Abstract
Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from the ginger rhizosphere. It degrades a broad range of N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching mechanisms in this bacterium.
GENOME ANNOUNCEMENT
Members of the genus Acinetobacter are always subjects of research because they have great potentials in biotechnology and environmental sciences. Acinetobacter is also a well-known emerging multidrug-resistant nosocomial infectious pathogen (2). Previous reports have shown that Acinetobacter spp. possess either quorum-sensing (QS) or quorum-quenching (QQ) activity (2, 5, 8). However, recently, our group has reported that Acinetobacter sp. strain GG2, isolated from the rhizosphere of ginger (Zingiber officinale) growing in the Malaysian rainforest, exhibits both QS and QQ activities (3). Strain GG2 can degrade various types of N-acylhomoserine lactone (AHL) molecules, ranging from C5-homoserine lactone (C5-HSL) to C14-HSL, via a broad-spectrum lactonase activity. The lactonase of strain GG2 degrades AHL molecules regardless of the substituent group at the C-3 position of the AHL molecules (3). Here, we sequenced the complete genome of Acinetobacter sp. strain GG2 as a step toward understanding the molecular regulation of QS systems and searching for the QQ gene in this bacterium.
Genomic DNA of Acinetobacter sp. strain GG2 was isolated using the QIAamp DNA minikit (Qiagen, Germany) per the manufacturer's instructions. The quality of DNA was examined using a Nanodrop spectrophotometer (Thermo Scientific) and a Qubit 2.0 fluorometer (Life Technologies). The whole-genome sequencing of strain GG2 was performed using the Illumina HiSeq 2000 platform after the construction of a sequencing library using the TruSeq DNA sample preparation kit, v2 (Illumina Inc., CA). This resulted in 2,466,436 filtered reads and approximately 56-fold coverage. The filtered reads were de novo assembled with the CLC Genomic Workbench v5.1, generating 57 contigs (N50, 168,611 bp), containing a total of 3,890,805 bp. The G+C content of this genome is 38.4%. Gene prediction was performed using Prodigal (v2.60), and a total of 3,572 open reading frames (ORFs) were predicted (6). Annotation was performed using Blast2GO (4) against the NCBI-NR sequence database (1). One complete rRNA operon and one copy each of the 5S rRNA gene, the 23S rRNA gene, and the 16S rRNA gene were identified using RNAmmer (9). A total of 49 tRNAs were identified using tRNAscan-SE (10).
Based on Blast2GO analysis, the AHL synthase gene of Acinetobacter sp. strain GG2 was found in contig 3. It has a high percentage of similarity (95%) to the AHL synthase gene of Acinetobacter sp. strain DR1 (7). Furthermore, a putative AHL-lactonase gene that has a metallo-beta-lactamase domain was found in silico in contig 2.
Nucleotide sequence accession numbers.
This Whole-Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ALOW00000000. The version described in this paper is the first version, ALOW01000000.
ACKNOWLEDGMENT
K.-G. Chan gratefully acknowledges the University of Malaya for financial support (High Impact Research Grant, A000001-50001).
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