Limits...
The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5.

Yan Q, Philmus B, Hesse C, Kohen M, Chang JH, Loper JE - Front Microbiol (2016)

Bottom Line: The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5.Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity.Furthermore, overexpression of tRNA[Formula: see text], the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA.

ABSTRACT
The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcriptional and post-transcriptional levels. In this study, we analyzed the genomic sequence of Pf-5 for codon usage patterns and observed that the six rarest codons in the genome are present in all seven known antibiotic biosynthesis gene clusters. In particular, there is an abundance of rare codons in pltR, which encodes a member of the LysR transcriptional regulator family that controls the expression of pyoluteorin biosynthetic genes. To test the hypothesis that rare codons in pltR influence pyoluteorin production, we generated a derivative of Pf-5 in which 23 types of rare codons in pltR were substituted with synonymous preferred codons. The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5. Accordingly, the promoter activity of the pyoluteorin biosynthetic gene pltL was 20 times higher in the codon-modified stain than in the wild-type. pltR has six AGA codons, which is the rarest codon in the Pf-5 genome. Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity. Furthermore, overexpression of tRNA[Formula: see text], the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5. A bias in codon usage has been linked to the regulation of many phenotypes in eukaryotes and prokaryotes but, to our knowledge, this is the first example of the role of a rare codon in the regulation of antibiotic production by a Gram-negative bacterium.

No MeSH data available.


Related in: MedlinePlus

The codon usage frequency of the six rarest codons in antibiotic gene clusters of P. protegens Pf-5. The codon usage frequency refers to the number of times a specified codon was identified per 1000 codons in the annotated coding sequences of Pf-5 (black bar) or within a specific gene cluster (colored markers).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4836200&req=5

Figure 1: The codon usage frequency of the six rarest codons in antibiotic gene clusters of P. protegens Pf-5. The codon usage frequency refers to the number of times a specified codon was identified per 1000 codons in the annotated coding sequences of Pf-5 (black bar) or within a specific gene cluster (colored markers).

Mentions: The arginine (Arg) codon AGA is the rarest codon in the annotated coding sequences (CDSs) of the Pf-5 genome, occurring at the level of 9.9 per 1000 Arg codons and 0.6 per 1000 codons (Table 2; Paulsen et al., 2005). AGA is present in 917 genes, which comprise approximately 15% of the 6144 annotated genes in the Pf-5 genome (Table 2). Six of the seven antibiotic biosynthesis gene clusters of Pf-5 include at least one AGA codon and 40% of the genes present in the seven gene clusters have an AGA codon (Table 2). The usage frequency of the AGA codon within four antibiotic biosynthesis gene clusters exceeds the average usage frequency of this rare codon in the genome of Pf-5 (Figure 1). Further, analysis revealed that each of the top six rarest codons in the Pf-5 genome is present in the six or more of the seven antibiotic biosynthesis gene clusters (Table 2). Fifty five of the 60 genes (92%) in the seven gene clusters have at least one of the six rarest codons of the Pf-5 genome (Table 2). The presence of rare codons in the antibiotic gene clusters of Pf-5 raised the possibility that rare codons may be involved in the regulation of antibiotic production in this bacterium.


The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5.

Yan Q, Philmus B, Hesse C, Kohen M, Chang JH, Loper JE - Front Microbiol (2016)

The codon usage frequency of the six rarest codons in antibiotic gene clusters of P. protegens Pf-5. The codon usage frequency refers to the number of times a specified codon was identified per 1000 codons in the annotated coding sequences of Pf-5 (black bar) or within a specific gene cluster (colored markers).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836200&req=5

Figure 1: The codon usage frequency of the six rarest codons in antibiotic gene clusters of P. protegens Pf-5. The codon usage frequency refers to the number of times a specified codon was identified per 1000 codons in the annotated coding sequences of Pf-5 (black bar) or within a specific gene cluster (colored markers).
Mentions: The arginine (Arg) codon AGA is the rarest codon in the annotated coding sequences (CDSs) of the Pf-5 genome, occurring at the level of 9.9 per 1000 Arg codons and 0.6 per 1000 codons (Table 2; Paulsen et al., 2005). AGA is present in 917 genes, which comprise approximately 15% of the 6144 annotated genes in the Pf-5 genome (Table 2). Six of the seven antibiotic biosynthesis gene clusters of Pf-5 include at least one AGA codon and 40% of the genes present in the seven gene clusters have an AGA codon (Table 2). The usage frequency of the AGA codon within four antibiotic biosynthesis gene clusters exceeds the average usage frequency of this rare codon in the genome of Pf-5 (Figure 1). Further, analysis revealed that each of the top six rarest codons in the Pf-5 genome is present in the six or more of the seven antibiotic biosynthesis gene clusters (Table 2). Fifty five of the 60 genes (92%) in the seven gene clusters have at least one of the six rarest codons of the Pf-5 genome (Table 2). The presence of rare codons in the antibiotic gene clusters of Pf-5 raised the possibility that rare codons may be involved in the regulation of antibiotic production in this bacterium.

Bottom Line: The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5.Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity.Furthermore, overexpression of tRNA[Formula: see text], the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA.

ABSTRACT
The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcriptional and post-transcriptional levels. In this study, we analyzed the genomic sequence of Pf-5 for codon usage patterns and observed that the six rarest codons in the genome are present in all seven known antibiotic biosynthesis gene clusters. In particular, there is an abundance of rare codons in pltR, which encodes a member of the LysR transcriptional regulator family that controls the expression of pyoluteorin biosynthetic genes. To test the hypothesis that rare codons in pltR influence pyoluteorin production, we generated a derivative of Pf-5 in which 23 types of rare codons in pltR were substituted with synonymous preferred codons. The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5. Accordingly, the promoter activity of the pyoluteorin biosynthetic gene pltL was 20 times higher in the codon-modified stain than in the wild-type. pltR has six AGA codons, which is the rarest codon in the Pf-5 genome. Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity. Furthermore, overexpression of tRNA[Formula: see text], the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5. A bias in codon usage has been linked to the regulation of many phenotypes in eukaryotes and prokaryotes but, to our knowledge, this is the first example of the role of a rare codon in the regulation of antibiotic production by a Gram-negative bacterium.

No MeSH data available.


Related in: MedlinePlus