Table S1. Enzyme kinetic parameters used in the model. In case values for parameters were assumed, a flux control coefficient was determined by increasing and decreasing the value by 20%.
EC / Paremeters / Reference1.2.1.9 / KmNADP+=0.017 mM / (Iglesias and Losada, 1988)
KmGAP=0.75 mM / (Iglesias and Losada, 1988)
KiPGA_GAP=0.75 mM / (Iglesias and Losada, 1988)
KiNADH_NADP+=0.0073 mM / (Iglesias and Losada, 1988)
Vmax=108 μmol m-2 s-1 / (Rosenberg and Arnon, 1955), Estimated
Flux control coefficient=0
1.2.1.12 / KmGAP=0.4 mM / (Speranza and Gozzer, 1978)
KmNAD+=0.25 mM / (Speranza and Gozzer, 1978)
Ke=0.156 / (Speranza and Gozzer, 1978)
Vmax=0.3 μmol m-2 s-1 / Assumed
Flux control coefficient=0
2.7.2.3cyt / KmADP=0.27 mM / (Kuntz and Krietsch, 1982)
KmATP=0.3 mM / (Kuntz and Krietsch, 1982)
KmPGA=1.1 mM / (Kuntz and Krietsch, 1982)
Ke=3.1*10-4 / (Kuntz and Krietsch, 1982)
Vmax=48.0 μmol m-2s-1 / (Laisk and Edwards, 2000), Estimated
Flux control coefficient=0
5.4.2.1 and 4.2.1.11 / KmPGA=0.1 mM / (Laisk and Edwards, 2000)
KmPEP=0.5 mM / (Laisk and Edwards, 2000)
Ke=0.4302 / (Laisk and Edwards, 2000)
Vmax=30.0 μmol m-2 s-1 / (Laisk and Edwards, 2000), Estimated
Flux control coefficient=0
2.7.1.40 / KmADP=0.037 mM / (Hu and Plaxton, 1996)
KmPEP=0.033 mM / (Hu and Plaxton, 1996)
Ke=6452 / (Hu and Plaxton, 1996)
Vmax=0.6 μmol m-2 s-1 / (Kowallik and Ruyters, 1976), Estimated
Flux control coefficient=0
4.1.1.31 / KmPEP=0.2 mM / (Tripodi et al., 2005)
Vmax=30.0 μmol m-2 s-1 / (Gehlen et al., 1996)
2.6.1.1 / KmGLU=13.2 mM / (Yagi et al., 1993)
KmOAA=0.048 mM / (Yagi et al., 1993)
KmASP=3.7 mM / (Yagi et al., 1993)
KmKG=0.105 mM / (Yagi et al., 1993)
Vmax=60.0 μmol m-2 s-1 / (Griffith and Vance, 1989),Estimated
Flux control coefficient=0
1.1.1.41 / KmICIT=0.12 mM / (Igamberdiev and Gardeström, 2003)
KmNAD+=0.2 mM / (Igamberdiev and Gardeström, 2003)
KiNADPH_NAD+=0.26 mM / (Igamberdiev and Gardeström, 2003)
KiNADH_NAD+=0.18 mM / (Igamberdiev and Gardeström, 2003)
Vmax=30.0 μmol m-2 s-1 / EstimatedFlux control coefficient=0
4.2.1.3 / KmICIT=0.031 mM / (Pickworth Glusker, 1971)
KmCIT=0.4 mM / (Pickworth Glusker, 1971)
Vmax=30.0 μmol m-2 s-1 / (Brouquisse et al., 1987)
2.3.3.1 / KmAceCoA=0.031 mM / (Iredale, 1979)
KmOAA=0.016 mM / (Iredale, 1979)
KiATP_AceCoA=5.0 mM / (Iredale, 1979)
Vmax=60.0 μmol m-2 s-1 / Assumed
Flux control coefficient=0
4.1.1.39 / KmCO2=0.008 mM / (Makino et al., 1985)
KmO2=0.37 mM / (Makino et al., 1985)
KmRuBP=0.020 mM / (Farquhar, 1979)
KiPGA=0.84 mM / (Badger and Lorimer, 1981)
KiFBP=0.04 mM / (Badger and Lorimer, 1981)
KiSBP=0.075 mM / (Badger and Lorimer, 1981)
KiPi=0.9 mM / (Badger and Lorimer, 1981)
KiNADPH=0.07 mM / (Badger and Lorimer, 1981)
VCmax=87.4 μmol m-2 s-1
VOmax=29.7 μmol m-2 s-1 / (Kanai and Edwards, 1999; Caemmerer, 2000)
2.7.2.3chl / KmGPA=0.24 mM / (Larsson-Raźnikiewicz, 1967; Köpke-Secundo et al., 1990)
KmATP=0.39 mM / (Larsson-Raźnikiewicz, 1967; Köpke-Secundo et al., 1990)
KmADP=0.23 mM / (Lee 1982)
Ke=7.6 * 10-4 / (Dietz and Heber, 1984; Laisk et al., 1989)
Vmax=600 μmol m-2 s-1 / (Laisk and Edwards, 2000), Estimated
Flux control coefficient=0
1.2.1.13 / KmBPGA=0.004 mM / (Trost et al., 1993)
KmNADPH=0.1 mM / (Zhu et al., 2007)
Vmax=121 μmol m-2 s-1 / (Laisk and Edwards, 2000), Estimated
Flux control coefficient=0
5.3.1.1 / Ke=0.05 / (Bassham and Krause, 1969)
KmGAP=0.68 mM / (Kurzok and Feierabend, 1984)
KmDHAP=2.5 mM / (Laisk and Edwards, 2000)
Vmax=3000 μmol m-2 s-1 / Assumed
Flux control coefficient=0
4.1.2.13FBP / KmGAP=0.3 mM / (Iwaki et al., 1991)
KmDHAP=0.4 mM / (Iwaki et al., 1991)
KmFBP=0.02 mM / (Brooks and Criddle, 1966; Schnarrenberger et al., 1986)
Ke=7.1 / (Bassham and Krause, 1969)
Vmax=58.5 μmol m-2 s-1 / (Wang et al, 2014)
3.1.3.11 / KmFBP=0.033 mM / (Charles and Halliwell, 1981)
KiF6P=0.7 mM / (Heldt 1983)
KiPi=12 mM / (Charles and Halliwell, 1981)
Ke=6.7*105 / Bassham and Krause (1969), Laisk et al. (1989)
Vmax=21.0 μmol m-2 s-1 / (Zhu et al., 2007),with modification1
Flux control coefficient=0
2.2.1.1F6P / KmF6P=0.1 mM / (Wang et al., 2014)
KmE4P=0.1 mM / (Wang et al., 2014)
KmXu5P=0.1 mM / (Laisk et al., 1989)
KmGAP=0.1 mM / (Sprenger et al., 1995)
Ke=0.08 / (Datta and Racker, 1961)
Vmax=93.0 μmol m-2 s-1 / (Zhu et al., 2007),with modification1
Flux control coefficient=0
4.1.2.13SBP / KmSBP=0.02 mM / (Brooks and Criddle, 1966)
KmDHAP=0.4 mM / (Iwaki et al., 1991)
KmE4P=0.2 mM / (Zhu et al., 2007)
Ke=1.07 / (Bassham and Krause, 1969; Laisk et al., 1989)
Vmax=36.6 μmol m-2 s-1 / (Zhu et al., 2007), with modification1
Flux control coefficient=0
3.1.3.37 / KmSBP=0.05 mM / (Woodrow and Walker, 1983; Cadet and Meunier, 1988)
KiPi=12 mM / (Woodrow and Walker, 1983)
Ke=6.7*105 / (Bassham and Krause, 1969; Laisk et al., 1989)
Vmax=29.2 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.2.1.1S7P / KmGAP=0.072 mM / (Laisk et al., 1989; Albe, 1991)
KmRi5P=1.5 mM / (Laisk et al., 1989; Albe, 1991)
KmS7P=0.46 mM / (Laisk et al., 1989; Albe, 1991)
KmXu5P=0.1 mM / (Laisk et al., 1989; Albe, 1991)
Ke=1.176 / (Bassham and Krause, 1969; Laisk et al., 1989)
Vmax=93.0 μmol m-2 s-1 / (Zhu et al., 2007),with modification1
Flux control coefficient=0
2.7.1.19 / KiADP=2.5 mM / (Gardemann et al., 1983)
KiADP=0.4 mM / (Gardemann et al., 1983)
KiPGA=2.0 mM / (Gardemann et al., 1983)
KiPi=4.0 mM / (Gardemann et al., 1983)
KiRuBP=0.7 mM / (Gardemann et al., 1983)
KmATP=0.625 mM / (Slabas and Walker, 1976)
KmRu5P=0.05 mM / (Gardemann et al., 1983; Omnaas et al., 1985)
Ke=6846 / (Bassham and Krause, 1969; Laisk et al., 1989)
Vmax=1170.0 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
3.6.3.14 / KmADP=0.014 mM / (Davenport and McCarty, 1986)
KmPi=0.3 mM / (Aflalo and Shavit, 1983)
KmATP=0.3 mM / (Laisk et al., 1989)
Ke=5.7 / (Bassham and Krause, 1969; Laisk et al., 1989)
Vmax=180 μmol m-2 s-1 / (Wang et al., 2014),with modification1
Flux control coefficient=0
5.3.1.9chl / Ke=2.3 / (Bassham and Krause 1969)
Vmax=49.4 μmol m-2 s-1 / (Zhu et al., 2007),with modification1
Flux control coefficient=0
5.4.2.2 / Ke=0.058 / (Colowick and Sutherland, 1942)
Vmax=300 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.7.7.27 / KmG1P=0.031 mM / (Copeland and Preiss, 1981)
KmATP=0.045 mM / (Copeland and Preiss, 1981)
KaPGA=0.2252 mM / (Wang et al., 2014)
KiPi_ATP=0.97 mM / (Copeland and Preiss, 1981)
KmPPi=0.033 mM / (Amir and Cherry, 1972)
KmADPG=0.24 mM / (Sowokinos, 1981)
KiADP_ATP=2.0 mM / (Ghosh and Preiss, 1966)
KiPPi_ATP=3.8*10-4 mM / (Amir and Preiss, 1982)
Ke=1.1 / (Espada, 1962)
Vmax=30 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
3.6.1.1 / KmPPi=0.154 mM / (Van et al., 2005)
Ke=1.57*10-4 / (Flodgaard and Fleron, 1974)
Vmax=3000 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.4.1.21 / KmADPG=0.077 mM / (Hawker et al., 1974)
Vmax=30 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
3.1.3.18 / KmPGCA=0.026 mM / (Christeller and Tolbert, 1978)
KiPi=2.55 mM / (Christeller and Tolbert, 1978)
KiGCA=94 mM / (Christeller and Tolbert, 1978)
Vmax=1572 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.7.1.31 / KmATP=0.21 mM / (Kleczkowski et al., 1985)
KmGCEA=0.25 mM / (Kleczkowski et al., 1985)
KiPGA=0.36 mM / (Kleczkowski et al., 1986)
Ke=300 / (Kleczkowski et al., 1985)
Vmax=300 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
1.1.3.15 / KmGCA=0.1 mM / (Tolbert, 1981)
Vmax=44 μmol m-2 s-1 / (Zhu et al., 2007), with modification1
Flux control coefficient=0
2.6.1.45 / Ke=0.24 / (Zhu et al., 2007)
KmGOA=0.15 mM / (Nakamura and Tolbert, 1983)
KmSER=2.7 mM / (Nakamura and Tolbert, 1983)
KiGLY=33 mM / (Nakamura and Tolbert, 1983)
Vmax=100 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
1.1.1.29 / KiHPR=12 mM / (Kleczkowski and Edwards, 1989)
KmHPR=0.09 mM / (Kleczkowski and Edwards, 1989)
Ke=2.5*10-5 / (Zhu et al., 2007)
Vmax=300 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.6.1.4 / Ke=607 / (Cooper and Meister, 1972)
Vmax=82.4 μmol m-2 s-1 / (Zhu et al., 2007), with modification1
Flux control coefficient=0
KmGOA=0.15 mM / (Nakamura and Tolbert 1983)
KmGLU=1.7 mM / (Nakamura and Tolbert 1983)
KiGLY=2.0 mM / (Zhu et al., 2007)
GLy_Ser / KmGLY=6.0 mM / (Douce et al., 2001)
KiSER=4.0 mM / (Douce et al., 2001)
Vmax=75 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
Tgca / KmGCA=0.2 mM / (Howitz and McCarty, 1985)
KiGCEA=0.22 mM / (Howitz and McCarty, 1985)
Vmax=300 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
Tgcea / KmGCEA=0.39 mM / (Howitz and McCarty, 1985)
KiGCA=0.28 mM / (Howitz and McCarty, 1985)
Vmax=250 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
4.1.2.13Cyt / KmFBP=0.02 mM / (Brooks and Criddle, 1966; Schnarrenberger et al., 1986)
KmGAP=0.3 mM / (Iwaki et al., 1991)
KmDHAP=0.45 mM / (Iwaki et al., 1991)
Ke=12 / (Zhu et al., 2007)
Vmax=21 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.7.7.9 / KmG1P=0.055 mM / (Sowokinos et al., 1993)
KmUTP=0.1 mM / (Nakano et al., 1989)
KmUDPG=0.12 mM / (Nakano et al., 1989)
KmPPi=0.11 mM / (Nakano et al., 1989)
Ke=0.31 / (Nakano et al., 1989)
Vmax=33.5 μmol m-2 s-1 / (Zhu et al., 2007), with modification1
Flux control coefficient=0
2.4.1.14 / KmF6P=0.8 mM / (Lunn and ap Rees, 1990)
KmUDPG=1.3 mM / (Lunn and ap Rees, 1990)
KiUDP=0.7 mM / (Harbron et al., 1981)
KiFBP=0.8 mM / (Harbron et al., 1981)
KiSUCP=0.4 mM / (Harbron et al., 1981)
KiPi=1.75 mM / (Amir and Preiss, 1982)
KiSucrose=50 mM / (Salerno and Pontis, 1978)
Ke=10 / (Lunn and ap Rees, 1990)
Vmax=46.6 μmol m-2 s-1 / (Zhu et al., 2007), with modification1
Flux control coefficient=0
3.1.3.24 / KmSUCP=0.105 mM / (Echeverria et al., 1997)
KiSUC=80 mM / (Whitaker, 1984)
Ke=780 / (Lunn and ap Rees, 1990)
Vmax=27.8 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
3.1.3.46 / KmF26BP=0.032 mM / (Macdonald et al., 1989)
KiF6P=0.1 mM / (Villadsen and Nielsen, 2001)
KiPi=0.5 mM / (Villadsen and Nielsen, 2001)
Vmax=21 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.7.1.105 / KiADP=0.16 mM / (Kretschmer and Hofmann, 1984)
KiDHAP=0.7 mM / (Markham and Kruger, 2002)
KmF6P=1.4 mM / (Markham and Kruger, 2002)
KmATP=1.32 mM / (Markham and Kruger, 2002)
KmF26BP=0.021 mM / (Defrutos and Baanante, 1994)
Ke=590 / (Cornish-Bowden 1997)
Vmax=33 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
2.7.1.90 / KmF6P=0.3 mM / (Mahajan and Singh, 1989)
KmPPi=0.025 mM / (Mahajan and Singh, 1989)
KmFBP=0.139 mM / (Mahajan and Singh, 1989)
KmPi=0.129 mM / (Mahajan and Singh, 1989)
KiPi_F6P=0.78 mM / (Mahajan and Singh, 1989)
KiPi_PPi=1.2 mM / (Mahajan and Singh, 1989)
Vmax=30 μmol m-2 s-1 / (Zhu et al., 2007), with modification1
Flux control coefficient=0
5.3.1.9Cyt / Ke=2.3 / (Bassham and Krause, 1969)
KmF6P=0.58 mM / (Backhausen et al., 1997)
KmG6P=8.0 mM / (Backhausen et al., 1997)
Vmax=30 μmol m-2 s-1 / (Zhu et al., 2007; Wang et al., 2014)
1.4.7.1 / KmGLN=0.53 mM / (Hirasawa and Tamura, 1984)
KmKG=0.062 mM / (Hirasawa and Tamura, 1984)
KmFDXH=0.002 mM / (Hirasawa et al., 1986)
Vmax=3 μmol m-2 s-1 / Assumed
Flux control coefficient=0
6.3.1.2 / Ke=3000 / (Ericson, 1985)
KmATP=1.8 mM / (Ericson, 1985)
KmGLU=6.7 mM / (Ericson, 1985)
KmNH3=0.4 mM / (Pushkin et al., 1985)
Vmax=45 μmol m-2 s-1 / Assumed
Flux control coefficient=0.00
1.4.1.3 / Ke=71429.0 / (Moyano et al., 1992)
KmNADPH=1.75*10-4 mM / (Moyano et al., 1992)
KmKG=0.59 mM / (Moyano et al., 1992)
KmNH3=0.0424 mM / (Engel and Dalziel, 1969)
Vmax=2.4 μmol m-2 s-1 / Assumed
Flux control coefficient=0
1.1.99.14 / KmGCA=0.04 mM / (Lord, 1972)
Vmax=15 μmol m-2 s-1 / Estimated to make sure 50% of the photorespiratory went through the bypass
4.1.1.47 / KmGOA=0.9 mM / (Kaplun et al., 2008)
Vmax=30 μmol m-2 s-1 / Assumed
Flux control coefficient=0 (Kebeish bypass and Carvalho bypass)
1.1.1.60 / Ke=1.6 * 10-5 / (Gotto and Kornberg, 1961)
KmGCEA=0.278 mM / (Njau et al., 2000)
KmNAD+=0.028 mM / (Njau et al., 2000)
kmTS=0.05 mM / (Kohn, 1968)
KmNADH=0.02 mM / (Kohn, 1968)
Vmax=300 μmol m-2 s-1 / Assumed
Flux control coefficient=0 (Kebeish bypass)
2.3.3.9 / KmGOA=2 mM / (Bowden and Lord, 1978)
KmAceCoA=0.01 mM / (Bowden and Lord, 1978)
KiGCA=0.15 mM / (Bowden and Lord, 1978)
Vmax=43.5 μmol m-2 s-1 / Assumed
Flux control coefficient=0.33 (Maier bypass)
1.1.1.40 / Ke=0.051 / (Harary et al., 1953)
kmMAL=0.23 mM / (Wheeler et al., 2005)
KmNADP+=0.0102 mM / (Wheeler et al., 2005)
KmPYR=26.3 mM / (Wheeler et al., 2005)
Vmax=30 μmol m-2 s-1 / Assumed
Flux control coefficient=0 (Maier bypass)
1.2.4.1 / KmPYR=0.09 mM / (Rapp et al., 1987)
KmCOA=0.003 mM / (Rapp et al., 1987)
KmNAD+=0.051 mM / (Rapp et al., 1987)
KiAceCoA=0.02 mM / (Rapp et al., 1987)
KiNADH=0.015 mM / (Rapp et al., 1987)
Vmax=300 μmol m-2 s-1 / Assumed
Flux control coefficient=0.01 (Maier bypass)
5.3.1.22 / Vmax=43.5 μmol m-2 s-1 / (Ashiuchi and Misono, 1999)
Ke=0.4 / (De Windt and Van Der Drift, 1980)
KmHPR=12.5 mM / (Ashiuchi and Misono, 1999)
KmTS=15 mM / Assumed
Flux control coefficient=0 (Carvalho bypass)
5.1.3.1 / Ke=0.67 / (Bassham and Krause 1969)
5.3.1.6 / Ke=0.4 / (Bassham and Krause 1969)
GDC / KmGLY=6.0 mM / (Zhu et al., 2007)
KISER=4.0 mM / (Zhu et al., 2007)
Vmax=75μmol m-2 s-1 / (Zhu et al., 2007)
Tglu / KmGLU=1.2 mM / (Flügge et al., 1988)
KIKG =0.7 mM / (Flügge et al., 1988)
KIMAL=1.2 mM / (Flügge et al., 1988)
Vmax=12.6 μmol m-2 s-1 / (Flügge et al., 1988)
Tkg / KmKG=0.3 mM / (Yu and Woo, 1992)
KIMAL=3.1 mM / (Flügge et al., 1988)
KIGLU=2.2 mM / (Flügge et al., 1988)
Vmax=58.2 μmol m-2 s-1 / (Yu and Woo, 1992)
2.7.4.6 / KmATP =0.89 mM / (Nomura et al., 1991)
KmUDP =0.091 mM / (Nomura et al., 1991)
Ke= 1.04 / (Lynn and Guynn, 1978)
Vmax=183 / (Zhu et al., 2007)
SucSink / KmSUC=1.5 mM / (Riesmeier et al., 1992)
Vmax=0.21μmol m-2 s-1 / (Zhu et al., 2007)
Tpga / KIGAP=0.3 mM / (Gross et al., 1990)
KmPi =0.28 mM / (Gross et al., 1990)
KIDHAP=0.3 mM / (Gross et al., 1990)
KI2PGA =3.9 mM / (Gross et al., 1990)
KIPGA =0.32 mM / (Gross et al., 1990)
KIPEP=4.7 mM / (Gross et al., 1990)
KmGAP=0.075 mM / (Fliege et al., 1978; Zhu et al., 2007)
kmPGA=0.25 mM / (Fliege et al., 1978; Zhu et al., 2007)
Vmax=42.6 μmol m-2 s-1 / (Zhu et al., 2007)
Tgap / KmPi =0.28 mM / (Gross et al., 1990)
KIGAP =0.3 mM / (Gross et al., 1990)
KIPEP =4.7 mM / (Gross et al., 1990)
KIPGA =3.9 mM / (Gross et al., 1990)
KIPGA =0.32 mM / (Gross et al., 1990)
KIDHAP =0.3 mM / (Gross et al., 1990)
KmGAP =0.075 mM / (Fliege et al., 1978; Zhu et al., 2007)
KmPGA =0.25 mM / (Fliege et al., 1978; Zhu et al., 2007)
KmDHAP =0.077 mM / (Fliege et al., 1978; Zhu et al., 2007)
Vmax=42.6 μmol m-2 s-1 / (Zhu et al., 2007)
Tdhap / KmPi =0.28 mM / (Gross et al., 1990)
KIGAP =0.3 mM / (Gross et al., 1990)
KIPEP =4.7 mM / (Gross et al., 1990)
KIPGA =3.9 mM / (Gross et al., 1990)
KIPGA =0.32 mM / (Gross et al., 1990)
KIDHAP =0.3 mM / (Gross et al., 1990)
KmGAP =0.075 mM / (Fliege et al., 1978; Zhu et al., 2007)
KmPGA =0.25 mM / (Fliege et al., 1978; Zhu et al., 2007)
KmDHAP =0.077 mM / (Fliege et al., 1978; Zhu et al., 2007)
Vmax=162.6 μmol m-2 s-1 / (Zhu et al., 2007)
1 Zhu et al. (2007) assumed a relatively high Rubisco capacity per unit area. To tailor our model closer to the Arabidopsis plants in which the bypasses were implemented, we reduced the Vcmax of Rubisco per unit area to a value more likely for Arabidopsis. Other enzyme activities from Zhu et al. were scaled with the same factor.
Table S2. Initial values of metabolite concentrations used in the model.
Metabolitename / Concentration (mM) / Compartment / Reference
CO2 / 0.004 / Chloroplast / Assumed
PGA / 6.188 / Chloroplast / (Zhu et al., 2007)
DPGA / 0.005 / Chloroplast / (Zhu et al., 2007)
RuBP / 2.0 / Chloroplast / (Bassham and Krause, 1969; Dietz and Heber, 1984; Woodrow and Mott, 1993)
ATP / 1.49 / Chloroplast / (Zhu et al., 2007)
ATP / 1.35 / Chloroplast / (Zhu et al., 2007)
PGCA / 1.29 / Chloroplast / (Zhu et al., 2007)
GCA / 5.22 / Chloroplast / (Zhu et al., 2007)
GCEA / 1.68 / Chloroplast / (Zhu et al., 2007)
PPi / 0 / Chloroplast / Assumed
ADPG / 0 / Chloroplast / Assumed
GAP / 0.15 / Chloroplast / (Zhu et al., 2007)
Pi / 0.35 / Chloroplast / (Zhu et al., 2007)
DHAP / 6 / Chloroplast / (Zhu et al., 2007)
GOA / 0 / Chloroplast / Assumed
TS / 0 / Chloroplast / Assumed
Ri5P / 0.415 / Chloroplast / (Zhu et al., 2007)
Xu5P / 0.05 / Chloroplast / (Zhu et al., 2007)
Ru5P / 0.07 / Chloroplast / (Zhu et al., 2007)
O2 / 0.2646 / Chloroplast / (Zhu et al., 2007)
NH3 / 0.2 / Chloroplast / Assumed
Malate / 3.0 / Chloroplast / (Heineke et al., 1991)
FDXH / 0.1 / Chloroplast / Assumed
FDX / 0.1 / Chloroplast / Assumed
KG / 0.16 / Chloroplast / (Heineke et al., 1991)
GLU / 25.2 / Chloroplast / (Heineke et al., 1991)
GLN / 20 / Chloroplast / (Winter et al., 1994)
NAD+ / 1 / Chloroplast / Assumed
NADH / 1 / Chloroplast / Assumed
NADPH / 0.21 / Chloroplast / (Woodrow and Mott, 1993; Zhu et al., 2007)
NADP+ / 0.79 / Chloroplast / (Woodrow and Mott, 1993; Zhu et al., 2007)
SBP / 0.3 / Chloroplast / (Bassham and Krause, 1969; Woodrow and Mott, 1993; Zhu et al., 2007)
S7P / 0.4 / Chloroplast / (Bassham and Krause, 1969; Woodrow and Mott, 1993; Zhu et al., 2007)
FBP / 0.03 / Chloroplast / (Leegood, 1985; Zhu et al., 2007)
E4P / 0.2 / Chloroplast / (Bassham and Krause, 1969; Woodrow and Mott, 1993)
Starch / 0 / Chloroplast / Assumed
F6P / 0.1 / Chloroplast / (Zhu et al., 2007)
G6P / 0.25 / Chloroplast / (Zhu et al., 2007)
G1P / 0.015 / Chloroplast / (Zhu et al., 2007)
AceCOA / 0.035 / Chloroplast / Assumed
CoA / 0.002 / Chloroplast / Assumed
GCA / 0.0185 / Peroxisome / (Zhu et al., 2007)
GOA / 0.0073 / Peroxisome / (Zhu et al., 2007)
O2 / 0.265 / Peroxisome / Assumed
GLY / 1.32 / Peroxisome / Assumed
GLU / 24 / Peroxisome / (Heineke et al., 1991; Hu and Plaxton, 1996)
KG / 0.4 / Peroxisome / (Heineke et al., 1991; Hu and Plaxton, 1996)
HPR / 0.0022 / Peroxisome / (Zhu et al., 2007)
GCEA / 0.667 / Peroxisome / (Zhu et al., 2007)
NADH / 0.47 / Peroxisome / Assumed
NAD+ / 0.4 / Peroxisome / Assumed
TS / 0 / Peroxisome / Assumed
DHAP / 9.15 / Cytosol / (Zhu et al., 2007)
Pi / 5 / Cytosol / (Zhu et al., 2007)
GAP / 0.42 / Cytosol / (Zhu et al., 2007)
PGA / 0.067 / Cytosol / (Zhu et al., 2007)
FBP / 1.4 / Cytosol / (Leegood, 1985)
F6P / 0.24 / Cytosol / (Zhu et al., 2007)
G6P / 0.068 / Cytosol / (Zhu et al., 2007)
G1P / 1 / Cytosol / (Zhu et al., 2007)
UDPG / 0.62 / Cytosol / (Zhu et al., 2007)
UTP / 0.75 / Cytosol / (Zhu et al., 2007)
SUCP / 0 / Cytosol / Assumed
SUC / 0 / Cytosol / Assumed
UDP / 0.13 / Cytosol / (Zhu et al., 2007)
F26BP / 0.037 / Cytosol / (Zhu et al., 2007)
ATP / 0.35 / Cytosol / (Zhu et al., 2007)
ADP / 0.65 / Cytosol / (Zhu et al., 2007)
PPi / 0 / Cytosol / Assumed
2PGA / 0 / Cytosol / Assumed
PEP / 0 / Cytosol / Assumed
PYR / 0 / Cytosol / Assumed
NAD+ / 0.6 / Cytosol / (Heineke et al., 1991)
NADH / 0.06 / Cytosol / (Heineke et al., 1991)
DPGA / 0 / Cytosol / Assumed
CO2 / 0.009 / Cytosol / Assumed
OAA / 0.098 / Cytosol / (Heineke et al., 1991)
Malate / 1 / Cytosol / (Hu and Plaxton, 1996)
ASP / 0 / Cytosol / Assumed
NADP+ / 0 / Cytosol / Assumed
NADPH / 0 / Cytosol / Assumed
CoA / 1 / Mitochondria / Assumed
AceCOA / 1 / Mitochondria / Assumed
NAD+ / 0.4 / Mitochondria / Assumed
NADH / 0.47 / Mitochondria / Assumed
CIT / 0 / Mitochondria / Assumed
ICIT / 0 / Mitochondria / Assumed
KG / 0 / Mitochondria / Assumed
SER / 0.14 / Mitochondria / Assumed
CO2 / 0 / Mitochondria / Assumed
Table S3. Additional parameters used in the model.
Parameter / Value / Referencepartial pressue of CO2 concentration in the intercellular airspace / 27 Pa / We assumed an ambient CO2 partial pressure of 38.5 Pa and that the ratio between intercellular and ambient partial pressures was 0.7(Wong et al., 1985)
Light intensity / 1000 μmol m-2 s-1 / Saturating light
O2 concentration / 21 kPa / Current ambient conditions
CO2 conductance between cytosol and chloroplast stroma / 2.5 * 10-4 m s-1 / Estimated, based on (Uehlein et al., 2008; Evans et al., 2009)
CO2 conductance between cytosol and mitochondria / 0.005 m s-1 / Assumed
CO2 conductance between cytosol and intercellular space / 0.001 m s-1 / Estimated, based on (Evans et al., 2009)
Cytosol volume per unit of chlorophyll / 24 μl (mg Chl)-1 / (Winter et al., 1994)
Mitochondria volume per unit of chlorophyll / 3.7 μl (mg Chl)-1 / (Winter et al., 1994)
Chloroplast volume per unit of chlorophyll / 66 μl (mg Chl)-1 / (Winter et al., 1994)
Mesophyll surface area per unit of leaf area / 15 m2 m-2 / (Slaton and Smith, 2002)
Mitochondria surface area per unit of leaf area / 9.48 m2 m-2 / (Slaton and Smith, 2002)
Table S4. Predicted photosynthesis of wild type plants under ambient conditions. Ci=27 Par, PAR=1000 μmol m-2 s-1.
Photosynthetic rate (μmol m-2 s-1) / Photorespiration rate (μmol m-2 s-1)Wild Type / 12.52 / 4.8
A
(μmol m-2 s-1) / Proportion of the photorespiratory fluxes through Carvalho-bypass flux
(μmol m-2 s-1)
With default parameters / 4.96 / 0.01 %
Vgcl× 1000 / 4.99 (+0.6%) / 7.63%
Kmgcl:GOA× 0.1 / 4.96 / 1.05%
Kmgcl:GOA× 0.001 / 5.10 (+2.8%) / 31.5%
Vhyi × 100 / 4.96 / 0.01 %
Vhyi × 1000 / 4.96 / 0.01 %
Kmhyi:HPR× 0.1 / 4.96 / 0.01 %
Kmhyi:HPR× 0.01 / 4.96 / 0.01 %
Kmhyi:HPR× 0.001 / 4.96 / 0.01 %
Table S5. The effects of glyoxylate carboligase (GCL) and hydroxypyruvate isomerase (HYI) enzyme parameters on the photosynthetic rate and on the proportion of the photorespiratory fluxes through the Carvalho-bypass under low light conditions (Ci=27 Pa and PAR=200 μmol m-2 s-1).
Table S6. The photosynthetic rate predicted for several scenarios where the energy cost for ammonia refixation was completely abolished and/or all photorespiratory CO2 release was relocated into chloroplasts. Results are calculated for different light intensities and CO2 partial pressures.
Ci (Pa) / High light(PAR = 1000 μmol m-2 s-1) / Low light
(PAR = 200 μmol m-2 s-1)
WT / Only reduced ATP cost / Only relocating CO2 release / WT / Only reduced ATP cost / Only relocating CO2 release
10 / 2.03 / 2.03 (+0%) / 4.46 (+119.7%) / 1.70 / 1.90 (+11.8%) / 2.20 (+29.4%)
27 / 12.52 / 12.52 (+0%) / 14.43 (+15.3%) / 4.96 / 5.19 (+4.6%) / 5.06 (+2.0%)
50 / 21.10 / 21.0 (+0%) / 21.41 (+1.5%) / 6.89 / 7.16 (+3.9%) / 6.90 (+0.1%)
Table S7. Effect of variation in the maximal enzyme activity (Vmax) on the photosynthetic rates of wild type and Kebeish-bypass plants under ambient conditions (Ci=27 Pa, PAR=1000 μmol m-2 s-1). With the default Vmax values, the predicted photosynthetic rate of wild type was 12.52 μmol m-2 s-1, and that of plants with a Kebeish-bypass was 13.53 μmol m-2 s-1. The Vmax of enzymes that were not listed had no significant effect on the photosynthetic rate.
Enzyme ID / Photosynthetic rate (μmol m-2 s-1)With 110% of the default Vmax / With 90% of the default Vmax
Wild Type / Bypass / Wild Type / Bypass
4.1.1.39O2 / 12.11 / 13.08 / 12.97 / 13.93
4.1.1.39CO2 / 13.15 / 14.16 / 11.80 / 12.77
1.1.99.14 / 12.52 / 13.58 / 12.52 / 13.47
3.1.3.37 / 12.56 / 13.63 / 12.31 / 13.07
2.7.2.3Chl / 12.52 / 13.53 / 12.52 / 13.53
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