PMID- 23825601
OWN - NLM
STAT- MEDLINE
DCOM- 20140207
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 8
IP  - 6
DP  - 2013
TI  - Genome analysis and physiological comparison of Alicycliphilus denitrificans 
      strains BC and K601(T.).
PG  - e66971
LID - 10.1371/journal.pone.0066971 [doi]
LID - e66971
AB  - The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and 
      K601(T) have been sequenced to get insight into the physiology of the two 
      strains. Strain BC degrades benzene with chlorate as electron acceptor. The 
      cyclohexanol-degrading denitrifying strain K601(T) is not able to use chlorate as 
      electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA 
      sequences of strains BC and K601(T) are identical and the fatty acid methyl ester 
      patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) 
      analysis of predicted open reading frames of both strains showed most hits with 
      Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes 
      include strain-specific plasmids (pAlide201 in strain K601(T) and pAlide01 and 
      pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located 
      on a 120 kb megaplasmid (pAlide01), which was absent in strain K601(T). Genes 
      involved in cyclohexanol degradation were only found in strain K601(T). Benzene 
      and toluene are degraded via oxygenase-mediated pathways in both strains. Genes 
      involved in the meta-cleavage pathway of catechol are present in the genomes of 
      both strains. Strain BC also contains all genes of the ortho-cleavage pathway. 
      The large number of mono- and dioxygenase genes in the genomes suggests that the 
      two strains have a broader substrate range than known thus far.
FAU - Oosterkamp, Margreet J
AU  - Oosterkamp MJ
AD  - Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
FAU - Veuskens, Teun
AU  - Veuskens T
FAU - Talarico Saia, Flavia
AU  - Talarico Saia F
FAU - Weelink, Sander A B
AU  - Weelink SA
FAU - Goodwin, Lynne A
AU  - Goodwin LA
FAU - Daligault, Hajnalka E
AU  - Daligault HE
FAU - Bruce, David C
AU  - Bruce DC
FAU - Detter, John C
AU  - Detter JC
FAU - Tapia, Roxanne
AU  - Tapia R
FAU - Han, Cliff S
AU  - Han CS
FAU - Land, Miriam L
AU  - Land ML
FAU - Hauser, Loren J
AU  - Hauser LJ
FAU - Langenhoff, Alette A M
AU  - Langenhoff AA
FAU - Gerritse, Jan
AU  - Gerritse J
FAU - van Berkel, Willem J H
AU  - van Berkel WJ
FAU - Pieper, Dietmar H
AU  - Pieper DH
FAU - Junca, Howard
AU  - Junca H
FAU - Smidt, Hauke
AU  - Smidt H
FAU - Schraa, Gosse
AU  - Schraa G
FAU - Davids, Mark
AU  - Davids M
FAU - Schaap, Peter J
AU  - Schaap PJ
FAU - Plugge, Caroline M
AU  - Plugge CM
FAU - Stams, Alfons J M
AU  - Stams AJ
LA  - eng
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20130625
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Chlorates)
RN  - 0 (Hydrocarbons, Alicyclic)
RN  - 0 (Nitrates)
RN  - S88TT14065 (Oxygen)
SB  - IM
MH  - Base Sequence
MH  - Chlorates/metabolism
MH  - Comamonadaceae/*genetics/metabolism/*physiology
MH  - Genome, Bacterial/genetics
MH  - *Genomics
MH  - Hydrocarbons, Alicyclic/metabolism
MH  - Nitrates/metabolism
MH  - Oxygen/metabolism
MH  - Species Specificity
PMC - PMC3692508
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2013/07/05 06:00
MHDA- 2014/02/08 06:00
PMCR- 2013/06/25
CRDT- 2013/07/05 06:00
PHST- 2013/03/07 00:00 [received]
PHST- 2013/05/14 00:00 [accepted]
PHST- 2013/07/05 06:00 [entrez]
PHST- 2013/07/05 06:00 [pubmed]
PHST- 2014/02/08 06:00 [medline]
PHST- 2013/06/25 00:00 [pmc-release]
AID - PONE-D-13-09945 [pii]
AID - 10.1371/journal.pone.0066971 [doi]
PST - epublish
SO  - PLoS One. 2013 Jun 25;8(6):e66971. doi: 10.1371/journal.pone.0066971. Print 2013.