scholarly journals Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by Dehalococcoides-Containing Cultures

2005 ◽  
Vol 71 (12) ◽  
pp. 8257-8264 ◽  
Author(s):  
Alison S. Waller ◽  
Rosa Krajmalnik-Brown ◽  
Frank E. Löffler ◽  
Elizabeth A. Edwards
Keyword(s):  
Vinyl Chloride ◽  
Electron Acceptor ◽  
Reductive Dechlorination ◽  
Amino Acid Identity ◽  
Degenerate Primers ◽  
Acid Identity ◽  
Reductive Dehalogenase ◽  
Homologous Genes ◽  
Differential Transcription ◽  
Transcribed Sequences

ABSTRACT Degenerate primers were used to amplify 14 distinct reductive-dehalogenase-homologous (RDH) genes from the Dehalococcoides-containing mixed culture KB1. Most of the corresponding predicted proteins were highly similar (97 to >99% amino acid identity) to previously reported Dehalococcoides reductive dehalogenases. To examine the differential transcription of these RDH genes, KB1 was split into five subcultures amended with either trichloroethene, cis-1,2-dichloroethene, vinyl chloride, 1,2-dichlorethane, or no chlorinated electron acceptor. Total RNA was extracted following the onset of reductive dechlorination, and RDH transcripts were reverse transcribed and amplified using degenerate primers. The results indicate that the transcription of RDH genes requires the presence of a chlorinated electron acceptor, and for all treatments, multiple RDH genes were simultaneously transcribed, with transcripts of two of the genes being present under all four electron-accepting conditions. Two of the transcribed sequences were highly similar to reported vinyl chloride reductase genes, namely, vcrA from Dehalococcoides sp. strain VS and bvcA from Dehalococcoides sp. strain BAV1. These findings suggest that multiple RDH genes are induced by a single chlorinated substrate and that multiple reductive dehalogenases contribute to chloroethene degradation in KB1.

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.

Reductive Dechlorination of Chlorinated Ethenes and 1,2-Dichloroethane by “Dehalococcoides ethenogenes” 195

1999 ◽  
Vol 65 (7) ◽  
pp. 3108-3113 ◽  
Author(s):  
Xavier Maymó-Gatell ◽  
Timothy Anguish ◽  
Stephen H. Zinder
Keyword(s):  
Vinyl Chloride ◽  
Growth Medium ◽  
Electron Acceptor ◽  
Reductive Dechlorination ◽  
Electron Acceptors ◽  
Chlorinated Compounds ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Ethenogenes ◽  
Over Time ◽  
Number Of Cells

ABSTRACT “Dehalococcoides ethenogenes” 195 can reductively dechlorinate tetrachloroethene (PCE) completely to ethene (ETH). When PCE-grown strain 195 was transferred (2% [vol/vol] inoculum) into growth medium amended with trichloroethene (TCE),cis-dichloroethene (DCE), 1,1-DCE, or 1,2-dichloroethane (DCA) as an electron acceptor, these chlorinated compounds were consumed at increasing rates over time, which indicated that growth occurred. Moreover, the number of cells increased when TCE, 1,1-DCE, or DCA was present. PCE, TCE, 1,1-DCE, and cis-DCE were converted mainly to vinyl chloride (VC) and then to ETH, while DCA was converted to ca. 99% ETH and 1% VC. cis-DCE was used at lower rates than PCE, TCE, 1,1-DCE, or DCA was used. When PCE-grown cultures were transferred to media containing VC ortrans-DCE, products accumulated slowly, and there was no increase in the rate, which indicated that these two compounds did not support growth. When the intermediates in PCE dechlorination by strain 195 were monitored, TCE was detected first, followed bycis-DCE. After a lag, VC, 1,1-DCE, andtrans-DCE accumulated, which is consistent with the hypothesis that cis-DCE is the precursor of these compounds. Both cis-DCE and 1,1-DCE were eventually consumed, and both of these compounds could be considered intermediates in PCE dechlorination, whereas the small amount oftrans-DCE that was produced persisted. Cultures grown on TCE, 1,1-DCE, or DCA could immediately dechlorinate PCE, which indicated that PCE reductive dehalogenase activity was constitutive when these electron acceptors were used.

scholarly journals Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Sara Kleindienst ◽  
Karuna Chourey ◽  
Gao Chen ◽  
Robert W. Murdoch ◽  
Steven A. Higgins ◽  
...  
Keyword(s):  
Amino Acid ◽  
Reductive Dechlorination ◽  
Bond Cleavage ◽  
Amino Acid Identity ◽  
Methyl Group ◽  
Acid Identity ◽  
Group Transfer ◽  
Degrading Bacterium ◽  
Chlorine Bond ◽  
Methyl Group Transfer

ABSTRACTDichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader “CandidatusDichloromethanomonas elyunquensis” strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM’s genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase ofDehalococcoides mccartyistrain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase ofDehalobactersp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.IMPORTANCENaturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader “CandidatusDichloromethanomonas elyunquensis” strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacteriumDehalobacterium formicoaceticumand “CandidatusDichloromethanomonas elyunquensis” strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.

scholarly journals First Report of Bidens mottle virus Infecting Calendula in Taiwan

Plant Disease ◽  
2011 ◽  
Vol 95 (3) ◽  
pp. 362-362 ◽  
Author(s):  
C.-H. Huang ◽  
F.-J. Jan
Keyword(s):  
Amino Acid ◽  
Inclusion Bodies ◽  
Amino Acid Identity ◽  
Mottle Virus ◽  
Rt Pcr ◽  
Degenerate Primers ◽  
Acid Identity ◽  
First Report ◽  
Cp Gene ◽  
Dna Fragment

In March of 2010, calendula (Calendula officinalis L.), a perennial herb known as the pot marigold, showing chlorotic spots on leaves, chlorosis, and stunting were collected from Puli Township, Nantou County, Taiwan. The disorder occurred in more than 50% of the calendula plants in the field. A virus culture isolated from one of the symptomatic calendulas was established in Chenopodium quinoa through triple single-lesion isolation and designated as TwCa1. With transmission electron microscopy (TEM), negatively stained flexuous filamentous virions approximately 12 × 720 nm were observed in the crude sap of TwCa1-infected C. quinoa leaves and pinwheel inclusion bodies were found in the infected cells. On the basis of the sizes of the viral particles and inclusion bodies, isolate TwCa1 was a suspected potyvirus. By reverse transcription (RT)-PCR and potyvirus degenerate primers (Hrp5/Pot1) (1,2), a 0.65-kb DNA fragment, which included the 3′-end of the NIb gene and the 5′-end of coat protein (CP) gene of the virus, was amplified from total RNA isolated from TwCa1-infected plants. The amplified DNA fragment was cloned and sequenced. A homology search indicated that the new calendula-infecting virus in Taiwan might belong to Bidens mottle virus (BiMoV) because its partial genomic sequence shared 94.9 to 97.3% nucleotide and 96.6 to 98.1% amino acid identity with 11 BiMoV isolates available in NCBI GenBank. Primer pairs Hrp5/oligo d(T) were used to amplify the 3′-end genome of BioMV TwCa1 including the 3′-end of the NIb gene, the full-length CP gene, and the 3′-nontranslatable region of the virus. The 807-nt CP gene of TwCa1 (Accession No. HQ117871) shared 97.3 to 98.6% nucleotide and 98.5 to 98.9% amino acid identity with those of 11 BiMoV isolates available in GenBank. Results from TEM observations and CP gene sequence analysis indicated that TwCa1 is an isolate of BiMoV. BiMoV was later detected by RT-PCR in eight symptomatic calendulas collected from the same field. To our knowledge, this is the first report of BiMoV infecting calendula in Taiwan. This newly identified calendula-infecting BiMoV could have a direct impact on the economically important vegetable and floral industry in Taiwan. References: (1) C. C. Chen et al. Bot. Stud. 947:369, 2006. (2) D. Colinet and J. Kummert. J. Virol. Methods 45:149, 1993.

scholarly journals First Report of Grapevine leafroll-associated virus 5 in Spain

Plant Disease ◽  
2010 ◽  
Vol 94 (12) ◽  
pp. 1507-1507 ◽  
Author(s):  
C. V. Padilla ◽  
E. Cretazzo ◽  
I. Hita ◽  
N. López ◽  
V. Padilla ◽  
...  
Keyword(s):  
United States ◽  
Amino Acid ◽  
The United States ◽  
Amino Acid Identity ◽  
Wine Industry ◽  
Rt Pcr ◽  
Acid Identity ◽  
First Report ◽  
Virus Indexing ◽  
Homologous Genes

Grapevine leafroll-associated viruses (GLRaVs) cause significant reductions in yield and quality in the wine industry worldwide. At least nine different GLRaVs have been found in different regions of the world. In the process of virus indexing of candidate grapevine clones for certification, which includes grafting of scions onto rootstocks, we observed strong leafroll symptoms 1 year after grafting with one vine of cv. Estaladina in Castilla y León, Spain and one vine of cv. Tempranillo in La Rioja, Spain, collected in 2008 and 2007, respectively. Both vines tested positive by real-time reverse transcription (RT)-PCR with TaqMan probes specific for Grapevine leafroll-associated virus 5 and double-antibody sandwich (DAS)-ELISA with a mix of monoclonal antibodies that recognizes GLRaV-4, 5, 6, 7, and 9 (Bioreba, Reinach, Switzerland). RNA extracts of both GLRaV-5 positive vines were analyzed by conventional RT-PCR with a pair of consensus degenerated primers derived from GLRaV-5 hsp70 sequences available in GenBank: LR5HYF (5′-TGGGATGAAYAARTTCAATGC-3′) and LR5HYR (5′-TGAAATTCCTCATRTARGAGC-3′) that amplified a 250-bp fragment. Amplicons were cloned and the comparison of the amino acid sequences (Estaladina isolate, Est110: Accession No. HM208622; Tempranillo isolate, Tem020: Accession No. HM208618) showed in the case of the Est110 isolate, 100 and 82.6% identity, respectively, with the homologous genes of one GLRaV-5 isolate from the United States (AF233934 [3]) and Argentina (EU815935 [2]). For isolate Tem020, the hsp70 gene showed 97.1 and 81.2% amino acid identity with the homologous hsp70 genes of the United States and Argentina isolates. The coat protein (cp) genes of both isolates were also amplified and cloned using the specific GLRaV-5 primers, LR53413 (5′-CGTGATACAAGGTAGGACAACCGT-3′) and LR53843 (5′-CTTGCACTATCGCTGCCGTGAAT-3′), designed according to the sequence of AF233934. Fragments were of the expected size (430 bp) and the nucleotide sequences were obtained (Est110: Accession No. HM363522; Tem020: Accession No. HM363523) and used for pairwise nucleotide comparisons. The Est110 isolate showed 96.7 and 97.5% amino acid identity with the isolates from the United States and Argentina, respectively, while the Tem020 isolate showed 94.8 and 95.6% identity, respectively. Amino acid identity of Est110 and Tem020 cp genes was 100% when compared with the homologous genes of isolates AF233934 and EU815935. To our knowledge this is the first report of GRLaV-5 in Spain. Since 2008, we have detected eight additional vines positive for this virus in 200 clones analyzed for certification, suggesting that the incidence of GLRaV-5 in Spain could be widespread. This research indicates that virus indexing for GLRaV should be included in certification schemes for grapevine candidate clones (1) in Spain. References: (1) Anonymous. OEPP/EPPO Bull. 38:422, 2008. (2) S. Gomez Talquenca et al. Virus Genes 38:184, 2009. (3) F. Osman et al. J. Virol. Methods 141:22, 2007.

scholarly journals Fraction of Electrons Consumed in Electron Acceptor Reduction and Hydrogen Thresholds as Indicators of Halorespiratory Physiology

1999 ◽  
Vol 65 (9) ◽  
pp. 4049-4056 ◽  
Author(s):  
Frank E. Löffler ◽  
James M. Tiedje ◽  
Robert A. Sanford
Keyword(s):  
Vinyl Chloride ◽  
Electron Acceptor ◽  
Reductive Dechlorination ◽  
Theoretical Calculations ◽  
Mixed Cultures ◽  
Lower Threshold ◽  
Chlorinated Compound ◽  
Hydrogen Consumption ◽  
Pure Cultures ◽  
Good Agreement

ABSTRACT Measurements of the hydrogen consumption threshold and the tracking of electrons transferred to the chlorinated electron acceptor (fe) reliably detected chlororespiratory physiology in both mixed cultures and pure cultures capable of using tetrachloroethene,cis-1,2-dichloroethene, vinyl chloride, 2-chlorophenol, 3-chlorobenzoate, 3-chloro-4-hydroxybenzoate, or 1,2-dichloropropane as an electron acceptor. Hydrogen was consumed to significantly lower threshold concentrations of less than 0.4 ppmv compared with the values obtained for the same cultures without a chlorinated compound as an electron acceptor. The fe values ranged from 0.63 to 0.7, values which are in good agreement with theoretical calculations based on the thermodynamics of reductive dechlorination as the terminal electron-accepting process. In contrast, a mixed methanogenic culture that cometabolized 3-chlorophenol exhibited a significantly lower fe value, 0.012.

Identification of a novel K-channel gene (KC22) that is highly expressed in distal tubule of rabbit kidney

1993 ◽  
Vol 264 (1) ◽  
pp. F128-F133 ◽  
Author(s):  
G. V. Desir ◽  
H. Velazquez
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
Rat Brain ◽  
Distal Tubule ◽  
Amino Acid Identity ◽  
Rabbit Kidney ◽  
Kidney Cortex ◽  
Degenerate Primers ◽  
Acid Identity ◽  
Partial Length

The Shaker gene family encodes voltage-gated K channels. Five partial-length Shaker-like cDNAs (KC2, 4, 10, 19, and 22) were previously isolated from rabbit kidney using polymerase chain reaction (PCR) [G. V. Desir, E. Hamlin, A.H. Puente, R.F. Reilly, F. Hiledebrandt, and P. Igarashi. Am. J. Physiol. 262 (Renal Fluid Electrolyte Physiol. 31): F151-F157, 1992]. We now report the cloning of another Shaker-like cDNA (KC6) from rabbit kidney and the identification of one isoform that is highly expressed in rabbit distal tubule cells grown in culture. A partial-length cDNA (859 bp) for KC6 was isolated by PCR amplification of rabbit kidney cDNA using Shaker-specific degenerate primers. KC6 was most similar to the rat brain clone RBK2 (77% amino acid identity) and to the rabbit clone KC19 (78% amino acid identity). Transcript levels for KC2, 4, 6, 10, 19, and 22 were quantified using the ribonuclease protection assay. Transcripts for all six isoforms were detected in renal tissues. KC22 was the most abundant isoform in kidney cortex and medulla (20- to 40-fold greater than the other isoforms). Furthermore, KC22 expression levels were fivefold higher in primary cultures of rabbit distal convoluted tubules and connecting tubules than in whole kidney cortex. Although the partial-length sequence for KC22 represents the most conserved regions in the Shaker gene family it only has 35-88% amino acid identity with other Shaker channels, suggesting that KC22 represents a novel isoform. In contrast, KC4 and KC19 (less abundant in kidney than KC22) are highly homologous to the rat brain clones RBK1 and RBK2, respectively (97% amino acid identity).(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Genome Sequence of “Candidatus Dehalogenimonas etheniformans” Strain GP, a Vinyl Chloride-Respiring Anaerobe

2020 ◽  
Vol 9 (50) ◽  
Author(s):  
Yi Yang ◽  
Jun Yan ◽  
Xiuying Li ◽  
Yan Lv ◽  
Yiru Cui ◽  
...  
Keyword(s):  
Vinyl Chloride ◽  
Genome Sequence ◽  
Reductive Dechlorination ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes

ABSTRACT “Candidatus Dehalogenimonas etheniformans” strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase genes.

scholarly journals First Report of Capsicum chlorosis virus Infecting Tomato in Taiwan

Plant Disease ◽  
2010 ◽  
Vol 94 (10) ◽  
pp. 1263-1263 ◽  
Author(s):  
C.-H. Huang ◽  
Y.-X. Zheng ◽  
Y.-H. Cheng ◽  
W.-S. Lee ◽  
F.-J. Jan
Keyword(s):  
Amino Acid ◽  
Amino Acid Identity ◽  
N Gene ◽  
Rt Pcr ◽  
Degenerate Primers ◽  
Tomato Plants ◽  
Acid Identity ◽  
First Report ◽  
Conserved Region ◽  
Capsicum Chlorosis Virus

In December 2009, two samples from tomato plants (Solanum lycopersicum cv. Known-you 301) showing symptoms of chlorosis and necrosis on leaves were collected from two different fields that exhibited 5% disease incidence in Wufeng Township, Taichung County. Reverse transcription (RT)-PCR was applied to detect the presence of potential viruses in collected samples using three degenerate primers (3), gL3637/gL4435c for tospoviruses, Tob-Uni1/Tob-Uni2 for tobamoviruses, and Hrp5/Pot1 for potyviruses, and one specific primer, FJJ2001-7/FJJ2001-8, for the coat protein gene of Cucumber mosaic virus (3). An 816-nt DNA fragment was amplified from each of these two field samples by RT-PCR with the tospovirus degenerate primers, gL3637/gL4435c, designed from the conserved region of L RNA. One of the amplified fragments was cloned and sequenced. A homology search indicated that the new tomato-infecting virus in Taiwan might belong to Capsicum chlorosis virus (CaCV) since the partial L RNA shared more than 87% nucleotide and 99.6% amino acid identity with two CaCV isolates from Thailand (GenBank Accession Nos. DQ256124 and NC_008302). A virus culture isolated from the symptomatic tomato was established in Chenopodium quinoa through triple single-lesion isolation and designated as TwTom1. The partial L RNA and full-length nucleocapsid (N) gene of TwTom1 were obtained by RT-PCR with primer pairs gL3637/gL4435c and FJJ 2010-2 (5′-TTAAAT(C/T)ACAC(C/T)TCTATAGA)/N3534c (1), respectively. The 816-nt L RNA conserved region of TwTom1 (Accession No. HM021140) also shared 87% nucleotide and 99.6% amino acid identity with those of the above mentioned two CaCV isolates available in GenBank. The 828-nt N gene of TwTom1 (Accession No. HM021139) shared 85 to 98.1% nucleotide and 92 to 100% amino acid identity with those of 26 CaCV isolates available in GenBank. TwTom1 shared the highest N gene nucleotide and amino acid identity, 98.1 and 100%, respectively, with a gloxinia isolate (Accession No. AY312061). Sequence analysis results indicated that TwTom1 is an isolate of CaCV. The TwTom1 isolate was back inoculated onto three tomato (cv. Known-you 301) plants for pathogenicity test. The inoculated tomato plants showed symptoms of chlorosis at 13 days postinoculation (dpi) and symptoms of chlorosis plus necrosis on leaves at 20 dpi, which were similar to that observed in the field. A protein band measuring approximately 30 kDa in the crude sap of the TwTom1-infected tomato was observed in western blotting using the antiserum against the N protein of CaCV. In addition, CaCV was later detected by RT-PCR in two symptomatic tomato samples collected from another field. CaCV was first found in Australia, then Thailand, Taiwan, China, and India (2). Although CaCV was found to infect several species of ornamental crops in Taiwan, to our knowledge, this is the first report of CaCV that could naturally infect tomato, a nonornamental plant in Taiwan. References: (1) Y. H. Lin et al. Phytopathology 95:1482, 2005. (2) H. R. Pappu et al. Virus Res. 141:219, 2009. (3) Y.-X. Zheng et al. Plant Dis. 94:920, 2010.

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