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
Reference
1.2.1.9
1.2.1.12
2.7.2.3cyt
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
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
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)
(Laisk and Edwards, 2000), Estimated
Vmax=48.0 μmol m-2 s-1
5.4.2.1 and 4.2.1.11
Flux control coefficient=0
KmPGA=0.1 mM
(Laisk and Edwards, 2000)
KmPEP=0.5 mM
(Laisk and Edwards, 2000)
Ke=0.4302
(Laisk and Edwards, 2000)
(Laisk and Edwards, 2000), Estimated
Vmax=30.0 μmol m-2 s-1
2.7.1.40
4.1.1.31
2.6.1.1
1.1.1.41
Flux control coefficient=0
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
KmPEP=0.2 mM
(Tripodi et al., 2005)
Vmax=30.0 μmol m-2 s-1
(Gehlen et al., 1996)
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
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 s
Estimated Flux control coefficient=0
KmICIT=0.031 mM
(Pickworth Glusker, 1971)
KmCIT=0.4 mM
(Pickworth Glusker, 1971)
Vmax=30.0 μmol m s
(Brouquisse et al., 1987)
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
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)
-2 -1
4.2.1.3
-2 -1
2.3.3.1
4.1.1.39
m-2 s-1
2.7.2.3chl
VCmax=87.4 μmol
VOmax=29.7 μmol m-2 s-1
(Kanai and Edwards, 1999; Caemmerer, 2000)
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)
(Laisk and Edwards, 2000), Estimated
Vmax=600 μmol m-2 s-1
1.2.1.13
Flux control coefficient=0
KmBPGA=0.004 mM
(Trost et al., 1993)
KmNADPH=0.1 mM
(Zhu et al., 2007)
(Laisk and Edwards, 2000), Estimated
Vmax=121 μmol
5.3.1.1
m-2 s-1
Flux control coefficient=0
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
3.1.3.11
2.2.1.1F6P
4.1.2.13SBP
3.1.3.37
2.2.1.1S7P
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)
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
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
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
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)
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)
2.7.1.19
3.6.3.14
5.3.1.9chl
5.4.2.2
Vmax=93.0 μmol m-2 s-1
(Zhu et al., 2007), with modification1
Flux control coefficient=0
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)
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
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
Ke=0.058
(Colowick and Sutherland, 1942)
Vmax=300 μmol
2.7.7.27
m-2 s-1
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)
-4
3.6.1.1
KiPPi_ATP=3.8*10 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)
KmPPi=0.154 mM
(Van et al., 2005)
Ke=1.57*10-4
(Flodgaard and Fleron, 1974)
Vmax=3000 μmol
2.4.1.21
3.1.3.18
(Zhu et al., 2007; Wang et al., 2014)
m-2 s-1
(Zhu et al., 2007; Wang et al., 2014)
KmADPG=0.077 mM
(Hawker et al., 1974)
Vmax=30 μmol m-2 s-1
(Zhu et al., 2007; Wang et al., 2014)
KmPGCA=0.026 mM
(Christeller and Tolbert, 1978)
2.7.1.31
1.1.3.15
2.6.1.45
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)
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)
KmGCA=0.1 mM
(Tolbert, 1981)
Vmax=44 μmol m-2 s-1
(Zhu et al., 2007), with modification1
Flux control coefficient=0
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
1.1.1.29
2.6.1.4
GLy_Ser
(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)
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)
KmGLY=6.0 mM
(Douce et al., 2001)
KiSER=4.0 mM
(Douce et al., 2001)
m-2 s-1
4.1.2.13Cyt
(Zhu et al., 2007; Wang et al., 2014)
KmGCA=0.2 mM
(Howitz and McCarty, 1985)
KiGCEA=0.22 mM
(Howitz and McCarty, 1985)
Vmax=300 μmol
Tgcea
(Zhu et al., 2007; Wang et al., 2014)
KiHPR=12 mM
Vmax=75 μmol
Tgca
m-2 s-1
m-2 s-1
(Zhu et al., 2007; Wang et al., 2014)
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)
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 s
(Zhu et al., 2007; Wang et al., 2014)
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
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
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)
KmF26BP=0.032 mM
(Macdonald et al., 1989)
KiF6P=0.1 mM
(Villadsen and Nielsen, 2001)
KiPi=0.5 mM
(Villadsen and Nielsen, 2001)
-2 -1
2.7.7.9
2.4.1.14
3.1.3.24
3.1.3.46
Vmax=21 μmol
2.7.1.105
(Zhu et al., 2007; Wang et al., 2014)
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
2.7.1.90
m-2 s-1
m-2 s-1
(Zhu et al., 2007; Wang et al., 2014)
KmF6P=0.3 mM
(Mahajan and Singh, 1989)
KmPPi=0.025 mM
(Mahajan and Singh, 1989)
KmFBP=0.139 mM
(Mahajan and Singh, 1989)
5.3.1.9Cyt
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
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
1.4.7.1
6.3.1.2
1.4.1.3
1.1.99.14
m-2 s-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
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
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
KmGCA=0.04 mM
(Lord, 1972)
Vmax=15 μmol m-2 s-1
4.1.1.47
KmGOA=0.9 mM
Vmax=30 μmol m-2 s-1
1.1.1.60
(Zhu et al., 2007; Wang et al., 2014)
Estimated to make sure 50% of the
photorespiratory went through the bypass
(Kaplun et al., 2008)
Assumed
Flux control coefficient=0 (Kebeish bypass
and Carvalho bypass)
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
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
1.1.1.40
Assumed
Flux control coefficient=0 (Kebeish bypass)
Assumed
Flux control coefficient=0.33 (Maier bypass)
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)
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)
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)
KmGLU=1.2 mM
(Flügge et al., 1988)
KIKG =0.7 mM
(Flügge et al., 1988)
1.2.4.1
5.3.1.22
Tglu
Tkg
2.7.4.6
SucSink
Tpga
Tgap
KIMAL=1.2 mM
(Flügge et al., 1988)
Vmax=12.6 μmol m-2 s-1
(Flügge et al., 1988)
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)
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)
KmSUC=1.5 mM
(Riesmeier et al., 1992)
Vmax=0.21μmol m-2 s-1
(Zhu et al., 2007)
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)
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)
Tdhap
1
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)
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)
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 V cmax 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.
Metabolite
Concentration
Compartment
Reference
name
(mM)
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
Reference
partial 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
10-4
2.5 *
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)
Chl)-1
(Winter et al., 1994)
Chloroplast volume per unit of chlorophyll
66 μl (mg
Mesophyll surface area per unit of leaf area
m2
Mitochondria surface area per unit of leaf area
15
m-2
9.48 m2 m-2
(Slaton and Smith, 2002)
(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
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).
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 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
Low light
(PAR = 1000 μmol m-2 s-1)
(PAR = 200 μmol m-2 s-1)
Only
WT
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 Kebeishbypass was 13.53 μmol m-2 s-1. The Vmax of enzymes that were not listed had no significant effect on the
photosynthetic rate.
Photosynthetic rate (μmol m-2 s-1)
Enzyme ID
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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