Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays.

BMC Genomics
Alexandra B GrafDiethard Mattanovich

Abstract

DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR) in this yeast species, as compared to S. cerevisiae. By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer). To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT) or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal me...Continue Reading

References

Nov 21, 2001·Journal of Microbiological Methods·R W YeK M Croker
Aug 15, 2002·Biochemical and Biophysical Research Communications·Hironori Higashio, Kenji Kohno
Oct 5, 2002·Nucleic Acids Research·Catherine MathéPierre Rouzé
Jan 10, 2003·Nucleic Acids Research·Ross OverbeekNikos Kyrpides
Jan 23, 2003·Bioinformatics·Jakob Skou Pedersen, Jotun Hein
May 16, 2003·FEMS Yeast Research·Daniel J ErasmusHennie J J van Vuuren
Jun 12, 2003·Nucleic Acids Research·Jean-Marie RouillardErdogan Gulari
Nov 5, 2003·Methods : a Companion to Methods in Enzymology·Gordon K Smyth, Terry Speed
Jan 21, 2004·Fungal Genetics and Biology : FG & B·Andrew H SimsManda E Gent
May 18, 2004·Bioinformatics·W H MajorosS L Salzberg
May 5, 2005·Applied and Environmental Microbiology·Andrew H SimsGeoffrey D Robson
Jun 28, 2005·Nucleic Acids Research·John Besemer, Mark Borodovsky
Nov 30, 2005·Nucleic Acids Research·Alexandre LomsadzeMark Borodovsky
Mar 30, 2006·Biotechnology and Bioengineering·Brigitte GasserDiethard Mattanovich
Apr 26, 2006·Metabolic Engineering·Marcel Tigges, Martin Fussenegger
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Aug 30, 2006·Methods in Enzymology·David P KreilSteven Russell
May 3, 2007·BMC Bioinformatics·Marianna ZahurakLeslie Cope
Sep 4, 2007·Applied and Environmental Microbiology·Brigitte GasserDiethard Mattanovich
Dec 15, 2007·Biotechnology and Bioengineering·Kristin BaumannDiethard Mattanovich
Dec 24, 2008·Nucleic Acids Research·Germán Gastón LeparcDavid P Kreil

❮ Previous
Next ❯

Citations

Jul 18, 2012·Applied Microbiology and Biotechnology·Silvia HeissBrigitte Gasser
Jan 5, 2010·BMC Genomics·Tim van ZutphenIda J van der Klei
Mar 30, 2010·BMC Genomics·Martin DragositsDiethard Mattanovich
Mar 24, 2010·BMC Microbiology·Sabine Lezar, Eugenia Barros
May 16, 2012·Microbial Cell Factories·Andrea MellitzerKarlheinz Flicker
Jan 26, 2013·Microbial Cell Factories·Roland PrielhoferDiethard Mattanovich
Mar 26, 2009·Microbial Cell Factories·Neus Ferrer-MirallesAntonio Villaverde
Oct 20, 2009·Microbial Cell Factories·Diethard MattanovichKristof De Schutter
Oct 26, 2010·BMC Systems Biology·Kristin BaumannPau Ferrer
Feb 5, 2013·Future Microbiology·Brigitte GasserDiethard Mattanovich
Jul 24, 2014·Applied Microbiology and Biotechnology·Andreas MaccaniWolfgang Ernst
Sep 11, 2014·Microbial Cell Factories·Claudia RuthBrigitte Gasser
Nov 21, 2012·New Biotechnology·Thomas Vogl, Anton Glieder
Sep 19, 2012·Biotechnology Advances·José Luis CorcheroAntonio Villaverde
May 20, 2014·Proteomics·Shuvadeep MaityShantanu Sengupta
Dec 11, 2013·Biotechnology Journal·Corinna RebneggerDiethard Mattanovich
Jan 5, 2010·Biotechnology and Applied Biochemistry·Yanina R SevastsyanovichJeffrey A Cole
Sep 25, 2015·BMC Biology·Hannes RußmayerBrigitte Gasser
Mar 14, 2013·FEMS Microbiology Reviews·Marizela DelicBrigitte Gasser
Dec 20, 2014·BMC Genomics·Tatiana Q AguiarLucília Domingues
Jun 16, 2014·Trends in Biotechnology·Duygu DikiciogluStephen G Oliver
Feb 28, 2015·Applied Microbiology and Biotechnology·Verena PuxbaumBrigitte Gasser
Mar 27, 2010·FEMS Microbiology Letters·Marizela DelicBrigitte Gasser
Apr 4, 2009·FEMS Yeast Research·Alexandra GrafDiethard Mattanovich

❮ Previous
Next ❯

Datasets Mentioned

BETA
A-MEXP-1157

Methods Mentioned

BETA
Affinity Capture
protein folding
glycosylation
Assay
Feature Extraction

Software Mentioned

Glimmer3
BioMart
Integrated Genomics
SGD GO slim
limma of
Glimmer
R
SGD GO slim tool
IG
Agilent

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.