scholarly journals Transcriptomic Assessment of Isozymes in the Biphenyl Pathway of Rhodococcus sp. Strain RHA1

2006 ◽  
Vol 72 (9) ◽  
pp. 6183-6193 ◽  
Author(s):  
Edmilson R. Gon�alves ◽  
Hirofumi Hara ◽  
Daisuke Miyazawa ◽  
Julian E. Davies ◽  
Lindsay D. Eltis ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Aromatic Compounds ◽  
Regulatory Mechanism ◽  
Sequence Analyses ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Pcr Assays ◽  
Alkyl Benzenes ◽  
Rhodococcus Sp

ABSTRACT Rhodococcus sp. RHA1 grows on a broad range of aromatic compounds and vigorously degrades polychlorinated biphenyls (PCBs). Previous work identified RHA1 genes encoding multiple isozymes for most of the seven steps of the biphenyl (BPH) pathway, provided evidence for coexpression of some of these isozymes, and indicated the involvement of some of these enzymes in the degradation of BPH, ethylbenzene (ETB), and PCBs. To investigate the expression of these isozymes and better understand how they contribute to the robust degradative capacity of RHA1, we comprehensively analyzed the 9.7-Mb genome of RHA1 for BPH pathway genes and characterized the transcriptome of RHA1 growing on benzoate (BEN), BPH, and ETB. Sequence analyses revealed 54 potential BPH pathway genes, including 28 not previously reported. Transcriptomic analysis with a DNA microarray containing 70-mer probes for 8,213 RHA1 genes revealed a suite of 320 genes of diverse functions that were upregulated during growth both on BPH and on ETB, relative to growth on the control substrate, pyruvate. By contrast, only 65 genes were upregulated during growth on BEN. Quantitative PCR assays confirmed microarray results for selected genes and indicated that some of the catabolic genes were upregulated over 10,000-fold. Our analysis suggests that up to 22 enzymes, including 8 newly identified ones, may function in the BPH pathway of RHA1. The relative expression levels of catabolic genes did not differ for BPH and ETB, suggesting a common regulatory mechanism. This study delineated a suite of catabolic enzymes for biphenyl and alkyl-benzenes in RHA1, which is larger than previously recognized and which may serve as a model for catabolism in other environmentally important bacteria having large genomes.

scholarly journals Transcriptomic Analysis Reveals a Bifurcated Terephthalate Degradation Pathway in Rhodococcus sp. Strain RHA1

2006 ◽  
Vol 189 (5) ◽  
pp. 1641-1647 ◽  
Author(s):  
Hirofumi Hara ◽  
Lindsay D. Eltis ◽  
Julian E. Davies ◽  
William W. Mohn
Keyword(s):  
Aromatic Compounds ◽  
Degradation Pathway ◽  
Transcriptomic Analysis ◽  
Ring Cleavage ◽  
Wide Range ◽  
Genes Encoding ◽  
Catechol 1,2 Dioxygenase ◽  
Rhodococcus Sp ◽  
Dioxygenase Activity ◽  
In Cells

ABSTRACT Phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. Rhodococcus sp. strain RHA1 is notable for its ability to degrade a wide range of aromatic compounds. RHA1 was previously shown to degrade phthalate (PTH) and to have genes putatively encoding terephthalate (TPA) degradation. Transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on PTH and that 521 were up-regulated during growth on TPA. Distinct ring cleavage dioxygenase systems were differentially expressed during growth on PTH and TPA. Genes encoding the protocatechuate (PCA) pathway were induced on both substrates, while genes encoding the catechol branch of the PCA pathway were additionally induced only on TPA. Accordingly, protocatechuate-3,4-dioxygenase activity was induced in cells grown on both substrates, while catechol-1,2-dioxygenase activity was induced only in cells grown on TPA. Knockout analysis indicated that pcaL, encoding 3-oxoadipate enol-lactone hydrolase and 4-carboxymuconolactone decarboxylase, was required for growth on both substrates but that pcaB, encoding β-carboxy-cis,cis-muconate lactonizing enzyme, was required for growth on PTH only. These results indicate that PTH is degraded solely via the PCA pathway, whereas TPA is degraded via a bifurcated pathway that additionally includes the catechol branch of the PCA pathway.

scholarly journals Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

2021 ◽  
Author(s):  
Junhui Li ◽  
Chongjian Jia ◽  
Qihong Lu ◽  
Bruce A Hungate ◽  
Paul Dijkstra ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Contaminated Soils ◽  
Microbial Processes ◽  
Positive Interactions ◽  
Ecological Strategies ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Micro Organisms ◽  
Xenobiotic Biodegradation

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely co-drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

scholarly journals Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Vikas D. Trivedi ◽  
Pramod Kumar Jangir ◽  
Rakesh Sharma ◽  
Prashant S. Phale
Keyword(s):  
Draft Genome ◽  
Degradation Pathway ◽  
Evolutionary Analysis ◽  
Extradiol Dioxygenase ◽  
Transfer Event ◽  
New Family ◽  
New Genes ◽  
Catabolic Genes ◽  
Soil Isolate ◽  
Genes Encoding

Abstract Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, ‘upper’, ‘middle’ and ‘lower’. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The ‘upper’ pathway genes were present as a part of a integron while the ‘middle’ and ‘lower’ pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.

scholarly journals Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. Strain Mel

2011 ◽  
Vol 78 (5) ◽  
pp. 1397-1403 ◽  
Author(s):  
Anthony G. Dodge ◽  
Lawrence P. Wackett ◽  
Michael J. Sadowsky
Keyword(s):  
454 Pyrosequencing ◽  
Minimal Medium ◽  
Doubling Time ◽  
Cyanuric Acid ◽  
Acid Hydrolase ◽  
Content Type ◽  
N Source ◽  
Genes Encoding ◽  
Rhodococcus Sp ◽  
Roche 454

ABSTRACTRhodococcussp. strain Mel was isolated from soil by enrichment and grew in minimal medium with melamine as the sole N source with a doubling time of 3.5 h. Stoichiometry studies showed that all six nitrogen atoms of melamine were assimilated. The genome was sequenced by Roche 454 pyrosequencing to 13× coverage, and a 22.3-kb DNA region was found to contain a homolog to the melamine deaminase genetrzA. Mutagenesis studies showed that the cyanuric acid hydrolase and biuret hydrolase genes were clustered together on a different 17.9-kb contig. Curing and gene transfer studies indicated that 4 of 6 genes required for the complete degradation of melamine were located on an ∼265-kb self-transmissible linear plasmid (pMel2), but this plasmid was not required for ammeline deamination. TheRhodococcussp. strain Mel melamine metabolic pathway genes were located in at least three noncontiguous regions of the genome, and the plasmid-borne genes encoding enzymes for melamine metabolism were likely recently acquired.

Genomic analysis of Rhodococcus sp. BH4 reveals two genes encoding different types of AHL-lactonase for quorum quenching

2018 ◽  
Vol 44 ◽  
pp. S77-S78
Author(s):  
D.H. Ryu ◽  
S.W. Lee ◽  
S.J. Lee ◽  
H. Jeong ◽  
C.H. Lee ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Quorum Quenching ◽  
Different Types ◽  
Genes Encoding ◽  
Rhodococcus Sp

Transcriptomic and metabolomic profiling reveals the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings

2020 ◽  
Author(s):  
Dejin Xie ◽  
Lingyan Chen ◽  
Chengcheng Zhou ◽  
Muhammad Waqqas Khan Tarin ◽  
Deming Yang ◽  
...  
Keyword(s):  
Leaf Area ◽  
Regulatory Mechanism ◽  
Substantial Reduction ◽  
Leaf Tissue ◽  
Influential Factor ◽  
Led Light ◽  
Metabolomic Profiling ◽  
Red Led ◽  
Genes Encoding ◽  
The Impact

Abstract Background: Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Light is one of the most influential factor affecting the growth and quality of herbs. In recent times, the introduction of Light Emission Diode (LED) technology has been widely used for plants in greenhouse. However, the impact of such lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds in S. glabra remain unclear. Results: The red LED light (RL) substantially increased the plant height and decreased the stem diameter and leaf area relative to the white LED light (WL), while the blue LED light (BL) significantly reduced the height and leaf area of S. glabra. According to transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs. leaf tissue under RL (RY), BY vs. leaf tissue under WL (WY), RY vs. WY, root tissue under WL (WG) vs. WY, stem tissue under WL (WJ) vs. WG, and WJ vs. WY, respectively. We identified 46 genes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and flavonol synthase (FLS). We found 53 genes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. A total of 454 metabolites were identified based on metabolomic profiling, of which 44, 87, and 296 compounds were differentially produced in WY vs. RY, WY vs. BY, and WY vs. WG. In BY there was a substantial reduction in the production of esculetin, caffeic acid, isofraxidin, and fraxidin, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol decreased significantly. Besides, in WG, the production of metabolites (e.g. chlorogenic acid, cryptochlorogenic acid, and scopolin) declined, while their yields increased significantly (e.g. esculetin, fraxetin, isofraxidin, and fraxidin).Conclusion: These results provide further insight into the regulatory mechanism of accumulation patterns of phenylpropanoid-derived compounds in S. glabra under various light conditions, allowing optimum breeding conditions to be developed for this plant.

scholarly journals DNA Microarray Assessment of Putative Borrelia burgdorferi Lipoprotein Genes

2002 ◽  
Vol 70 (6) ◽  
pp. 3300-3303 ◽  
Author(s):  
Fang Ting Liang ◽  
F. Kenneth Nelson ◽  
Erol Fikrig
Keyword(s):  
Lyme Disease ◽  
Borrelia Burgdorferi ◽  
Dna Microarray ◽  
Sensu Stricto ◽  
Borrelia Garinii ◽  
Borrelia Afzelii ◽  
Genes Encoding ◽  
The Individual

ABSTRACT A DNA microarray containing fragments of 137 Borrelia burgdorferi B31 putative lipoprotein genes was used to examine Lyme disease spirochetes. DNA from B. burgdorferi sensu stricto B31, 297, and N40; Borrelia garinii IP90; and Borrelia afzelii P/Gau was fluorescently labeled and hybridized to the microarray, demonstrating the degree to which the individual putative lipoprotein genes were conserved among the genospecies. These data show that a DNA microarray can globally examine the genes encoding B. burgdorferi lipoproteins.

scholarly journals Regulation of freA, acoA, lysF, and cycA Expression by Iron Availability in Aspergillus nidulans

2002 ◽  
Vol 68 (11) ◽  
pp. 5769-5772 ◽  
Author(s):  
Harald Oberegger ◽  
Michelle Schoeser ◽  
Ivo Zadra ◽  
Markus Schrettl ◽  
Walther Parson ◽  
...  
Keyword(s):  
Aspergillus Nidulans ◽  
Iron Homeostasis ◽  
Regulatory Mechanism ◽  
Growth Conditions ◽  
Iron Limitation ◽  
Transcriptional Level ◽  
Iron Availability ◽  
Gata Factor ◽  
Genes Encoding ◽  
Encoding Gene

ABSTRACT In the filamentous fungus Aspergillus nidulans, iron homeostasis is regulated at the transcriptional level by the negative-acting GATA factor SREA. In this study the expression of a putative heme-containing metalloreductase-encoding gene, freA, was found to be upregulated by iron limitation independently of SREA, demonstrating the existence of an iron-regulatory mechanism which does not involve SREA. In contrast to freA, various other genes encoding proteins in need of iron-containing cofactors—acoA, lysF, and cycA—were downregulated in response to iron depletion. Remarkably, SREA deficiency led to increased expression of acoA, lysF, and cycA under iron-replete growth conditions.

scholarly journals Expression Patterns of Convergently Overlapping Arabidopsis Thaliana Gene Pairs OHP-NDP1 and OHP2-MES14

2014 ◽  
Vol 56 (1) ◽  
pp. 80-89 ◽  
Author(s):  
Karol Stawski ◽  
Mariusz Banach ◽  
Anna Goc
Keyword(s):  
Regulatory Mechanism ◽  
Expression Patterns ◽  
Transcript Level ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Gene Pairs ◽  
Etiolated Seedlings ◽  
Genes Encoding ◽  
Prolonged Heat ◽  
Prolonged Heat Treatment

Abstract The function of one-helix proteins (OHPs) in the thylakoid membrane remains poorly understood but may be linked to plant photosystem protection. In Arabidopsis, the 3'UTRs of the genes encoding OHP and OHP2 partially overlap with NDP1 and MES14 respectively. Antisense orientation of genes has the potential to form double-stranded transcript (dsRNA) molecules which can be processed to siRNA and trigger RNA interference (RNAi). Natural siRNAs are induced by abiotic and biotic stresses. We examined whether the expression of the OHP-NDP1 and OHP2-MES14 gene pairs is regulated in this way. Both OHP genes, but neither NDP1 nor MES14, were activated by light in etiolated seedlings, whereas cold and prolonged heat treatment elevated the OHP transcript level. Expression of OHP2 was down-regulated after 2 h of osmotic and heat stress, while salt and osmotic stress increased MES14 transcript levels. No inverse regulation of these overlapping gene pairs was observed, excluding RNAi as a regulatory mechanism in the tested conditions. The presence of alternatively polyadenylat-ed transcripts of the studied genes raises the possibility of another regulatory mechanism of 3'UTR overlap.

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