Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain

Procópio, Luciano; Silva, Michele de Cássia Pereira e; Elsas, Jan Dirk van; Seldin, Lucy

doi:10.1590/s1517-83822013000200044

Cited by 19 publications

(10 citation statements)

References 45 publications

(64 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…(Cappelletti et al 2011) and transcript analysis in Dietzia sp. (Procopio et al 2013), as well. Our results serve as novel, additional, indirect proof for the role of this TetR-type protein in the transcriptional control of genes related to hydrocarbon catabolism.…”

Section: Discussionmentioning

confidence: 92%

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Laczi

Kis

Horváth

et al. 2015

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

Rhodococcus erythropolis PR4 is able to degrade diesel oil, normal-, iso-and cycloparaffins and aromatic compounds. The complete DNA content of the strain was previously sequenced and numerous oxygenase genes were identified. In order to identify the key elements participating in biodegradation of various hydrocarbons, we performed a comparative whole transcriptome analysis of cells grown on hexadecane, diesel oil and acetate. The transcriptomic data for the most prominent genes were validated by RT-qPCR. The expression of two genes coding for alkane-1-monooxygenase enzymes was highly upregulated in the presence of hydrocarbon substrates. The transcription of eight phylogenetically diverse cytochrome P450 (cyp) genes was upregulated in the presence of diesel oil. The transcript levels of various oxygenase genes were determined in cells grown in an artificial mixture, containing hexadecane, cycloparaffin and aromatic compounds and six cyp genes were induced by this hydrocarbon mixture. Five of them were not upregulated by linear and branched hydrocarbons. The expression of fatty acid synthase I genes was downregulated by hydrocarbon substrates, indicating the utilization of external alkanes for fatty acid synthesis. Moreover, the transcription of genes involved in siderophore synthesis, iron transport and exopolysaccharide biosynthesis was also upregulated, indicating their important role in hydrocarbon metabolism. Based on the results, complex metabolic response profiles were established for cells grown on various hydrocarbons. Our results represent a functional annotation of a rhodococcal genome, provide deeper insight into molecular events in diesel/hydrocarbon utilization and suggest novel target genes for environmental monitoring projects.

show abstract

Section: Discussionmentioning

confidence: 92%

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Laczi

Kis

Horváth

et al. 2015

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

show abstract

“…The M. vanbaalenii PYR-1 genome has two genes encoding a membrane-bound AlkB alkane monooxygenase (Mvan_1742 and Mvan_3100), and our proteome analysis confirmed that only one AlkB alkane monooxygenase (Mvan_1742) was upregulated. The gene encoding this monooxygenase enzyme (Mvan_1742) constitutes an alkB gene cluster with other genes, including two rubredoxins (Mvan_1743 and Mvan_1744) and a TetR-type transcriptional regulator, AlkU (Mvan_1745), which is known to activate expression of alkB (49,50). As shown in Data Set S3 in the supplemental material, all the proteins in this gene cluster were upregulated together, suggesting their functional interaction for alkane hydroxylation.…”

Section: Resultsmentioning

confidence: 97%

Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil

Kim

Kweon

Sutherland

et al. 2015

Appl Environ Microbiol

View full text Add to dashboard Cite

We investigated the response of the hydrocarbon-degrading Mycobacterium vanbaalenii PYR-1 to crude oil from the BP Deepwater Horizon (DWH) spill, using substrate depletion, genomic, and proteome analyses. M. vanbaalenii PYR-1 cultures were incubated with BP DWH crude oil, and proteomes and degradation of alkanes and polycyclic aromatic hydrocarbons (PAHs) were analyzed at four time points over 30 days. Gas chromatography-mass spectrometry (GC-MS) analysis showed a chain length-dependent pattern of alkane degradation, with C 12 and C 13 being degraded at the highest rate, although alkanes up to C 28 were degraded. Whereas phenanthrene and pyrene were completely degraded, a significantly smaller amount of fluoranthene was degraded. Proteome analysis identified 3,948 proteins, with 876 and 1,859 proteins up-and downregulated, respectively. We observed dynamic changes in protein expression during BP crude oil incubation, including transcriptional factors and transporters potentially involved in adaptation to crude oil. The proteome also provided a molecular basis for the metabolism of the aliphatic and aromatic hydrocarbon components in the BP DWH crude oil, which included upregulation of AlkB alkane hydroxylase and an expression pattern of PAH-metabolizing enzymes different from those in previous proteome expression studies of strain PYR-1 incubated with pure or mixed PAHs, particularly the ring-hydroxylating oxygenase (RHO) responsible for the initial oxidation of aromatic hydrocarbons. Based on these results, a comprehensive cellular response of M. vanbaalenii PYR-1 to BP crude oil was proposed. This study increases our fundamental understanding of the impact of crude oil on the cellular response of bacteria and provides data needed for development of practical bioremediation applications.

show abstract

“…Members of Dietzia and Rhodococcus obtained their competitive advantages along with a decrease in short‐chain alkanes and an increase in oxygen concentration in the artificial ecosystem model due to aeration and agitation, which is not beneficial to the growth of members of Marinobacter (Klein et al ., ; Grimaud et al ., ). Although the Dietzia alk B genotype became the dominant ADB in the early chemostat cultivation stage due to its high relative abundance in oil‐well products, the longer generation time of members of Dietzia predestinated their failure in competition with members of Rhodococcus (Koerner et al ., ; Solyanikova et al ., ; Solyanikova and Golovleva, ; Wang et al ., ; Procópio et al ., ). In addition, the constant biodegradability under nutrient starvation conditions and active membrane transport systems enable members of Rhodococcus to outcompete other ADB (De Carvalho et al ., ).…”

Section: Discussionmentioning

confidence: 97%

The relative abundance of alkane‐degrading bacteria oscillated similarly to a sinusoidal curve in an artificial ecosystem model from oil‐well products

Gao

Zhi

et al. 2018

Environmental Microbiology

View full text Add to dashboard Cite

Microbial phylogenetic diversity and species interactions in natural ecosystems have been investigated extensively, but our knowledge about their ecological roles, community dynamics and succession patterns is far from complete. This knowledge is essential to understand the complicated interactions of microorganisms in natural ecosystems. Here, an artificial ecosystem model of microorganisms was constructed from oil-well products and cultivated in a chemostat to investigate the succession pattern of alkane-degrading bacteria, a functional population in oil reservoirs. Their abundance was quantified by an improved qPCR technique. Our results showed that the phylogenetic structure of this artificial ecosystem model is stable during most of the chemostat cultivation process, while the genotype structure of alkane-degrading bacteria containing alkB genes shifted and their relative abundance oscillated similarly to a sinusoidal curve, like the succession pattern of producers in the Lotka-Volterra model. These results suggest that some theoretical frameworks of macroecology may work well in microbial ecosystems and be an efficient tool to understand them.

show abstract

Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain

Cited by 19 publications

References 45 publications

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil

The relative abundance of alkane‐degrading bacteria oscillated similarly to a sinusoidal curve in an artificial ecosystem model from oil‐well products

Contact Info

Product

Resources

About