scholarly journals Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1

2019 ◽  
Vol 7 (11) ◽  
pp. 479 ◽  
Author(s):  
Gibu ◽  
Kasai ◽  
Ikawa ◽  
Akiyama ◽  
Fukuda
Keyword(s):  
Transcriptional Regulation ◽  
Gene Cluster ◽  
Constitutive Expression ◽  
Sole Source ◽  
Degradation Pathway ◽  
Alkane Hydroxylase ◽  
Alkane Degradation ◽  
Putative Promoter Region ◽  
Rhodococcus Jostii Rha1 ◽  
Rhodococcus Jostii

Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway—a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation—was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster.

scholarly journals The Hydroxyquinol Degradation Pathway in Rhodococcus jostii RHA1 and Agrobacterium Species Is an Alternative Pathway for Degradation of Protocatechuic Acid and Lignin Fragments

2020 ◽  
Vol 86 (19) ◽  
Author(s):  
Edward M. Spence ◽  
Heather T. Scott ◽  
Louison Dumond ◽  
Leonides Calvo-Bado ◽  
Sabrina di Monaco ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Protocatechuic Acid ◽  
Alternative Pathway ◽  
Degradation Pathway ◽  
Oxidative Decarboxylation ◽  
Content Type ◽  
Genes Encoding ◽  
Rhodococcus Jostii Rha1 ◽  
Similar Gene ◽  
Rhodococcus Jostii

ABSTRACT Deletion of the pcaHG genes, encoding protocatechuate 3,4-dioxygenase in Rhodococcus jostii RHA1, gives a gene deletion strain still able to grow on protocatechuic acid as the sole carbon source, indicating a second degradation pathway for protocatechuic acid. Metabolite analysis of wild-type R. jostii RHA1 grown on medium containing vanillin or protocatechuic acid indicated the formation of hydroxyquinol (benzene-1,2,4-triol) as a downstream product. Gene cluster ro01857-ro01860 in Rhodococcus jostii RHA1 contains genes encoding hydroxyquinol 1,2-dioxygenase and maleylacetate reductase for degradation of hydroxyquinol but also putative mono-oxygenase (ro01860) and putative decarboxylase (ro01859) genes, and a similar gene cluster is found in the genome of lignin-degrading Agrobacterium species. Recombinant R. jostii mono-oxygenase and decarboxylase enzymes in combination were found to convert protocatechuic acid to hydroxyquinol. Hence, an alternative pathway for degradation of protocatechuic acid via oxidative decarboxylation to hydroxyquinol is proposed. IMPORTANCE There is a well-established paradigm for degradation of protocatechuic acid via the β-ketoadipate pathway in a range of soil bacteria. In this study, we have found the existence of a second pathway for degradation of protocatechuic acid in Rhodococcus jostii RHA1, via hydroxyquinol (benzene-1,2,4-triol), which establishes a metabolic link between protocatechuic acid and hydroxyquinol. The presence of this pathway in a lignin-degrading Agrobacterium sp. strain suggests the involvement of the hydroxyquinol pathway in the metabolism of degraded lignin fragments.

scholarly journals LaoABCR, a Novel System for Oxidation of Long-Chain Alcohols Derived from SDS and Alkane Degradation inPseudomonas aeruginosa

2018 ◽  
Vol 84 (13) ◽  
pp. e00626-18 ◽  
Author(s):  
Gianna Panasia ◽  
Bodo Philipp
Keyword(s):  
Gene Cluster ◽  
Distribution Systems ◽  
Sodium Dodecyl ◽  
Constitutive Expression ◽  
Opportunistic Pathogen ◽  
Alkane Degradation ◽  
Content Type ◽  
Cell Extracts ◽  
Growth Substrates ◽  
Long Chain

ABSTRACTThe opportunistic pathogenPseudomonas aeruginosastrain PAO1 is able to use a variety of organic pollutants as growth substrates, including the anionic detergent sodium dodecyl sulfate (SDS) and long-chain alkanes. While the enzymes initiating SDS and alkane degradation are well known, the subsequent enzymatic steps for degradation of the derived primary long-chain alcohols have not yet been identified. By evaluating genes specifically induced during growth with SDS, a gene cluster encoding a putative alcohol dehydrogenase (PA0364/LaoA), a probable inner membrane protein (PA0365/LaoB), and a presumable aldehyde dehydrogenase (PA0366/LaoC) was identified and designated the Lao (long-chain-alcohol/aldehyde-oxidation) system. Growth experiments with deletion mutants with SDS, 1-dodecanol, and alkanes revealed that LaoA and LaoB are involved in the degradation of primary long-chain alcohols. Moreover, detection of 1-dodecanol oxidation in cell extracts by activity staining revealed an interdependency of LaoA and LaoB for efficient 1-dodecanol oxidation. Anin silicoanalysis yielded no well-characterized homologue proteins for LaoA and LaoB. Furthermore, a gene adjacent to thelaogene cluster encodes a putative transcriptional regulator (PA0367/LaoR). AlaoRdeletion mutant exhibited constitutive expression of LaoA and LaoB, indicating that LaoR is a repressor for the expression oflaoABC. Taken together, these results showed that the proteins LaoA and LaoB constitute a novel oxidation system for long-chain alcohols derived from pollutants.IMPORTANCEThe versatile and highly adaptive bacteriumPseudomonas aeruginosa is able to colonize a variety of habitats, including anthropogenic environments, where it is often challenged with toxic compounds. Its ability to degrade such compounds and to use them as growth substrates can significantly enhance spreading of this opportunistic pathogen in hygienic settings, such as clinics or water distribution systems. Thus, knowledge about the metabolism ofP. aeruginosacan contribute to novel approaches for preventing its growth and reducing nosocomial infections. As the Lao system is important for the degradation of two different classes of pollutants, the identification of these novel enzymes can be a useful contribution for developing effective antibacterial strategies.

scholarly journals Specific Gene Responses of Rhodococcus jostii RHA1 during Growth in Soil

2012 ◽  
Vol 78 (19) ◽  
pp. 6954-6962 ◽  
Author(s):  
Toju Iino ◽  
Yong Wang ◽  
Keisuke Miyauchi ◽  
Daisuke Kasai ◽  
Eiji Masai ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Transcriptome Analysis ◽  
Growth Retardation ◽  
Soil Classification ◽  
Specific Gene ◽  
Content Type ◽  
Rhodococcus Jostii Rha1 ◽  
Nitrite Nitrate ◽  
Nitrate And Nitrite ◽  
Rhodococcus Jostii

ABSTRACTTranscriptome analysis ofRhodococcus jostiiRHA1 during growth in sterilized soil was performed. A total of 165 soil-specific genes were identified by subtracting genes upregulated in late growth phases and on solid medium from 264 genes commonly upregulated during growth on biphenyl or pyruvate in sterilized soil. Classification of the 165 genes into functional categories indicated that this soil-specific group is rich in genes for the metabolism of fatty acids, amino acids, carbohydrates, and nitrogen and relatively poor in those for cellular processes and signaling. The ro06365–ro06369 gene cluster, in which ro06365 to ro06368 were highly upregulated in transcriptome analysis, was characterized further. ro06365 and ro06366 show similarity to a nitrite/nitrate transporter and a nitrite reductase, respectively, suggesting their involvement in nitrogen metabolism. A strain with an ro06366 deletion, D6366, showed growth retardation when we used nitrate as the sole nitrogen source and no growth when we used nitrite. A strain with a deletion of ro06365 to ro06368, DNop, utilized neither nitrite nor nitrate and recovered growth using nitrite and nitrate by introduction of the deleted genes. Both of the mutants showed growth retardation in sterilized soil, and the growth retardation of DNop was more significant than that of D6366. When these mutants were cultivated in medium containing the same proportions of ammonium, nitrate, and nitrite ions as those in the sterilized soil, they showed growth retardation similar to that in the soil. These results suggest that the ro06365–ro06369 gene cluster has a significant role in nitrogen utilization in sterilized soil.

Insight into the sugar transport and metabolism in Biphenyl/PCB degrader, Rhodococcus jostii RHA1

2009 ◽  
Vol 108 ◽  
pp. S93
Author(s):  
Naoto Araki ◽  
Toru Suzuki ◽  
Keisuke Miyauchi ◽  
Daisuke Kasai ◽  
Eiji Masai ◽  
...  
Keyword(s):  
Sugar Transport ◽  
Rhodococcus Jostii Rha1 ◽  
Insight Into ◽  
Rhodococcus Jostii

scholarly journals Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective β-Estradiol-Degrading Bacterium

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Hongyan Zhao ◽  
Kejian Tian ◽  
Qing Qiu ◽  
Yu Wang ◽  
Hongyan Zhang ◽  
...  
Keyword(s):  
Sole Source ◽  
Rhodococcus Opacus ◽  
Whole Genome ◽  
Metabolic Potential ◽  
Protein Coding ◽  
Degrading Enzymes ◽  
Degrading Bacterium ◽  
Rhodococcus Jostii Rha1 ◽  
Multiple Strains ◽  
Rhodococcus Sp

We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4 Mbp with G + C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5.2, 0.09, and 0.09, respectively. The results showed that there were ten steroid-degrading enzymes distributed in the whole genome of the strain. The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. It was found that Rhodococcus DSSKP-R-001 had the highest similarity to Rhodococcus sp. P14 and there were 2070 core genes shared with Rhodococcus sp. P14, Rhodococcus jostii RHA1, Rhodococcus opacus B4, and Rhodococcus equi 103S, showing evolutionary homology. In summary, this study provides a comprehensive understanding of the role of Rhodococcus DSSKP-R-001 in estradiol-efficient degradation of these assays for Rhodococcus. DSSKP-R-001 in bioremediation and evolution within Rhodococcus has important meaning.

scholarly journals Novel Pathway for the Degradation of 2-Chloro-4-Nitrobenzoic Acid by Acinetobacter sp. Strain RKJ12

2011 ◽  
Vol 77 (18) ◽  
pp. 6606-6613 ◽  
Author(s):  
Dhan Prakash ◽  
Ravi Kumar ◽  
R. K. Jain ◽  
B. N. Tiwary
Keyword(s):  
Salicylic Acid ◽  
Tricarboxylic Acid Cycle ◽  
Sole Source ◽  
Degradation Pathway ◽  
Ring Cleavage ◽  
Muconic Acid ◽  
Content Type ◽  
Nitrobenzoic Acid ◽  
Catabolic Genes ◽  
Catechol 1,2 Dioxygenase

ABSTRACTThe organismAcinetobactersp. RKJ12 is capable of utilizing 2-chloro-4-nitrobenzoic acid (2C4NBA) as a sole source of carbon, nitrogen, and energy. In the degradation of 2C4NBA by strain RKJ12, various metabolites were isolated and identified by a combination of chromatographic, spectroscopic, and enzymatic activities, revealing a novel assimilation pathway involving both oxidative and reductive catabolic mechanisms. The metabolism of 2C4NBA was initiated by oxidativeorthodehalogenation, leading to the formation of 2-hydroxy-4-nitrobenzoic acid (2H4NBA), which subsequently was metabolized into 2,4-dihydroxybenzoic acid (2,4-DHBA) by a mono-oxygenase with the concomitant release of chloride and nitrite ions. Stoichiometric analysis indicated the consumption of 1 mol O2per conversion of 2C4NBA to 2,4-DHBA, ruling out the possibility of two oxidative reactions. Experiments with labeled H218O and18O2indicated the involvement of mono-oxygenase-catalyzed initial hydrolytic dechlorination and oxidative denitration mechanisms. The further degradation of 2,4-DHBA then proceeds via reductive dehydroxylation involving the formation of salicylic acid. In the lower pathway, the organism transformed salicylic acid into catechol, which was mineralized by theorthoring cleavage catechol-1,2-dioxygenase tocis, cis-muconic acid, ultimately forming tricarboxylic acid cycle intermediates. Furthermore, the studies carried out on a 2C4NBA−derivative and a 2C4NBA+transconjugant demonstrated that the catabolic genes for the 2C4NBA degradation pathway possibly reside on the ∼55-kb transmissible plasmid present in RKJ12.

scholarly journals Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the ocean

2021 ◽  
Author(s):  
Maria Pinto ◽  
Zihao Zhao ◽  
Katja Klun ◽  
Eugen Libowitzky ◽  
Gerhard J Herndl
Keyword(s):  
Relative Abundance ◽  
Low Density Polyethylene ◽  
Low Density ◽  
Alkane Hydroxylase ◽  
Alkane Degradation ◽  
Electron Microscopic ◽  
Genes Encoding ◽  
Diverse Community ◽  
Metagenomics Analysis ◽  
Over Time

Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analysed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for two years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harboured genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This study identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential of utilizing LDPE-associated compounds as carbon and energy source.

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