Low degree metabolites explain essential reactions and enhance modularity in biological networks

BMC Bioinformatics
Areejit SamalSanjay Jain

Abstract

Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explanation of specific modules and essential genes and reactions in terms of specific structural or evolutionary constraints. In the metabolic networks of Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus, we identified metabolites with a low degree of connectivity, particularly those that are produced and/or consumed in just a single reaction. Using flux balance analysis (FBA) we also determined reactions essential for growth in these metabolic networks. We find that most reactions identified as essential in these networks turn out to be those involving the production or consumption of low degree metabolites. Applying graph theoretic methods to these metabolic networks, we identified connected clusters of these low degree metabolites. The genes involved in several operons in E. coli are correctly predicted as those of enzymes catalyzing the reactions of these clusters. Furthermore, we find that larger sized clu...Continue Reading

References

Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
May 1, 1999·Bioinformatics·T PfeifferS Schuster
Dec 11, 1999·Nature·L H HartwellA W Murray
May 11, 2000·Proceedings of the National Academy of Sciences of the United States of America·J S Edwards, B O Palsson
Oct 18, 2000·Nature·H JeongA L Barabási
May 3, 2001·Nature·H JeongZ N Oltvai
Aug 28, 2001·Proceedings. Biological Sciences·A Wagner, D A Fell
Dec 26, 2001·Nucleic Acids Research·Peter D KarpSocorro Gama-Castro
Feb 28, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Sanjay Jain, Sandeep Krishna
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
May 4, 2002·Science·Sergei Maslov, Kim Sneppen
Jul 23, 2002·Nature Genetics·Jan IhmelsNaama Barkai
Nov 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Daniel SegrèGeorge M Church
Nov 15, 2002·Nature·Jörg StellingErnst Dieter Gilles
Dec 6, 2002·Genome Research·Jason A PapinBernhard Ø Palsson
May 23, 2003·Bioinformatics·Julien GagneurGeorg Casari
Sep 4, 2003·Genome Biology·Jennifer L ReedBernhard O Palsson
Jan 14, 2004·Genome Research·Anthony P BurgardCostas D Maranas
Mar 6, 2004·Science·Ron MiloUri Alon
May 7, 2004·Nature·Markus W CovertBernhard O Palsson
Dec 3, 2004·Biophysical Journal·R Mahadevan, B O Palsson
Feb 25, 2005·Nature·Roger Guimerà, Luís A Nunes Amaral
May 12, 2005·Metabolic Engineering·Dong-Yup LeeFerenc Friedler
Dec 20, 2005·PLoS Computational Biology·Eivind AlmaasAlbert-László Barabási

❮ Previous
Next ❯

Citations

Jul 19, 2013·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Sergey A Marakushev, Ol'ga V Belonogova
Jun 10, 2008·Nature Biotechnology·Adam M Feist, Bernhard Ø Palsson
Sep 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ashley G SmartJulio M Ottino
Apr 18, 2012·Proceedings of the National Academy of Sciences of the United States of America·Aditya BarveAndreas Wagner
Aug 17, 2012·Journal of the Royal Society, Interface·Moritz Emanuel BeberMarc-Thorsten Hütt
Nov 4, 2008·Journal of Bacteriology·Julio Collado-VidesAlberto Santos-Zavaleta
Aug 23, 2007·BMC Bioinformatics·Kazuhiro TakemotoTatsuya Akutsu
May 5, 2010·BMC Systems Biology·Kitiporn PlaimasRainer König
Aug 26, 2011·BMC Systems Biology·Areejit SamalOlivier C Martin
Mar 24, 2011·BMC Systems Biology·Rui-Sheng Wang, Réka Albert
Aug 14, 2010·Journal of Biomedicine & Biotechnology·A De MartinoV Van Kerrebroeck
Jul 26, 2008·BMC Systems Biology·Kitiporn PlaimasRainer König
Feb 3, 2015·IEEE Transactions on Nanobioscience·Lin WuFang-Xiang Wu
Jan 1, 2012·Metabolites·Nikolaus SonnenscheinMarc-Thorsten Hütt
Nov 21, 2007·Chemistry & Biodiversity·Seth B RobertsGregory A Buck
Nov 6, 2009·Molecular Systems Biology·Matthew A OberhardtJason A Papin
Jun 19, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shalini SinghSanjay Jain
Mar 28, 2009·Journal of the Royal Society, Interface·Patrick M Boyle, Pamela A Silver
Aug 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Marco BardosciaAreejit Samal
Aug 23, 2018·NPJ Systems Biology and Applications·Mariano Beguerisse-DíazMauricio Barahona
Mar 5, 2009·Physical Review Letters·André A MoreiraJoseph O Indekeu
Feb 12, 2021·Frontiers in Bioengineering and Biotechnology·Varshit DusadDiego A Oyarzún

❮ Previous
Next ❯

Methods Mentioned

BETA
gene knockouts

Software Mentioned

Ecocyc
UC

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.