From genomes to systems: the path with yeast

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Stephen G Oliver

Abstract

Metabolic Control Analysis (MCA) is a conceptual and mathematical formalism that models the relative contributions of individual effectors in a pathway to both the flux through the pathway and the concentrations of individual intermediates within it. To exploit MCA in an initial Systems Biology analysis of the eukaryotic cell, two categories of experiments are required. In category 1 experiments, flux is changed and the impact on the levels of the direct and indirect products of gene action is measured. We have measured the impact of changing the flux on the transcriptome, proteome and metabolome of Saccharomyces cerevisiae. In this whole-cell analysis, flux equates to growth rate. In category 2 experiments, the levels of individual gene products are altered, and the impact on the flux is measured. We have used competition analyses between the complete set of heterozygous yeast deletion mutants to reveal genes encoding proteins with high flux control coefficients. These genes may be exploited, in a top-down analysis, to build a coarse-grained model of the eukaryotic cell, as exemplified by yeast. More detailed modelling requires that 'natural' biological systems be identified. The combination of flux balance analysis with both ...Continue Reading

References

Jan 1, 1973·Annals of the New York Academy of Sciences·J J BellB W Harding
May 1, 1995·Biochemical Society Transactions·H Kacser
Jul 1, 1996·Trends in Genetics : TIG·S Oliver
Oct 25, 1996·Science·A GoffeauS G Oliver
Sep 23, 1998·Trends in Biotechnology·S G OliverF Baganz
Dec 23, 1998·Molecular & General Genetics : MGG·K SanyalP Sinha
May 14, 1999·Current Opinion in Microbiology·T Ferenci
Feb 22, 2001·Science·J C VenterX Zhu
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Jun 11, 2002·Methods : a Companion to Methods in Enzymology·Alan J Whitmarsh
Jun 11, 2002·Methods : a Companion to Methods in Enzymology·Andrew HayesStephen G Oliver
Jun 21, 2002·Methods in Enzymology·Fred Sherman
Jul 26, 2002·Nature·Guri GiaeverMark Johnston
Sep 13, 2002·Genome Biology·Paul T SpellmanAlvis Brazma
Jan 2, 2003·Molecular and Cellular Biology·Fei-Ling LimAndrew D Sharrocks
Feb 5, 2003·Genome Research·Jochen FörsterJens Nielsen
Mar 1, 2003·Nature Biotechnology·Chris F TaylorStephen G Oliver
Jul 23, 2003·Proteomics·Sandra OrchardRolf Apweiler
Aug 22, 2003·Nature·Paul Nurse
Dec 30, 2003·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Douglas B Kell, Stephen G Oliver
Jan 14, 2004·Genome Research·Anthony P BurgardCostas D Maranas
Feb 6, 2004·Journal of Biochemistry and Molecular Biology·Juan I Castrillo, Stephen G Oliver
Feb 7, 2004·Science·Amy Hin Yan TongCharles Boone
Feb 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jian WuStephen G Oliver
May 18, 2004·Bioinformatics·Andrew JonesChristian J Stoeckert
Jun 16, 2004·Current Opinion in Microbiology·Douglas B Kell
Sep 24, 2004·Experimental Neurology·Liu-Gen LeiYu-Qiu Zhang
Dec 8, 2004·Nature Biotechnology·Helen JenkinsDouglas B Kell
Dec 14, 2004·Nature Genetics·Daniel SegrèRoy Kishony
Jun 15, 2005·Nature Reviews. Microbiology·Douglas B KellStephen G Oliver
May 27, 2006·Molecular Systems Biology·Hiroaki Kitano
Apr 19, 2007·Journal of Biology·Juan I CastrilloStephen G Oliver

❮ Previous
Next ❯

Citations

Jul 16, 2009·Médecine sciences : M/S·François IrisPablo Santamaria
Mar 10, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David T JonesJanet M Thornton
Sep 6, 2008·Microbiology and Molecular Biology Reviews : MMBR·Elke Nevoigt
Jun 26, 2007·Trends in Biotechnology·Anthony R BornemanIsak S Pretorius
Jan 25, 2007·The New Phytologist·Ralf T Voegele, Kurt W Mendgen
Jun 17, 2008·Journal of Cellular and Molecular Medicine·Ignasi BarbaDavid Pozo
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Duccio Cavalieri
Jul 4, 2006·Current Opinion in Chemical Biology·Julian L Griffin
Jan 24, 2015·Nature Reviews. Drug Discovery·Alan L HarveyRonald J Quinn
May 11, 2007·Expert Review of Molecular Diagnostics·Laura K Schnackenberg
Jul 9, 2020·Progress in Lipid Research·Sandra M CorreaYariv Brotman

❮ 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.

Related Papers

Nature Reviews. Microbiology
Jeremy K NicholsonIan D Wilson
Trends in Plant Science
Raoul J BinoLloyd W Sumner
Proceedings of the National Academy of Sciences of the United States of America
G GiaeverR W Davis
Science
A GoffeauStephen G Oliver
© 2021 Meta ULC. All rights reserved