Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9.

Journal of Proteome Research
Katarzyna H KucharzykFrank E Löffler

Abstract

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and ha...Continue Reading

References

Apr 1, 1984·Applied and Environmental Microbiology·D R Shelton, J M Tiedje
Dec 16, 2000·Nature·L AdrianH Görisch
Aug 7, 2003·Applied and Environmental Microbiology·Julien MaillardChristof Holliger
Sep 4, 2004·Applied and Environmental Microbiology·Melanie DuhamelElizabeth A Edwards
Oct 7, 2004·Applied and Environmental Microbiology·Rosa Krajmalnik-BrownFrank E Löffler
Nov 14, 2006·Applied and Environmental Microbiology·R M MorrisR E Richardson
Nov 24, 2007·Bioinformatics·Pedro AlvesPredrag Radivojac
Nov 29, 2007·The ISME Journal·Dirk BenndorfMartin von Bergen
Mar 5, 2009·Microbiology and Molecular Biology Reviews : MMBR·Martin Keller, Robert Hettich
Jun 13, 2009·Journal of Industrial Microbiology & Biotechnology·Simon VainbergRobert J Steffan
Mar 2, 2012·The ISME Journal·Vanessa L BrissonLisa Alvarez-Cohen
Jul 21, 2012·Environmental Science & Technology·Annette R RoweRuth E Richardson
Aug 7, 2012·Molecular & Cellular Proteomics : MCP·Amelia C PetersonJoshua J Coon
Mar 13, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Laura A HugLorenz Adrian
Dec 4, 2014·Applied Microbiology and Biotechnology·Annette R RoweRuth E Richardson
Feb 11, 2015·International Journal of Molecular Sciences·Peter Feist, Amanda B Hummon
Apr 4, 2015·Analytical Chemistry·Jacek R Wiśniewski, Fabienne Z Gaugaz
Mar 8, 2016·Current Opinion in Biotechnology·Jean Armengaud
Apr 14, 2016·Nature Communications·Peter MenzelAnders Krogh

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.