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Sains Malaysiana 47(10)(2018):
2269–2289 http://dx.doi.org/10.17576/jsm-2018-4710-04
Dissection of Synechococcus
Rubisco Large Subunit Sections Involved in Holoenzyme Formation
in Escherichia coli by Combinatorial Section Swapping and
Sequence Analyses (Pembahagian Synechococcus
Rubisco Seksyen Subunit Besar
Terlibat dalam
Pembentukan holoenzim dalam Escherichia coli oleh
Seksyen Kombinatori
Tertukar dan Jujukan
Analisis) YEE HUNG
YEAP1,
TENG
WEI
KOAY1,
HANN
LING
WONG2
& BOON HOE LIM1*
1Department
of Chemical Science, Universiti Tunku
Abdul Rahman, 31900 Kampar, Perak Darul
Ridzuan, Malaysia 2Department
of Biological Science, Universiti Tunku
Abdul Rahman, 31900 Kampar, Perak Darul
Ridzuan, Malaysia Received:
14 March 2018/Accepted: 4 June 2018 ABSTRACT Engineering the CO2-fixing
enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase
(Rubisco) to improve photosynthesis has long been sought. Rubisco
large subunits (RbcL) are highly-conserved
but because of certain undefined sequence differences, plant Rubisco
research cannot fully utilise the robust heterologous Escherichia coli expression system and its GroEL
folding machinery. Previously, a series of chimeric cyanobacteria
Synechococcus elongatus Rubisco,
incorporated with sequences from the green alga Chlamydomonas
reinhardtii, were expressed in E.
coli; differences in RbcL sections
essential for holoenzyme formation were pinpointed. In this study,
the remaining sections, presumably not crucial for holoenzyme
formation and also the small subunit (RbcS), are substituted to further
ascertain the possible destabilising
effects of multiple section mutations. To that end, combinations
of Synechococcus RbcL Sections
1 (residues 1-47), 2 (residues 48-97), 5 (residues 198-247) and
10 (residues 448-472), and RbcS, were
swapped with collinear Chlamydomonas
sections and expressed in E. coli. Interestingly, only
the chimera with Sections 1 and 2 together produces holoenzyme
and an interaction network of complementing amino acid changes
is delineated by crystal structure analysis. Furthermore, sequence-based
analysis also highlighted possible GroEL
binding site differences between the two RbcLs.
Keywords: Chaperone;
Chlamydomonas reinhardtii;
protein assembly; ribulose bisphosphate carboxylase/oxygenase
(Rubisco); Synechococcus elongatus PCC6301
ABSTRAK Kajian untuk mengubah
suai ribulosa-1,5-bisfosfat
karboksilase/oksigenase (Rubisco)
bagi memperbaiki
proses fotosintesis adalah usaha yang telah lama dijalankan. Subunit- besar
Rubisco amat konservatif
tetapi disebabkan perbezaan jujukan asid amino yang tertentu, Rubisco
tumbuh-tumbuhan tidak
dapat dikaji dengan
menggunakan sistem
pengekspresan Escherichia
coli yang serba-boleh serta
mekanisme penglipatan
GroEL-nya. Sebelum ini, satu siri
Rubisco kimerik yang menggabungkan
jujukan daripada
cyanobacteria Synechococcus elongatus dengan
alga hijau Chlamydomonas
reinhardtii telah
diekspreskan ke
dalam E. coli; dalam uji kaji tersebut,
perbezaan yang merangkumi
seksyen RbcL yang mustahak dalam pembentukan holoenzim telah ditentukan. Dalam uji kaji
ini, seksyen
lain yang mungkin tidak penting
untuk pembentukan
holoenzim, bersama-sama subunit
kecil (RbcS) telah
digantikan untuk
menentukan kemungkinan kesan ketidakstabilan akibat mutasi seksyen
berbilang. Untuk itu, kombinasi
Synechococcus RbcL Seksyen 1 (residu 1-47), 2 (residu 48-97), 5 (residu 198-247)
dengan 10 (residu
448-472) dan RbcS, telah
digantikan dengan
seksyen Chlamydomonas yang kolinear dan diekspreskan dalam E. coli.
Kesimpulannya, hanya
kimera yang ditukarkan kedua-dua Seksyen 1 dan 2 dapat membentuk
holoenzim dan
rangkaian interaksi yang meliputi perubahan asid amino yang saling melengkapkan berdasarkan analisis struktur kristal telah dikemukakan.
Selain
itu, analisis berasaskan
jujukan asid
amino juga menunjukkan bahawa perbezaan tapak ikatan GroEL yang mungkin bagi RbcL.
Kata kunci: Chaperone; Chlamydomonas reinhardtii; himpunan protein;
ribulosa-1,5-bisfosfat karboksilase/oksigenase (Rubisco); Synechococcus
elongatus PCC6301 REFERENCES Aigner,
H., Wilson, R.H., Bracher, A. Calisse,
L., Bhat, J.Y., Hartl, F.U. & Hayer-Hartl,
M. 2017. Plant RuBisCo assembly in
E. coli with five chloroplast chaperones including BSD2.
Science 358: 1272-1278. Andersson,
I. & Backlund, A. 2008. Structure and function of Rubisco. Plant Physiology and
Biochemistry 46: 275-291. Bainbridge,
G., Madgwick, P.J., Parmar,
S., Mitchell, R., Paul, M., Pitts, J., Keys, A.J. & Parry,
M.A.J. 1995. Engineering Rubisco to change its catalytic properties. Journal
of Experimental Botany 46: 1269-1276. Bloom,
J.D., Silberg, J.J., Wilke, C.O., Drummond,
D.A., Adami, C. & Arnold, F.H. 2005. Thermodynamic prediction of protein neutrality. Proceedings
of the National Academy of Science of the United States of America
102: 606-611. Burger,
R., Willensdorfer, M. & Nowak, M.A.
2006. Why
are phenotypic mutation rates much higher than genotypic mutation
rates? Genetics 172: 197-206. Campbell,
W.J. & Ogren, W.L. 1992. Light
activation of Rubisco by Rubisco activase
and thylakoid membranes. Plant Cell Physiology 33: 751-756.
Chaudhuri,
T.K. & Gupta, P. 2005. Factors governing the substrate recognition
by GroEL chaperone: A sequence correlation approach. Cell
Stress Chaperones 10: 24-36. Chen,
Z. & Spreitzer, R.J. 1992. How
various factors influence the CO2/O2 specificity
of ribulose-1, 5-bisphosphate carboxylase/ oxygenase.
Photosynthesis Research 31: 157-164. Cloney,
L.P., Bekkaoui, D.R. & Hemmingsen,
S.M. 1993. Co-expression of plastid chaperonin
genes and a synthetic plant Rubisco operon in Escherichia coli.
Plant Molecular Biology 23: 1285-1290. Cohen,
I., Sapir, Y. & Shapira, M. 2006. A conserved
mechanism controls translation of Rubisco large subunit in different
photosynthetic organisms. Plant Physiology 141: 1089-1097.
Cordes,
M.H. & Sauer, R.T. 1999. Tolerance of
a protein to multiple polar-to-hydrophobic surface substitutions.
Protein Science 8: 318-325. Curmi,
P.M.G., Cascio, D., Sweet, R.M., Eisenberg,
D. & Schreuder, H. 1992. Crystal structure
of the unactivated form of ribulose-
1,5-bisphosphate carboxylase/ oxygenase from tobacco refined
at 20-Å resolution. Journal of Biological Chemistry 267:
16980-16989. Ellis,
R.J. 1979. The most abundant protein in the
world. Trends in Biochemical Science 4: 241-244.
Esquivel,
M.G., Genkov, T., Nogueira,
A.S., Salvucci, M.E. & Spreitzer,
R.J. 2013. Substitutions at the opening of the Rubisco central
solvent channel affect holoenzyme stability and CO2/O2 specificity
but not activation by Rubisco activase.
Photosynthesis Research 118: 209-218. Feller,
U., Anders, I. & Mae, T. 2008. Rubiscolytics: Fate of Rubisco after its enzymatic function
in a cell is terminated. Journal of Experimental Botany 59:
1615-1624. Genkov,
T., Du, Y.C. & Spreitzer, R.J. 2006. Small
subunit cysteine-65 substitutions can suppress or induce alterations
in the large-subunit catalytic efficiency and holoenzyme thermal
stability of ribulose-1,5-bisphosphate
carboxylase/oxygenase. Archives of Biochemistry and Biophysics
451: 167-174. Genkov,
T. & Spreitzer, R.J. 2009. Highly
conserved small subunit residues influence Rubisco large subunit
catalysis. Journal of Biological Chemistry 284: 30105-30112.
Genkov,
T., Meyer, M., Griffiths, H. & Spreitzer,
R.J. 2010.
Functional hybrid Rubisco enzymes with plant small subunits and
algal large subunits: Engineered rbcS
cDNA for expression in Chlamydomonas. Journal of Biological Chemistry 285:
19833-19841. Goloubinoff, P.,
Gatenby, A.A. & Lorimer, G.H. 1989. GroE
heat-shock proteins promote assembly of foreign prokaryotic ribulose
bisphosphate carboxylase oligomers in Escherichia coli.
Nature 337: 44-47. Gutteridge, S., Rhoades, D.F. & Herrmann, C. 1993. Site-specific mutations in a loop region
of the C-terminal domain of the large subunit of ribulose bisphosphate
carboxylase/oxygenase that influence substrate partitioning.
Journal of Biological Chemistry 268: 7818-7824. Jordan,
D.B. & Ogren, W.L. 1981. Species variation in the specificity of ribulose biphosphate carboxylase/oxygenase. Nature 291: 513-515.
Kannappan,
B. & Gready, J.E. 2008. Redefinition
of Rubisco carboxylase reaction reveals origin of water for hydration
and new roles for active-site residues. Journal of the American
Chemical Society 130: 15063-15080. Knight,
S., Andersson, I. & Brändén,
C.I. 1990. Crystallographic analysis of ribulose 1,5-bisphosphate
carboxylase from spinach at 2·4 Å resolution. Journal of Molecular
Biology 215: 113-160. Koay,
T.W., Wong, H.L. & Lim, B.H. 2016. Engineering of chimeric eukaryotic/bacterial Rubisco large subunits
in Escherichia coli. Genes & Genetic Systems 91: 139-150.
Kumar,
V., Punetha, A., Sundar,
D. & Chaudhuri, T.K. 2012. In silico engineering
of aggregation-prone recombinant proteins for substrate recognition
by the chaperonin GroEL. BMC
Genomics 13: S22. Kyte,
J. & Doolittle, R.F. 1982. A simple method
for displaying the hydropathic character of a protein.
Journal of Molecular Biology 157: 105-132. Laing,
W.A., Ogren, W.L. & Hageman, R.H.
1974. Regulation
of soybean net photosynthetic CO2 fixation
by the interaction of CO2, O2,
and ribulose 1,5-diphosphate carboxylase.
Plant Physiology 54: 678-685. Lin,
Z. & Rye, H.S. 2006. GroEL-mediated
protein folding: Making the impossible, possible. Critical Reviews
in Biochemistry and Molecular Biology 41: 211-239. Long,
S.P., Zhu, X-G., Naidu, S.L. & Ort, D.R. 2006. Can
improvement in photosynthesis increase crop yields? Plant, Cell
and Environment 29: 315-330. Marin-Navarro,
J. & Moreno, J. 2006. Cysteines 449 and 459 modulate the reduction-oxidation
conformational changes of ribulose 1.5-bisphosphate carboxylase/oxygenase
and the translocation of the enzyme to membranes during stress.
Plant, Cell and Environment 29: 898-908. Meyer,
M.T., Genkov, T., Skepper,
J.N., Jouhet, J., Mitchell, M.C., Spreitzer,
R.J. & Griffiths, H. 2012. Rubisco small-subunit α-helices
control pyrenoid formation in Chlamydomonas. Proceedings of the National Academy of Science
of the United States of America 109: 19474-19479. Mueller-Cajar, O. & Whitney, S.M. 2008. Evolving
improved Synechococcus Rubisco functional
expression in Escherichia coli. Biochemical Journal 414: 205-214.
Ogren, W.L.
1984. Photorespiration: Pathways, regulation, and modification.
Annual Review of Plant Physiology and Plant Molecular Biology
35: 415-442. Ott,
C.M., Smith, B.D., Portis, A.R. & Spreitzer,
R.J. 2000.
Activase region on chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase. Journal of Biological
Chemistry 275: 26241-26244. Pace,
C.N. 2001. Polar group burial contributes more to protein stability
than nonpolar group burial. Biochemistry 40:
310- 313. Pakula,
A.A. & Sauer, R.T. 1990. Reverse hydrophobic effects relieved
by amino-acid substitutions at a protein surface. Nature 344:
363-364. Parikh,
M.R., Greene, D.A., Woods, K.K. & Matsumura, I. 2006. Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.
coli. Protein Engineering, Design and Selection
19: 113-119. Parry,
M.A.J., Madgwick, P.J., Carvalho,
J.F.C. & Andralojc, P.J.
2007. Prospects for increasing photosynthesis
by overcoming the limitations of Rubisco. Journal of
Agricultural Science 145: 31-43. Peterhansel,
C., Niessen, M. & Kebeish,
R.M. 2008. Metabolic engineering towards the
enhancement of photosynthesis. Photochemistry and Photobiology
84: 1317-1323. Rasineni,
G.K., Loh, P.C. & Lim, B.H. 2017. Characterization
of Chlamydomonas ribulose-1,5-bisphosphate carboxylase/ oxygenase variants mutated at
residues that are post-translationally modified. Biochimica
et Biophysica
Acta 1861(2): 79-85. Saschenbrecker,
S., Bracher, A., Rao, K.V., Rao, B.V.,
Hartl, F.U. & Hayer-Hartl, M.
2007.
Structure and function of RbcX, an assembly
chaperone for hexadecameric Rubisco.
Cell 129: 1189-1200. Smith,
S.A. & Tabita, F.R. 2003. Positive
and negative selection of mutant forms of prokaryotic (cyanobacterial)
ribulose-1,5- bisphosphate carboxylase/oxygenase.
Journal of Molecular Biology 331: 557-569. Spreitzer,
R.J., Thow, G. & Zhu, G. 1995. Pseudoreversion substitution at large-subunit residue 54 influences
the CO2/O2 specificity
of chloroplast ribulose bisphosphate carboxylase/ oxygenase. Plant
Physiology 109: 681-685. Stan,
G., Brooks, B.R., Lorimer, G.H. & Thirumalai,
D. 2006.
Residues in substrate proteins that interact with GroEL
in the capture process are buried in the native state. Proceedings
of the National Academy of Science of the United States of America
103: 4433-4438. Stan,
G., Brooks, B.R., Lorimer, G.H. & Thirumalai,
D. 2004.
Identifying natural substrates for chaperonins
using a sequence-based approach. Protein Science 14:
193-201. Tabita, F.R.,
Hanson, T.E., Satagopan, S., Witte,
B.H. & Kreel, N.E. 2008. Phylogenetic and evolutionary
relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided
by diverse molecular forms. Philosophical Transactions
of the Royal Society B 363: 2629-2640. Tabita, F.R.,
Hanson, T.E., Li, H., Satagopan, S.,
Singh, J. & Chan, S. 2007a. Function, structure,
and evolution of the RubisCO-like proteins
and their RubisCO homologs. Microbiology and Molecular Biology
Reviews 71(4): 576-599. Tabita, F.R.,
Satagopan, S., Hanson, T.E., Kreel, N.E. & Scott, S.S. 2007b. Distinct form I, II,
III, and IV Rubisco proteins from the three kingdoms of life provide
clues about Rubisco evolution and structure/function relationships.
Journal of Experimental Botany 59: 1515-1524. Takano,
K., Yamagata, Y. & Yutani, K. 2001. Contribution of polar groups in the interior of a protein to the conformational
stability. Biochemistry 40: 4853-4858. Taylor,
T.C., Backlund, A., Bjorhall,
K., Spreitzer, R.J. & Andersson,
I. 2001. First crystal structure of Rubisco
from a green alga, Chlamydomonas
reinhardtii. Journal of Biological Chemistry
276: 48159-48164. Tcherkez, G.G.B.,
Farquhar, G.D. & Andrews, T.J. 2006. Despite slow catalysis and confused
substrate specificity, all ribulose bisphosphate carboxylases
may be nearly perfectly optimized. Proceedings of the National
Academy of Science of the United States of America 103: 7246-7251. Whitney,
S.M., Baldet, P., Hudson, G.S. &
Andrews, T.J. 2001. Form I Rubiscos from non-green algae are expressed abundantly
but not assembled in tobacco chloroplasts. Plant Journal 26:
535-547. Whitney,
S.M., Houtz, R.L. & Alonso, H. 2011. Advancing our understanding and capacity to engineer nature’s CO2-
sequestering enzyme, Rubisco. Plant Physiology 155:
27-35. Wilson,
R.H., Martin-Avila, E., Conlan, C. &
Whitney, S.M. 2017. An improved Escherichia coli screen for Rubisco
identifies a protein-protein interface that can enhance CO2-
fixation kinetics. Journal of Biological Chemistry 293:
18-27. Wostrikoff,
K. & Stern, D. 2007. Rubisco large-subunit translation is autoregulated in response to its assembly state in tobacco
chloroplasts. Proceedings of the National Academy of Science
of the United States of America 104: 6466-6471. Zhu,
X.G., Portis, A.R. & Long, S.P. 2004. Would transformation
of C3 crop plants with foreign Rubisco increase productivity?
A computational analysis extrapolating from
kinetic properties to canopy photosynthesis. Plant,
Cell and Environment 27: 155-165. *Corresponding author; email: bhlim@utar.edu.my
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