Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential

Abstract

The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO2 fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-011-9633-7) contains supplementary material, which is available to authorized users.

Regulation of the Alkane Hydroxylase CYP153 Gene in a Gram-Positive Alkane-Degrading Bacterium, Dietzia sp. Strain DQ12-45-1b

“…Sequence analysis revealed a putative AraC family transcriptional-regulator gene located upstream of the CYP153 gene cluster in both Actinobacteria and Proteobacteria, such as in Dietzia (15,18), Rhodococcus (27), Mycobacterium (28), Amycolicicoccus (29), Acinetobacter (13), and Alcanivorax (17,23,30). These findings implied a link between AraC family regulators (AFRs) and CYP153 proteins in bacterial alkane degradation, as reported previously (29).…”

“…Although CYP153 was widely detected in alkane-degrading bacteria lacking AlkB (16), more and more researches revealed its existence in many broad-spectrum alkane-degrading species expressing AlkB, such as Alcanivorax (17), Dietzia (18,19), Rhodococcus (20), and Nocardia (21) species. This wide distribution of the diverse CYP153 genes was attributed to the numerous potential horizontal gene transfer (HGT) events in bacteria containing both alkB and CYP153 genes, particularly in the phylum Actinobacteria (22).…”

Comparison of the Vitek MS and Bruker Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems for Identification of Rhodococcus equi and Dietzia spp

“…This strain was identified as D. cinnamea by 16S rRNA sequencing. D. cinnamea was first isolated from a perianal swab of a patient with a bone marrow transplant (15), but it is mostly known for its ability to degrade a wide variety of organic compounds and rarely for its pathogenic potential (16). The performance of the Biotyper in identification of R. equi, distinguishing it from Dietzia spp., is comparable to the performances of PCR choE and 16S rRNA sequencing.…”

Cloning and expression of a Baeyer–Villiger monooxygenase oxidizing linear aliphatic ketones from Dietzia sp. D5

“…strains are known to have a variety of oxygenases [17][18][19]. This work presents cloning, expression and substrate scope of a BVMO isolated from Dietzia sp.…”