doi.org/10.1111/j.1365-3040.1994.
tb00144.x
54. Marcus Y, Altman-Gueta H, Wolff Y, Gurevitz
M (2011) Rubisco mutagenesis provides new
insight into limitations on photosynthesis and
growth in Synechocystis PCC6803. J Exp Bot
62:4173–4182.
https://doi.org/10.1093/
jxb/err116
55. Paul MJ (2001) Sink regulation of photosynthesis. J Exp Bot 52:1383–1400. https://doi.
org/10.1093/jexbot/52.360.1383
56. Stitt M (1986) Limitation of photosynthesis by
carbon metabolism: I. Evidence for excess electron transport capacity in leaves carrying out
photosynthesis in saturating light and CO(2).
Plant Physiol 81:1115–1122
57. Farquhar GD, Sharkey TD (1982) Stomatal
conductance and photosynthesis. Annu Rev
Plant Physiol 33:317–345. https://doi.org/
10.1146/annurev.pp.33.060182.001533
58. Tennessen DJ, Bula RJ, Sharkey TD (1995)
Efficiency of photosynthesis in continuous
and pulsed light emitting diode irradiation.
Photosynth Res 44:261–269. https://doi.
org/10.1007/BF00048599
59. Bruhn A, Dahl J, Nielsen HB, Nikolaisen L,
Rasmussen MB, Markager S, Olesen B,
Arias C, Jensen PD (2011) Bioenergy potential
of Ulva lactuca: biomass yield, methane production and combustion. Bioresour Technol
102:2595–2604. https://doi.org/10.1016/j.
biortech.2010.10.010
60. Sforza E, Simionato D, Giacometti GM,
Bertucco A, Morosinotto T (2012) Adjusted
light and dark cycles can optimize photosynthetic efficiency in algae growing in photobioreactors. PLoS One 7:e38975. https://doi.
org/10.1371/journal.pone.0038975
61. Carvalho AP, Silva SO, Baptista JM, Malcata
FX (2011) Light requirements in microalgal
photobioreactors: an overview of biophotonic
aspects.
Appl
Microbiol
Biotechnol
89:1275–1288.
https://doi.org/10.1007/
s00253-010-3047-8
62. van Maris AJA, Abbott DA, Bellissimi E, van
den Brink J, Kuyper M, Luttik MAH, Wisselink
HW, Scheffers WA, van Dijken JP, Pronk JT
(2006) Alcoholic fermentation of carbon
sources in biomass hydrolysates by Saccharomyces cerevisiae: current status. Antonie Van
Leeuwenhoek 90(4):391–418
63. Bond-Watts BB, Bellerose RJ, Chang MCY
(2011) Enzyme mechanism as a kinetic control
element for designing synthetic biofuel pathways. Nat Chem Biol 7:222–227. https://doi.
org/10.1038/nchembio.537
64. Kim Y, Ingram LO, Shanmugam KT (2007)
Construction of an Escherichia coli K-12
mutant for homoethanologenic fermentation
of glucose or xylose without foreign genes.
Appl Environ Microbiol 73:1766–1771.
https://doi.org/10.1128/AEM.02456-06
65. Talebnia F, Niklasson C, Taherzadeh MJ
(2005) Ethanol production from glucose and
dilute-acid hydrolyzates by encapsulated
S. cerevisiae. Biotechnol Bioeng 90:345–353.
https://doi.org/10.1002/bit.20432
66. Zomorrodi AR, Maranas CD (2012) OptCom:
a multi-level optimization framework for the
metabolic modeling and analysis of microbial
communities. PLoS Comput Biol 8:e1002363.
https://doi.org/10.1371/journal.pcbi.
1002363
67. Durinck S, Spellman PT, Birney E, Huber W
(2009) Mapping identifiers for the integration
of genomic datasets with the R/Bioconductor
package biomaRt. Nat Protoc 4:1184–1191.
https://doi.org/10.1038/nprot.2009.97
68. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I,
Hanspers K, Conklin BR, Evelo CT (2010)
The BridgeDb framework: standardized access
to gene, protein and metabolite identifier
mapping services. BMC Bioinformatics 11:5.
https://doi.org/10.1186/1471-2105-11-5
69. Khandelwal RA, Olivier BG, Ro ¨ling WFM,
Teusink B, Bruggeman FJ (2013) Community
flux balance analysis for microbial consortia at
balanced growth. PLoS One. https://doi.org/
10.1371/journal.pone.0064567
70. Zarecki R, Oberhardt MA, Yizhak K,
Wagner A, Segal ES, Freilich S, Henry CS,
Gophna U, Ruppin E (2014) Maximal sum of
metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of
microorganisms. PLoS One. https://doi.org/
10.1371/journal.pone.0098372
71. Hanly TJ, Henson MA (2011) Dynamic flux
balance modeling of microbial co-cultures for
efficient batch fermentation of glucose and
xylose
mixtures.
Biotechnol
Bioeng
108:376–385. https://doi.org/10.1002/bit.
22954
72. Vitkin E, Golberg A, Yakhini Z (2015) BioLEGO—a web-based application for biorefinery design and evaluation of serial biomass
fermentation. Technology 1–10. doi: https://
doi.org/10.1142/S2339547815400038
73. Vitkin E, Shlomi T (2012) MIRAGE: a functional genomics-based approach for metabolic
network model reconstruction and its application to cyanobacteria networks. Genome Biol
13:R111.
https://doi.org/10.1186/gb2012-13-11-r111
32
Alexander Golberg et al.
tb00144.x
54. Marcus Y, Altman-Gueta H, Wolff Y, Gurevitz
M (2011) Rubisco mutagenesis provides new
insight into limitations on photosynthesis and
growth in Synechocystis PCC6803. J Exp Bot
62:4173–4182.
https://doi.org/10.1093/
jxb/err116
55. Paul MJ (2001) Sink regulation of photosynthesis. J Exp Bot 52:1383–1400. https://doi.
org/10.1093/jexbot/52.360.1383
56. Stitt M (1986) Limitation of photosynthesis by
carbon metabolism: I. Evidence for excess electron transport capacity in leaves carrying out
photosynthesis in saturating light and CO(2).
Plant Physiol 81:1115–1122
57. Farquhar GD, Sharkey TD (1982) Stomatal
conductance and photosynthesis. Annu Rev
Plant Physiol 33:317–345. https://doi.org/
10.1146/annurev.pp.33.060182.001533
58. Tennessen DJ, Bula RJ, Sharkey TD (1995)
Efficiency of photosynthesis in continuous
and pulsed light emitting diode irradiation.
Photosynth Res 44:261–269. https://doi.
org/10.1007/BF00048599
59. Bruhn A, Dahl J, Nielsen HB, Nikolaisen L,
Rasmussen MB, Markager S, Olesen B,
Arias C, Jensen PD (2011) Bioenergy potential
of Ulva lactuca: biomass yield, methane production and combustion. Bioresour Technol
102:2595–2604. https://doi.org/10.1016/j.
biortech.2010.10.010
60. Sforza E, Simionato D, Giacometti GM,
Bertucco A, Morosinotto T (2012) Adjusted
light and dark cycles can optimize photosynthetic efficiency in algae growing in photobioreactors. PLoS One 7:e38975. https://doi.
org/10.1371/journal.pone.0038975
61. Carvalho AP, Silva SO, Baptista JM, Malcata
FX (2011) Light requirements in microalgal
photobioreactors: an overview of biophotonic
aspects.
Appl
Microbiol
Biotechnol
89:1275–1288.
https://doi.org/10.1007/
s00253-010-3047-8
62. van Maris AJA, Abbott DA, Bellissimi E, van
den Brink J, Kuyper M, Luttik MAH, Wisselink
HW, Scheffers WA, van Dijken JP, Pronk JT
(2006) Alcoholic fermentation of carbon
sources in biomass hydrolysates by Saccharomyces cerevisiae: current status. Antonie Van
Leeuwenhoek 90(4):391–418
63. Bond-Watts BB, Bellerose RJ, Chang MCY
(2011) Enzyme mechanism as a kinetic control
element for designing synthetic biofuel pathways. Nat Chem Biol 7:222–227. https://doi.
org/10.1038/nchembio.537
64. Kim Y, Ingram LO, Shanmugam KT (2007)
Construction of an Escherichia coli K-12
mutant for homoethanologenic fermentation
of glucose or xylose without foreign genes.
Appl Environ Microbiol 73:1766–1771.
https://doi.org/10.1128/AEM.02456-06
65. Talebnia F, Niklasson C, Taherzadeh MJ
(2005) Ethanol production from glucose and
dilute-acid hydrolyzates by encapsulated
S. cerevisiae. Biotechnol Bioeng 90:345–353.
https://doi.org/10.1002/bit.20432
66. Zomorrodi AR, Maranas CD (2012) OptCom:
a multi-level optimization framework for the
metabolic modeling and analysis of microbial
communities. PLoS Comput Biol 8:e1002363.
https://doi.org/10.1371/journal.pcbi.
1002363
67. Durinck S, Spellman PT, Birney E, Huber W
(2009) Mapping identifiers for the integration
of genomic datasets with the R/Bioconductor
package biomaRt. Nat Protoc 4:1184–1191.
https://doi.org/10.1038/nprot.2009.97
68. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I,
Hanspers K, Conklin BR, Evelo CT (2010)
The BridgeDb framework: standardized access
to gene, protein and metabolite identifier
mapping services. BMC Bioinformatics 11:5.
https://doi.org/10.1186/1471-2105-11-5
69. Khandelwal RA, Olivier BG, Ro ¨ling WFM,
Teusink B, Bruggeman FJ (2013) Community
flux balance analysis for microbial consortia at
balanced growth. PLoS One. https://doi.org/
10.1371/journal.pone.0064567
70. Zarecki R, Oberhardt MA, Yizhak K,
Wagner A, Segal ES, Freilich S, Henry CS,
Gophna U, Ruppin E (2014) Maximal sum of
metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of
microorganisms. PLoS One. https://doi.org/
10.1371/journal.pone.0098372
71. Hanly TJ, Henson MA (2011) Dynamic flux
balance modeling of microbial co-cultures for
efficient batch fermentation of glucose and
xylose
mixtures.
Biotechnol
Bioeng
108:376–385. https://doi.org/10.1002/bit.
22954
72. Vitkin E, Golberg A, Yakhini Z (2015) BioLEGO—a web-based application for biorefinery design and evaluation of serial biomass
fermentation. Technology 1–10. doi: https://
doi.org/10.1142/S2339547815400038
73. Vitkin E, Shlomi T (2012) MIRAGE: a functional genomics-based approach for metabolic
network model reconstruction and its application to cyanobacteria networks. Genome Biol
13:R111.
https://doi.org/10.1186/gb2012-13-11-r111
32
Alexander Golberg et al.