Rohwer2001_SucroseView the 2009-05 Model of the Month entry for this model
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To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
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- Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data.
- Rohwer JM, Botha FC
- The Biochemical journal , 9/ 2001 , Volume 358 , pages: 437-445 , PubMed ID: 11513743
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, 7602 Matieland, South Africa. email@example.com
- Sucrose accumulation in developing sugar cane (Saccharum officinarum) is accompanied by a continuous synthesis and cleavage of sucrose in the storage tissues. Despite numerous studies, the factors affecting sucrose accumulation are still poorly understood, and no consistent pattern has emerged which pinpoints certain enzyme activities as important controlling steps. Here, we develop an approach based on pathway analysis and kinetic modelling to assess the biochemical control of sucrose accumulation and futile cycling in sugar cane. By using the concept of elementary flux modes, all possible routes of futile cycling of sucrose were enumerated in the metabolic system. The available kinetic data for the pathway enzymes were then collected and assembled in a kinetic model of sucrose accumulation in sugar cane culm tissue. Although no data were fitted, the model agreed well with independent experimental results: in no case was the difference between calculated and measured fluxes and concentrations greater than 2-fold. The model thus validated was then used to assess different enhancement strategies for increasing sucrose accumulation. First, the control coefficient of each enzyme in the system on futile cycling of sucrose was calculated. Secondly, the activities of those enzymes with the numerically largest control coefficients were varied over a 5-fold range to determine the effect on the degree of futile cycling, the conversion efficiency from hexoses into sucrose, and the net sucrose accumulation rate. In view of the modelling results, overexpression of the fructose or glucose transporter or the vacuolar sucrose import protein, as well as reduction of cytosolic neutral invertase levels, appear to be the most promising targets for genetic manipulation. This offers a more directed improvement strategy than cumbersome gene-by-gene manipulation. The kinetic model can be viewed and interrogated on the World Wide Web at http://jjj.biochem.sun.ac.za.
|BIOMD0000000023_url.xml||SBML L2V4 representation of Rohwer2001_Sucrose||54.57 KB||Preview | Download|
|BIOMD0000000023-biopax2.owl||Auto-generated BioPAX (Level 2)||33.79 KB||Preview | Download|
|BIOMD0000000023.pdf||Auto-generated PDF file||193.97 KB||Preview | Download|
|BIOMD0000000023_urn.xml||Auto-generated SBML file with URNs||53.80 KB||Preview | Download|
|BIOMD0000000023.m||Auto-generated Octave file||11.34 KB||Preview | Download|
|BIOMD0000000023.svg||Auto-generated Reaction graph (SVG)||25.55 KB||Preview | Download|
|BIOMD0000000023-biopax3.owl||Auto-generated BioPAX (Level 3)||46.41 KB||Preview | Download|
|BIOMD0000000023.sci||Auto-generated Scilab file||9.67 KB||Preview | Download|
|BIOMD0000000023.vcml||Auto-generated VCML file||55.45 KB||Preview | Download|
|BIOMD0000000023.png||Auto-generated Reaction graph (PNG)||98.72 KB||Preview | Download|
|BIOMD0000000023.xpp||Auto-generated XPP file||7.87 KB||Preview | Download|
- Model originally submitted by : Nicolas Le Novère
- Submitted: 13-Sep-2005 14:28:04
- Last Modified: 20-May-2012 13:43:33
- Submitted on: 20-May-2012 13:43:33
- Submitted by: Nicolas Le Novère
- With comment: Current version of Rohwer2001_Sucrose
- Submitted on: 13-Sep-2005 14:28:04
- Submitted by: Nicolas Le Novère
- With comment: Original import of Rohwer2001_Sucrose
(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
sucrose ; Sucrose
UDP ; UDP
ADP ; ADP
ATP ; ATP
D-fructose ; D-Fructose
D-fructose ; D-Fructose
D-glucose ; D-Glucose
beta-D-glucose 1-phosphate ; keto-D-fructose 6-phosphate ; D-glucose 6-phosphate ; UDP-glucose ; alpha-D-Glucose 6-phosphate ; D-Fructose 6-phosphate ; D-Glucose 1-phosphate ; UDP-D-glucose
|Suc6P => Suc + phos||compartment*Vmax7*Suc6P/(Km7Suc6P+Suc6P)||Vmax7=0.5; Km7Suc6P=0.1|
|HexP + Fru => Suc + UDP||compartment*(-Vmax8f)*(Suc*UDP-Fru*0.8231*HexP/Keq8)/(Suc*UDP*(1+Fru/Ki8Fru)+Km8Suc*(UDP+Ki8UDP)+Km8UDP*Suc+Vmax8f/(Vmax8r*Keq8)*(Km8UDPGlc*Fru*(1+UDP/Ki8UDP)+0.8231*HexP*(Km8Fru*(1+Km8UDP*Suc/(Ki8UDP*Km8Suc))+Fru*(1+Suc/Ki8Suc))))||Ki8Suc=40.0; Vmax8f=0.677; Km8Suc=50.0; Keq8=5.0; Ki8Fru=4.0; Ki8UDP=0.3; Km8UDP=0.3; Km8UDPGlc=0.3; Vmax8r=0.3; Km8Fru=4.0|
|Suc => Fru + Glc||compartment*Vmax9/(1+Glc/Ki9Glc)*Suc/(Km9Suc*(1+Fru/Ki9Fru)+Suc)||Ki9Glc=15.0; Vmax9=0.372; Km9Suc=10.0; Ki9Fru=15.0|
|Suc => Sucvac||compartment*Vmax11*Suc/(Km11Suc+Suc)||Km11Suc=100.0; Vmax11=1.0|
|HexP => UDP + Suc6P; phos||compartment*Vmax6f*(0.0575*HexP*0.8231*HexP-Suc6P*UDP/Keq6)/(0.0575*HexP*0.8231*HexP*(1+Suc6P/Ki6Suc6P)+Km6F6P*(1+phos/Ki6Pi)*(0.8231*HexP+Ki6UDPGlc)+Km6UDPGlc*0.0575*HexP+Vmax6f/(Vmax6r*Keq6)*(Km6UDP*Suc6P*(1+0.8231*HexP/Ki6UDPGlc)+UDP*(Km6Suc6P*(1+Km6UDPGlc*0.0575*HexP/(Ki6UDPGlc*Km6F6P*(1+phos/Ki6Pi)))+Suc6P*(1+0.0575*HexP/Ki6F6P))))||Km6UDP=0.3; Ki6Suc6P=0.07; Km6F6P=0.6; Ki6F6P=0.4; Keq6=10.0; Vmax6r=0.2; Km6UDPGlc=1.8; Km6Suc6P=0.1; Ki6Pi=3.0; Vmax6f=0.379; Ki6UDPGlc=1.4|
|ATP + Glc => HexP + ADP; Fru||compartment*Vmax3*Glc/Km3Glc*ATP/Km3ATP/((1+ATP/Km3ATP)*(1+Glc/Km3Glc+Fru/Km4Fru+0.113*HexP/Ki3G6P+0.0575*HexP/Ki4F6P))||Km3ATP=0.25; Ki3G6P=0.1; Km3Glc=0.07; Km4Fru=10.0; Vmax3=0.197; Ki4F6P=10.0|
|Fru + ATP => HexP + ADP||compartment*Vmax5/(1+Fru/Ki5Fru)*Fru/Km5Fru*ATP/Km5ATP/(1+Fru/Km5Fru+ATP/Km5ATP+Fru*ATP/(Km5Fru*Km5ATP)+ADP/Ki5ADP)||Ki5Fru=12.0; Km5Fru=0.1; Vmax5=0.164; Km5ATP=0.085; Ki5ADP=2.0|
|Fru + ATP => HexP + ADP; Glc||compartment*Vmax4*Fru/Km4Fru*ATP/Km4ATP/((1+ATP/Km4ATP)*(1+Glc/Km3Glc+Fru/Km4Fru+0.113*HexP/Ki3G6P+0.0575*HexP/Ki4F6P))||Vmax4=0.197; Ki3G6P=0.1; Km3Glc=0.07; Km4Fru=10.0; Km4ATP=0.25; Ki4F6P=10.0|
|Fruex => Fru||compartment*Vmax1*Fruex/(Km1Fruex*(1+Fru/Ki1Fru)+Fruex)||Km1Fruex=0.2; Ki1Fru=1.0; Vmax1=0.286|
(added: 18 Jan 2010, 12:55:48, updated: 18 Jan 2010, 12:55:48)