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Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation

Gan, Han Ming, Hudson, Andre O., Rahman, Ahmad Yamin Abdul, Chan, Kok Gan and Savka, Michael A. 2013, Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation, BMC genomics, vol. 14, pp. 1-14, doi: 10.1186/1471-2164-14-431.

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Title Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation
Author(s) Gan, Han Ming
Hudson, Andre O.
Rahman, Ahmad Yamin Abdul
Chan, Kok Gan
Savka, Michael A.
Journal name BMC genomics
Volume number 14
Article ID 431
Start page 1
End page 14
Total pages 14
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2013-06-28
ISSN 1471-2164
Keyword(s) Adaptation, Physiological
Alphaproteobacteria
Amino Acid Sequence
Bacterial Proteins
Biodegradation, Environmental
Conserved Sequence
Dioxygenases
Gene Transfer, Horizontal
Genes, Bacterial
Genomics
Molecular Sequence Data
Oceans and Seas
Phenotype
Phylogeny
Quorum Sensing
Salts
Sequence Homology, Nucleic Acid
Signal Transduction
Species Specificity
Summary Background
Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures.

Results
The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme.

Conclusions
The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation. The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.
Language eng
DOI 10.1186/1471-2164-14-431
Field of Research 060408 Genomics
060503 Microbial Genetics
060501 Bacteriology
06 Biological Sciences
11 Medical And Health Sciences
08 Information And Computing Sciences
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2013, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30101907

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.