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Open Access Research article

New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures

Andy Hesketh1, Giselda Bucca2, Emma Laing2, Fiona Flett3, Graham Hotchkiss2, Colin P Smith2 and Keith F Chater1*

Author Affiliations

1 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

2 School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK

3 Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK

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BMC Genomics 2007, 8:261  doi:10.1186/1471-2164-8-261

Published: 2 August 2007

Additional files

Additional file 1:

Transcript abundance profiles for all 74 genes identified as being differentially expressed between M600 and M600 ΔbldA. Provides a summary of the transcript abundance profiles for all 74 genes identified as being differentially expressed between M600 and M600 ΔbldA using DNA microarrays.

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Additional file 2:

Transcription profiles determined for SCO4295, SCO5013, SCO6808, SCO7657, SCO 3088, SCO 3285, SCO 3286, SCO 5166, SCO 6958, SCO 6638, SCO 4660, SCO 4702 and SCO 4648 using either a) Q-RT-PCR, or B) DNAmicroarrays. A comparison for a subset of genes of transcript abundance profiles determined using DNA microarrays with results obtained using quantitative RT-PCR.

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Additional file 3:

A list of ribosomal protein genes present in the S. coelicolor genome, and the predicted physical properties of their gene products. Illustrates that the vast majority of ribosomal proteins would not be expected to be detected in the protomics analysis undertaken in this study.

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Additional file 4:

Normalized spot volume data for the 336 protein spots identified in the proteome analysis. A spreadsheet of quantitative protein spot measurements from the proteome analysis.

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Additional file 5:

Summary of the protein spots identified as being differentially represented between M600 and M600 ΔbldA. Lists proteins that were found to be statistically differentially represented between the two strains using the Mann-Whitney test; those found to be reproducibly differentially expressed using the complementary mathematical approach detailed in the Methods; and a combined list summarising all differences. Functional assignments are noted, based on KEGG [56], and on the Sanger Institute classifications [57], and information given on: (a) occurrence of more than one gene product per gene; (b) 2-fold up- or down-regulated relative to the bldA mutant; and (c) membership of the M600 expression profile group (see Additional File 6).

Format: XLS Size: 144KB Download file

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Additional file 6:

Classification of the time-course data for the 336 identified protein spots according to their abundance profiles in strain M600. Provides information on: (a) occurrence of more than one gene product per gene; (b) 2-fold up- or down-regulated relative to the bldA mutant; and (c) P-value for any statistically different protein spot observed. A list of all genes for which more than one protein spot was identified is also presented.

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Additional file 7:

Time-course abundance profiles showing changes in the post-translational processing of certain proteins as a result of bldA mutation. Illustrates the changes observed in post-translational processing of 11 proteins during growth of the wild-type and bldA mutant strains.

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Additional file 8:

Summary of the identification of changes in transcription or protein synthesis from 147 genes as a result of bldA mutation. Functional assignments are noted, based on KEGG [56] and on the Sanger Institute classifications [57], and operon membership is also indicated. Differences identified from the transcriptome and proteome analyses are listed separately, and also combined into a masterlist of all differences. Functional assignments are noted, based on KEGG [56] and on the Sanger Institute classifications [57]. For the proteome data information is given on: a) occurrence of more than one gene product per gene; b) 2-fold up- or down-regulated relative to the bldA mutant; and c) membership of the M600 expression profile group (see Additional File 6). Significance P-values are given where appropriate.

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Additional file 9:

Comparison of transcript and protein abundance profiles for the eleven genes identified by both transcriptome and proteome analyses as being differentially expressed in the ΔbldA mutant. Compares the transcript and protein spot abundance profiles for the eleven genes identified by both transcriptome and proteome analysis as being differentially expressed in the bldA mutant.

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Additional file 10:

Abundance data for protein spots belonging to genes responsible for the production of secondary metabolites in S. coelicolor. Illustrates differential representation of many proteins associated with secondary metabolite production as a result of bldA mutation.

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Additional file 11:

Consensus DNA sequence motifs identified upstream of the 40 differentially transcribed genes determined from the ANOVA transcriptomics analysis. The top ten most significant motifs are listed, and figures for how frequently each motif is found in the genome are given.

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