. Buchnera sp. APS was originally annotated to have ffh and ftsY, which encode the protein components of the signal recognition particle (SRP) (Shigenobu et al., 2000). We found the gene encoding the RNA component of the SRP, ffs, between mdlB and dnaX and have defined the CDS based on the coordinates provided by SRPDB (Rosenblad et al., 2003). Also, based on the presence of smpB, we identified the gene for the tmRNA, ssrA, and confirmed this using the tmRNA website (Gueneau and Williams, 2004).
|
COMPARATIVE ANALYSIS OF INSECT SYMBIONT GENOMES |
|---|
|
TOPABSTRACTINTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
To aid understanding of the APS genome and its products, we have included the genomes of four additional insect symbionts, B.aphidicola str. SG (Schizaphis graminum) (Tamas et al., 2002), B.aphidicola str. BP (Baizongia pistaciae) (van Ham et al., 2003), Wigglesworthia glossinidia (Akman et al., 2002) and Blochmannia floridanus NL (Gil et al., 2003), which were parsed and added to the database as for Buchnera sp. APS. A manually curated non-redundant table of genes was created for the products of the five genomes with mapping of all orthologous genes across the genomes. This allows rapid assessment of the distribution of individual genes within the sequenced insect symbionts, displayed on the genes page. These data can also be viewed in a summary table providing referencing across the five genomes to allow rapid determination of genes shared between or particular to certain symbionts genomes. More limited gene pages are available for genes for all four of the additional symbionts.
We have updated the function lines of the Wigglesworthia gene products for the 618 genes that have clear orthologues in E. coli, based on the current E. coli function lines. This improves the usefulness of the annotation, which included non-specific descriptions of many gene products in the original submission (Akman et al., 2002).
|
MAPPING OF BUCHNERA SP. APS GENE PRODUCTS TO AN E.COLI METABOLIC MODEL (IJR904) |
|---|
|
TOPABSTRACTINTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
We have mapped all metabolic reactions from Buchnera sp. APS to a metabolic model of E. coli (iJR904) created for flux-balance analysis (Reed et al., 2003). A total of 233 gene/enzyme relationships were mapped by matching of gene names and then by manual checks. The mappings are shown on the gene pages for the genes that encode these activities, displaying the reaction equation, reaction name (and synonyms) and reaction pathway. This includes 182 distinct biochemical reactions encoded by the products of 193 distinct APS genes. This will allow examination of the properties of the metabolic network with graph analysis tools and facilitate use of the mapping in flux-balance modeling of Buchnera metabolism.
|
NOTE ADDED IN PROOF |
|---|
|
TOPABSTRACTINTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
While this manuscript was being reviewed the genome sequence of Blochmannia pennsylvanicus was published [Degnan, Lazarns and Wernegreen (2005) Genome Research, 15 1023–1033], which has been added to BuchneraBASE.
|
Acknowledgments |
|---|
We thank Raju Misra and Richard Horler for advice in setting up the database.
Conflict of Interest: none declared.
|
FOOTNOTES |
|---|
Current address: UCB, 216 Bath Road, Slough, Berkshire SL1 4EN, UK 
Associate Editor: Nikolaus Rajewsky
Received on October 19, 2005; revised on December 22, 2005; accepted on December 22, 2005
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONCREATION AND ORGANIZATION OF...SUMMARY OF ANNOTATION CHANGES...COMPARATIVE ANALYSIS OF INSECT...MAPPING OF BUCHNERA SP....NOTE ADDED IN PROOFREFERENCES |
|---|
Akman, L., et al. (2002) Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat. Genet, . 32, 402–407[CrossRef][ISI][Medline].
Gil, R., et al. (2003) The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc. Natl Acad. Sci. USA, 100, 9388–9393
Gueneau, D.N. and Williams, K.P. (2004) The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Res, . 32, D104–D108
Misra, R.V., et al. (2005) EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res, . 33, D329–D333
Reed, J.L., et al. (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol, . 4, R54[CrossRef][Medline].
Rosenblad, M.A., et al. (2003) SRPDB: Signal Recognition Particle Database. Nucleic Acids Res, . 31, 363–364
Serres, M.H. and Riley, M. (2000) MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb Comp. Genomics, 5, 205–222[Medline].
Shigenobu, S., et al. (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature, 407, 81–86[CrossRef][Medline].
Tamas, I., et al. (2002) 50 million years of genomic stasis in endosymbiotic bacteria. Science, 296, 2376–2379
Thomason, L.C., et al. (2004) Identification of the Escherichia coli K-12 ybhE gene as pgl, encoding 6-phosphogluconolactonase. J Bacteriol, . 186, 8248–8253
van Ham, R.C., et al. (2003) Reductive genome evolution in Buchnera aphidicola. Proc. Natl Acad. Sci. USA, 100, 581–586
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Y. Galperin The Molecular Biology Database Collection: 2008 update Nucleic Acids Res., January 11, 2008; 36(suppl_1): D2 - D4. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Reymond, F. Calevro, J. Vinuelas, N. Morin, Y. Rahbe, G. Febvay, C. Laugier, A. Douglas, J.-M. Fayard, and H. Charles Different Levels of Transcriptional Regulation Due to Trophic Constraints in the Reduced Genome of Buchnera aphidicola APS Appl. Envir. Microbiol., December 1, 2006; 72(12): 7760 - 7766. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Toft and M. A. Fares GRAST: a new way of genome reduction analysis using comparative genomics Bioinformatics, July 1, 2006; 22(13): 1551 - 1561. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||