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A Genomic, Transcriptomic and Proteomic Look at the GE2270 Producer Planobispora rosea, an Uncommon Actinomycete.

Tocchetti A, Bordoni R, Gallo G, Petiti L, Corti G, Alt S, Cruz JC, Salzano AM, Scaloni A, Puglia AM, De Bellis G, Peano C, Donadio S, Sosio M - PLoS ONE (2015)

Bottom Line: The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs.While GE2270 production starts during the exponential phase, most pbt genes, as analyzed by qRT-PCR, are down-regulated.The exception is represented by pbtA, encoding the precursor peptide of the ribosomally synthesized GE2270, whose expression reached the highest level at the entry into stationary phase.

View Article: PubMed Central - PubMed

Affiliation: NAICONS Srl, Milano, Italy; KtedoGen Srl, Milano, Italy.

ABSTRACT
We report the genome sequence of Planobispora rosea ATCC 53733, a mycelium-forming soil-dweller belonging to one of the lesser studied genera of Actinobacteria and producing the thiopeptide GE2270. The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs. Patterns of gene expression in P. rosea cultures during exponential and stationary phase have been analyzed using whole transcriptome shotgun sequencing and by proteome analysis. Among the differentially abundant proteins, those involved in protein metabolism are particularly represented, including the GE2270-insensitive EF-Tu. Two proteins from the pbt cluster, directing GE2270 biosynthesis, slightly increase their abundance values over time. While GE2270 production starts during the exponential phase, most pbt genes, as analyzed by qRT-PCR, are down-regulated. The exception is represented by pbtA, encoding the precursor peptide of the ribosomally synthesized GE2270, whose expression reached the highest level at the entry into stationary phase.

No MeSH data available.


Representation of the P. rosea genome.Outer grey circle corresponds to the scaffolds and nucleotide length, with the replication origin (oriC) placed as nucleotide 1. Blue segments designate secondary metabolite clusters as reported in Table 2. The other circles denote the distribution of CDSs according to the functional categories of S1 Table (from edge to center): C to R, T and U. GC skew is represented by the inner circle.
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pone.0133705.g001: Representation of the P. rosea genome.Outer grey circle corresponds to the scaffolds and nucleotide length, with the replication origin (oriC) placed as nucleotide 1. Blue segments designate secondary metabolite clusters as reported in Table 2. The other circles denote the distribution of CDSs according to the functional categories of S1 Table (from edge to center): C to R, T and U. GC skew is represented by the inner circle.

Mentions: The four largest P. rosea scaffolds, which account for 97.4% of the genome, show considerable synteny (see below) with the single-scaffold genome of Streptosporangium roseum NRRL B-2638 [12]. The P. rosea scaffolds were thus in silico ordered using the latter genome as template, creating an 8,466,550-bp superscaffold. The remaining 6 scaffolds, which overall account for 224,158 bp, could not be ordered on the basis of synteny with S. roseum and were arbitrarily placed at the end of the superscaffold, resulting in the draft genome depicted in Fig 1.


A Genomic, Transcriptomic and Proteomic Look at the GE2270 Producer Planobispora rosea, an Uncommon Actinomycete.

Tocchetti A, Bordoni R, Gallo G, Petiti L, Corti G, Alt S, Cruz JC, Salzano AM, Scaloni A, Puglia AM, De Bellis G, Peano C, Donadio S, Sosio M - PLoS ONE (2015)

Representation of the P. rosea genome.Outer grey circle corresponds to the scaffolds and nucleotide length, with the replication origin (oriC) placed as nucleotide 1. Blue segments designate secondary metabolite clusters as reported in Table 2. The other circles denote the distribution of CDSs according to the functional categories of S1 Table (from edge to center): C to R, T and U. GC skew is represented by the inner circle.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4514598&req=5

pone.0133705.g001: Representation of the P. rosea genome.Outer grey circle corresponds to the scaffolds and nucleotide length, with the replication origin (oriC) placed as nucleotide 1. Blue segments designate secondary metabolite clusters as reported in Table 2. The other circles denote the distribution of CDSs according to the functional categories of S1 Table (from edge to center): C to R, T and U. GC skew is represented by the inner circle.
Mentions: The four largest P. rosea scaffolds, which account for 97.4% of the genome, show considerable synteny (see below) with the single-scaffold genome of Streptosporangium roseum NRRL B-2638 [12]. The P. rosea scaffolds were thus in silico ordered using the latter genome as template, creating an 8,466,550-bp superscaffold. The remaining 6 scaffolds, which overall account for 224,158 bp, could not be ordered on the basis of synteny with S. roseum and were arbitrarily placed at the end of the superscaffold, resulting in the draft genome depicted in Fig 1.

Bottom Line: The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs.While GE2270 production starts during the exponential phase, most pbt genes, as analyzed by qRT-PCR, are down-regulated.The exception is represented by pbtA, encoding the precursor peptide of the ribosomally synthesized GE2270, whose expression reached the highest level at the entry into stationary phase.

View Article: PubMed Central - PubMed

Affiliation: NAICONS Srl, Milano, Italy; KtedoGen Srl, Milano, Italy.

ABSTRACT
We report the genome sequence of Planobispora rosea ATCC 53733, a mycelium-forming soil-dweller belonging to one of the lesser studied genera of Actinobacteria and producing the thiopeptide GE2270. The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs. Patterns of gene expression in P. rosea cultures during exponential and stationary phase have been analyzed using whole transcriptome shotgun sequencing and by proteome analysis. Among the differentially abundant proteins, those involved in protein metabolism are particularly represented, including the GE2270-insensitive EF-Tu. Two proteins from the pbt cluster, directing GE2270 biosynthesis, slightly increase their abundance values over time. While GE2270 production starts during the exponential phase, most pbt genes, as analyzed by qRT-PCR, are down-regulated. The exception is represented by pbtA, encoding the precursor peptide of the ribosomally synthesized GE2270, whose expression reached the highest level at the entry into stationary phase.

No MeSH data available.