Limits...
Genomic analysis reveals versatile organisms for quorum quenching enzymes: acyl-homoserine lactone-acylase and -lactonase.

Kalia VC, Raju SC, Purohit HJ - Open Microbiol J (2011)

Bottom Line: Mining sequenced genome databases has revealed organisms possessing conserved domains for AHL-lactonases and -acylases: i) Streptomyces (Actinobacteria), ii) Deinococcus (Deinococcus-Thermus), iii) Hyphomonas (α-Proteobacteria), iv) Ralstonia (β-Proteobacteria), v) Photorhabdus (γ-Proteobacteria), and certain marine gamma proteobacterium.Presence of genes for both the enzymes within an organism was observed in the following: i) Deinococcus radiodurans R1, ii) Hyphomonas neptunium ATCC 15444 and iii) Photorhabdus luminescens subsp. laumondii TTO1.Phylogenetic analysis and multiple sequence alignment of the gene sequences for AHL-lactonases and -acylases have revealed consensus sequences which can be used to design primers for amplifying these genes even among mixed cultures and metagenomes.

View Article: PubMed Central - PubMed

Affiliation: Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India.

ABSTRACT
Microbial virulence and their resistance to multiple drugs have obliged researchers to look for novel drug targets. Virulence of pathogenic microbes is regulated by signal molecules such as acylated homoserine lactone (AHL) produced during a cell density dependent phenomenon of quorum sensing (QS). In contrast, certain microbes produce AHL-lactonases and -acylases to degrade QS signals, also termed as quorum quenching. Mining sequenced genome databases has revealed organisms possessing conserved domains for AHL-lactonases and -acylases: i) Streptomyces (Actinobacteria), ii) Deinococcus (Deinococcus-Thermus), iii) Hyphomonas (α-Proteobacteria), iv) Ralstonia (β-Proteobacteria), v) Photorhabdus (γ-Proteobacteria), and certain marine gamma proteobacterium. Presence of genes for both the enzymes within an organism was observed in the following: i) Deinococcus radiodurans R1, ii) Hyphomonas neptunium ATCC 15444 and iii) Photorhabdus luminescens subsp. laumondii TTO1. These observations are supported by the presence motifs for lactonase and acylase in these strains. Phylogenetic analysis and multiple sequence alignment of the gene sequences for AHL-lactonases and -acylases have revealed consensus sequences which can be used to design primers for amplifying these genes even among mixed cultures and metagenomes. Quorum quenching can be exploited to prevent food spoilage, bacterial infections and bioremediation.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree (Upper half) based on protein sequences of organisms containing conserved domains with respect to Ralstonia sp. XJ12B AHL acylase as reference (For Taxonomic details refer to Additional file 3). A Neighbor-Joining analysis with Jukes-Cantor correction and bootstrap support was performed on the protein sequences. Bootstrap values are given at nodes, 1000 bootstrap replicates were run. The leaf contains Accession number and name of the organism.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3106361&req=5

Figure 4: Phylogenetic tree (Upper half) based on protein sequences of organisms containing conserved domains with respect to Ralstonia sp. XJ12B AHL acylase as reference (For Taxonomic details refer to Additional file 3). A Neighbor-Joining analysis with Jukes-Cantor correction and bootstrap support was performed on the protein sequences. Bootstrap values are given at nodes, 1000 bootstrap replicates were run. The leaf contains Accession number and name of the organism.

Mentions: The phylogenetic trees (Figs. 2-5) based on organisms found to possess AHL-lactonase and AHL-acylase followed the taxonomic distribution, which is expected on the basis of their 16S rDNA sequences. A few phylogenetic discrepancies were observed for AHL-lactonase (Figs. 2,3, Table 2), the notable being the associations between i) Moorella thermoacetica ATCC 39073 (Firmicutes) and Burkholderia graminis C4D1M (β-Proteobacteria) (Boot Strap Value, BV 1000), ii) Actinobacteria (Mycobacterium sp. MCS and Rubrobacter xylanophilus DSM9941) and members of α-Proteobacteria (Granulibacter bethesdensis CGDNIH1, Acidiphilum cryptum Jf-5 and Agrobacterium tumefaciens) (BV 820), and iii) Deinococcus radiodurans R1 (Deinococcus-Thermus) and Xylella fastidiosa (γ-Proteobacteria) (BV 1000). Similarly, certain taxonomic discrepancies were also recorded in the phylogenetic tree (Figs. 4,5, Table 2) drawn with respect to sequences of organisms possessing AHL-acylase: i) Solibacter usitatus Ellin 6076 (Acidobacteria) and Plesiocystis pacifica SIR-1 (δ-Proteobacteria) (BV 1000), ii) D. radiodurans R1 (Deinococcus-Thermus) and Ralstonia metallidurans CH34, R. solanacearum GMI1000 and Ralstonia sp. XJ12B (β-Proteobacteria (BV 1000). Since these associations between widely distributed organisms show very high BVs, these may be interesting cases of horizontal gene transfers.


Genomic analysis reveals versatile organisms for quorum quenching enzymes: acyl-homoserine lactone-acylase and -lactonase.

Kalia VC, Raju SC, Purohit HJ - Open Microbiol J (2011)

Phylogenetic tree (Upper half) based on protein sequences of organisms containing conserved domains with respect to Ralstonia sp. XJ12B AHL acylase as reference (For Taxonomic details refer to Additional file 3). A Neighbor-Joining analysis with Jukes-Cantor correction and bootstrap support was performed on the protein sequences. Bootstrap values are given at nodes, 1000 bootstrap replicates were run. The leaf contains Accession number and name of the organism.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3106361&req=5

Figure 4: Phylogenetic tree (Upper half) based on protein sequences of organisms containing conserved domains with respect to Ralstonia sp. XJ12B AHL acylase as reference (For Taxonomic details refer to Additional file 3). A Neighbor-Joining analysis with Jukes-Cantor correction and bootstrap support was performed on the protein sequences. Bootstrap values are given at nodes, 1000 bootstrap replicates were run. The leaf contains Accession number and name of the organism.
Mentions: The phylogenetic trees (Figs. 2-5) based on organisms found to possess AHL-lactonase and AHL-acylase followed the taxonomic distribution, which is expected on the basis of their 16S rDNA sequences. A few phylogenetic discrepancies were observed for AHL-lactonase (Figs. 2,3, Table 2), the notable being the associations between i) Moorella thermoacetica ATCC 39073 (Firmicutes) and Burkholderia graminis C4D1M (β-Proteobacteria) (Boot Strap Value, BV 1000), ii) Actinobacteria (Mycobacterium sp. MCS and Rubrobacter xylanophilus DSM9941) and members of α-Proteobacteria (Granulibacter bethesdensis CGDNIH1, Acidiphilum cryptum Jf-5 and Agrobacterium tumefaciens) (BV 820), and iii) Deinococcus radiodurans R1 (Deinococcus-Thermus) and Xylella fastidiosa (γ-Proteobacteria) (BV 1000). Similarly, certain taxonomic discrepancies were also recorded in the phylogenetic tree (Figs. 4,5, Table 2) drawn with respect to sequences of organisms possessing AHL-acylase: i) Solibacter usitatus Ellin 6076 (Acidobacteria) and Plesiocystis pacifica SIR-1 (δ-Proteobacteria) (BV 1000), ii) D. radiodurans R1 (Deinococcus-Thermus) and Ralstonia metallidurans CH34, R. solanacearum GMI1000 and Ralstonia sp. XJ12B (β-Proteobacteria (BV 1000). Since these associations between widely distributed organisms show very high BVs, these may be interesting cases of horizontal gene transfers.

Bottom Line: Mining sequenced genome databases has revealed organisms possessing conserved domains for AHL-lactonases and -acylases: i) Streptomyces (Actinobacteria), ii) Deinococcus (Deinococcus-Thermus), iii) Hyphomonas (α-Proteobacteria), iv) Ralstonia (β-Proteobacteria), v) Photorhabdus (γ-Proteobacteria), and certain marine gamma proteobacterium.Presence of genes for both the enzymes within an organism was observed in the following: i) Deinococcus radiodurans R1, ii) Hyphomonas neptunium ATCC 15444 and iii) Photorhabdus luminescens subsp. laumondii TTO1.Phylogenetic analysis and multiple sequence alignment of the gene sequences for AHL-lactonases and -acylases have revealed consensus sequences which can be used to design primers for amplifying these genes even among mixed cultures and metagenomes.

View Article: PubMed Central - PubMed

Affiliation: Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India.

ABSTRACT
Microbial virulence and their resistance to multiple drugs have obliged researchers to look for novel drug targets. Virulence of pathogenic microbes is regulated by signal molecules such as acylated homoserine lactone (AHL) produced during a cell density dependent phenomenon of quorum sensing (QS). In contrast, certain microbes produce AHL-lactonases and -acylases to degrade QS signals, also termed as quorum quenching. Mining sequenced genome databases has revealed organisms possessing conserved domains for AHL-lactonases and -acylases: i) Streptomyces (Actinobacteria), ii) Deinococcus (Deinococcus-Thermus), iii) Hyphomonas (α-Proteobacteria), iv) Ralstonia (β-Proteobacteria), v) Photorhabdus (γ-Proteobacteria), and certain marine gamma proteobacterium. Presence of genes for both the enzymes within an organism was observed in the following: i) Deinococcus radiodurans R1, ii) Hyphomonas neptunium ATCC 15444 and iii) Photorhabdus luminescens subsp. laumondii TTO1. These observations are supported by the presence motifs for lactonase and acylase in these strains. Phylogenetic analysis and multiple sequence alignment of the gene sequences for AHL-lactonases and -acylases have revealed consensus sequences which can be used to design primers for amplifying these genes even among mixed cultures and metagenomes. Quorum quenching can be exploited to prevent food spoilage, bacterial infections and bioremediation.

No MeSH data available.


Related in: MedlinePlus