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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

A. Conserved domains on AHL-lactonase (Bacillus sp. SB4) [gi/40388447/gb/AAR85482.1], B. Conserved domains on AHL-acylase (Ralstonia sp. XJ12B) [gi/28376389/gb/AAO41113.1].
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Figure 1: A. Conserved domains on AHL-lactonase (Bacillus sp. SB4) [gi/40388447/gb/AAR85482.1], B. Conserved domains on AHL-acylase (Ralstonia sp. XJ12B) [gi/28376389/gb/AAO41113.1].

Mentions: From the literature available in public domains, we collected protein sequences for AHL-lactonase from Bacillus sp. SB4 (Accession No. AAR85482.1) and AHL-acylase from Ralstonia sp. XJ12B (Accession No. AAO41113.1) from NCBI Protein database. The nucleotide sequences of corresponding protein sequences for the MEME signature analysis were downloaded from the NCBI Genbank. The conserved domains of these enzymes from reference organisms have been presented in Fig. (1). We used BLASTP for the similarity searches and NCBI Conserved Domains [36, 37], for conserved domain search. The selected sequences were analyzed to get similar sequences and Conserved Domains of each BLAST hit. We selected parameter for Max target sequences in BLASTP as ~250 hits (BLOSUM 62 Matrix), as it gives results with large number of sequences from same species.


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)

A. Conserved domains on AHL-lactonase (Bacillus sp. SB4) [gi/40388447/gb/AAR85482.1], B. Conserved domains on AHL-acylase (Ralstonia sp. XJ12B) [gi/28376389/gb/AAO41113.1].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: A. Conserved domains on AHL-lactonase (Bacillus sp. SB4) [gi/40388447/gb/AAR85482.1], B. Conserved domains on AHL-acylase (Ralstonia sp. XJ12B) [gi/28376389/gb/AAO41113.1].
Mentions: From the literature available in public domains, we collected protein sequences for AHL-lactonase from Bacillus sp. SB4 (Accession No. AAR85482.1) and AHL-acylase from Ralstonia sp. XJ12B (Accession No. AAO41113.1) from NCBI Protein database. The nucleotide sequences of corresponding protein sequences for the MEME signature analysis were downloaded from the NCBI Genbank. The conserved domains of these enzymes from reference organisms have been presented in Fig. (1). We used BLASTP for the similarity searches and NCBI Conserved Domains [36, 37], for conserved domain search. The selected sequences were analyzed to get similar sequences and Conserved Domains of each BLAST hit. We selected parameter for Max target sequences in BLASTP as ~250 hits (BLOSUM 62 Matrix), as it gives results with large number of sequences from same species.

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