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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

Genomic Visualization of various RNAs identified.The 1st ring from inside depicts genomic size maker; 2nd ring in black indicates DNA GC content; 3rd ring in purple and green indicates GC skew (+/-); 4th ring in grey indicates housekeeping rRNA and tRNAs; 5th and 6th ring indicates primary TSS (in red) and genes located on the leading strand (black arrows clockwise), 7th ring with oliver arrows indicates the re-annotated genes on the leading strand, including corrected CDS, leaderless mRNAs and proposed operons; 8th and 9th ring indicates primary TSS(in red) and genes (black arrows counterclockwise) located on the lagging strand; 10th ring with Olive green arrows indicates re-annotated genes on the lagging strand; 11th-12th ring show nucleotide conservation patterns with genomes of B. amyloliquefaciens DSM7 (NC_014551.1), B. amyloliquefaciens subsp. plantarum CAU B946 (NC_016784.1) and B. subtilis 168 (NC_000964.3), respectively; 13th ring in orange depicts all the cis-encoded RNAs annotated in this study, including riboswitches and all the antisense RNAs; 14th ring (the most outer-ring in red) depicts experimentally validated sRNAs in this study and their names are labeled.
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pone.0142002.g005: Genomic Visualization of various RNAs identified.The 1st ring from inside depicts genomic size maker; 2nd ring in black indicates DNA GC content; 3rd ring in purple and green indicates GC skew (+/-); 4th ring in grey indicates housekeeping rRNA and tRNAs; 5th and 6th ring indicates primary TSS (in red) and genes located on the leading strand (black arrows clockwise), 7th ring with oliver arrows indicates the re-annotated genes on the leading strand, including corrected CDS, leaderless mRNAs and proposed operons; 8th and 9th ring indicates primary TSS(in red) and genes (black arrows counterclockwise) located on the lagging strand; 10th ring with Olive green arrows indicates re-annotated genes on the lagging strand; 11th-12th ring show nucleotide conservation patterns with genomes of B. amyloliquefaciens DSM7 (NC_014551.1), B. amyloliquefaciens subsp. plantarum CAU B946 (NC_016784.1) and B. subtilis 168 (NC_000964.3), respectively; 13th ring in orange depicts all the cis-encoded RNAs annotated in this study, including riboswitches and all the antisense RNAs; 14th ring (the most outer-ring in red) depicts experimentally validated sRNAs in this study and their names are labeled.

Mentions: B. amyloliquefaciens FZB42 is a Gram-positive representative of rhizobacteria that colonize plant roots and promote plant growth. Understanding its transcriptome structure and dynamics is critical to study the symbiotic relationship between rhizobacteria and host plants. In this work we have employed dRNA-seq and investigated the primary transcriptome of strain FZB42 under several conditions mimicking plant root environments. Our analyses established a comprehensive transcriptome structure for FZB42 (Fig 5) by determining primary TSSs for 60% of all FZB42 genes, assigning 5'-UTRs and operon structures, and identifying a large number of cis-encoded and trans-encoded RNAs which may be regulators of gene expression in B. amyloliquefaciens. Our analyses at the transcriptome level also improved the genome annotation of FZB42; for example, we proposed 46 new genes and corrected 10 mis-annotated genes (S13 Table).


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)

Genomic Visualization of various RNAs identified.The 1st ring from inside depicts genomic size maker; 2nd ring in black indicates DNA GC content; 3rd ring in purple and green indicates GC skew (+/-); 4th ring in grey indicates housekeeping rRNA and tRNAs; 5th and 6th ring indicates primary TSS (in red) and genes located on the leading strand (black arrows clockwise), 7th ring with oliver arrows indicates the re-annotated genes on the leading strand, including corrected CDS, leaderless mRNAs and proposed operons; 8th and 9th ring indicates primary TSS(in red) and genes (black arrows counterclockwise) located on the lagging strand; 10th ring with Olive green arrows indicates re-annotated genes on the lagging strand; 11th-12th ring show nucleotide conservation patterns with genomes of B. amyloliquefaciens DSM7 (NC_014551.1), B. amyloliquefaciens subsp. plantarum CAU B946 (NC_016784.1) and B. subtilis 168 (NC_000964.3), respectively; 13th ring in orange depicts all the cis-encoded RNAs annotated in this study, including riboswitches and all the antisense RNAs; 14th ring (the most outer-ring in red) depicts experimentally validated sRNAs in this study and their names are labeled.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0142002.g005: Genomic Visualization of various RNAs identified.The 1st ring from inside depicts genomic size maker; 2nd ring in black indicates DNA GC content; 3rd ring in purple and green indicates GC skew (+/-); 4th ring in grey indicates housekeeping rRNA and tRNAs; 5th and 6th ring indicates primary TSS (in red) and genes located on the leading strand (black arrows clockwise), 7th ring with oliver arrows indicates the re-annotated genes on the leading strand, including corrected CDS, leaderless mRNAs and proposed operons; 8th and 9th ring indicates primary TSS(in red) and genes (black arrows counterclockwise) located on the lagging strand; 10th ring with Olive green arrows indicates re-annotated genes on the lagging strand; 11th-12th ring show nucleotide conservation patterns with genomes of B. amyloliquefaciens DSM7 (NC_014551.1), B. amyloliquefaciens subsp. plantarum CAU B946 (NC_016784.1) and B. subtilis 168 (NC_000964.3), respectively; 13th ring in orange depicts all the cis-encoded RNAs annotated in this study, including riboswitches and all the antisense RNAs; 14th ring (the most outer-ring in red) depicts experimentally validated sRNAs in this study and their names are labeled.
Mentions: B. amyloliquefaciens FZB42 is a Gram-positive representative of rhizobacteria that colonize plant roots and promote plant growth. Understanding its transcriptome structure and dynamics is critical to study the symbiotic relationship between rhizobacteria and host plants. In this work we have employed dRNA-seq and investigated the primary transcriptome of strain FZB42 under several conditions mimicking plant root environments. Our analyses established a comprehensive transcriptome structure for FZB42 (Fig 5) by determining primary TSSs for 60% of all FZB42 genes, assigning 5'-UTRs and operon structures, and identifying a large number of cis-encoded and trans-encoded RNAs which may be regulators of gene expression in B. amyloliquefaciens. Our analyses at the transcriptome level also improved the genome annotation of FZB42; for example, we proposed 46 new genes and corrected 10 mis-annotated genes (S13 Table).

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