Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72
Version of Record online: 23 MAY 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Thematic issue: Sulfur Metabolism
Volume 14, Issue 10, pages 2775–2787, October 2012
How to Cite
Shidore, T., Dinse, T., Öhrlein, J., Becker, A. and Reinhold-Hurek, B. (2012), Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72. Environmental Microbiology, 14: 2775–2787. doi: 10.1111/j.1462-2920.2012.02777.x
- Issue online: 3 OCT 2012
- Version of Record online: 23 MAY 2012
- Received 27 December, 2011; revised 13 April, 2012; accepted 17 April, 2012.
Fig. S1. Schematic representation of the workflow followed for transcriptomic profiling of responses of Azoarcus sp. strain BH72 upon exposure to exudates. Exponentially growing cells of Azoarcus sp. strain BH72 were grown for 1 or 4 h on growth medium with and without exudates. Harvested cells were subjected to RNA isolation. From equal amount of RNA, cDNA was synthesized and fluorescent labelling with Cy3 or Cy5 was done. This was followed by combining the cDNAs and hybridization onto a 70mer oligonucleotide array comprising of probes for 3992 protein coding genes of Azoarcus sp. strain BH72.
Fig. S2. Distribution of differentially regulated genes of Azoarcus sp. strain BH72 in COG categories. Number of genes with modulated expression (up/downregulation) on exposure to exudates for 1 or 4 h is represented as black or white bars respectively. Different COG categories are, A: RNA processing and modification, B: Chromatin structure and dynamics, C: Energy production and conversion, D: Cell cycle control, mitosis and meiosis, E: Amino acid transport and metabolism, F: Nucleotide transport and metabolism, G: Carbohydrate transport and metabolism, H: Coenzyme transport and metabolism, I: Lipid transport and metabolism, J: Translation, K: Transcription, L: Replication, recombination and repair, M: Cell wall/membrane biogenesis, N: Cell motility, O: Posttranslational modification, protein turnover, chaperones, P: Inorganic ion transport and metabolism, Q: Secondary metabolites biosynthesis, transport and catabolism, R: General function prediction only, S: Function unknown, T: Signal transduction mechanisms, U: Intracellular trafficking and secretion, no: not in COG.
Fig. S3. Type VI secretion gene clusters in Azoarcus sp. strain BH72. Two gene clusters encoding for proteins of type VI secretion systems, the sci cluster (named for its similarity to Salmonella enterica's centisome 7 genomic island 7) and the imp cluster (similar to Rhizobium leguminosarum's imp cluster, named for its impaired nodulation).
Fig. S4. Cross-reactivity of three antisera produced against each of the overexpressed Hcp proteins. Purified recombinant proteins (0.15 μg) were focused using SDS-PAGE and subjected to Western blot analysis. The membranes were cut into strips and incubated with the indicated null or antisera. The approximate molecular weights of each band are marked.
Fig. S5. The null sera do not react non-specifically with BH72 proteins. 100 μg of total cellular extracts of wild type (BH72) were focused using SDS-PAGE and subjected to Western blot analysis. The membranes were cut into strips and incubated with the indicated null sera. Bottom panel, Coomassie-Brilliant Blue stained membranes.
Table S1. Strains and plasmids used in this study.
Table S2. Primers used in this study.
Table S3. List of genes differentially regulated in response to exudates.
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