Metabolic network modelling - AbsoluteAstronomy.com

Metabolic network reconstruction and simulation allows for an in depth insight into comprehending the molecular mechanisms of a particular organism, especially correlating the genome

Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

with molecular physiology

Physiology

Physiology is the science of the function of living systems. This includes how organisms, organ systems, organs, cells, and bio-molecules carry out the chemical or physical functions that exist in a living system. The highest honor awarded in physiology is the Nobel Prize in Physiology or...

(Francke, Siezen, and Teusink 2005). A reconstruction breaks down metabolic pathways into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. Examples of various metabolic pathways include glycolysis

Glycolysis

Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+...

, Krebs cycle

Citric acid cycle

The citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or the Szent-Györgyi-Krebs cycle — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and...

, pentose phosphate pathway

Pentose phosphate pathway

The pentose phosphate pathway is a process that generates NADPH and pentoses . There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of 5-carbon sugars...

. In simplified terms, a reconstruction involves collecting all of the relevant metabolic information of an organism and then compiling it in a way that makes sense for various types of analyses to be performed. The correlation between the genome and metabolism is made by searching gene databases, such as KEGG http://www.genome.ad.jp, GeneDB http://www.genedb.org, for particular genes by inputting enzyme or protein names. For example, a search can be conducted based on the protein name or the EC number

EC number

The Enzyme Commission number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze....

(a number that represents the catalytic function of the enzyme of interest) in order to find the associated gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

(Francke et al. 2005).

Resources

Below is more detailed description of a few gene/enzyme/reaction/pathway databases that are crucial to a metabolic reconstruction:

Kyoto Encyclopedia of Genes and Genomes (KEGG): This is a bioinformatics database containing information on genes, proteins, reactions, and pathways. The ‘KEGG Organisms’ section, which is divided into eukaryotes and prokaryotes, encompasses many organisms for which gene and DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

information can be searched by typing in the enzyme of choice. This resource can be extremely useful when building the association between metabolism enzymes, reactions and genes.

BioCyc, EcoCyc, and MetaCyc: BioCyc is a collection of 1,000 pathway/genome databases (as of Oct 2010), with each database dedicated to one organism. For example, EcoCyc is a highly detailed bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

database on the genome and metabolic reconstruction of Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...

, including thorough descriptions of E. coli signaling pathways and regulatory network. The EcoCyc database can serve as a paradigm and model for any reconstruction. Additionally, MetaCyc, an encyclopedia of experimentally defined metabolic pathways and enzymes, contains 1,500 metabolic pathways and 8,700 metabolic reactions (Oct 2010).

Pathway Tools http://bioinformatics.ai.sri.com/ptools/: A bioinformatics software package that assists in the construction of pathway/genome databases such as EcoCyc (Karp 2010). Developed by Peter Karp and associates at the SRI International Bioinformatics Group, Pathway Tools comprises several separate units. First, PathoLogic takes an annotated genome for an organism and infers probable metabolic pathways to produce a new pathway/genome database. This can be followed by application of the Pathway Hole Filler, which predicts likely genes to fill "holes" (missing steps) in predicted pathways. Afterward, the Pathway Tools Navigator and Editor functions let users visualize, analyze, access and update the database. Thus, using PathoLogic and encyclopedias like MetaCyc, an initial fast reconstruction can be developed automatically, and then using the other units of Pathway Tools, a very detailed manual update, curation and verification step can be carried out (SRI 2005).

ERGO: ERGO http://ergo.integratedgenomics.com integrates data from every level including genomic, biochemical data, literature, and high-throughput analysis into a comprehensive user friendly network of metabolic and nonmetabolic pathways.

metaTIGER http://www.bioinformatics.leeds.ac.uk/metatiger/: is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes. Phylogenomic information is provided by 2,257 large phylogenetic trees which can be interactively explored. High-throughput tree analysis can also be carried out to identify trees of interest, e.g. trees containing horizontal gene transfers. metaTIGER also provides novel facilities for viewing and comparing the metabolic profiles.

ENZYME: This is an enzyme nomenclature database (part of the ExPASY http://ca.expasy.org/ proteonomics server of the Swiss Institute of Bioinformatics). After searching for a particular enzyme on the database, this resource gives you the reaction that is catalyzed. Additionally, ENZYME has direct links to various other gene/enzyme/medical literature databases such as KEGG, BRENDA, PUBMED, and PUMA2 to name a few.

BRENDA: A comprehensive enzyme database, BRENDA, allows you to search for an enzyme by name or EC number. You can also search for an organism and find all the relevant enzyme information. Moreover, when an enzyme search is carried out, BRENDA provides a list of all organisms containing the particular enzyme of interest.

PUBMED: This is an online library developed by the National Center for Biotechnology Information
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...

, which contains a massive collection of medical journals. Using the link provided by ENZYME, the search can be directed towards the organism of interest, thus recovering literature on the enzyme and its use inside of the organism.

Model SEED http://www.theseed.org/models/: This is an online resource for the analysis, comparison, reconstruction, and curation of genome-scale metabolic models (Henry et al. 2010). Users can submit genome sequences to the RAST annotation system, and the resulting annotation can be automatically piped into the Model SEED to produce a draft metabolic model. The Model SEED automatically constructs a network of metabolic reactions, gene-protein-reaction associations for each reaction, and a biomass composition reaction for each genome to produce a model of microbial metabolism that can be simulated using Flux Balance Analysis.

Next steps of the reconstruction

After the initial stages of the reconstruction, a systematic verification is made in order to make sure no inconsistencies are present and that all the entries listed are correct and accurate (Francke et al. 2005). Furthermore, previous literature can be researched in order to support any information obtained from one of the many metabolic reaction and genome databases. This provides an added level of assurance for the reconstruction that the enzyme and the reaction it catalyzes do actually occur in the organism.

Any new reactions not present in the databases need to be added to the reconstruction. The presence or absence of certain reactions of the metabolism will affect the amount of reactants/products that are present for other reactions within the particular pathway. This is because products in one reaction go on to become the reactants for another reaction, i.e. products of one reaction can combine with other proteins or compounds to form new proteins/compounds in the presence of different enzymes or catalysts (Francke et al. 2005).

Francke et al. (2005) provide an excellent example as to why the verification step of the project needs to be performed in significant detail. During a metabolic network reconstruction of Lactobacillus plantarum
Lactobacillus plantarum
Lactobacillus plantarum is a widespread member of the genus Lactobacillus, commonly found in many fermented food products as well as anaerobic plant matter. It is also present in saliva . It has the ability to liquefy gelatin. L...

, the model showed that succinyl-CoA

Succinyl-CoA

Succinyl-Coenzyme A, abbreviated as Succinyl-CoA or SucCoA, is a combination of succinic acid and coenzyme A.-Source:It is an important intermediate in the citric acid cycle, where it is synthesized from α-Ketoglutarate by α-ketoglutarate dehydrogenase through decarboxylation...

was one of the reactants for a reaction that was a part of the biosynthesis of methionine

Methionine

Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...

. However, an understanding of the physiology of the organism would have revealed that due to an incomplete tricarboxylic acid pathway, Lactobacillus plantarum does not actually produce succinyl-CoA, and the correct reactant for that part of the reaction was acetyl-CoA

Acetyl-CoA

Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. Its main function is to convey the carbon atoms within the acetyl group to the citric acid cycle to be oxidized for energy production. In chemical structure, acetyl-CoA is the thioester...

.

Therefore, systematic verification of the initial reconstruction will bring to light several inconsistencies that can adversely affect the final interpretation of the reconstruction, which is to accurately comprehend the molecular mechanisms of the organism. Furthermore, the simulation

Simulation

Simulation is the imitation of some real thing available, state of affairs, or process. The act of simulating something generally entails representing certain key characteristics or behaviours of a selected physical or abstract system....

step also ensures that all the reactions present in the reconstruction are properly balanced. To sum up, a reconstruction that is fully accurate can lead to greater insight about understanding the functioning of the organism of interest (Francke et al. 2005).

Advantages of a reconstruction

Several inconsistencies exist between gene, enzyme, and reaction databases and published literature sources regarding the metabolic information of an organism. A reconstruction is a systematic verification and compilation of data from various sources that takes into account all of the discrepancies.
A reconstruction combines the relevant metabolic and genomic information of an organism.
A reconstruction also allows for metabolic comparisons to be performed between various organisms of the same species as well as between different organisms.

Metabolic network simulation

A metabolic network can be broken down into a stoichiometric matrix where the rows represent the compounds of the reactions, while the columns of the matrix correspond to the reactions themselves. Stoichiometry

Stoichiometry

Stoichiometry is a branch of chemistry that deals with the relative quantities of reactants and products in chemical reactions. In a balanced chemical reaction, the relations among quantities of reactants and products typically form a ratio of whole numbers...

is a quantitative relationship between substrate

Substrate (chemistry)

In chemistry, a substrate is the chemical species being observed, which reacts with a reagent. This term is highly context-dependent. In particular, in biochemistry, an enzyme substrate is the material upon which an enzyme acts....

s of a chemical reaction (Merriam 2002). In order to deduce what the metabolic network suggests, recent research has centered on two approaches; namely extreme pathways and elementary mode analysis (Papin, Stelling, Price, Klamt, Schuster, and Palsson 2004).

Extreme Pathways

Price, Reed, Papin, Wiback and Palsson (2003) use a method of singular value decomposition (SVD) of extreme pathways in order to understand regulation of a human red blood cell

Red blood cell

Red blood cells are the most common type of blood cell and the vertebrate organism's principal means of delivering oxygen to the body tissues via the blood flow through the circulatory system...

metabolism. Extreme pathways are convex basis vectors

Basis (linear algebra)

In linear algebra, a basis is a set of linearly independent vectors that, in a linear combination, can represent every vector in a given vector space or free module, or, more simply put, which define a "coordinate system"...

that consist of steady state

Steady state

A system in a steady state has numerous properties that are unchanging in time. This implies that for any property p of the system, the partial derivative with respect to time is zero:...

functions of a metabolic network (Papin, Price, and Palsson 2002). For any particular metabolic network, there is always a unique set of extreme pathways available (Papin et al. 2004). Furthermore, Price et al. (2003) define a constraint-based approach, where through the help of constraints

Constraint (mathematics)

In mathematics, a constraint is a condition that a solution to an optimization problem must satisfy. There are two types of constraints: equality constraints and inequality constraints...

like mass balance

Mass balance

A mass balance is an application of conservation of mass to the analysis of physical systems. By accounting for material entering and leaving a system, mass flows can be identified which might have been unknown, or difficult to measure without this technique...

and maximum reaction rates, it is possible to develop a ‘solution space’ where all the feasible options fall within. Then, using a kinetic model approach, a single solution that falls within the extreme pathway solution space can be determined (Price et al. 2003). Therefore, in their study, Price et al. (2003) use both constraint and kinetic

Kinetic energy

The kinetic energy of an object is the energy which it possesses due to its motion.It is defined as the work needed to accelerate a body of a given mass from rest to its stated velocity. Having gained this energy during its acceleration, the body maintains this kinetic energy unless its speed changes...

approaches to understand the human red blood cell metabolism. In conclusion, using extreme pathways, the regulatory mechanisms of a metabolic network can be studied in further detail.

Elementary mode analysis

Elementary mode analysis closely matches the approach used by extreme pathways. Similar to extreme pathways, there is always a unique set of elementary modes available for a particular metabolic network (Papin et al. 2004). These are the smallest sub-networks that allow a metabolic reconstruction network to function in steady state (Schuster, Fell, and Dandekar 2000; Stelling, Klamt, Bettenbrock, Schuster, and Gilles 2002). According to Stelling et al. (2002), elementary modes can be used to understand cellular objectives for the overall metabolic network. Furthermore, elementary mode analysis takes into account stoichiometrics

Stoichiometry

and thermodynamics

Thermodynamics

Thermodynamics is a physical science that studies the effects on material bodies, and on radiation in regions of space, of transfer of heat and of work done on or by the bodies or radiation...

when evaluating whether a particular metabolic route or network is feasible and likely for a set of proteins/enzymes (Schuster et al. 2000).

Minimal metabolic behaviors (MMBs)

Recently, Larhlimi and Bockmayr (2009) presented a new approach called "minimal metabolic behaviors" for the analysis of metabolic networks. Like elementary modes or extreme pathways, these are uniquely determined by the network, and yield a complete description of the flux cone. However, the new description is much more compact. In contrast with elementary modes and extreme pathways, which use an inner description based on generating vectors of the flux cone, MMBs are using an outer description of the flux cone. This approach is based on sets of non-negativity constraints. These can be identified with irreversible reactions, and thus have a direct biochemical interpretation. One can characterize a metabolic network by MMBs and the reversible metabolic space.

Flux balance analysis

A different technique to simulate the metabolic network is to perform flux balance analysis

Flux balance analysis

Flux balance analysis is a mathematical method for analysing metabolism. It does not require knowledge of metabolite concentration or details of the enzyme kinetics of the system...

. This method uses linear programming

Linear programming

Linear programming is a mathematical method for determining a way to achieve the best outcome in a given mathematical model for some list of requirements represented as linear relationships...

, but in contrast to elementary mode analysis and extreme pathways, only a single solution results in the end. Linear programming is usually used to obtain the maximum potential of the objective function that you are looking at, and therefore, when using flux balance analysis, a single solution is found to the optimization problem (Stelling et al. 2002). In a flux balance analysis approach, exchange flux

Flux

In the various subfields of physics, there exist two common usages of the term flux, both with rigorous mathematical frameworks.* In the study of transport phenomena , flux is defined as flow per unit area, where flow is the movement of some quantity per time...

es are assigned to those metabolites that enter or leave the particular network only. Those metabolites that are consumed within the network are not assigned any exchange flux value. Also, the exchange fluxes along with the enzymes can have constraints ranging from a negative to positive value (ex: -10 to 10).

Furthermore, this particular approach can accurately define if the reaction stoichiometry is in line with predictions by providing fluxes for the balanced reactions. Also, flux balance analysis can highlight the most effective and efficient pathway through the network in order to achieve a particular objective function. In addition, gene knockout

Gene knockout

A gene knockout is a genetic technique in which one of an organism's genes is made inoperative . Also known as knockout organisms or simply knockouts, they are used in learning about a gene that has been sequenced, but which has an unknown or incompletely known function...

studies can be performed using flux balance analysis. The enzyme that correlates to the gene that needs to be removed is given a constraint value of 0. Then, the reaction that the particular enzyme catalyzes is completely removed from the analysis.

Dynamic simulation and parameter estimation

In order to perform a dynamic simulation with such a network it is necessary to construct an ordinary differential equation
system that describes the rates of change in each metabolite's concentration or amount. To this end, a rate law, i.e., a kinetic equation is required for each reaction. Often these rate laws contain kinetic parameters with uncertain values. In many cases it is desired to estimate these parameter values with respect to given time-series data of metabolite concentrations. The system is then supposed to reproduce the given data. For this purpose the distance between the given data set and the result of the simulation, i.e., the numerically or in few cases analytically obtained solution of the differential equation system is computed. The values of the parameters are then estimated to minimize this distance (Dräger et al. 2009). One step further, it may be desired to estimate the mathematical structure of the differential equation system because the real rate laws are not known for the reactions within the system under study. To this end, the program SBMLsqueezer allows automatic creation of appropriate rate laws for all reactions with the network.

Conclusion

In conclusion, metabolic network reconstruction and simulation can be effectively used to understand how an organism or parasite functions inside of the host cell. For example, if the parasite serves to compromise the immune system

Immune system

An immune system is a system of biological structures and processes within an organism that protects against disease by identifying and killing pathogens and tumor cells. It detects a wide variety of agents, from viruses to parasitic worms, and needs to distinguish them from the organism's own...

by lysing macrophages, then the goal of metabolic reconstruction/simulation would be to determine the metabolites that are essential to the organism's proliferation inside of macrophages. If the proliferation cycle is inhibited, then the parasite would not continue to evade the host's immune system. A reconstruction model serves as a first step to deciphering the complicated mechanisms surrounding disease. The next step would be to use the predictions and postulates generated from a reconstruction model and apply it to drug delivery

Drug delivery

Drug delivery is the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals. Drug delivery technologies modify drug release profile, absorption, distribution and elimination for the benefit of improving product efficacy and safety, as well...

and drug-engineering techniques.

Currently, many tropical diseases affecting third world nations are very inadequately characterized, and thus poorly understood. Therefore, a metabolic reconstruction and simulation of the parasites that cause the tropical diseases would aid in developing new and innovative cures and treatments.

External links

ERGO
GeneDB
KEGG
PathCase Case Western Reserve University
BRENDA
BioCyc and Cyclone - provides an open source Java API to the pathway tool BioCyc to extract Metabolic graphs.
EcoCyc
MetaCyc
SEED
Model SEED
ENZYME
SBRI Bioinformatics Tools and Software
TIGR
Pathway Tools
metaTIGER
Stanford Genomic Resources
Pathway Hunter Tool
IMG The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI.
Systems Analysis, Modelling and Prediction Group at the University of Oxford, Biochemical reaction pathway inference techniques.
EFMtool provided by Marco Terzer
SBMLsqueezer
Cellnet analyzer from Klamt and von Kamp
Copasi

The source of this article is wikipedia, the free encyclopedia. The text of this article is licensed under the GFDL.

Resources

Next steps of the reconstruction

Advantages of a reconstruction

Metabolic network simulation

Extreme Pathways

Elementary mode analysis

Minimal metabolic behaviors (MMBs)

Flux balance analysis

Dynamic simulation and parameter estimation

Conclusion

See also

External links