7/31/2019 Rubisco Like Proteins
1/12
Journal of Experimental Botany, Vol. 59, No. 7, pp. 15431554, 2008
doi:10.1093/jxb/ern104 Advance Access publication 9 April, 2008
SPECIAL ISSUE REVIEW PAPER
RuBisCO-like proteins as the enolase enzyme in the
methionine salvage pathway: functional and evolutionary
relationships between RuBisCO-like proteins andphotosynthetic RuBisCO
Hiroki Ashida1,*, Yohtaro Saito1, Toshihiro Nakano1, Nicole Tandeau de Marsac2, Agnieszka Sekowska3,
Antoine Danchin4 and Akiho Yokota1
1 Nara Institute of Science and Technology (NAIST), Graduate School of Biological Sciences, 8916-5 Takayama,
Ikoma, Nara, 630-0101 Japan2 Unitedes Cyanobacteries, CNRS URA 2172, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15,France3 Unitede Genetique in silico, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France4 Genetics of Bacterial Genomics, CNRS URA 2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex15, France
Received 30 January 2008; Revised 26 February 2008; Accepted 28 February 2008
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase
(RuBisCO) is the key enzyme in the fixation of CO2 in
the Calvin cycle of plants. Many genome projects have
revealed that bacteria, including Bacillus subtilis,
possess genes for proteins that are similar to the largesubunit of RuBisCO. These RuBisCO homologues are
called RuBisCO-like proteins (RLPs) because they are
not able to catalyse the carboxylase or the oxygenase
reactions that are catalysed by photosynthetic
RuBisCO. It has been demonstrated that B. subtilis
RLP catalyses the 2,3-diketo-5-methylthiopentyl-
1-phosphate (DK-MTP-1-P) enolase reaction in the
methionine salvage pathway. The structure of
DK-MTP-1-P is very similar to that of ribulose-
1,5-bisphosphate (RuBP) and the enolase reaction is
a part of the reaction catalysed by photosynthetic
RuBisCO. In this review, functional and evolutionary
relationships between B. subtilis RLP of the methio-
nine salvage pathway, other RLPs, and photosynthetic
RuBisCO are discussed. In addition, the fundamental
question, How has RuBisCO evolved? is also consid-
ered, and evidence is presented that RuBisCOs
evolved from RLPs.
Key words: Bacillus subtilis, CO2 fixation, 2,3-diketo-5-
methylthiopentyl-1-phosphate enolase, methionine salvage
pathway, molecular evolution, photosynthesis, RuBisCO,
RuBisCO-like protein.
Introduction
Ribulose-1,5-bisphosphate carboxylase/oxygenase
(RuBisCO) is the key enzyme in the Calvin cycle.
RuBisCO catalyses the carboxylase reaction that fixes
CO2 on RuBP and produces two molecules of
3-phosphoglycerate (Andrews and Lorimer, 1987; Hartman
and Harpel, 1994; Roy and Andrews, 2000). The
carboxylase reaction is the initial reaction in the Calvin
cycle, and fixed CO2 is utilized as the carbon source to
synthesize sugars and/or starch for the growth of photo-
synthetic organisms. Nevertheless, RuBisCO has ineffi-
cient enzymatic properties (Andrews and Whitney, 2003).
In particular, RuBisCO catalyses an oxygenase reaction
that fixes O2 into RuBP, and this reaction antagonizes thecarboxylase reaction in atmospheres in which O2 is much
more abundant than CO2 (Andrews and Lorimer, 1987;
Hartman and Harpel, 1994; Roy and Andrews, 2000).
The oxygenase reaction is the starting reaction of
* To whom correspondence should be addressed. E-mail: [email protected]
The Author [2008]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.For Permissions, please e-mail: [email protected]
7/31/2019 Rubisco Like Proteins
2/12
photorespiration, which releases CO2 and NH3 and wastes
energy. In addition, the turnover of the carboxylasereaction by RuBisCO is a few to several times per second,
even when substrates are saturating (Andrews and
Whitney, 2003). Therefore, the photosynthetic CO2assimilation rate in plants can be limited by RuBisCO
(Hudson et al., 1992; Von Caemmerer et al., 1997). Plants
manage to perform photosynthetic CO2 fixation byaccumulating large amounts of RuBisCO protein to
compensate for the inefficient properties of RuBisCO.
Indeed, the RuBisCO protein constitutes ;50% of the
soluble proteins in plant leaves and is the most abundant
protein on earth (Ellis, 1979). Given these observations,
RuBisCO is the critical target for the improvement of
photosynthetic efficiency and productivity of plants.
Manipulation of RuBisCO to increase the carboxylation
rate and/or achieve high CO2 and low O2 affinity would
promote the efficiency of photosynthesis (Andrews and
Whitney, 2003).
Why has RuBisCO failed to evolve into an efficient
enzyme that does not catalyse the oxygenase reaction?Has there been an opportunity to evolve a more efficient
enzyme? The answers to these questions should be
resolved by a study of the molecular evolution of
RuBisCO. RuBisCO is classified into three forms, forms
I, II, and III, based on amino acid sequences and protein
structures, and all RuBisCOs in these groups catalyse both
carboxylase and oxygenase reactions. CO2 and O2 are
freely diffusible gasses, and O2 is smaller than CO2,
making it difficult to create a physical barrier to dioxygen
where CO2 has to be present; but why did RuBisCO not
acquire some sort of chemical barrier to prevent the action
of O2? This question cannot be answered by only
considering the evolutionary relationships among the threeforms of RuBisCO. Instead there is a need to understand
the emergence of RuBisCO in terms of its molecular
evolution.
Interestingly, there are proteins that are suitable for the
analysis of the molecular evolution of RuBisCO. Bacteria
and Archaea possess genes encoding proteins that have
considerable sequence identity to the large subunit of
photosynthetic RuBisCO. These proteins cannot catalyseeither the carboxylase or the oxygenase reactions of
RuBisCO, and are named RuBisCO-like proteins (RLPs).
RLPs represent a fourth class of the RuBisCO enzyme
family (Hanson and Tabita, 2001). Among the Bacteria
and Archaea, the function of RLP has been revealed onlyin Bacillus subtilis. Bacillus subtilis RLP catalyses the2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P)
enolase reaction, which is the fourth step in the methionine
salvage pathway (Ashida et al., 2003). Bacillus subtilisRLP catalyses an analogous reaction to photosynthetic
RuBisCO since its substrate resembles the structure of
RuBP, rationalizing the tight linkage between RLPs and
RuBisCO.
Until recently, the molecular evolution of RuBisCO had
been discussed using an evolutionary clock involving the
emergence of form I and form II RuBisCOs. It was not
possible to discuss the molecular evolution of RuBisCO
before the enzyme acquired the ability to fix CO2 because
ancestor proteins of RuBisCO had not yet been found.
The finding of RLPs, as a fourth form of the RuBisCO
family of enzymes, has enabled discussion of themolecular evolutionary relationship between RLPs and
RuBisCO. In Guptas hypothesis for the evolution of
Bacteria, low G+C Gram-positive bacteria, including
B. subtilis, were predicted to be the most ancient bacteria,which emerged near the root of the phylogenetic tree of
life. Considering the molecular evolution of RuBisCO,
based on Guptas hypothesis (Gupta, 1998; Gupta et al.,1999), RLPs may still retain features of the ancestor
protein of RuBisCO, because low G+C Gram-positive
bacteria and Archaea, possessing RLP genes, emerged
before cyanobacteria and photosynthetic bacteria, which
both utilize RuBisCO in the Calvin cycle. Thus, the
discovery of RLPs and determination of RLP functionprovide a new approach to elucidate the evolution of
RuBisCO. However, the methionine salvage pathway, to
recycle reduced sulphur in sulphur-deprived environ-
ments, may not be a more ancient metabolic pathway,
with respect to evolutionary processes. This is because
hydrogen sulphide, a reduced form of sulphur, was
presumably abundant early on Earth when the most
primitive organisms were living with minimal numbers of
genes and metabolic pathways (Delano, 2001). It is
possible, therefore, that an unknown ancestor protein of
RuBisCO already existed before RLPs emerged as the
enolase enzyme in the methionine salvage pathway, and
that RuBisCO has evolved from this ancestor protein,rather than via RLP in the methionine salvage pathway.
Thus, discussion of the evolutionary relationship between
RuBisCO and RLPs in the methionine salvage pathway
still cannot answer such fundamental questions as: Has
RuBisCO evolved via RLPs? and What is the origin of
RuBisCO? In this review, functional and evolutionary
relationships between RLPs and photosynthetic RuBisCO
are discussed, and a hypothesis is also proposed for this
fundamental question of RuBisCO evolution.
RuBisCO-like proteins are widely distributed in
Bacteria and in ArchaeaGenome projects have revealed that many of them possess
genes encoding RLPs that show similarity to the large
subunit of RuBisCO. In a phylogenetic tree, produced
using deduced amino acid sequences from the large
subunits of RuBisCO and RLPs, RuBisCOs are classified
into three forms, forms I, II, and III (Fig. 1) (Hanson and
Tabita, 2001; Ashida et al., 2003, 2005). Form I consistsof eight large and eight small subunits of 5055 kDa and
1544 Ashidaet al.
7/31/2019 Rubisco Like Proteins
3/12
1218 kDa, respectively, and is distributed widely among
photosynthetic organisms such as plants, algae, cyanobac-
teria, and photosynthetic and chemoautotrophic proteo-
bacteria (Tabita, 1999). Form II is composed only of large
subunits and is found mainly in some photosynthetic
proteobacteria and chemoautotrophic bacteria (Tabita,
1999). Form III is composed of only large subunits and is
found in Archaea (Tabita, 1999). On the other hand, RLPs
form three clades, groups a, b, and c, that are differentfrom the clades of photosynthetic RuBisCO (Fig. 1).
Group a includes RLPs from Bacillus species, thecyanobacterium Microcystis aeruginosa, the sulphate-reducing Archaeon Archaeoglobus fulgidus, and thephotosynthetic bacteria Rhodopseudomonas palustris and
Rhodospirillum rubrum. Group b contains RLPs fromnon-photosynthetic proteobacteria Palaromonas sp.,
Fig. 1. Phylogenetic tree constructed from the amino acid sequences of the large subunits of RuBisCO and of RLPs. The multiple sequencealignment and the phylogenetic tree were produced with CLUSTALW and TREE VIEW. Full names of species are as follows: B. subtilis, Bacillussubtilis; B. licheniformis, Bacillus licheniformis; Bacillus sp., Bacillus sp. NRRL B-14911; B. thuringiensis, Bacillus thuringiensis; B. anthracis,Bacillus anthracis; B. weihenstephanesis, Bacillus weihenstephanesis; B. cereus, Bacillus cereus; G. kaustrophilus, Geobacillus kaustrophilus;
B. clausii, Bacillus clausii; E. sibiricum, Exiguobacterium sibiricum; Lyngbya sp., Lyngbya sp. PCC8106; M. aeruginosa, Microcystis aeruginosaPCC7806; A. fulgidus, Archaeoglobus fulgidus; H. mobilis, Heliobacillus mobilis; O. tauri, Ostreococcus tauri; O. granulosus, Oceanicolagranulosus; N. mobilis, Nitrococcus mobilis; H. halophila, Halorhodospira halophila; R. palustris, Rhodopseudomonas palustris; R. rubrum,Rhodospirillum rubrum; Aurantimonas, Aurantimonas sp. SI85-9A1; F. pelagi, Fulvimarina pelagi; Polaromonas sp., Polaromonas sp. JS666;C. salexigens, Chromohalobacter salexigens; P. putida, Pseudomonas putida; D. acidovorans, Delftia acidovorans; B. bronchiseptica, Bordetellabronchiseptica; M. loti, Mesorhizobium loti; S. meliloti, Sinorhizobium meliloti; A. aurescens, Arthrobacter aurescens; P. luteolum, Pelodictyonluteolum; C. chlorochromatii, Chlorobium chlorochromatii; C. phaeobacteroides, Chlorobium phaeobacteroides; P. aestuarii, Prosthecochlorisaestuarii; C. tepidum, Chlorobium tepidum; R. sphaeroides, Rhodobacter sphaeroides; T. denitrificans, Thiobacillus denitrificans; D. aromatica,Dechloromonas aromatica; N. hamburgensis, Nitrobacter hamburgensis; S. WH8102, Synechococcus sp. WH8102; P. marinus, Prochlorococcusmarinus; N. punctifome, Nostoc punctiforme PCC73102; T. elongatus, Thermosynechococcus elongatus; S. PCC6803, Synechocystis sp. PCC6803; S.elongatus, Synechococcus elongatus PCC6301; R. sphaeroides, Rhodobacter sphaeroides; R. gelatinosus, Rubrivivax gelatinosus; B. japonicum,Bradyrhizobium japonicum; M. jannaschii, Methanocaldococcus jannaschii; M. barkeri, Methanosarcina barkeri; M. mazei, Methanosarcina mazei;M. acetivorans, Methanosarcina acetivorans; T. kodakarensis, Thermococcus kodakarensis; H. butylicus, Hyperthermus butylicus; N. pharaonis,Natronomonas pharaonis; P abyssi, Pyrococcus abyssi; P. horikoshii, Pyrococcus horikoshii; P. furiosus, Pyrococcus furiosus; M. marisnigri,Methanoculleus marisnigri.
RuBisCO-like proteins 1545
7/31/2019 Rubisco Like Proteins
4/12
Bordetella bronchiseptica, and Mesorhizobium loti. RLPs
from green non-sulphur bacteria of the genus Chlorobiumand the proteobacteria Rhodopseudomonas sp. are classi-fied in group c.
Comparing amino acid sequences between B. subtilisRLP and photosynthetic RuBisCO, B. subtilis RLP shows
;23% identity to form I and II RuBisCOs and ;30%
identity to form III RuBisCOs. In the same group a, B.subtilis RLP shows 78.5, 62.0, 59.4, 22.7, 35.6, 34.8,23.2, and 22.7% identity to RLPs of Bacillus lichen-iformis, Geobacillus kaustophilis, Bacillus anthracis,
Bacillus clausii, M. aeruginosa, A. fulgidus, R. rubrum,and R. palustris, respectively. On the other hand, B.subtilis RLP shows 27.5, 26.6, and 23.5% identity to
RLPs in group b, from Palaromonas sp., B. bronchisep-tica, and M. loti, respectively, and 25.1% and 26.8%identity to RLPs in group c, from R. palustris and
Chlorobium tepidum, respectively. Considering this distri-
bution and in the absence of horizontal gene transfer,
RLPs should have evolved widely, because the three
clades of RLPs show a greater distance from each other
compared with that with each form of RuBisCO (Fig. 1).
Using X-ray crystallography and point mutational
analysis, Hanson and Tabita (2001) proposed 19 amino
acid residues of photosynthetic RuBisCO as essential for
catalysis (Fig. 2). Alignment of RLPs sequences fromRLPs shows conservation of 918 of the 19 residues.
Bacillus subtilis RLP has 11 conserved residues (Fig. 2).These observations indicate that RLPs are very unlikely to
catalyse the carboxylase and oxygenase reactions that are
catalysed by photosynthetic RuBisCO.
What is the function of RLPs? Is there a functional and
evolutionary relationship between RLPs and photosyn-
thetic RuBisCO? The answers to these questions have
interested us with respect to the molecular evolution of
RuBisCO.
Fig. 2. Partial multiple sequence alignment of the large subunits of RuBisCO and RLPs. Sequences flanking the residues involved in the carboxylasereaction catalysed by RuBisCO are aligned. Active site residues conserved in RuBisCO are shown in grey letters on a black background. Residuesinvolved in catalysis and enolization of RuBP are indicated above the alignment by C and E, respectively. Lys201 for carbamylation is indicated by*. 1 and 5 above the alignment indicate residues involved in binding of the phosphate groups on C1 and C5 of RuBP, respectively. White colouredletters indicate residues that are not conserved in RLPs. The alignment is numbered according to the sequence of the large subunit of spinachRuBisCO.
1546 Ashidaet al.
7/31/2019 Rubisco Like Proteins
5/12
The road to identification of the function ofB. subtilis RLP
In order to identify the function of RLP, the B. subtilisgenome was explored when it was completed. When the
analysis began, the gene encoding RLP in B. subtilis wasannotated as a gene of unknown function, now named
mtnW, coding for a protein similar to the large subunit of
RuBisCO. It was initially predicted that B. subtilis RLPcould not catalyse the carboxylase and oxygenase reactions
of photosynthetic RuBisCOs, because this RLP has only
11 of 19 amino acid residues that are essential for this
catalysis (Fig. 2). In order to confirm this prediction, an
analysis was carried out to determine whether B. subtilisRLP can catalyse the carboxylase reaction using recombi-
nant protein expressed in Escherichia coli. Indeed,
B. subtilis RLP showed no carboxylase activity. This resultclearly showed that B. subtilis RLP functions as an enzymein a different metabolic pathway from that of RuBisCO.
The mtnW gene for the RLP of B. subtilis is the firstgene of the mtnWXBD operon (Fig. 3a). The mtnKAoperon lies in the vicinity of the mtnWXBD operon
(Fig. 3a). It has been predicted that both operons have
a leader mRNA, the S box, known to regulate the
expression of the genes involved in methionine metabo-
lism (Murphy et al., 2002; Sekowska and Danchin,
2002) (Fig. 3a). The S box is a riboswitch that regulates
gene expression via transcription termination (Winkler
et al., 2003; Montange and Batey, 2006), and enhances
the expression of target genes in response to methioninestarvation by detection of the concentration of S-
adenosylmethionine, a metabolite indicator for methionine
levels in vivo. In order to analyse the response of the
mtnWXBD operon to methionine starvation, lacZ was
inserted into the internal region of mtnW. Analysis of the
expression of the mtnWXBDlacZ operon showed that
expression of lacZ was not induced on growth medium
containing methionine but was induced on medium
containing NH4Cl, glutamine, and serine (Fig. 4a). In
addition, lacZ expression was enhanced by removing
methionine from the culture medium after pre-culture on
medium including methionine (Fig. 4b). These results
clearly suggested that this operon was involved in
Fig. 3. The methionine salvage pathway and related operons in B. subtilis. The mtnWXBD and mtnKA operons consist of genes involved in themethionine salvage pathway. The expression of genes in both operons is regulated by S boxes. (b) The methionine salvage pathway in B. subtilis.
RuBisCO-like proteins 1547
7/31/2019 Rubisco Like Proteins
6/12
methionine metabolism. Furthermore, in mtnWXBD and
mtnKA operons, MtnD showed high similarity to1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase,
and MtnK has been identified as the methylthioribose
(MTR) kinase (Sekowska et al., 2001), suggesting thatboth operons function in the methionine salvage pathway
(Fig. 3b) (Grundy and Henkin, 2002; Murphy et al., 2002;Sekowska and Danchin, 2002). These data indicate that
B. subtilis RLP would catalyse a reaction step somewhere
in this pathway. Many organisms, including bacteria
(Sekowska et al., 2000; Grundy and Henkin, 2002), yeast(Marchitto and Ferro, 1985), plants (Burstenbinder et al.,
2007), and mammals (Wray and Abeles, 1995; Garcia-
Castellano et al., 2002), utilize the methionine salvagepathway to recycle organic sulphur from MTR. In this
pathway, organic sulphur is salvaged from MTR, which is
produced from methylthioadenosine (MTA), a waste prod-
uct of polyamine (Sekowska et al., 2000; Grundy andHenkin, 2002), mugineic acid (Ma et al., 1995), and
ethylene synthesis (Burstenbinder et al., 2007). In themethionine salvage pathway that has been proposed in
Klebsiella, MTR is phosphorylated to MTR-1-phosphate(MTR-1-P) by the MTR kinase, and then MTR-1-P
is isomerized by an isomerase to methylthioribulose-1-
phosphate (MTRu-1-P) (Saito et al., 2007). MTRu-1-Pundergoes a dehydration that is catalysed by a dehydratase
and produces DK-MTP-1-P (Furfine and Abeles, 1988;Ashida et al., 2003, 2005, 2007; Sekowska et al., 2004).DK-MTP-1-P is converted to 1,2-dihydroxy-3-keto-5-
methylthiopentene (DHK-MTPene), via the intermediate,
2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-
MTPenyl-1-P), by a bi-functional enzyme, enolase/phos-
phatase (Balakrishnan et al., 1993; Myers et al., 1993). In
the final step, DHK-MTPene is converted to formate and
2-keto-4-methylthiobutyrate (KMTB) by a dioxygenase
(Wray and Abeles, 1993), and KMTB is transaminated to
methionine (Berger et al., 2003). In Klebsiella, each stephas been predicted based on the analysis of metabolites,
but this pathway remains to be fully understood. The
structures of MTRu-1-P and of DK-MTP-1-P are similar tothe structure of RuBP, and D-glycero-2,3-pentodiulose-
1,5-bisphosphate, is a by-product of the oxygenase re-
action catalysed by RuBisCO (Pearce and Andrews, 2003).
It is therefore predicted that B. subtilis RLP is MTRu-1-Pdehydratase or DK-MTP-1-P enolase/phosphatase.
Growth assays were used to examine whether RLP was
involved in the methionine salvage pathway, using an
RLP-deficient mutant of B. subtilis and pathway metabo-lites. The wild type grew in the culture medium contain-
ing methionine, MTA, or KMTB as a sole source of
sulphur (Fig. 5a, b). The RLP-deficient mutant grew in
culture medium containing methionine or KMTB, but not
in medium containing MTA as a sole source of sulphur(Fig. 5a, b) (Ashida et al., 2003). This result clearly
showed that B. subtilis RLP catalyses a reaction stepbetween MTA and KMTB in the methionine salvage
pathway. To determine this step, enzymes, their sub-
strates, and products in the methionine salvage pathway of
B. subtilis were identified, step-by-step, using recombinantproteins encoded in the mtnWXBD and mtnKS operonsand employing 1H-NMR and UV-VIS spectroscopy(Ashida et al., 2003). All reaction steps and enzymeswere determined in the methionine salvage pathway,
consisting of mtnA, mtnW, mtnX, mtnB, and mtnD genes,which encode MTR-1-P isomerase, DK-MTP-1-P enolase,
HK-MTPenyl-1-P phosphatase, MTRu-1-P dehydratase,and DHK-MTPene dioxygenase, respectively (Fig. 3b)
(Ashida et al., 2003). In this way, B. subtilis RLP wasidentified as the DK-MTP-1-P enolase. The enolase/
phosphatase activities in other organisms were different
from that in the methionine salvage pathway of B. subtilis,in that these steps were catalysed by two enzymes in
B. subtilis, RLP for enolization and HK-MTPenyl-1-Pphosphatase for deposphorylation (Fig. 3b).
Fig. 4. Induction of the mtnWXBD operon. (a) A Bacillus subtilismutant with lacZ inserted into the mtnW gene was grown on culturemedium containing 40 mg ml1 X-gal and 1 mM NH4Cl, glutamine,serine, or methionine. Blue colonies were produced (black colour in thismonochromatic figure) by the expression of a lacZ reporter gene withinthe mtnWXBD operon, when the mtnWXBD operon was induced. (b)The same mutant was grown in Spizizen minimal medium containingmethionine (0.3 mM), split at 0 h, and grown in the presence (opencircles) or absence (filled squares) of methionine (0.3 mM). Cells werecollected every 1 h, and b-galactosidase activities were measured using
the total soluble fraction extracted from cells.
1548 Ashidaet al.
7/31/2019 Rubisco Like Proteins
7/12
The function of RLP from the cyanobacterium Micro-cystis aeruginosa PCC7806 was also identified, based onanalysis of B. subtilis RLP. Interestingly, this cyanobacte-
rium possesses genes for both RLP and photosyntheticRuBisCO. The gene for RLP of M. aeruginosa couldrescue an RLP-deficient mutant of B. subtilis when they
were grown in culture medium including MTA as the sole
source of sulphur (Fig. 5c) (Carre-Mlouka et al., 2006).The recombinant M. aeruginosa RLP showed DK-MTP-1-P enolase activity (Carre-Mlouka et al., 2006), suggest-ing that M. aeruginosa RLP is the DK-MTP-1-P enolasein this cyanobacterium. This was the first report that RLP,
functioning in the methionine salvage pathway, co-existed
with a photosynthetic RuBisCO in the same organism. Inaddition, cyanobacteria are considered to be the ancestors
of photosynthetic eukaryotic chloroplasts. These facts are
interesting, with respect to the evolutionary relationship
between RLPs and photosynthetic RuBisCO. Assuming
that RLP, in the methionine salvage pathway, is related to
the ancestor protein of RuBisCO, based on Guptas
bacterial evolution hypothesis, the examination of this
cyanobacterium may provide the missing link between
micro-organisms utilizing RLPs for methionine salvage
and photosynthetic organisms with RuBisCO. However, it
is unclear whether this cyanobacterium has retained the
gene for RLP from an ancestral organism or acquired it
from recent lateral transfer. Further analysis of cyanobac-
teria possessing both genes for RLP and RuBisCO are
needed to settle this question.
What is the comparison of catalysing reactionsbetween B. subtilis RLP and photosyntheticRuBisCO telling us?
It seems that there is no linkage between B. subtilis and
M. aeruginosa RLPs and photosynthetic RuBisCO,because RLPs function in the methionine salvage path-
way, which is far from the Calvin cycle for CO2 fixation.
However, interesting observations can be made about the
catalysing reactions of these RLPs and photosynthetic
RuBisCO. DK-MTP-1-P, a substrate of RLPs, has
structural similarity to RuBP, the substrate for photosyn-thetic RuBisCO, except that in DK-MTP-1-P, the OH
group and proton on C3 of RuBP are replaced by
a carbonyl group (Fig. 6) (Ashida et al., 2005). Addition-ally, in DK-MTP-1-P, the OH group on C4 and the
phosphate group on C5 of RuBP are replaced by a proton
and a methylthio group, respectively (Fig. 6). The
functional similarities between DK-MTP-1-P enolase and
RuBisCO are found not only by comparing substrates, but
also by comparing steps in the catalytic cycle. The
carboxylase reaction, catalysed by RuBisCO, consists of
five sequential reactions: (i) enolization of RuBP by
abstraction of a proton on C3; (ii) carboxylation of C2;
(iii) hydration of C3; (iv) cleavage of the C2C3 bond;and (v) protonation of the C2 of the upper aci-acid formof 3-phosphoglycerate (Mauser et al., 2001). The firstcatalysing reaction, enolization of RuBP, is the same
reaction as enolization of DK-MTP-1-P in RLP, except
that the proton on C1 of DK-MTP-1-P is abstracted in the
RLP-catalysed reaction. Lys175, Lys201, Asp203, and
Glu204 are essential residues for RuBP enolization inRuBisCO (Cleland et al., 1998). In particular, Lys201 is
carbamylated by CO2, and this carbamate is stabilized by
co-ordination of an Mg2+ ion (Andrews and Lorimer,
1987; Hartman and Harpel, 1994; Roy and Andrews,
2000). The carbamylated Lys201, Asp203, and Glu204
are essential residues to bind the Mg2+ ion, whichstabilizes the endiol form of RuBP (Cleland et al., 1998).
In the proposed mechanism for the enolization of RuBP,the carbamylated Lys201 is the base that abstracts the
proton of C3, while the amino group of Lys175 initially
stabilizes the resultant endiol of RuBP and then acts as the
acid that protonates the oxygen anion (Cleland et al.,1998) (Fig. 6). Mutation of these residues leads to a lack
of RuBP enolization activity in RuBisCO (Estelle et al.,
Fig. 5. Rescue of the RLP-deficient mutant of B. subtilis by thegene for photosynthetic RuBisCO or by cyanobacterium RLP. Weused two RLP-deficient mutants of B. subtilis, DRLP1 (mtnW::spcamyE::mtnXBD) (Carre-Mlouka et al., 2006) and DRLP2 (mtnW::pMu-tinT3) (Ashida et al., 2003). Strain DRLP1 was transformed with theexpression vector, pDG148 (Stragier et al., 1998), harbouring the RLPgene from M. aeruginosa PCC7806, yielding DRLP/MaRLP+. The genefor photosynthetic RuBisCO from the photosynthetic bacterium Rhodo-spirillum rubrum was integrated into the amyE gene in DRLP2, givingstrain DRLP/RuBisCO+. Wild type (a), DRLP1 (b), DRLP/MaRLP+ (c),and DRLP/RuBisCO+ (d) were grown for 35 h in Spizizen minimalmedium (Anagnostopoulos and Spizizen, 1961) containing 1 mMisopropyl-b-D-thiogalactopyranoside and 0.5 mM MTA as the solesource of sulphur. When required, spectinomycin, erythromycin,kanamycin, and chloramphenicol were added to a final concentration of100, 0.5, 5, and 5 mg ml1, respectively.
RuBisCO-like proteins 1549
7/31/2019 Rubisco Like Proteins
8/12
1985; Hartman et al., 1987; Gutteridge et al., 1988).Interestingly, B. subtilis and M. aeruginosa RLPs con-serve these residues that are predicted to be essential
residues for the DK-MTP-1-P enolase reaction (Fig. 2). It
was easy to predict that Lys201 was also the catalytic
residue for abstraction of a proton in B. subtilis RLP.Recently, Imker et al. (2007) reported the X-ray crystal
structure of Geobacillus kaustophilus RLP, complexedwith an analogue of DK-MTP-1-P, 2,3-diketohexane-1-
phosphate (DK-H-1-P). Geobacillus kaustophilus belongsto the same clade Bacillaceae as B. subtilis. Geobacillus
kaustophilus RLP catalyses the DK-MTP-1-P enolase
reaction and has conserved residues Lys175, Lys201,
Asp203, and Glu204, which are also conserved in
B. subtilis and M. aeruginosa RLPs (Fig. 2). Lys201 wascarbamylated, and carbamylated Lys201, Asp203, and
Glu204 were Mg2+ ligands in the 3D structure of G.kaustophilus RLP (Imker et al., 2007). The arrangementof Lys175, carbamylated Lys201, Asp203, and Glu204 in
the active site was very similar to that in RuBisCO.Therefore, carbamylated Lys201 was located too far from
C1 of DK-H-1-P to abstract a proton, and Lys175 was
also located at a distance from C1. In this RLP, Asn123,
conserved in RuBisCO, was replaced by lysine (Fig. 2),
and Lys123 was appropriately positioned to abstract
a proton from C1 of DK-H-1-P. In fact, the enolase
activity was retained by alanine substitutions for Lys175
and Lys201, but alanine substitution for Lys123 resulted
Fig. 6. Proposed mechanism for the enolization of RuBP by RuBisCO and of DK-MTP-1-P by Bacillus RLP. In enolization of RuBP by RuBisCO,the carbamate group attached to Lys201 is the base that abstracts a proton from C3, while the amino group of Lys175 initially stabilizes the resultantenolate and then acts as the acid that protonates the oxygen anion. In the reaction catalysed by RLP, if RLPs utilize the same residues as RuBisCO,de-protonation at C1 and re-protonation at the oxygen anion are carried out by carbamylated Lys201 and Lys175, respectively. In the reactionmechanism proposed by Imker et al. (2007), Lys123 is the residue for de-protonation at C1.
1550 Ashidaet al.
7/31/2019 Rubisco Like Proteins
9/12
in a lack of enolization activity (Imker et al., 2007).
Therefore, Imker et al. proposed that a candidate residueto abstract the proton is Lys123, while the carbamylated
Lys201 is involved in de-protonation in photosynthetic
RuBisCO (Fig. 6). Interestingly, Lys123 is conserved in
RLPs of B. subtilis, M. aeruginosa, and G. kaustophilus,which all show DK-MTP-1-P enolase activity (Fig. 2),
suggesting that Lys123 is the essential residue for DK-MTP-1-P enolase activity in all RLPs. Considering
conservation of Lys123, Lys175, and Lys201 in DK-
MTP-1-P enolase activity, all three residues should
contribute to the enolization of DK-MTP-1-P. However,
it is unclear whether Lys175 and Lys201 are involved in
re- and de-protonation, as they are in photosynthetic
RuBisCO (Fig. 6). If Lys123 played a role in the
abstraction of protons in DK-MTP-1-P enolase, in spite
of the fact that Lys201 was carbamylated, why was
Lys201 carbamylated in RLP, as it is in photosynthetic
RuBisCO? It was reported by Imkar et al. (2007) thatthe carbamylation at Lys201 increased the kcat/Km for the
enolase reaction of G. kaustophilus RLP. However, therole of carbamylation on Lys201 is still unknown in
RLP. Further analysis will reveal the functional relation-
ship of carbamylation on Lys201 between RLPs and
photosynthetic RuBisCO. Three RLPs also had conserved
residues at Gly401 and Gly403, relative to the P1
phosphate-binding motif of photosynthetic RuBisCO
(Fig. 2) (Hartman and Harpel, 1994). In G. kaustophilusRLP, the P1 phosphate oxygens of DK-H-1-P form
hydrogen bonds to amide groups of the backbone of
Gly401 and Gly403 (Imker et al., 2007). DK-MTP-1-Penolase and photosynthetic RuBisCO utilize the common
conserved P1-binding motif to bind the substrate P1
phosphate group.
Are all RLPs acting as the DK-MTP-1-P enolases?
Many bacteria possess genes for RLPs, as shown in the
phylogenetic tree (Fig. 1). Are all RLPs acting as DK-
MTP-1-P enolases, as is the case in B. subtilis,
M. aeruginosa, and G. kaustophilus?As described above, RLPs from B. subtilis, M. aeruginosa,
and G. kaustophilus have conserved residues Lys123,Lys175, Lys201, Asp203, and Glu204 that are essential
for the enolization reaction of DK-MTP-1-P enolase
(Fig. 2). Other RLPs from group a together with those ofBacillus species and of cyanobacteria also have conservedresidues Lys123, Lys175, Lys201, Asp203, and Glu204
(Fig. 2). In addition, the genes for RLPs from B.licheniformis, B. cereus, and B. anthracis, and from other
Bacillus species are members of the mtnWXBD operon. Thegene for RLP from the cyanobacterium Lyngbya sp. PCC8106 is also predicted to form this operon with homologous
genes for mtnB and mtnE. These observations suggest that
these RLPs in group a also function as the DK-MTP-1-Penolase in the methionine salvage pathway. However, the
RLPs of R. rubrum and R. palustris, in the same group a,have conserved residues Lys175, Lys201, and Asp203, but
Lys123 and Glu204 are replaced with asparagine and
histidine, respectively (Fig. 2). Interestingly, it was reported
that R. rubrum and R. palustris utilize the methionine
salvage pathway because they can grow using MTA as thesole source of sulphur (Tabita et al., 2007). This resultimplies that R. rubrum and R. palustris RLPs function asthe DK-MTP-1-P enolase in these bacteria. Considering the
result of mutational analysis at Lys123 in G. kaustophilusRLP, these RLPs may not be the DK-MTP-1-P enolase,
because they do not have conserved Lys123. In R. rubrumand R. palustris, the reaction step of DK-MTP-1-P enolasemay be catalysed by a photosynthetic form II RuBisCO and
not by RLPs, because R. rubrum RuBisCO can catalyse thisreaction, although at a very low rate (described below)
(Ashida et al., 2003). As in the case of R. rubrum and
R. palustris, group a seem to include RLPs with other
functions, distinct from DK-MTP-1-P enolase. Tabita et al.(2007) reported a phylogenetic tree of RLPs produced using
a large number of RLP sequences. In Tabitas phylogenetic
tree, group a was further classified into two subgroups,
RLPs for DK-MTP-1-P enolase and photosynthetic bacterial
RLPs. If the phylogenetic tree is examined in detail, RLPs
of group a can be divided into two subgroups, a1 including
B. subtilis DK-MTP-1-P enolase and a2 including RLPsfrom photosynthetic bacteria, in agreement with Tabitas
classification. This classification of RLPs is in accord with
the prediction of function. RLP is the DK-MTP-1-P enolase,
based on conservation of predicted essential residues,
and, therefore, it is predicted that RLPs in group a1 are
DK-MTP-1-P enolases, but group a2 RLPs are not.However, Lys201 is replaced by glutamine in B. clausiiRLP of group a1 (Fig. 2) and this micro-organism does
not possess homologous genes for other enzymes
functioning in the methionine salvage pathway, in spite
of B. clausii being a Bacillus species. Likewise,
A. fulgidus RLP in group a1 is exceptional in thatLys123 is not conserved (Fig. 2) and, in addition, the
homologous genes encoding other enzymes for
methionine salvage cannot be found. These facts
suggest that these RLPs may not function as DK-MTP-1-P
enolase and that some RLPs classified in group a1
possess a different function. On the other hand, in RLPs in
groups b and c, Lys123 is replaced by asparagine, and,therefore, these RLP groups should not function as DK-
MTP-1-P enolase.
The function of RLPs from species other than Bacillusspecies and cyanobacteria is unclear. Hanson and Tabita
(2001) reported that C. tepidum RLP, included in RLPgroup c, is involved in sulphur oxidation and oxidativestress, suggesting that this RLP functions in other
biological process.
RuBisCO-like proteins 1551
7/31/2019 Rubisco Like Proteins
10/12
Evolutionary and functional linkage between RLPand photosynthetic RuBisCO
Evolutionary and functional linkage between RLP and
photosynthetic RuBisCO has attracted interest. It is con-
cluded that there is functional linkage of RLP and RuBisCO
in the DK-MTP-1-P enolase reaction, because the catalytic
reaction and the substrate of DK-MTP-1-P enolase resemble
those of RuBisCO. Surprisingly, introduction of the gene forRuBisCO from the photosynthetic bacterium R. rubrumrescued the growth of an RLP-deficient B. subtilis mutant
on medium containing MTA as the sole sulphur source (Fig.
5d). In addition, recombinant R. rubrum RuBisCO showed
a very low, but significant level of DK-MTP-1-P activity in
vitro (Ashida et al., 2003). This suggested that photosyn-
thetic RuBisCO could catalyse the DK-MTP-1-P enolase
reaction, and that there is a functional link between RLP and
RuBisCO. It is therefore speculated that RLP and photosyn-
thetic RuBisCO evolved from the same ancestor protein.
Gupta proposed a hypothesis for linear evolution of
bacteria by indel analysis using highly conserved domains
of proteins that all bacteria commonly possess (Gupta,
1998; Gupta et al., 1999). In this hypothesis, low G+C
Gram-positive bacteria, including Bacillus species, would
have features of the most ancient bacteria, rather than
Archaea and Bacteria possessing RLPs and RuBisCO. If
the molecular evolution of RLP and photosynthetic
RuBisCO is discussed following Guptas hypothesis, RLP
in the methionine salvage pathway might have evolved
earlier than photosynthetic RuBisCO. Furthermore, photo-
synthetic RuBisCO might have evolved from an ancestral
DK-MTP-1-P enolase (Ashida et al., 2005).If this hypothesis is correct, the methionine salvage
pathway would be one of the most ancient metabolicpathways. However, ancient organisms might not have
utilized this pathway to recycle the reduced sulphur source,
because the concentration of hydrogen sulphide would have
been high in the environments where the most ancient
organisms initially emerged (Delano, 2001). It is therefore
thought that the methionine salvage pathway was not part of
ancient metabolism and that a catalytically distinct ancestor
protein of RLPs, functioning in the methionine salvage
pathway, might have already existed. Interestingly, the
methionine-salvaging enzymes, MtnK, A, B, and W, from
B. subtilis can catalyse sequential reactions for ribose,
in addition to the substrate, MTR (Imker et al., 2007).
Ribose is converted to 2-hydroxy-3-keto-5-hydroxypent-1-ene 1-phosphate by sequential reactions catalysed by four
methionine-salvaging enzymes including RLP (Imker et al.,
2007). It has been predicted that ribose was formed in the
chemical evolution era and was an essential compound in the
RNA world (Joyce, 2002). Ribose is one of the most ancient
compounds on earth, older than MTR. Considering that
methionine-salvaging enzymes can utilize ribose, an ances-
tral metabolic pathway of the methionine salvage pathway
might have been involved in some form of ribose metabo-
lism, incorporating the sequential reactions catalysed by themethionine-salvaging enzymes. In other words, an ancestral
RLP protein might be an enolase enzyme that functioned in
ancient ribose metabolism.
Concluding remarks
Many genome projects have revealed that Bacteria and
Archaea possess genes for RLPs that cannot catalyse either
the carboxylase or the oxygenase reactions of photosyn-
thetic RuBisCO. These facts provide the fourth form of
RuBisCO enzymes. The present studies have revealed that
one member of the fourth form, B. subtilis RLP, is theenolase enzyme functioning in the methionine salvage
pathway. In addition, RLPs from the cyanobacterium,
M. aeruginosa, and G. kaustophilis catalyse the enolasereaction in methionine salvage. Comparing the steps in the
catalytic cycle between these RLPs and RuBisCO, it was
found that RLPs catalysed a very similar reaction to
photosynthetic RuBisCO, for a substrate with a similarstructure to RuBP. In addition, both enzymes utilized the
same amino acid residues to catalyse each reaction,
suggesting that RLP and photosynthetic RuBisCO might
have evolved from the same ancestral protein. Further-
more, considering the molecular evolution of RuBisCObased on Guptas evolutionary hypothesis of micro-
organisms, the hypothesis is proposed that RLP, function-
ing as an enolase, is the ancestral protein of RuBisCO.
Thus, studies on RLPs have suggested an answer to the
fundamental question What is the origin of photosynthetic
RuBisCO? However, there remains limited information
about RLPs and, therefore, further analysis of evolutionary
and functional relationships between RLPs and RuBisCOis needed to answer to this question fully. In particular,
functional characterization of many RLPs is required to
establish the molecular evolution of RuBisCO.
Research on RLPs should provide useful information, not
only for evolutionary studies, but also to improve RuBisCO
efficiency. CO2 fixation by RuBisCO is the limiting step in
plant photosynthesis. Hence, inefficient RuBisCO is the
obvious target to improve efficiency of photosynthesis in
plants. To improve RuBisCO to Super-RuBisCO with
high CO2 specificity, depressed reactivity for O2, and
a high CO2-fixing catalytic rate, it is necessary to know the
amino acid residues involved in catalysis of RuBisCO.
Analysis of the functional and structural relationships
between RLPs and photosynthetic RuBisCO should pro-
vide important information on the structure and amino acid
residues involved in carboxylase or oxygenase reactions.
Acknowledgements
The authors thank Drs Naotake Ogasawara and Kazuo Kobayashifor help and discussion in molecular manipulation of Bacillus. We
1552 Ashidaet al.
7/31/2019 Rubisco Like Proteins
11/12
are grateful to Dr Chojiro Kojima for 1H-NMR analysis. This workwas supported partly by a Grant in Aid (17208031 and 18688021)for Scientific Research from the Japan Society for the Promotion ofScience (JSPS), partly by a grant (FY2004-2006) for GeneralScience and Technology from the Asahi Glass Foundation, andpartly by a grant (FY2005-2007) from the Nissan ScienceFoundation.
References
Andrews TJ, Lorimer GH. 1987. Rubisco: structure, mechanisms,and prospects for improvement. In: Hatch M, Boardman N, eds.The biochemistry of plants, Vol. 10. New York: Academic Press,131218.
Andrews TJ, Whitney SM. 2003. Manipulating ribulose bisphos-phate carboxylase/oxygenase in the chloroplasts of higher plants.Archives of Biochemistry and Biophysics 414, 159169.
Ashida H, Danchin A, Yokota A. 2005. Was photosyntheticRuBisCO recruited by acquisitive evolution from RuBisCO-likeproteins involved in sulfur metabolism? Research in Microbiol-ogy 156, 611618.
Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N,
Yokota A. 2003. A functional link between RuBisCO-like proteinof Bacillus and photosynthetic RuBisCO. Science 302, 286290.Ashida H, Saito Y, Kojima C, Yokota A. 2007. Enzymatic
characterization of 5-methylthioribulose-1-phosphate dehydrataseof the methionine salvage pathway from Bacillus subtilis.Bioscience, Biotechnology and Biochemistry 71, 20212028.
Balakrishnan R, Frohlich M, Rahaim PT, Backman K,Yocum RR. 1993. Appendix. Cloning and sequence of the geneencoding enzyme E-1 from the methionine salvage pathway ofKlebsiella oxytoca. Journal of Biological Chemistry 268, 2479224795.
Berger BJ, English S, Chan G, Knodel MH. 2003. Methionineregeneration and aminotransferases in Bacillus subtilis, Bacilluscereus, and Bacillus anthracis. Journal of Bacteriology 185,24182431.
Burstenbinder K, Rzewuski G, Wirtz M, Hell R, Sauter M.2007. The role of methionine recycling for ethylene synthesis inArabidopsis. The Plant Journal 49, 238249.
Carre-Mlouka A, Mejean A, Quillardet P, et al. 2006. A newRubisco-like protein coexists with a photosynthetic Rubisco inthe planktonic cyanobacteria Microcystis. Journal of BiologicalChemistry 281, 2446224471.
Cleland WW, Andrews TJ, Gutteridge S, Hartman FC,Lorimer GH. 1998. Mechanism of Rubisco: the carbamate asgeneral base. Chemical Reviews 98, 549562.
Delano JW. 2001. Redox history of the Earths interior sinceapproximately 3900 Ma: implications for prebiotic molecules.Origins of Life and Evolution of the Biosphere 31, 311341.
Ellis RJ. 1979. Most abundant protein in the world. Trends inBiochemical Sciences 4, 241244.
Estelle M, Hanks J, McIntosh L, Somerville C. 1985. Site-
specific mutagenesis of ribulose-1,5-bisphosphate carboxylase/oxygenase. Evidence that carbamate formation at Lys191 isrequired for catalytic activity. Journal of Biological Chemistry260, 95239526.
Furfine ES, Abeles RH. 1988. Intermediates in the conversion of5#-S-methylthioadenosine to methionine in Klebsiella pneumo-niae. Journal of Biological Chemistry 263, 95989606.
Garcia-Castellano JM, Villanueva A, Healey JH, Sowers R,Cordon-Cardo C, Huvos A, Bertino JR, Meyers P, Gorlick R.2002. Methylthioadenosine phosphorylase gene deletions arecommon in osteosarcoma. Clinical Cancer Research 8, 782787.
Grundy F, Henkin T. 2002. Synthesis of serine, glycine, cysteine,and methionine. In: Sonenshein A, Hoch J, Losick R, eds.
Bacillus subtilis and its closest relatives: from genes to cells.Washington, DC: American Society for Microbiology, 245254.
Gupta RS. 1998. Protein phylogenies and signature sequences:a reappraisal of evolutionary relationships among archaebacteria,
eubacteria, and eukaryotes. Microbiology and Molecular BiologyReviews 62, 14351491.
Gupta RS, Mukhtar T, Singh B. 1999. Evolutionary relationships
among photosynthetic prokaryotes (Heliobacterium chlorum,Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidumand proteobacteria): implications regarding the origin of photo-
synthesis. Molecular Microbiology 32, 893906.Gutteridge S, Lorimer G, Pierce J. 1988. Details of the reactions
catalyzed by mutant forms of Rubisco. Plant Physiology andBiochemistry 26, 675682.
Hanson TE, Tabita FR. 2001. A ribulose-1,5-bisphosphatecarboxylase/oxygenase (RubisCO)-like protein from Chlorobiumtepidum that is involved with sulfur metabolism and the responseto oxidative stress. Proceedings of the National Academy ofSciences, USA 98, 43974402.
Hartman FC, Harpel MR. 1994. Structure, function, regulation,and assembly ofD-ribulose-1,5-bisphosphate carboxylase/oxygen-
ase. Annual Review of Biochemistry 63, 197234.
Hartman FC, Soper TS, Niyogi SK, Mural RJ, Foote RS,Mitra S, Lee EH, Machanoff R, Larimer FW. 1987. Functionof Lys-166 of Rhodospirillum rubrum ribulosebisphosphatecarboxylase/oxygenase as examined by site-directed mutagenesis.
Journal of Biological Chemistry 262, 34963501.Hudson GS, Evans JR, von Caemmerer S, Arvidsson YB,
Andrews TJ. 1992. Reduction of ribulose-1,5-bisphosphatecarboxylase/oxygenase content by antisense RNA reduces photo-
synthesis in transgenic tobacco plants. Plant Physiology andBiochemistry 98, 294302.
Imker HJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. 2007.Mechanistic diversity in the RuBisCO superfamily: the enolase
in the methionine salvage pathway in Geobacillus kaustophilus.Biochemistry 46, 40774089.
Joyce GF. 2002. The antiquity of RNA-based evolution. Nature
418, 214221.Ma JF, Shinada T, Matsuda C, Nomoto K. 1995. Biosyn-
thesis of phytosiderophores, mugineic acids, associated withmethionine cycling. Journal of Biological Chemistry 270,1654916554.
Marchitto KS, Ferro AJ. 1985. The metabolism of 5#-methyl-thioadenosine and 5-methylthioribose 1-phosphate in Saccharo-myces cerevisiae. Journal of General Microbiology 131, 21532164.
Mauser H, King WA, Gready JE, Andrews TJ. 2001. CO(2)fixation by Rubisco: computational dissection of the key steps of
carboxylation, hydration, and CC bond cleavage. Journal of theAmerican Chemical Society 123, 1082110829.
Montange RK, Batey RT. 2006. Structure of the S-adenosylme-thionine riboswitch regulatory mRNA element. Nature 441,
11721175.Murphy BA, Grundy FJ, Henkin TM. 2002. Prediction of gene
function in methylthioadenosine recycling from regulatory sig-
nals. Journal of Bacteriology 184, 23142318.Myers RW, Wray JW, Fish S, Abeles RH. 1993. Purification and
characterization of an enzyme involved in oxidative carbon
carbon bond cleavage reactions in the methionine salvage
pathway of Klebsiella pneumoniae. Journal of Biological Chem-istry 268, 2478524791.
Pearce FG, Andrews TJ. 2003. The relationship betweenside reactions and slow inhibition of ribulose-bisphosphate
RuBisCO-like proteins 1553
7/31/2019 Rubisco Like Proteins
12/12
carboxylase revealed by a loop 6 mutant of the tobacco enzyme.Journal of Biological Chemistry 278, 3252632536.
Roy H, Andrews TJ. 2000. Rubisco: assembly and mechanism. In:Leegood R, Sharkey T, von Caemmerer S, eds. Photosynthesis:physiology and metabolism, Vol. 9. Springer: Dordrecht, TheNetherlands, 5383.
Saito Y, Ashida H, Kojima C, Tamura H, Matsumura H, Kai Y,Yokota A. 2007. Enzymatic characterization of 5-methylthio-ribose 1-phosphate isomerase from Bacillus subtilis. Bioscience,
Biotechnology and Biochemistry 71, 20212028.Sekowska A, Danchin A. 2002. The methionine salvage pathway
in Bacillus subtilis. BMC Microbiology 2, 8.Sekowska A, Denervaud V, Ashida H, Michoud K, Haas D,
Yokota A, Danchin A. 2004. Bacterial variations on themethionine salvage pathway. BMC Microbiology 4, 9.
Sekowska A, Kung HF, Danchin A. 2000. Sulfur metabolism inEscherichia coli and related bacteria: facts and fiction. Journal ofMolecular Microbiology and Biotechnology 2, 145177.
Sekowska A, Mulard L, Krogh S, Tse JK, Danchin A. 2001.MtnK, methylthioribose kinase, is a starvation-induced protein inBacillus subtilis. BMC Microbiology 1, 15.
Tabita FR. 1999. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynthesis Research 60, 128.
Tabita FR, Hanson TE, Li H, Satagopan S, Singh J, Chan S.2007. Function, structure, and evolution of the RubisCO-likeproteins and their RubisCO homologs. Microbiology and Molec-ular Biology Reviews 71, 576599.
von Caemmerer S, Millgate A, Farquhar GD, Furbank RT.1997. Reduction of ribulose-1,5-bisphosphate carboxylase/oxy-genase by antisense RNA in the C4 plant Flaveria bidentis leads
to reduced assimilation rates and increased carbon isotopediscrimination. Plant Physiology 113, 469477.
Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR.2003. An mRNA structure that controls gene expression by bindingS-adenosylmethionine. Nature Structural Biology 10, 701707.
Wray JW, Abeles RH. 1993. A bacterial enzyme that catalyzesformation of carbon monoxide. Journal of Biological Chemistry268, 2146621469.
Wray JW, Abeles RH. 1995. The methionine salvage pathway inKlebsiella pneumoniae and rat liver. Identification and character-ization of two novel dioxygenases. Journal of BiologicalChemistry 270, 31473153.
1554 Ashidaet al.