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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

A subset of operons antisense to known genes.Two operons identified antisense to a known operon (A) or to known genes (B). cDNA reads in each library without (-TEX) or with (+TEX) terminator exonuclease treatment were mapped to B. amyloliquefaciens FZB42 chromosome and visualized by IGB 8.1. Vertical bars indicate cDNA recovery detected in each library and were adjusted to the same scale of 20. The genes indicated above the horizontal coordinates are located on the forward strand while the genes indicated below the horizontal coordinates are located on the reverse strand. Bacterial cultures were sampled for total RNA extraction at two time points (#6h?  h) from four conditions: i) in 1CM medium; ii) 1CM medium supplemented with the maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil extract (+RS). The time point #6h corresponded to early stationary phase while #9h corresponded to middle stationary phase.
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pone.0142002.g003: A subset of operons antisense to known genes.Two operons identified antisense to a known operon (A) or to known genes (B). cDNA reads in each library without (-TEX) or with (+TEX) terminator exonuclease treatment were mapped to B. amyloliquefaciens FZB42 chromosome and visualized by IGB 8.1. Vertical bars indicate cDNA recovery detected in each library and were adjusted to the same scale of 20. The genes indicated above the horizontal coordinates are located on the forward strand while the genes indicated below the horizontal coordinates are located on the reverse strand. Bacterial cultures were sampled for total RNA extraction at two time points (#6h? h) from four conditions: i) in 1CM medium; ii) 1CM medium supplemented with the maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil extract (+RS). The time point #6h corresponded to early stationary phase while #9h corresponded to middle stationary phase.

Mentions: We found 730 operons for the FZB42 genome predicted by the DOOR database [68]. We manually checked the 730operon loci with our visualized dRNA-seq data and thus validated 78 polycistronic transcripts covering a total of 210 genes (S14 Table). Most of the confirmed operons (53 out of the 78) are bicistronic. Intriguingly, we observed two long asRNA that resemble excludon structures (Fig 3A and 3B). Excludon is a transcriptome organization where divergent genes with mutually exclusive or related functions transcribe long antisense RNAs in order to suppress the expression of the other gene in the same locus [69, 70]. In addition, we found that 13 genes, which are listed within a polycistronic operon by DBTBS [55], were actually transcribed as a monocistronic unit (S15 Table). This indicates that alternative TSSs could be used to initiate their gene transcription in a certain environment. For example, the polycistronic operon of yhaA-yhfA-yhgC varied their transcript initiation from different TSSs at ESP (#6h) or MSP (#9h) (S2 Fig).


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)

A subset of operons antisense to known genes.Two operons identified antisense to a known operon (A) or to known genes (B). cDNA reads in each library without (-TEX) or with (+TEX) terminator exonuclease treatment were mapped to B. amyloliquefaciens FZB42 chromosome and visualized by IGB 8.1. Vertical bars indicate cDNA recovery detected in each library and were adjusted to the same scale of 20. The genes indicated above the horizontal coordinates are located on the forward strand while the genes indicated below the horizontal coordinates are located on the reverse strand. Bacterial cultures were sampled for total RNA extraction at two time points (#6h?  h) from four conditions: i) in 1CM medium; ii) 1CM medium supplemented with the maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil extract (+RS). The time point #6h corresponded to early stationary phase while #9h corresponded to middle stationary phase.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4634765&req=5

pone.0142002.g003: A subset of operons antisense to known genes.Two operons identified antisense to a known operon (A) or to known genes (B). cDNA reads in each library without (-TEX) or with (+TEX) terminator exonuclease treatment were mapped to B. amyloliquefaciens FZB42 chromosome and visualized by IGB 8.1. Vertical bars indicate cDNA recovery detected in each library and were adjusted to the same scale of 20. The genes indicated above the horizontal coordinates are located on the forward strand while the genes indicated below the horizontal coordinates are located on the reverse strand. Bacterial cultures were sampled for total RNA extraction at two time points (#6h? h) from four conditions: i) in 1CM medium; ii) 1CM medium supplemented with the maize root exudates (+RE); iii) 1CM medium supplemented with soil extract (+SE); iv) 1CM medium supplemented with both maize root exudates and soil extract (+RS). The time point #6h corresponded to early stationary phase while #9h corresponded to middle stationary phase.
Mentions: We found 730 operons for the FZB42 genome predicted by the DOOR database [68]. We manually checked the 730operon loci with our visualized dRNA-seq data and thus validated 78 polycistronic transcripts covering a total of 210 genes (S14 Table). Most of the confirmed operons (53 out of the 78) are bicistronic. Intriguingly, we observed two long asRNA that resemble excludon structures (Fig 3A and 3B). Excludon is a transcriptome organization where divergent genes with mutually exclusive or related functions transcribe long antisense RNAs in order to suppress the expression of the other gene in the same locus [69, 70]. In addition, we found that 13 genes, which are listed within a polycistronic operon by DBTBS [55], were actually transcribed as a monocistronic unit (S15 Table). This indicates that alternative TSSs could be used to initiate their gene transcription in a certain environment. For example, the polycistronic operon of yhaA-yhfA-yhgC varied their transcript initiation from different TSSs at ESP (#6h) or MSP (#9h) (S2 Fig).

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