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dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42.

Fan B, Li L, Chao Y, Förstner K, Vogel J, Borriss R, Wu XQ - PLoS ONE (2015)

Bottom Line: Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments.We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus.Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.

View Article: PubMed Central - PubMed

Affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.

ABSTRACT
Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizosphere-mimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.

No MeSH data available.


Related in: MedlinePlus

Growth conditions of Bacillus amyloliquefaciens FZB42.(A) Schematic diagram of the dRNA-seq workflow of B. amyloliquefaciens FZB42. FZB42 was cultured in four media: i) 1CM medium; ii) 1CM medium supplemented with maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil (+RS). (B) Growth curves of FZB42 growing in the four media. The cultures were collected for total RNA preparation at different time points (#6h & #9h) as indicated by the arrows. TEX: terminator exonuclease; ESP: early stationary phase; MSP: middle stationary phase.
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pone.0142002.g001: Growth conditions of Bacillus amyloliquefaciens FZB42.(A) Schematic diagram of the dRNA-seq workflow of B. amyloliquefaciens FZB42. FZB42 was cultured in four media: i) 1CM medium; ii) 1CM medium supplemented with maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil (+RS). (B) Growth curves of FZB42 growing in the four media. The cultures were collected for total RNA preparation at different time points (#6h & #9h) as indicated by the arrows. TEX: terminator exonuclease; ESP: early stationary phase; MSP: middle stationary phase.

Mentions: B. amyloliquefaciens FZB42 was cultured under four conditions [43]: i) in 1CM medium (1% peptone, 0.05% yeast extract, 0.5% NaCl); ii) 1CM medium supplemented with maize root exudates (RE) of 0.25 mg/ml; iii) 1CM medium supplemented with 10% soil extract (SE) prepared from soil collected from the farmland (with the permission of farmland owner Mrs Constanze Ackermann) in Wuerzburg, Germany; iv) 1CM medium supplemented with both the maize root exudates (0.25 mg/ml) and the soil extract (10%). The maize root exudates were collected from the cultivar “DengHai 11” as described in our previous work [43]. The cultures were incubated at 210 rpm and 28°C and collected at early stationary phase and at middle stationary phase, respectively, for total RNA preparation (Fig 1).


dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42.

Fan B, Li L, Chao Y, Förstner K, Vogel J, Borriss R, Wu XQ - PLoS ONE (2015)

Growth conditions of Bacillus amyloliquefaciens FZB42.(A) Schematic diagram of the dRNA-seq workflow of B. amyloliquefaciens FZB42. FZB42 was cultured in four media: i) 1CM medium; ii) 1CM medium supplemented with maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil (+RS). (B) Growth curves of FZB42 growing in the four media. The cultures were collected for total RNA preparation at different time points (#6h & #9h) as indicated by the arrows. TEX: terminator exonuclease; ESP: early stationary phase; MSP: middle stationary phase.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4634765&req=5

pone.0142002.g001: Growth conditions of Bacillus amyloliquefaciens FZB42.(A) Schematic diagram of the dRNA-seq workflow of B. amyloliquefaciens FZB42. FZB42 was cultured in four media: i) 1CM medium; ii) 1CM medium supplemented with maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil (+RS). (B) Growth curves of FZB42 growing in the four media. The cultures were collected for total RNA preparation at different time points (#6h & #9h) as indicated by the arrows. TEX: terminator exonuclease; ESP: early stationary phase; MSP: middle stationary phase.
Mentions: B. amyloliquefaciens FZB42 was cultured under four conditions [43]: i) in 1CM medium (1% peptone, 0.05% yeast extract, 0.5% NaCl); ii) 1CM medium supplemented with maize root exudates (RE) of 0.25 mg/ml; iii) 1CM medium supplemented with 10% soil extract (SE) prepared from soil collected from the farmland (with the permission of farmland owner Mrs Constanze Ackermann) in Wuerzburg, Germany; iv) 1CM medium supplemented with both the maize root exudates (0.25 mg/ml) and the soil extract (10%). The maize root exudates were collected from the cultivar “DengHai 11” as described in our previous work [43]. The cultures were incubated at 210 rpm and 28°C and collected at early stationary phase and at middle stationary phase, respectively, for total RNA preparation (Fig 1).

Bottom Line: Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments.We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus.Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.

View Article: PubMed Central - PubMed

Affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.

ABSTRACT
Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizosphere-mimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.

No MeSH data available.


Related in: MedlinePlus