298 Marine Macro- and Microalgae: An Overview
Surzycki, R., L. Cournac, G. Peltier and J.D. Rochaix. 2007. Potential for hydrogen production with inducible chloroplast
gene expression in Chlamydomonas. Proc. Natl. Acad. Sci. USA 104: 17548–17553.
Tabita, F.R., S. Satagopan, T.E. Hanson, N.E. Kreel and S.S. Scott. 2008. Distinct form I, II, III, and IV Rubisco proteins
from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. J. Exp. Bot.
59: 1515–1524.
Tamoi, M., M. Nagaoka, Y. Miyagawa and S. Shigeoka. 2006. Contribution of fructose-1,6-bisphosphatae and sedoheptulose1,7-bisphosphatase to the photosynthetic rate and carbon flow in the Calvin cycle in transgenic plants. Plant Cell Physiol.
47: 380–390.
Tan, C., S. Qin, Q. Zhang, P. Jiang and F. Zhao. 2005. Establishment of a micro-particle bombardment transformation system
for Dunaliella salina. J. Microbiol. 43: 361–365.
Tcherkez, G.G., G.D. Farquhar and T.J. Andrews. 2006. Despite slow catalysis and confused substrate specificity, all ribulose
bisphosphate carboxylases may be nearly perfectly optimized. Proc Natl. Acad. Sci. USA 103: 7246–7251.
Thauer, R.K. 2007. A fifth pathway for carbon fixation. Science 318: 1732–1733.
Thelen, J.J. and J.B. Ohlrogge. 2002. Metabolic engineering of fatty acid biosynthesis in plants. Metabolic Engineering 4: 12–21.
Timmins, M., S.R. Thomas-Hall, A. Darling, E. Zhang, B. Hankamer, U.C. Marx and P.M. Schenk. 2009a. Phylogenetic and
molecular analysis of hydrogen-producing green algae. J. Exp. Bot. 60: 1691–1702.
Timmins, M., W. Zhou, J. Rupprecht, L. Lim, S.R. Thomas-Hall, A. Doebbe, O. Kruse, B. Hankamer, U.C. Marx, S.M. Smith
and P.M. Schenk. 2009b. The metabolome of Chlamydomonas reinhardtii following induction of anaerobic H 2 production
by sulfur depletion. J. Biol. Chem. 284: 23415–23425.
Torzillo, G., A. Scoma, C. Faraloni, A. Ena and U. Johanningmeier. 2009. Increased hydrogen photoproduction by means of
a sulfur-deprived Chlamydomonas reinhardtii D1 protein mutant. Int. J. Hydrogen Energy 34: 4529–4536.
Uemura, K., M. Anwaruzzaman, S. Miyachi and A. Yokota. 1997. Ribulose-1,5-bisphosphate carboxylase/oxygenase from
thermophilic red algae with a strong specificity for CO 2 fixation. Biochem. Biophys. Res. Commun. 233: 568–571.
Uji, T., H. Mizuta and N. Saga. 2013. Characterization of the sporophyte-preferential gene promoter from the red alga Porphyra
yezoensis using transient gene expression. Mar. Biotechnol. (NY) 15: 188–196.
van Ooijen, G., K. Knox, K. Kis, F.Y. Bouget and A.J. Millar. 2012. Genomic transformation of the picoeukaryote Ostreococcus
tauri. J. Vis. Exp. (65): e4074, doi:10.3791/4074.
Varaljay, V.A., S. Satagopan, J.A. North, B. Witte, M.N. Dourado, K. Anantharaman, M.A. Arbing, S.H. McCann, R.S. Oremland,
J.F. Banfield, K.C. Wrighton and F.R. Tabita. 2016. Functional metagenomic selection of ribulose 1,5-bisphosphate
carboxylase/oxygenase from uncultivated bacteria. Environ. Microbiol. 18: 1187–1199.
Volgusheva, A., S. Styring and F. Mamedov. 2013. Increased photosystem II stability promotes H 2 production in sulfur-deprived
Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 110: 7223–7228.
Wang, Q., Y. Lu, Y. Xin, L. Wei, S. Huang and J. Xu. 2016. Genome editing of model oleaginous microalgae Nannochloropsis
spp. by CRISPR/Cas9. Plant J. 88: 1071–1081.
Wargacki, A.J., E. Leonard, M.N. Win, D.D. Regitsky, C.N. Santos, P.B. Kim, S.R. Cooper, R.M. Raisner, A. Herman, A.B.
Sivitz, A. Lakshmanaswamy, Y. Kashiyama, D. Baker and Y. Yoshikuni. 2012. An engineered microbial platform for
direct biofuel production from brown macroalgae. Science 335: 308–313.
Warnecke, F., P. Luginbuhl, N. Ivanova, M. Ghassemian, T.H. Richardson, J.T. Stege, M. Cayouette, A.C. McHardy,
G. Djordjevic, N. Aboushadi, R. Sorek, S.G. Tringe, M. Podar, H.G. Martin, V. Kunin, D. Dalevi, J. Madejska, E.
Kirton, D. Platt, E. Szeto, A. Salamov, K. Barry, N. Mikhailova, N.C. Kyrpides, E.G. Matson, E.A. Ottesen, X. Zhang,
M. Hernandez, C. Murillo, L.G. Acosta, I. Rigoutsos, G. Tamayo, B.D. Green, C. Chang, E.M. Rubin, E.J. Mathur, D.E.
Robertson, P. Hugenholtz and J.R. Leadbetter. 2007. Metagenomic and functional analysis of hindgut microbiota of a
wood-feeding higher termite. Nature 450: 560–565.
Weyman, P.D., W.A. Vargas, Y. Tong, J. Yu, P.C. Maness, H.O. Smith and Q. Xu. 2011. Heterologous expression of Alteromonas
macleodii and Thiocapsa roseopersicina [NiFe] hydrogenases in Synechococcus elongatus. PLoS. One. 6: e20126.
Wilson, R.H., H. Alonso and S.M. Whitney. 2016. Evolving Methanococcoides burtonii archaeal Rubisco for improved
photosynthesis and plant growth. Sci. Rep. 6: 22284, doi:10.1038/srep22284.
Whitney, S.M., P. Baldet, G.S. Hudson and T.J. Andrews. 2001. Form I Rubiscos from non-green algae are expressed abundantly
but not assembled in tobacco chloroplasts. Plant J. 26: 535–547.
Whitney, S.M., R.L. Houtz and H. Alonso. 2011. Advancing our understanding and capacity to engineer nature’s CO 2 -
sequestering enzyme, Rubisco. Plant Physiol. 155: 27–35.
Work, V.H., S. D’Adamo, R. Radakovits, R.E. Jinkerson and M.C. Posewitz. 2012. Improving photosynthesis and metabolic
networks for the competitive production of phototroph-derived biofuels. Curr. Op. Biotechnol. 23: 290–297.
Wu, S., R. Huang, L. Xu, G. Yan and Q. Wang. 2010. Improved hydrogen production with expression of hemH and lba genes
in chloroplast of Chlamydomonas reinhardtii. J. Biotechnol. 146: 120–125.
Wu, S., L. Xu, R. Huang and Q. Wang. 2011. Improved biohydrogen production with an expression of codon-optimized hemH
and lba genes in the chloroplast of Chlamydomonas reinhardtii. Bioresour. Technol. 102: 2610–2616.
Yacoby, I., S. Pochekailov, H. Toporik, M.L. Ghirardi, P.W. King and S. Zhang. 2011. Photosynthetic electron partitioning
between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro. Proc. Natl. Acad. Sci.
USA 108: 9396–9401.
Surzycki, R., L. Cournac, G. Peltier and J.D. Rochaix. 2007. Potential for hydrogen production with inducible chloroplast
gene expression in Chlamydomonas. Proc. Natl. Acad. Sci. USA 104: 17548–17553.
Tabita, F.R., S. Satagopan, T.E. Hanson, N.E. Kreel and S.S. Scott. 2008. Distinct form I, II, III, and IV Rubisco proteins
from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. J. Exp. Bot.
59: 1515–1524.
Tamoi, M., M. Nagaoka, Y. Miyagawa and S. Shigeoka. 2006. Contribution of fructose-1,6-bisphosphatae and sedoheptulose1,7-bisphosphatase to the photosynthetic rate and carbon flow in the Calvin cycle in transgenic plants. Plant Cell Physiol.
47: 380–390.
Tan, C., S. Qin, Q. Zhang, P. Jiang and F. Zhao. 2005. Establishment of a micro-particle bombardment transformation system
for Dunaliella salina. J. Microbiol. 43: 361–365.
Tcherkez, G.G., G.D. Farquhar and T.J. Andrews. 2006. Despite slow catalysis and confused substrate specificity, all ribulose
bisphosphate carboxylases may be nearly perfectly optimized. Proc Natl. Acad. Sci. USA 103: 7246–7251.
Thauer, R.K. 2007. A fifth pathway for carbon fixation. Science 318: 1732–1733.
Thelen, J.J. and J.B. Ohlrogge. 2002. Metabolic engineering of fatty acid biosynthesis in plants. Metabolic Engineering 4: 12–21.
Timmins, M., S.R. Thomas-Hall, A. Darling, E. Zhang, B. Hankamer, U.C. Marx and P.M. Schenk. 2009a. Phylogenetic and
molecular analysis of hydrogen-producing green algae. J. Exp. Bot. 60: 1691–1702.
Timmins, M., W. Zhou, J. Rupprecht, L. Lim, S.R. Thomas-Hall, A. Doebbe, O. Kruse, B. Hankamer, U.C. Marx, S.M. Smith
and P.M. Schenk. 2009b. The metabolome of Chlamydomonas reinhardtii following induction of anaerobic H 2 production
by sulfur depletion. J. Biol. Chem. 284: 23415–23425.
Torzillo, G., A. Scoma, C. Faraloni, A. Ena and U. Johanningmeier. 2009. Increased hydrogen photoproduction by means of
a sulfur-deprived Chlamydomonas reinhardtii D1 protein mutant. Int. J. Hydrogen Energy 34: 4529–4536.
Uemura, K., M. Anwaruzzaman, S. Miyachi and A. Yokota. 1997. Ribulose-1,5-bisphosphate carboxylase/oxygenase from
thermophilic red algae with a strong specificity for CO 2 fixation. Biochem. Biophys. Res. Commun. 233: 568–571.
Uji, T., H. Mizuta and N. Saga. 2013. Characterization of the sporophyte-preferential gene promoter from the red alga Porphyra
yezoensis using transient gene expression. Mar. Biotechnol. (NY) 15: 188–196.
van Ooijen, G., K. Knox, K. Kis, F.Y. Bouget and A.J. Millar. 2012. Genomic transformation of the picoeukaryote Ostreococcus
tauri. J. Vis. Exp. (65): e4074, doi:10.3791/4074.
Varaljay, V.A., S. Satagopan, J.A. North, B. Witte, M.N. Dourado, K. Anantharaman, M.A. Arbing, S.H. McCann, R.S. Oremland,
J.F. Banfield, K.C. Wrighton and F.R. Tabita. 2016. Functional metagenomic selection of ribulose 1,5-bisphosphate
carboxylase/oxygenase from uncultivated bacteria. Environ. Microbiol. 18: 1187–1199.
Volgusheva, A., S. Styring and F. Mamedov. 2013. Increased photosystem II stability promotes H 2 production in sulfur-deprived
Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 110: 7223–7228.
Wang, Q., Y. Lu, Y. Xin, L. Wei, S. Huang and J. Xu. 2016. Genome editing of model oleaginous microalgae Nannochloropsis
spp. by CRISPR/Cas9. Plant J. 88: 1071–1081.
Wargacki, A.J., E. Leonard, M.N. Win, D.D. Regitsky, C.N. Santos, P.B. Kim, S.R. Cooper, R.M. Raisner, A. Herman, A.B.
Sivitz, A. Lakshmanaswamy, Y. Kashiyama, D. Baker and Y. Yoshikuni. 2012. An engineered microbial platform for
direct biofuel production from brown macroalgae. Science 335: 308–313.
Warnecke, F., P. Luginbuhl, N. Ivanova, M. Ghassemian, T.H. Richardson, J.T. Stege, M. Cayouette, A.C. McHardy,
G. Djordjevic, N. Aboushadi, R. Sorek, S.G. Tringe, M. Podar, H.G. Martin, V. Kunin, D. Dalevi, J. Madejska, E.
Kirton, D. Platt, E. Szeto, A. Salamov, K. Barry, N. Mikhailova, N.C. Kyrpides, E.G. Matson, E.A. Ottesen, X. Zhang,
M. Hernandez, C. Murillo, L.G. Acosta, I. Rigoutsos, G. Tamayo, B.D. Green, C. Chang, E.M. Rubin, E.J. Mathur, D.E.
Robertson, P. Hugenholtz and J.R. Leadbetter. 2007. Metagenomic and functional analysis of hindgut microbiota of a
wood-feeding higher termite. Nature 450: 560–565.
Weyman, P.D., W.A. Vargas, Y. Tong, J. Yu, P.C. Maness, H.O. Smith and Q. Xu. 2011. Heterologous expression of Alteromonas
macleodii and Thiocapsa roseopersicina [NiFe] hydrogenases in Synechococcus elongatus. PLoS. One. 6: e20126.
Wilson, R.H., H. Alonso and S.M. Whitney. 2016. Evolving Methanococcoides burtonii archaeal Rubisco for improved
photosynthesis and plant growth. Sci. Rep. 6: 22284, doi:10.1038/srep22284.
Whitney, S.M., P. Baldet, G.S. Hudson and T.J. Andrews. 2001. Form I Rubiscos from non-green algae are expressed abundantly
but not assembled in tobacco chloroplasts. Plant J. 26: 535–547.
Whitney, S.M., R.L. Houtz and H. Alonso. 2011. Advancing our understanding and capacity to engineer nature’s CO 2 -
sequestering enzyme, Rubisco. Plant Physiol. 155: 27–35.
Work, V.H., S. D’Adamo, R. Radakovits, R.E. Jinkerson and M.C. Posewitz. 2012. Improving photosynthesis and metabolic
networks for the competitive production of phototroph-derived biofuels. Curr. Op. Biotechnol. 23: 290–297.
Wu, S., R. Huang, L. Xu, G. Yan and Q. Wang. 2010. Improved hydrogen production with expression of hemH and lba genes
in chloroplast of Chlamydomonas reinhardtii. J. Biotechnol. 146: 120–125.
Wu, S., L. Xu, R. Huang and Q. Wang. 2011. Improved biohydrogen production with an expression of codon-optimized hemH
and lba genes in the chloroplast of Chlamydomonas reinhardtii. Bioresour. Technol. 102: 2610–2616.
Yacoby, I., S. Pochekailov, H. Toporik, M.L. Ghirardi, P.W. King and S. Zhang. 2011. Photosynthetic electron partitioning
between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro. Proc. Natl. Acad. Sci.
USA 108: 9396–9401.