Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1

Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs). Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that ma...

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Published in:PloS one 2014-03, Vol.9 (6), p.e90812
Main Authors: Yun, Sung Ho, Choi, Chi-Won, Lee, Sang-Yeop, Lee, Yeol Gyun, Kwon, Joseph, Leem, Sun Hee, Chung, Young Ho, Kahng, Hyung-Yeel, Kim, Sang Jin, Kwon, Kae Kyoung, Kim, Seung Il
Format: Article
Language:English
Subjects:
Bacteria
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biodegradation
Biodegradation, Environmental
Biology
Biphenyl
Biphenyl (Compound)
Biphenyl-2,3-diol 1,2-dioxygenase
Catechin
Catechol
Catechol 2,3-dioxygenase
Cleavage
Cluster Analysis
Comparative analysis
Enzymes
Gene Expression Regulation, Bacterial
Genes
Genomes
Genomics
Hydrocarbon-degrading bacteria
Life sciences
Mycobacterium
Novosphingobium
Novosphingobium pentaromativorans
Nucleotide sequence
Peptides
Phenanthrene
Plasmids
Plasmids - genetics
Polycyclic aromatic hydrocarbons
Polycyclic Aromatic Hydrocarbons - metabolism
Proteins
Proteome - genetics
Proteome - metabolism
Proteomics
Protocatechuate 4,5-dioxygenase
Pseudomonas putida
Sphingomonadaceae - genetics
Sphingomonadaceae - metabolism
Sphingomonas
Streptococcus infections
Transcriptional Activation
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cited_by cdi_FETCH-LOGICAL-c758t-a80c6e5e48e4e56267b9dbde0e0804eabb6e7f0f91504911ad7c3d93a48a41e43
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container_title PloS one
container_volume 9
creator Yun, Sung Ho
Choi, Chi-Won
Lee, Sang-Yeop
Lee, Yeol Gyun
Kwon, Joseph
Leem, Sun Hee
Chung, Young Ho
Kahng, Hyung-Yeel
Kim, Sang Jin
Kwon, Kae Kyoung
Kim, Seung Il
description Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs). Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that may be involved in PAH degradation. 1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs) identified approximately 1,000 and 1,400 proteins, respectively. Up-regulated biodegradation enzymes, including those belonging to pLA1, were quantitatively compared. Among the PAHs, phenanthrene induced the strongest up-regulation of extradiol cleavage pathway enzymes such as ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase in pLA1. These enzymes lead the initial step of the lower catabolic pathway of aromatic hydrocarbons through the extradiol cleavage pathway and participate in the attack of PAH ring cleavage, respectively. However, N. pentaromativorans US6-1 cultured with p-hydroxybenzoate induced activation of another extradiol cleavage pathway, the protocatechuate 4,5-dioxygenase pathway, that originated from chromosomal genes. These results suggest that N. pentaromativorans US6-1 utilizes two different extradiol pathways and plasmid pLA1 might play a key role in the biodegradation of PAH in N. pentaromativorans US6-1.
doi_str_mv 10.1371/journal.pone.0090812
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Academic</collection><collection>ProQuest Engineering Collection</collection><collection>Biological Sciences</collection><collection>Agriculture Science Database</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>ProQuest Engineering Database</collection><collection>Nursing &amp; Allied Health Premium</collection><collection>ProQuest advanced technologies &amp; aerospace journals</collection><collection>test</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ (Directory of Open Access Journals)</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yun, Sung Ho</au><au>Choi, Chi-Won</au><au>Lee, Sang-Yeop</au><au>Lee, Yeol Gyun</au><au>Kwon, Joseph</au><au>Leem, Sun Hee</au><au>Chung, Young Ho</au><au>Kahng, Hyung-Yeel</au><au>Kim, Sang Jin</au><au>Kwon, Kae Kyoung</au><au>Kim, Seung Il</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-03-07</date><risdate>2014</risdate><volume>9</volume><issue>6</issue><spage>e90812</spage><pages>e90812-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs). Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that may be involved in PAH degradation. 1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs) identified approximately 1,000 and 1,400 proteins, respectively. Up-regulated biodegradation enzymes, including those belonging to pLA1, were quantitatively compared. Among the PAHs, phenanthrene induced the strongest up-regulation of extradiol cleavage pathway enzymes such as ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase in pLA1. These enzymes lead the initial step of the lower catabolic pathway of aromatic hydrocarbons through the extradiol cleavage pathway and participate in the attack of PAH ring cleavage, respectively. However, N. pentaromativorans US6-1 cultured with p-hydroxybenzoate induced activation of another extradiol cleavage pathway, the protocatechuate 4,5-dioxygenase pathway, that originated from chromosomal genes. These results suggest that N. pentaromativorans US6-1 utilizes two different extradiol pathways and plasmid pLA1 might play a key role in the biodegradation of PAH in N. pentaromativorans US6-1.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24608660</pmid><doi>10.1371/journal.pone.0090812</doi><tpages>e90812</tpages><oa>free_for_read</oa></addata></record>
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identifier ISSN: 1932-6203
ispartof PloS one, 2014-03, Vol.9 (6), p.e90812
issn 1932-6203
1932-6203
language eng
recordid cdi_plos_journals_1504977652
source PubMed (Medline); Publicly Available Content Database
subjects Bacteria
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biodegradation
Biodegradation, Environmental
Biology
Biphenyl
Biphenyl (Compound)
Biphenyl-2,3-diol 1,2-dioxygenase
Catechin
Catechol
Catechol 2,3-dioxygenase
Cleavage
Cluster Analysis
Comparative analysis
Enzymes
Gene Expression Regulation, Bacterial
Genes
Genomes
Genomics
Hydrocarbon-degrading bacteria
Life sciences
Mycobacterium
Novosphingobium
Novosphingobium pentaromativorans
Nucleotide sequence
Peptides
Phenanthrene
Plasmids
Plasmids - genetics
Polycyclic aromatic hydrocarbons
Polycyclic Aromatic Hydrocarbons - metabolism
Proteins
Proteome - genetics
Proteome - metabolism
Proteomics
Protocatechuate 4,5-dioxygenase
Pseudomonas putida
Sphingomonadaceae - genetics
Sphingomonadaceae - metabolism
Sphingomonas
Streptococcus infections
Transcriptional Activation
title Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1
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