Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots
Article first published online: 10 APR 2013
© 2013 John Wiley & Sons Ltd and Society for Applied Microbiology
Environmental Microbiology Reports
Thematic Issue: Plant-Microbe Interactions
Volume 5, Issue 3, pages 393–403, June 2013
How to Cite
Marchi, M., Boutin, M., Gazengel, K., Rispe, C., Gauthier, J.-P., Guillerm-Erckelboudt, A.-Y., Lebreton, L., Barret, M., Daval, S. and Sarniguet, A. (2013), Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots. Environmental Microbiology Reports, 5: 393–403. doi: 10.1111/1758-2229.12048
- Issue published online: 22 APR 2013
- Article first published online: 10 APR 2013
- Accepted manuscript online: 8 MAR 2013 07:57AM EST
- Manuscript Accepted: 23 FEB 2013
- Manuscript Revised: 21 FEB 2013
- Manuscript Received: 12 DEC 2012
Fig. S1. Evolutionary relationships between P. fluorescens RscN sequences. RscN (T3SS ATPase) amino acid sequences were aligned with clustalw. A Neighbour-Joining phylogenic analysis with a Poisson correction model was performed using MEGA5 software. Nodal robustness of the tree was assessed using 1000 bootstrap replicates. Bootstrap values lower than 50% were not shown. The blue outlined group corresponds to Pseudomonas KD T3SS subgroup including P. syringae strains whereas the Pf29A strain is in the red outlined group with ‘P. brassicacearum like’ strain.
Fig. S2. Evolutionary relationships between P. fluorescens VipA sequences. VipA amino acid sequences were aligned with clustalw. A Neighbour-Joining phylogenic analysis with a Poisson correction model was performed using MEGA5 software. Nodal robustness of the tree was assessed using 1000 bootstrap replicates. The underlined strains correspond to Pf29Arp VipA sequences, and numbers in parenthesis correspond to laboratory sequence annotation that distinguished each VipA sequence. Bootstrap values lower than 50% were not shown. Type I (1.1 and 1.2), II, III, IV (4.A and 4.B) and V correspond to the main T6SS clades described by Boyer and colleagues (2009) and Barret and colleagues (2011).
Table S1. Number of orthologous hits between Pseudomonas spp. strain genomes. Sequence pairs were identified as Reciprocal Best Hit between genome of P. fluorescens Pf29Arp, P. brassicacearum NFM421, P. brassicacearum Q8r1-96, P. fluorescens Q2-87, P. fluorescens F113, P. fluorescens Pf0-1, P. fluorescens Pf-5, P. fluorescens SBW25, P. fluorescens WH6, P. syringae pv. syringae str. B728a, P. syringae pv. tomato str. DC3000, P. aeruginosa PAO1, P. putida W619 which contain respectively, 5497, 6095, 5788, 5699, 5864, 5722, 6108, 5921, 5089, 5481, 5571, 5182 protein-coding sequences.
Table S2. Genes involved in the PGPR activity and absent from the Pf29Arp genome.
Table S3. In silico analysis of the T3SS gene cluster. The percentage of identity is based on the BLASTp alignment with P. brassicacearum NMF421, P. fluorescens Q2-87, P. brassicacearum Q1r8-96, P. fluorescens F113, P. fluorescens SBW25, P. syringae DC3000, P. fluorescens BBc6r8 and P. fluorescens WH6.
Table S4. Correspondence between the different annotations of the T6SS core component proteins from Boyer and colleagues (2009) and Cascales and Cambillau (2012).
Table S5. Summary of VipA identity values from sequence blast. The percentage of identity is calculated using a BLASTp alignment with the VipA protein sequence from each strain. Numbers in parenthesis correspond to the laboratory sequence annotation that distinguished each VipA sequences and AA corresponds to Amino Acid.
Table S6. Primers used in this study.
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