References

Project:

Rhodococcus erythropolis PR4 (= NBRC 100887)

About this genome

*Sequence analysis of three plasmids harboured in Rhodococcus erythropolis* strain PR4.**
Sekine M.,Tanikawa S.,Omata S.,Saito M.,Fujisawa T.,Tsukatani N.,Tajima T.,Sekigawa T.,Kosugi H.,Matsuo Y.,Nishiko R.,Imamura K.,Ito M.,Narita H.,Tago S.,Fujita N.,Harayama S. Environ. Microbiol. 8 (2006) 334-46 [PMID: 16423019] Abstract
Abstract: Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The strain harbours one linear plasmid, pREL1 (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637 bp), all with some sequence similarities to other Rhodococcus plasmids. For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames, respectively, were predicted. Linear plasmid pREL1 has several regions homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis of pREL1 and pBD2 identified common metal-resistance genes on both, but pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme constituents some of which are quite different from those of other organisms. The alkane hydroxylase consisted of a cytochrome P450 monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin reductase) sequence. A zinc-containing alcohol dehydrogenase further oxydizes alkanols, alkane oxidation products catalysed by alkane hydroxylase. Of the circular plasmids, the pREC1 sequence is partially similar to the sequence of pREAT701, the virulence plasmid found in Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded by pREL1 and pREC1 may enable efficient mineralization of alkanes.

Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4.

Sekine M.,Tanikawa S.,Omata S.,Saito M.,Fujisawa T.,Tsukatani N.,Tajima T.,Sekigawa T.,Kosugi H.,Matsuo Y.,Nishiko R.,Imamura K.,Ito M.,Narita H.,Tago S.,Fujita N.,Harayama S.
Environ. Microbiol. 8 (2006) 334-46 [PMID: 16423019] Abstract

Journal

A comparison of various methods to predict bacterial predilection for organic solvents used as reaction media.
Hamada T.,Sameshima Y.,Honda K.,Omasa T.,Kato J.,Ohtake H. J. Biosci. Bioeng. 106 (2008) 357-62 [PMID: 19000611] Abstract
Abstract: Bacterial predilection for organic solvents is important in whole-cell biocatalysis in organic media. Although various methods of measuring bacterial hydrophobicity have been proposed, it is not fully determined whether they are applicable to the assessment of bacterial predilection for organic solvents in whole-cell biocatalytic processes. In this study, bacterial predilection for organic solvents was assessed by bacterial adhesion to hydrocarbon (BATH), contact angle measurement (CAM), hydrophobic interaction chromatography (HIC), and glass adhesion test (GAT). These methods were applied to the cultures of four bacterial species of industrial importance, namely, Rhodococcus opacus B-4, R. erythropolis PR4, Pseudomonas putida T-57, and Escherichia coli JM109, in organic media. Experimental results revealed that CAM assays could be used to predict the dispersibility of bacterial cells in anhydrous organic solvents. However, when bacteria were suspended in aqueous-organic (A/O) two-phase media, the results of BATH assays provided the most reliable assessment of bacterial predilection for organic solvents. This discrepancy noted between CAM and BATH assays was attributed to the effect of electrostatic interaction between bacteria and oil droplets. In A/O two-phase media, the accessibility of a water-immiscible dye, nile red, to the bacterial cell surface, correlated well with BATH assay results.
*Structural analysis of an acidic, fatty acid ester-bonded extracellular polysaccharide produced by a pristane-assimilating marine bacterium, Rhodococcus erythropolis* PR4.**
Urai M.,Yoshizaki H.,Anzai H.,Ogihara J.,Iwabuchi N.,Harayama S.,Sunairi M.,Nakajima M. Carbohydr. Res. 342 (2007) 933-42 [PMID: 17316581] Abstract
Abstract: Rhodococcus erythropolis PR4 is a marine bacterium that can degrade various alkanes including pristane, a C(19) branched alkane. This strain produces a large quantity of extracellular polysaccharides, which are assumed to play an important role in the hydrocarbon tolerance of this bacterium. The strain produced two acidic extracellular polysaccharides, FR1 and FR2, and the latter showed emulsifying activity toward clove oil, whereas the former did not. FR2 was composed of D-galactose, D-glucose, D-mannose, D-glucuronic acid, and pyruvic acid at a molar ratio of 1:1:1:1:1, and contained 2.9% (w/w) stearic acid and 4.3% (w/w) palmitic acid attached via ester bonds. Therefore, we designated FR2 as a PR4 fatty acid-containing extracellular polysaccharide or FACEPS. The chemical structure of the PR4 FACEPS polysaccharide chain was determined by 1D (1)H and (13)C NMR spectroscopies as well as by 2D DQF-COSY, TOCSY, HMQC, HMBC, and NOESY experiments. The sugar chain of PR4 FACEPS was shown to consist of tetrasaccharide repeating units having the following structure: [structure: see text].
*Structural analysis of mucoidan, an acidic extracellular polysaccharide produced by a pristane-assimilating marine bacterium, Rhodococcus erythropolis* PR4.**
Urai M.,Yoshizaki H.,Anzai H.,Ogihara J.,Iwabuchi N.,Harayama S.,Sunairi M.,Nakajima M. Carbohydr. Res. 342 (2007) 927-32 [PMID: 17316584] Abstract
Abstract: Rhodococcus erythropolis PR4 is a marine bacterium that can degrade various alkanes including pristane, a C(19) branched alkane. This strain produces a large quantity of extracellular polysaccharides (EPS), which are assumed to play an important role in the hydrocarbon tolerance of R. erythropolis PR4. The strain produced an acidic EPS, mucoidan, together with a fatty acid-containing EPS, PR4 FACEPS. The chemical structure of the mucoidan was determined using (1)H and (13)C NMR spectroscopy and by conducting 2D DQF-COSY, TOCSY, HMQC, HMBC, and NOESY experiments. The mucoidan was shown to consist of a pentasaccharide repeating unit with the following structure: [structure: see text].
*Characterization of four Rhodococcus* alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols.**
Peng X.,Taki H.,Komukai S.,Sekine M.,Kanoh K.,Kasai H.,Choi SK.,Omata S.,Tanikawa S.,Harayama S.,Misawa N. Appl. Microbiol. Biotechnol. 71 (2006) 824-32 [PMID: 16292529] Abstract
Abstract: Four genes were isolated and characterized for alcohol dehydrogenases (ADHs) catalyzing the oxidation of aromatic alcohols such as benzyl alcohol to their corresponding aldehydes, one from o-xylene-degrading Rhodococcus opacus TKN14 and the other three from n-alkane-degrading Rhodococcus erythropolis PR4. Various aromatic alcohols were bioconverted to their corresponding carboxylic acids using Escherichia coli cells expressing each of the four ADH genes together with an aromatic aldehyde dehydrogenase gene (phnN) from Sphingomonas sp. strain 14DN61. The ADH gene (designated adhA) from strain TKN14 had the ability to biotransform a wide variety of aromatic alcohols, i.e., 2-hydroxymethyl-6-methylnaphthalene, 2-hydroxymethylnaphthalene, xylene-alpha,alpha'-diol, 3-chlorobenzyl alcohol, and vanillyl alcohol, in addition to benzyl alcohol with or without a hydroxyl, methyl, or methoxy substitution. In contrast, the three ADH genes of strain PR4 (designated adhA, adhB, and adhC) exhibited lower ability to degrade these alcohols: these genes stimulated the conversion of the alcohol substrates by only threefold or less of the control value. One exception was the conversion of 3-methoxybenzyl alcohol, which was stimulated sevenfold by adhB. A phylogenetic analysis of the amino acid sequences of these four enzymes indicated that they differed from other Zn-dependent ADHs.
Construction of bacterial consortia that degrade Arabian light crude oil.
Komukai-Nakamura S., Sugiura K., Yamauchi-Inomata Y., Toki H., Venkateswaran K., Yamamoto S., Tanaka H., Harayama H. Abstract
Abstract: Four bacteria capable of degrading certain components of crude oil were examined with respect to their degradation abilities. Acinetobacter sp. T4 and Rhodococcus sp. PR4 could degrade various alkanes, while Pseudomonas putida PB4 was able to degrade benzene and alkylbenzens with a C1 to C4 side chain. Sphingomonas sp. AJ1 has been shown to be capable of degrading naphthalene and phenanthrene. The biodegradation of Arabian light crude oil by a mixed bacterial population constituted of these four bacteria was examined. This population degraded 40% of the saturated fraction and 21% of the aromatic fraction of the crude oil in 10 d, a degree of degradation equivalent to that attained by many microbial consortia specifically enriched for the biodegradation of crude oil. In a mixed culture of the four strains, Acinetobacter sp. T4 and P. putida PB4 grew, but the growth of the other two strains was not significant. A consortium of Acinetobacter sp. T4 and P. putida PB4 exhibited the same degree of biodegradation as that of the mixed population of the four bacteria. In this two-strain consortium, Acinetobacter sp. T4 degraded components in both the saturated and aromatic fractions, and produced metabolites that could support the growth of P. putida PB4. The latter strain grew on these metabolites, and degraded aromatic compounds present in the crude oil.