Genome sequences of triacylglycerol metabolism in Rhodococcus as a platform for comparative genomics

María S Villalba, Martín A Hernández, Roxana A Silva, Héctor M. Alvarez


Bacteria belonging to the Rhodococcus genus are usually able to synthesize and accumulate variable amounts of triacylglycerols (TAG) from diverse carbon sources. Although some significant advances in the basic knowledge on TAG metabolism in rhodococci have been made, the fundamental understanding of this process and its regulation remains to be clarified. The abundantly available genomic information for several rhodococcal species provides the possibility for comparative genome analysis on the occurrence and distribution of key genes and pathways involved in TAG metabolism. Our bioinformatic analyses of available databases from six rhodococcal strains demonstrated that genes/enzymes for reactions related to TAG biosynthesis and degradation, and fatty acid β-oxidation are surprisingly abundant in rhodococcal genomes. Several genes/enzymes of glycerolipids and fatty acid metabolism are highly represented in the analyzed genomes. A number of previously undescribed, new putative genes for glycerolipid metabolism in rhodococci have been identified and the size of each family has been estimated.


Rhodococcus, triacylglycerols, comparative genomics, biosynthesis and degradation genes


Alvarez AF, Alvarez HM, Kalscheuer R, Wältermann M & Steinbüchel A 2008 Cloning and characterization of a gene involved in triacylglycerol biosynthesis and identification of additional homologous genes in the oleaginous bacterium Rhodococcus opacus PD630. Microbiology 154 2327-2335

Alvarez HM 2003 Relationship between b-oxidation pathway and the hydrocarbon-degrading profile in actinomycetes bacteria. Intern Biodeter & Biodeg 52 35- 42

Alvarez HM 2010 Biotechnological production and significance of triacylglycerols and wax esters. In: Kenneth N. Timmis (ed) Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds. Springer Verlag, Heidelberg, Germany, Volume 3 Chapter 44 pp 2995-3002

Alvarez HM, Mayer F, Fabritius D & Steinbüchel A 1996 Formation of intracytoplasmic lipid inclusions by Rhodococcus opacus strain PD630. Arch Microbiol 165 377-386

Alvarez HM, Kalscheuer R & Steinbüchel A 1997 Accumulation of storage lipids in species of Rhodococcus and Nocardia and effect of inhibitors and polyethylene glycol. Fett/Lipid 99 239-246

Alvarez HM, Kalscheuer R & Steinbüchel A 2000 Accumulation and mobilization of storage lipids by Rhodococcus opacus PD630 and Rhodococcus ruber NCIMB 40126. Appl Microbiol Biotechnol 54 218-223

Alvarez HM, Luftmann H, Silva RA, Cesari AC, Viale A, Wältermann M & Steinbüchel A 2002 Identification of phenyldecanoic acid as constituent of triacylglycerols and wax ester produced by Rhodococcus opacus PD630. Microbiology 148 1407-1412

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A & Zagnitko O 2008 The RAST Server: rapid annotations using Subsystems Technology. BMC Genomics 9 75

Bassegoda A, Pastor FI & Diaz P 2012 Rhodococcus sp. strain CR-53 LipR, the first member of a new bacterial lipase family (family X) displaying an unusual Y-type oxyanion hole, similar to the Candida antarctica lipase clan. Appl Environ Microbiol 78 1724-1732

DiRusso CC 1990 Primary sequence of the Escherichia coli fadBA operon, encoding the fatty acid-oxidizing multienzyme complex, indicates a high degree of homology to eucaryotic enzymes. J Bacteriol 172 6459-6468

Felsenstein J 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368-376

Felsenstein J 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783-791

Felsenstein J 1993 Phylip: phylogeny inference package, version 3.67. Seattle: University of Washington

Hernández MA & Alvarez HM 2010 Glycogen formation by Rhodococcus species and effect of inhibition of lipid biosynthesis on glycogen accumulation in R. opacus PD630. FEMS Microbiol Lett 312 93-99

Hernández MA, Arabolaza A, Rodríguez E, Gramajo H & Alvarez HM 2012 The atf2 gene is involved in triacylglycerol biosynthesis and accumulation in the oleaginous Rhodococcus opacus PD630. Appl Microbiol Biotechnol DOI 10.1007/s00253-012-4360-1

Hernández MA, Mohn WW, Martínez E, Rost E, Alvarez AF & Alvarez HM 2008 Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism. BMC Genomics 12 9 600

Holder JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J, Zeng Q, Leach AL, Ghiviriga I, Dancel C, Abeel T, Gevers D, Kodira CD, Desany B, Affourtit JP, Birren BW & Sinskey AJ 2011 Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genet 7 e1002219

Kanehisa M & Goto S 2000 KEGG: Kyoto encyclopedia of genes and genomes. Nucleic acids Research 28 27-30

Kelly BG, Wall DM, Boland CA & Meijer WG 2002 Isocitrate lyase of the facultative intracellular pathogen Rhodococcus equi. Microbiology 148 793-798

Kim HJ, Kim TH, Kim Y, Lee HS 2004 Identification and characterization of glxR, a gene involved in regulation of glyoxylate bypass in Corynebacterium glutamicum. J Bacteriol 186 3453-3460

Kluge AG & Farris FS 1969 Quantitative phyletics and the evolution of the anurans. Syst Zool 18 1-32

Larkin MJ, Kulakov LA & Allen CCR 2005 Biodegradation and Rhodococcus-masters of catabolic versatility. Curr Opin Biotechnol 16 282-290

Letek M, González P, Macarthur I, Rodríguez H, Freeman TC, Valero-Rello A, Blanco M, Buckley T, Cherevach I, Fahey R, Hapeshi A, Holdstock J, Leadon D, Navas J, Ocampo A, Quail MA, Sanders M, Scortti MM, Prescott JF, Fogarty U, Meijer WG, Parkhill J, Bentley SD & Vázquez-Boland JA 2010 The genome of a pathogenic Rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genet 6 e1001145

Low KL, Shui G, Natter K, Yeo WK, Kohlwein SD, Dick T, Rao SP & Wenk MR 2010 Lipid droplet-associated proteins are involved in the biosynthesis and hydrolysis of triacylglycerol in Mycobacterium bovis bacillus Calmette-Guerin. J Biol Chem 285 21662-21670

MacEachran DP, Prophete ME & Sinskey AJ 2010 The Rhodococcus opacus PD630 heparin-binding hemagglutinin homolog TadA mediates lipid body formation. Appl Environ Microbiol 76 7217-7225

Martínková L, Uhnáková B, Pátek M, Nešvera J & Křen V 2009 Biodegradation potential of the genus Rhodococcus. Environ Int 35 162-177

McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW & Eltis LD 2006 The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA 103 15582-15587

Na KS, Nagayasu K, Kuroda A, Takiguchi N, Ikeda T, Ohtake H & Kato J 2005 Development of a genetic transformation system for benzene-tolerant Rhodococcus opacus strains. J Biosc Bioeng 99 408-414

Nicholas KB, Nicholas HB Jr. & Deerfield DW II 1997 GeneDoc: Analysis and visualization of Genetic Variation. EMBNEW.NEWS 4 14- Version 2.7.000

Petersen TN, Brunak S, von Heijne G & Nielsen H 2011 SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods 8 785-786

Ruiz C, Pastor FI & Diaz P 2005 Isolation of lipid- and polysaccharide-degrading micro-organisms from subtropical forest soil, and analysis of lipolytic strain Bacillus sp. CR-179. Lett Appl Microbiol 40 218-227

Saitou N & Nei M 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406-425

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 2006 Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ Microbiol 8 334-346

Silva RA, Grossi V, Olivera N & Alvarez HM 2010 Characterization of the indigenous Rhodococcus sp. 602, a strain able to accumulate triacylglycerides from naphthyl-compounds under nitrogen-starved conditions. Res Microbiol 161 198-207

Taylor RC, Brown AK, Singh A, Bhatt A & Besra GS 2010 Characterization of a β-hydroxybutyryl-CoA dehydrogenase from Mycobacterium tuberculosis. Microbiology 156 1975-1982

Thompson JD, Higgins DG & Gibson TJ 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 4673-4680

Warhurst AM & Fewson CA 1994 Biotransformations catalyzed by the genus Rhodococcus. Crit Rev Biotechnol 14 29-73

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