scholarly journals Temporal Expression of Respiratory Genes in an Enrichment Culture Containing Dehalococcoides ethenogenes

2006 ◽  
Vol 72 (8) ◽  
pp. 5486-5491 ◽  
Author(s):  
Brian G. Rahm ◽  
Robert M. Morris ◽  
Ruth E. Richardson
Keyword(s):  
Temporal Variability ◽  
Enrichment Culture ◽  
Transcript Level ◽  
Mixed Cultures ◽  
Temporal Expression ◽  
Expression Levels ◽  
Reductive Dehalogenase ◽  
Expression Of Genes ◽  
Dehalococcoides Ethenogenes ◽  
Rdase Genes

ABSTRACT Multiple reductive dehalogenase (RDase), hydrogenase (H2ase), and other respiration-associated (RA) oxidoreductase genes have been identified in cultured representatives of Dehalococcoides. Although their products are likely to play key roles in the environmentally important process of reductive dechlorination, very little information is available about their regulation and specific functions. Here we show increased expression and temporal variability in the expression of five RDase genes and in the expression of genes for a putative formate dehydrogenase (Fdh) and two H2ases, including a periplasmic [Ni/Fe] H2ase (Hup) and a cytoplasmic [Fe] H2ase (Vhu). mRNA transcripts extracted from tetrachloroethene-dechlorinating mixed cultures corresponding to Fdh, the H2ase Hup, and the RDase targets TceA and DET0162 were expressed most highly, with average levels 34 (± 7.5)-, 23 (± 6.7)-, 16 (± 3.3)-, and 13 (± 3.3)-fold higher, respectively, than that for RNA polymerase (RpoB). H2ase and RA transcripts reached their respective expression maxima within the first 2 h after feeding. RDase transcripts, however, were most highly expressed after 3 h and exhibited greater temporal variability than other transcripts. Comparison with D. ethenogenes strain 195 pure culture expression levels indicated that RDase DET1545 was more highly expressed in mixed cultures, where, on average, its transcript level was sixfold higher than that of RpoB. While the specific functions of several of these gene products remain elusive, the high expression levels and temporal variability reported here suggest that these groups of enzymes are metabolically important for the respiration of chlorinated ethenes in mixed cultures containing Dehalococcoides.

scholarly journals Genetic Identification of a Putative Vinyl Chloride Reductase in Dehalococcoides sp. Strain BAV1

2004 ◽  
Vol 70 (10) ◽  
pp. 6347-6351 ◽  
Author(s):  
Rosa Krajmalnik-Brown ◽  
Tina Hölscher ◽  
Ivy N. Thomson ◽  
F. Michael Saunders ◽  
Kirsti M. Ritalahti ◽  
...  
Keyword(s):  
Vinyl Chloride ◽  
Reductive Dechlorination ◽  
Complete Sequence ◽  
Mixed Cultures ◽  
Genetic Identification ◽  
Degenerate Primers ◽  
Transcription Analysis ◽  
Reductive Dehalogenase ◽  
Conserved Regions ◽  
Rdase Genes

ABSTRACT Dehalococcoides sp. strain BAV1 couples growth with the reductive dechlorination of vinyl chloride (VC) to ethene. Degenerate primers targeting conserved regions in reductive dehalogenase (RDase) genes were designed and used to PCR amplify putative RDase genes from strain BAV1. Seven unique RDase gene fragments were identified. Transcription analysis of VC-grown BAV1 cultures suggested that bvcA was involved in VC reductive dechlorination, and the complete sequence of bvcA was obtained. bvcA was absent in Dehalococcoides isolates that failed to respire VC, yet was detected in four of eight VC-respiring mixed cultures.

scholarly journals Isolation and Characterization of “Dehalococcoides” sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene

2009 ◽  
Vol 75 (18) ◽  
pp. 5910-5918 ◽  
Author(s):  
Dan Cheng ◽  
Jianzhong He
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Anaerobic Respiration ◽  
Rrna Gene ◽  
Reductive Dehalogenase ◽  
Isolation And Characterization ◽  
Dehalococcoides Ethenogenes ◽  
Pure Cultures ◽  
Microbial Group ◽  
Rdase Genes

ABSTRACT In an attempt to understand the microorganisms involved in the generation of trans-1,2-dichloroethene (trans-DCE), pure-culture “Dehalococcoides” sp. strain MB was isolated from environmental sediments. In contrast to currently known tetrachloroethene (PCE)- or trichloroethene (TCE)-dechlorinating pure cultures, which generate cis-DCE as the predominant product, Dehalococcoides sp. strain MB reductively dechlorinates PCE to trans-DCE and cis-DCE at a ratio of 7.3 (±0.4):1. It utilizes H2 as the sole electron donor and PCE or TCE as the electron acceptor during anaerobic respiration. Strain MB is a disc-shaped, nonmotile bacterium. Under an atomic force microscope, the cells appear singly or in pairs and are 1.0 μm in diameter and ∼150 nm in depth. The purity was confirmed by culture-based approaches and 16S rRNA gene-based analysis and was corroborated further by putative reductive dehalogenase (RDase) gene-based, quantitative real-time PCR. Although strain MB shares 100% 16S rRNA gene sequence identity with Dehalococcoides ethenogenes strain 195, these two strains possess different dechlorinating pathways. Microarray analysis revealed that 10 putative RDase genes present in strain 195 were also detected in strain MB. Successful cultivation of strain MB indicates that the biotic process could contribute significantly to the generation of trans-DCE in chloroethene-contaminated sites. It also enhances our understanding of the evolution of this unusual microbial group, Dehalococcoides species.

scholarly journals Reductive Dehalogenase Gene Expression as a Biomarker for Physiological Activity of Dehalococcoides spp

2006 ◽  
Vol 72 (9) ◽  
pp. 6161-6168 ◽  
Author(s):  
Patrick K. H. Lee ◽  
David R. Johnson ◽  
Victor F. Holmes ◽  
Jianzhong He ◽  
Lisa Alvarez-Cohen
Keyword(s):  
Gene Expression ◽  
Enrichment Culture ◽  
Physiological Activity ◽  
Physiological State ◽  
Background Level ◽  
Chlorinated Ethenes ◽  
Chlorinated Ethene ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Ethenogenes ◽  
Gene Transcripts

ABSTRACT This study characterizes the transcriptional expression of the reductive dehalogenase (RDase)-encoding tceA and vcrA genes and evaluates their applicability as potential biological markers of Dehalococcoides activity. When Dehalococcoides ethenogenes 195 was provided with trichloroethene (TCE) as the electron acceptor, the expression of the tceA gene increased by 90-fold relative to that in cells starved of chlorinated ethenes, demonstrating that tceA gene expression is indicative of the active physiological state of this strain. In a Dehalococcoides-containing enrichment culture that contains both the tceA and vcrA genes, the tceA gene was up-regulated in response to TCE and cis-1,2-dichloroethene (cDCE) exposure, while the vcrA gene was up-regulated in response to TCE, cDCE, and vinyl chloride (VC). When chlorinated ethenes were depleted, the RDase-encoding gene transcripts decayed exponentially, with a half-life between 4.8 and 6.1 h, until they reached a stable background level after 2 days. We found that while gene expression correlated generally to the presence of chlorinated ethenes, there was no apparent direct relationship between RDase-encoding transcript numbers and respective rates of TCE, cDCE, and VC dechlorination activities. However, elevated tceA and vcrA expression did correlate with chlorinated-ethene reduction beyond cDCE, suggesting that elevated RDase-encoding transcript numbers could serve as a biomarker for the physiological ability of Dehalococcoides spp. to dechlorinate beyond cDCE.

scholarly journals Reductive Dechlorination of Tetrachloroethene to Ethene by a Two-Component Enzyme Pathway

1998 ◽  
Vol 64 (4) ◽  
pp. 1270-1275 ◽  
Author(s):  
Jon K. Magnuson ◽  
Robert V. Stern ◽  
James M. Gossett ◽  
Stephen H. Zinder ◽  
David R. Burris
Keyword(s):  
Enrichment Culture ◽  
Reductive Dehalogenation ◽  
Reductive Dehalogenase ◽  
Reversible Inhibition ◽  
Isolation And Characterization ◽  
Dehalococcoides Ethenogenes ◽  
Membrane Bound ◽  
Catalytic Mechanisms ◽  
Insight Into

ABSTRACT Two membrane-bound, reductive dehalogenases that constitute a novel pathway for complete dechlorination of tetrachloroethene (perchloroethylene [PCE]) to ethene were partially purified from an anaerobic microbial enrichment culture containing Dehalococcoides ethenogenes 195. When titanium(III) citrate and methyl viologen were used as reductants, PCE-reductive dehalogenase (PCE-RDase) (51 kDa) dechlorinated PCE to trichloroethene (TCE) at a rate of 20 μmol/min/mg of protein. TCE-reductive dehalogenase (TCE-RDase) (61 kDa) dechlorinated TCE to ethene. TCE,cis-1,2-dichloroethene, and 1,1-dichloroethene were dechlorinated at similar rates, 8 to 12 μmol/min/mg of protein. Vinyl chloride and trans-1,2-dichloroethene were degraded at rates which were approximately 2 orders of magnitude lower. The light-reversible inhibition of TCE-RDase by iodopropane and the light-reversible inhibition of PCE-RDase by iodoethane suggest that both of these dehalogenases contain Co(I) corrinoid cofactors. Isolation and characterization of these novel bacterial enzymes provided further insight into the catalytic mechanisms of biological reductive dehalogenation.

scholarly journals Comparative Genomics of “Dehalococcoides ethenogenes” 195 and an Enrichment Culture Containing Unsequenced “Dehalococcoides” Strains

2008 ◽  
Vol 74 (11) ◽  
pp. 3533-3540 ◽  
Author(s):  
Kimberlee A. West ◽  
David R. Johnson ◽  
Ping Hu ◽  
Todd Z. DeSantis ◽  
Eoin L. Brodie ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Microbial Consortium ◽  
Enrichment Culture ◽  
Gene Encoding ◽  
Protein Coding ◽  
Groundwater Contaminants ◽  
Reductive Dehalogenase ◽  
Effective Strategies ◽  
Dehalococcoides Ethenogenes ◽  
Tryptophan Operon

ABSTRACT Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by some “Dehalococcoides” organisms. A Dehalococcoides-organism-containing microbial consortium (referred to as ANAS) with the ability to degrade TCE to ethene, an innocuous end product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of “Dehalococcoides ethenogenes” 195. This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray results revealed that the genes associated with central metabolism, including an apparently incomplete carbon fixation pathway, cobalamin-salvaging system, nitrogen fixation pathway, and five hydrogenase complexes, are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase, tceA, was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria, which is essential in developing effective strategies for the bioremediation of PCE and TCE in the environment.

DNA methyltransferase inhibitors modulate histone methylation: epigenetic crosstalk between H3K4me3 and DNA methylation during sperm differentiation

Zygote ◽  
2021 ◽  
pp. 1-6
Author(s):  
Liliana Burlibaşa ◽  
Alina-Teodora Nicu ◽  
Carmen Domnariu
Keyword(s):  
Dna Methylation ◽  
Histone Methylation ◽  
Dna Methyltransferase ◽  
Integrated Approach ◽  
Regulatory Mechanisms ◽  
Temporal Expression ◽  
Dna Methyltransferase Inhibitors ◽  
Expression Of Genes ◽  
Species Survival ◽  
Advanced Stages

Summary The process of cytodifferentiation in spermatogenesis is governed by a unique genetic and molecular programme. In this context, accurate ‘tuning’ of the regulatory mechanisms involved in germ cells differentiation is required, as any error could have dramatic consequences on species survival and maintenance. To study the processes that govern the spatial–temporal expression of genes, as well as analyse transmission of epigenetic information to descendants, an integrated approach of genetics, biochemistry and cytology data is necessary. As information in the literature on interplay between DNA methylation and histone H3 lysine 4 trimethylation (H3K4me3) in the advanced stages of murine spermatogenesis is still scarce, we investigated the effect of a DNA methyltransferase inhibitor, 5-aza-2′-deoxycytidine, at the cytological level using immunocytochemistry methodology. Our results revealed a particular distribution of H3K4me3 during sperm cell differentiation and highlighted an important role for regulation of DNA methylation in controlling histone methylation and chromatin remodelling during spermatogenesis.

scholarly journals Differential Expression of Benzophenone Synthase and Chalcone Synthase in Hypericum Sampsonii

2012 ◽  
Vol 7 (12) ◽  
pp. 1934578X1200701 ◽  
Author(s):  
Lili Huang ◽  
Hong Wang ◽  
Hechun Ye ◽  
Zhigao Du ◽  
Yansheng Zhang ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Differential Expression ◽  
Chalcone Synthase ◽  
Quantitative Polymerase Chain Reaction ◽  
Transcript Level ◽  
Reproductive Stage ◽  
Vegetative Stage ◽  
Chain Reaction ◽  
Expression Levels ◽  
Polymerase Chain

cDNAs encoding Hypericum sampsonii benzophenone synthase (HsBPS) and chalcone synthase (HsCHS) were isolated and functionally characterized. Differential expressions of HsBPS and HsCHS were monitored using quantitative polymerase chain reaction (PCR). In the vegetative stage, HsBPS was highly expressed in the roots; its transcript level was approx. 100 times higher than that of HsCHS. Relatively high transcript amounts of HsBPS were also detected in older leaves, whereas the youngest leaves contained higher transcript amounts of HsCHS. In the reproductive stage, maximum HsCHS expression was detected in flowers, the transcript level being approx. 5 times higher than that of HsBPS. The inversed situation with a 10-fold difference in the expression levels was observed with fruits. High transcript amounts for both proteins were found in roots.

scholarly journals Drought Stress Enhances Up-Regulation of Anthocyanin Biosynthesis in Grapevine leafroll-associated virus 3-Infected in vitro Grapevine (Vitis vinifera) Leaves

Plant Disease ◽  
2017 ◽  
Vol 101 (9) ◽  
pp. 1606-1615 ◽  
Author(s):  
Zhen-Hua Cui ◽  
Wen-Lu Bi ◽  
Xin-Yi Hao ◽  
Peng-Min Li ◽  
Ying Duan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Vitis Vinifera ◽  
Anthocyanin Biosynthesis ◽  
Anthocyanin Accumulation ◽  
Expression Levels ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Regulated Gene Expression

Reddish-purple coloration on the leaf blades and downward rolling of leaf margins are typical symptoms of grapevine leafroll disease (GLD) in red-fruited grapevine cultivars. These typical symptoms are attributed to the expression of genes encoding enzymes for anthocyanins synthesis, and the accumulation of flavonoids in diseased leaves. Drought has been proven to accelerate development of GLD symptoms in virus-infected leaves of grapevine. However, it is not known how drought affects GLD expression nor how anthocyanin biosynthesis in virus-infected leaves is altered. The present study used HPLC to determine the types and levels of anthocyanins, and applied reverse transcription quantitative polymerase chain reaction (RT-qPCR) to analyze the expression of genes encoding enzymes for anthocyanin synthesis. Plantlets of Grapevine leafroll-associated virus 3 (GLRaV-3)-infected Vitis vinifera ‘Cabernet Sauvignon’ were grown in vitro under PEG-induced drought stress. HPLC found no anthocyanin-related peaks in the healthy plantlets with or without PEG-induced stress, while 11 peaks were detected in the infected plantlets with or without PEG-induced drought stress, but the peaks were significantly higher in infected drought-stressed plantlets. Increased accumulation of total anthocyanin compounds was related to the development of GLD symptoms in the infected plantlets under PEG stress. The highest level of up-regulated gene expression was found in GLRaV-3-infected leaves with PEG-induced drought stress. Analyses of variance and correlation of anthocyanin accumulation with related gene expression levels found that GLRaV-3-infection was the key factor in increased anthocyanin accumulation. This accumulation involved the up-regulation of two key genes, MYBA1 and UFGT, and their expression levels were further enhanced by drought stress.

scholarly journals A Novel Reductive Dehalogenase, Identified in a Contaminated Groundwater Enrichment Culture and in Desulfitobacterium dichloroeliminans Strain DCA1, Is Linked to Dehalogenation of 1,2-Dichloroethane

2007 ◽  
Vol 73 (9) ◽  
pp. 2990-2999 ◽  
Author(s):  
Massimo Marzorati ◽  
Francesca de Ferra ◽  
Hilde Van Raemdonck ◽  
Sara Borin ◽  
Elena Allifranchini ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Enrichment Culture ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Chlorinated Ethenes ◽  
Gene Copy ◽  
Direct Pcr ◽  
Reductive Dehalogenase

ABSTRACT A mixed culture dechlorinating 1,2-dichloroethane (1,2-DCA) to ethene was enriched from groundwater that had been subjected to long-term contamination. In the metagenome of the enrichment, a 7-kb reductive dehalogenase (RD) gene cluster sequence was detected by inverse and direct PCR. The RD gene cluster had four open reading frames (ORF) showing 99% nucleotide identity with pceB, pceC, pceT, and orf1 of Dehalobacter restrictus strain DSMZ 9455T, a bacterium able to dechlorinate chlorinated ethenes. However, dcaA, the ORF encoding the catalytic subunit, showed only 94% nucleotide and 90% amino acid identity with pceA of strain DSMZ 9455T. Fifty-three percent of the amino acid differences were localized in two defined regions of the predicted protein. Exposure of the culture to 1,2-DCA and lactate increased the dcaA gene copy number by 2 log units, and under these conditions the dcaA and dcaB genes were actively transcribed. A very similar RD gene cluster with 98% identity in the dcaA gene sequence was identified in Desulfitobacterium dichloroeliminans strain DCA1, the only known isolate that selectively dechlorinates 1,2-DCA but not chlorinated ethenes. The dcaA gene of strain DCA1 possesses the same amino acid motifs as the new dcaA gene. Southern hybridization using total genomic DNA of strain DCA1 with dcaA gene-specific and dcaB- and pceB-targeting probes indicated the presence of two identical or highly similar dehalogenase gene clusters. In conclusion, these data suggest that the newly described RDs are specifically adapted to 1,2-DCA dechlorination.

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