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 Vanillin Catabolism in Rhodococcus jostii RHA1

2011 ◽  
Vol 78 (2) ◽  
pp. 586-588 ◽  
Author(s):  
Hao-Ping Chen ◽  
Mindy Chow ◽  
Chi-Chun Liu ◽  
Alice Lau ◽  
Jie Liu ◽  
...  
Keyword(s):  
Enzyme Activities ◽  
Gene Disruption ◽  
Lignin Degradation ◽  
Content Type ◽  
Genes Encoding ◽  
Rhodococcus Jostii Rha1 ◽  
Rhodococcus Jostii

ABSTRACTGenes encoding vanillin dehydrogenase (vdh) and vanillateO-demethylase (vanAB) were identified inRhodococcus jostiiRHA1 using gene disruption and enzyme activities. During growth on vanillin or vanillate,vanAwas highly upregulated whilevdhwas not. This study contributes to our understanding of lignin degradation by RHA1 and other actinomycetes.

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.

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 Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway

2014 ◽  
Vol 80 (11) ◽  
pp. 3341-3349 ◽  
Author(s):  
Tony Campillo ◽  
Sébastien Renoud ◽  
Isabelle Kerzaon ◽  
Ludovic Vial ◽  
Jessica Baude ◽  
...  
Keyword(s):  
Ferulic Acid ◽  
Protocatechuic Acid ◽  
Coenzyme A ◽  
Degradation Pathway ◽  
Hydroxycinnamic Acid ◽  
Plant Materials ◽  
Toxic Compounds ◽  
Content Type ◽  
Acid Degradation ◽  
Species Specific

ABSTRACTThe soil- and rhizosphere-inhabiting bacteriumAgrobacterium fabrum(genomospecies G8 of theAgrobacterium tumefaciensspecies complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl–CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl–CoA, vanillic acid, and protocatechuic acid. The genesatu1416,atu1417, andatu1420have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genesatu1415andatu1421have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)–CoA β-keto-thiolase, respectively. We thus demonstrated that theA. fabrumhydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transformp-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.

scholarly journals Oxidation of the Cyclic Ethers 1,4-Dioxane and Tetrahydrofuran by a Monooxygenase in Two Pseudonocardia Species

2013 ◽  
Vol 79 (24) ◽  
pp. 7702-7708 ◽  
Author(s):  
Christopher M. Sales ◽  
Ariel Grostern ◽  
Juanito V. Parales ◽  
Rebecca E. Parales ◽  
Lisa Alvarez-Cohen
Keyword(s):  
Gene Cluster ◽  
Transcriptional Analysis ◽  
Energy Sources ◽  
Cyclic Ethers ◽  
Oxidation Activity ◽  
Content Type ◽  
Dead End ◽  
Rhodococcus Jostii

ABSTRACTThe bacteriumPseudonocardia dioxanivoransCB1190 grows on the cyclic ethers 1,4-dioxane (dioxane) and tetrahydrofuran (THF) as sole carbon and energy sources. Prior transcriptional studies indicated that an annotated THF monooxygenase (THF MO) gene cluster,thmADBC, located on a plasmid in CB1190 is upregulated during growth on dioxane. In this work, transcriptional analysis demonstrates that upregulation ofthmADBCoccurs during growth on the dioxane metabolite β-hydroxyethoxyacetic acid (HEAA) and on THF. Comparison of the transcriptomes of CB1190 grown on THF and succinate (an intermediate of THF degradation) permitted the identification of other genes involved in THF metabolism. Dioxane and THF oxidation activity of the THF MO was verified inRhodococcus jostiiRHA1 cells heterologously expressing the CB1190thmADBCgene cluster. Interestingly, thesethmADBCexpression clones accumulated HEAA as a dead-end product of dioxane transformation, indicating that despite its genes being transcriptionally upregulated during growth on HEAA, the THF MO enzyme is not responsible for degradation of HEAA in CB1190. Similar activities were also observed in RHA1 cells heterologously expressing thethmADBCgene cluster fromPseudonocardia tetrahydrofuranoxydansK1.

scholarly journals Selection for Growth on 3-Nitrotoluene by 2-Nitrotoluene-Utilizing Acidovorax sp. Strain JS42 Identifies Nitroarene Dioxygenases with Altered Specificities

2014 ◽  
Vol 81 (1) ◽  
pp. 309-319 ◽  
Author(s):  
Kristina M. Mahan ◽  
Joseph T. Penrod ◽  
Kou-San Ju ◽  
Natascia Al Kass ◽  
Watumesa A. Tan ◽  
...  
Keyword(s):  
Active Site ◽  
Sole Source ◽  
Degradation Pathway ◽  
Short Term ◽  
Gene Encoding ◽  
Α Subunit ◽  
Content Type ◽  
Term Selection ◽  
Genes Encoding ◽  
Related Enzyme

ABSTRACTAcidovoraxsp. strain JS42 uses 2-nitrotoluene as a sole source of carbon and energy. The first enzyme of the degradation pathway, 2-nitrotoluene 2,3-dioxygenase, adds both atoms of molecular oxygen to 2-nitrotoluene, forming nitrite and 3-methylcatechol. All three mononitrotoluene isomers serve as substrates for 2-nitrotoluene dioxygenase, but strain JS42 is unable to grow on 3- or 4-nitrotoluene. Using both long- and short-term selections, we obtained spontaneous mutants of strain JS42 that grew on 3-nitrotoluene. All of the strains obtained by short-term selection had mutations in the gene encoding the α subunit of 2-nitrotoluene dioxygenase that changed isoleucine 204 at the active site to valine. Those strains obtained by long-term selections had mutations that changed the same residue to valine, alanine, or threonine or changed the alanine at position 405, which is just outside the active site, to glycine. All of these changes altered the regiospecificity of the enzymes with 3-nitrotoluene such that 4-methylcatechol was the primary product rather than 3-methylcatechol. Kinetic analyses indicated that the evolved enzymes had enhanced affinities for 3-nitrotoluene and were more catalytically efficient with 3-nitrotoluene than the wild-type enzyme. In contrast, the corresponding amino acid substitutions in the closely related enzyme nitrobenzene 1,2-dioxygenase were detrimental to enzyme activity. When cloned genes encoding the evolved dioxygenases were introduced into a JS42 mutant lacking a functional dioxygenase, the strains acquired the ability to grow on 3-nitrotoluene but with significantly longer doubling times than the evolved strains, suggesting that additional beneficial mutations occurred elsewhere in the genome.

scholarly journals Global Response to Desiccation Stress in the Soil Actinomycete Rhodococcus jostii RHA1

2008 ◽  
Vol 74 (9) ◽  
pp. 2627-2636 ◽  
Author(s):  
Justin C. LeBlanc ◽  
Edmilson R. Gonçalves ◽  
William W. Mohn
Keyword(s):  
Relative Humidity ◽  
Contaminated Soils ◽  
Expression Profiles ◽  
Transcriptional Response ◽  
Stress Protection ◽  
Genes Encoding ◽  
Soil Actinomycete ◽  
Rhodococcus Jostii Rha1 ◽  
Microarray Expression ◽  
Rhodococcus Jostii

ABSTRACT Rhodococcus jostii RHA1 is a soil-residing actinomycete with many favorable metabolic capabilities that make it an ideal candidate for the bioremediation of contaminated soils. Arguably the most basic requirement for life is water, yet some nonsporulating bacteria, like RHA1, can survive lengthy droughts. Here we report the first transcriptomic analysis of a gram-positive bacterium during desiccation. Filtered RHA1 cells incubated at either low relative humidity (20%), as an air-drying treatment, or high relative humidity (100%), as a control, were transcriptionally profiled over a comprehensive time series. Also, the morphology of RHA1 cells was characterized by cryofixation scanning electron microscopy during each treatment. Desiccation resulted in a transcriptional response of approximately 8 times more differentially regulated genes than in the control (819 versus 106 genes, respectively). Genes that were differentially expressed during only the desiccation treatment primarily had expression profiles that were maximally up-regulated upon complete drying of the cells. The microarray expression ratios for some of the highly up-regulated genes were verified by reverse transcriptase quantitative PCR. These genes included dps1, encoding an oxidative stress protection protein which has not previously been directly associated with desiccation, and the two genes encoding sigma factors SigF1 and SigF3, possibly involved in the regulatory response to desiccation. RHA1 cells also induced the biosynthetic pathway for the compatible solute ectoine. These desiccation-specific responses represent the best candidates for important mechanisms of desiccation resistance in RHA1.

scholarly journals Malic Enzyme and Malolactic Enzyme Pathways Are Functionally Linked but Independently Regulated in Lactobacillus casei BL23

2013 ◽  
Vol 79 (18) ◽  
pp. 5509-5518 ◽  
Author(s):  
José María Landete ◽  
Sergi Ferrer ◽  
Vicente Monedero ◽  
Manuel Zúñiga
Keyword(s):  
Carbon Source ◽  
Gene Cluster ◽  
Malic Enzyme ◽  
Lactobacillus Casei ◽  
Growth Defect ◽  
Two Component System ◽  
Content Type ◽  
Malolactic Enzyme ◽  
Genes Encoding ◽  
Malate Metabolism

ABSTRACTLactobacillus caseiis the only lactic acid bacterium in which two pathways forl-malate degradation have been described: the malolactic enzyme (MLE) and the malic enzyme (ME) pathways. Whereas the ME pathway enablesL. caseito grow onl-malate, MLE does not support growth. Themlegene cluster consists of three genes encoding MLE (mleS), the putativel-malate transporter MleT, and the putative regulator MleR. Themaegene cluster consists of four genes encoding ME (maeE), the putative transporter MaeP, and the two-component system MaeKR. Since both pathways compete for the same substrate, we sought to determine whether they are coordinately regulated and their role inl-malate utilization as a carbon source. Transcriptional analyses revealed that themleandmaegenes are independently regulated and showed that MleR acts as an activator and requires internalization ofl-malate to induce the expression ofmlegenes. Notwithstanding, bothl-malate transporters were required for maximall-malate uptake, although only anmleTmutation caused a growth defect onl-malate, indicating its crucial role inl-malate metabolism. However, inactivation of MLE resulted in higher growth rates and higher final optical densities onl-malate. The limited growth onl-malate of the wild-type strain was correlated to a rapid degradation of the availablel-malate tol-lactate, which cannot be further metabolized. Taken together, our results indicate thatL. caseil-malate metabolism is not optimized for utilization ofl-malate as a carbon source but for deacidification of the medium by conversion ofl-malate intol-lactate via MLE.

scholarly journals Ethylene Glycol Metabolism in the Acetogen Acetobacterium woodii

2016 ◽  
Vol 198 (7) ◽  
pp. 1058-1065 ◽  
Author(s):  
Dragan Trifunović ◽  
Kai Schuchmann ◽  
Volker Müller
Keyword(s):  
Ethylene Glycol ◽  
Gene Cluster ◽  
Dual Function ◽  
Acetobacterium Woodii ◽  
Acetyl Coa ◽  
Terminal Electron Acceptor ◽  
Content Type ◽  
Bacterial Microcompartments ◽  
Genes Encoding ◽  
Acetogenic Bacterium

ABSTRACTThe acetogenic bacteriumAcetobacterium woodiiis able to grow by the oxidation of diols, such as 1,2-propanediol, 2,3-butanediol, or ethylene glycol. Recent analyses demonstrated fundamentally different ways for oxidation of 1,2-propanediol and 2,3-butanediol. Here, we analyzed the metabolism of ethylene glycol. Our data demonstrate that ethylene glycol is dehydrated to acetaldehyde, which is then disproportionated to ethanol and acetyl coenzyme A (acetyl-CoA). The latter is further converted to acetate, and this pathway is coupled to ATP formation by substrate-level phosphorylation. Apparently, the product ethanol is in part further oxidized and the reducing equivalents are recycled by reduction of CO2to acetate in the Wood-Ljungdahl pathway. Biochemical data as well as the results of protein synthesis analysis are consistent with the hypothesis that the propane diol dehydratase (PduCDE) and CoA-dependent propionaldehyde dehydrogenase (PduP) proteins, encoded by thepdugene cluster, also catalyze ethylene glycol dehydration to acetaldehyde and its CoA-dependent oxidation to acetyl-CoA. Moreover, genes encoding bacterial microcompartments as part of thepdugene cluster are also expressed during growth on ethylene glycol, arguing for a dual function of the Pdu microcompartment system.IMPORTANCEAcetogenic bacteria are characterized by their ability to use CO2as a terminal electron acceptor by a specific pathway, the Wood-Ljungdahl pathway, enabling in most acetogens chemolithoautotrophic growth with H2and CO2. However, acetogens are very versatile and can use a wide variety of different substrates for growth. Here we report on the elucidation of the pathway for utilization of ethylene glycol by the model acetogenAcetobacterium woodii. This diol is degraded by dehydration to acetaldehyde followed by a disproportionation to acetate and ethanol. We present evidence that this pathway is catalyzed by the same enzyme system recently described for the utilization of 1,2-propanediol. The enzymes for ethylene glycol utilization seem to be encapsulated in protein compartments, known as bacterial microcompartments.

scholarly journals Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Erik Borchert ◽  
Antonio García-Moyano ◽  
Sergio Sanchez-Carrillo ◽  
Thomas G. Dahlgren ◽  
Beate M. Slaby ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Marine Environment ◽  
Field Experiments ◽  
Bone Matrix ◽  
Taxonomic Diversity ◽  
Bone Surface ◽  
Metagenomic Sequence ◽  
Content Type ◽  
Bone Degradation ◽  
Genes Encoding

ABSTRACT The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia. IMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.

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