JXB Advance Access originally published online on April 9, 2008
Journal of Experimental Botany 2008 59(7):1543-1554; doi:10.1093/jxb/ern104
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SPECIAL ISSUE REVIEW PAPER |
RuBisCO-like proteins as the enolase enzyme in the methionine salvage pathway: functional and evolutionary relationships between RuBisCO-like proteins and photosynthetic RuBisCO
1Nara Institute of Science and Technology (NAIST), Graduate School of Biological Sciences, 8916-5 Takayama, Ikoma, Nara, 630-0101 Japan
2Unité des Cyanobactéries, CNRS URA 2172, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
3Unité de Génétique in silico, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
4Genetics of Bacterial Genomics, CNRS URA 2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
* To whom correspondence should be addressed. E-mail: ashida{at}bs.naist.jp
Received 30 January 2008; Revised 26 February 2008 Accepted 28 February 2008
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Abstract |
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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 large subunit 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 methionine salvage pathway, other RLPs, and photosynthetic RuBisCO are discussed. In addition, the fundamental question, ‘How has RuBisCO evolved?’ is also considered, 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
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Introduction |
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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 photosynthetic organisms. Nevertheless, RuBisCO has inefficient enzymatic properties (Andrews and Whitney, 2003). In particular, RuBisCO catalyses an oxygenase reaction that fixes O2 into RuBP, and this reaction antagonizes the carboxylase 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 photorespiration, which releases CO2 and NH3 and wastes energy. In addition, the turnover of the carboxylase reaction by RuBisCO is a few to several times per second, even when substrates are saturating (Andrews and Whitney, 2003). Therefore, the photosynthetic CO2 assimilation rate in plants can be limited by RuBisCO (Hudson et al., 1992; Von Caemmerer et al., 1997). Plants manage to perform photosynthetic CO2 fixation by accumulating 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 three forms 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 catalyse either 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 only in Bacillus subtilis. Bacillus subtilis RLP catalyses the 2,3-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 subtilis RLP 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 the molecular evolutionary relationship between RLPs and RuBisCO. In Gupta's 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 Gupta's 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 function provide a new approach to elucidate the evolution of RuBisCO. However, the methionine salvage pathway, to recycle reduced sulphur in sulphur-deprived environments, 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.
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RuBisCO-like proteins are widely distributed in Bacteria and in Archaea |
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 TopAbstractIntroduction RuBisCO-like proteins are widely... The road to identification...What is the comparison...Are all RLPs acting...Evolutionary and functional...Concluding remarksReferences |
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Genome 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 consists of eight large and eight small subunits of 50–55 kDa and 12–18 kDa, respectively, and is distributed widely among photosynthetic organisms such as plants, algae, cyanobacteria, and photosynthetic and chemoautotrophic proteobacteria (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
, β, and 
, that are different from the clades of photosynthetic RuBisCO (Fig. 1). Group includes RLPs from Bacillus species, the cyanobacterium Microcystis aeruginosa, the sulphate-reducing Archaeon Archaeoglobus fulgidus, and the photosynthetic bacteria Rhodopseudomonas palustris and Rhodospirillum rubrum. Group β contains RLPs from non-photosynthetic proteobacteria Palaromonas sp., Bordetella bronchiseptica, and Mesorhizobium loti. RLPs from green non-sulphur bacteria of the genus Chlorobium and the proteobacteria Rhodopseudomonas sp. are classified in group .
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Comparing amino acid sequences between B. subtilis RLP 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 , 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 licheniformis, 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 β, from Palaromonas sp., B. bronchiseptica, and M. loti, respectively, and 25.1% and 26.8% identity to RLPs in group , from R. palustris and Chlorobium tepidum, respectively. Considering this distribution 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 from RLPs shows conservation of 9–18 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.
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What is the function of RLPs? Is there a functional and evolutionary relationship between RLPs and photosynthetic RuBisCO? The answers to these questions have interested us with respect to the molecular evolution of RuBisCO.
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The road to identification of the function of B. subtilis RLP |
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In order to identify the function of RLP, the B. subtilis genome was explored when it was completed. When the analysis began, the gene encoding RLP in B. subtilis was annotated 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 RLP could 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. subtilis RLP can catalyse the carboxylase reaction using recombinant protein expressed in Escherichia coli. Indeed, B. subtilis RLP showed no carboxylase activity. This result clearly showed that B. subtilis RLP functions as an enzyme in a different metabolic pathway from that of RuBisCO.
The mtnW gene for the RLP of B. subtilis is the first gene of the mtnWXBD operon (Fig. 3a). The mtnKA operon 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 metabolism (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 methionine starvation 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 mtnWXBD–lacZ 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 methionine metabolism. Furthermore, in mtnWXBD and mtnKA operons, MtnD showed high similarity to 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase, and MtnK has been identified as the methylthioribose (MTR) kinase (Sekowska et al., 2001), suggesting that both 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 salvage pathway to recycle organic sulphur from MTR. In this pathway, organic sulphur is salvaged from MTR, which is produced from methylthioadenosine (MTA), a waste product of polyamine (Sekowska et al., 2000; Grundy and Henkin, 2002), mugineic acid (Ma et al., 1995), and ethylene synthesis (Burstenbinder et al., 2007). In the methionine 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-P undergoes 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/phosphatase (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 step has 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 to the structure of RuBP, and D-glycero-2,3-pentodiulose-1,5-bisphosphate, is a by-product of the oxygenase reaction catalysed by RuBisCO (Pearce and Andrews, 2003). It is therefore predicted that B. subtilis RLP is MTRu-1-P dehydratase or DK-MTP-1-P enolase/phosphatase.
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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 metabolites. The wild type grew in the culture medium containing 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 step between MTA and KMTB in the methionine salvage pathway. To determine this step, enzymes, their substrates, and products in the methionine salvage pathway of B. subtilis were identified, step-by-step, using recombinant proteins encoded in the mtnWXBD and mtnKS operons and employing 1H-NMR and UV-VIS spectroscopy (Ashida et al., 2003). All reaction steps and enzymes were 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 was identified 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-P phosphatase for deposphorylation (Fig. 3b).
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The function of RLP from the cyanobacterium Microcystis aeruginosa PCC7806 was also identified, based on analysis of B. subtilis RLP. Interestingly, this cyanobacterium possesses genes for both RLP and photosynthetic RuBisCO. The gene for RLP of M. aeruginosa could rescue an RLP-deficient mutant of B. subtilis when they were grown in culture medium including MTA as the sole source of sulphur (Fig. 5c) (Carré-Mlouka et al., 2006). The recombinant M. aeruginosa RLP showed DK-MTP-1-P enolase activity (Carré-Mlouka et al., 2006), suggesting that M. aeruginosa RLP is the DK-MTP-1-P enolase in 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. In addition, 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 Gupta's 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 cyanobacteria possessing both genes for RLP and RuBisCO are needed to settle this question.
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What is the comparison of catalysing reactions between B. subtilis RLP and photosynthetic RuBisCO telling us? |
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It seems that there is no linkage between B. subtilis and M. aeruginosa RLPs and photosynthetic RuBisCO, because RLPs function in the methionine salvage pathway, 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 photosynthetic 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). Additionally, 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 C2–C3 bond; and (v) protonation of the C2 of the upper aci-acid form of 3-phosphoglycerate (Mauser et al., 2001). The first catalysing 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 in RuBisCO (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, which stabilizes 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., 1985; Hartman et al., 1987; Gutteridge et al., 1988). Interestingly, B. subtilis and M. aeruginosa RLPs conserve 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.
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Recently, Imker et al. (2007) reported the X-ray crystal structure of Geobacillus kaustophilus RLP, complexed with an analogue of DK-MTP-1-P, 2,3-diketohexane-1-phosphate (DK-H-1-P). Geobacillus kaustophilus belongs to 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 was carbamylated, and carbamylated Lys201, Asp203, and Glu204 were Mg2+ ligands in the 3D structure of G. kaustophilus RLP (Imker et al., 2007). The arrangement of 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 in a lack of enolization activity (Imker et al., 2007). Therefore, Imker et al. proposed that a candidate residue to 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) that the carbamylation at Lys201 increased the kcat/Km for the enolase reaction of G. kaustophilus RLP. However, the role of carbamylation on Lys201 is still unknown in RLP. Further analysis will reveal the functional relationship 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. kaustophilus RLP, 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-P enolase and photosynthetic RuBisCO utilize the common conserved P1-binding motif to bind the substrate P1 phosphate group.
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Are all RLPs acting as the DK-MTP-1-P enolases? |
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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 together with those of Bacillus species and of cyanobacteria also have conserved residues 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. The gene for RLP from the cyanobacterium Lyngbya sp. PCC 8106 is also predicted to form this operon with homologous genes for mtnB and mtnE. These observations suggest that these RLPs in group also function as the DK-MTP-1-P enolase in the methionine salvage pathway. However, the RLPs of R. rubrum and R. palustris, in the same group , 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 the sole source of sulphur (Tabita et al., 2007). This result implies that R. rubrum and R. palustris RLPs function as the DK-MTP-1-P enolase in these bacteria. Considering the result of mutational analysis at Lys123 in G. kaustophilus RLP, these RLPs may not be the DK-MTP-1-P enolase, because they do not have conserved Lys123. In R. rubrum and R. palustris, the reaction step of DK-MTP-1-P enolase may be catalysed by a photosynthetic form II RuBisCO and not by RLPs, because R. rubrum RuBisCO can catalyse this reaction, although at a very low rate (described below) (Ashida et al., 2003). As in the case of R. rubrum and R. palustris, group 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 Tabita's phylogenetic tree, group 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 can be divided into two subgroups, 1 including B. subtilis DK-MTP-1-P enolase and 2 including RLPs from photosynthetic bacteria, in agreement with Tabita's 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 1 are DK-MTP-1-P enolases, but group 2 RLPs are not. However, Lys201 is replaced by glutamine in B. clausii RLP of group 1 (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 1 is exceptional in that Lys123 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 1 possess a different function. On the other hand, in RLPs in groups β and , 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 Bacillus species and cyanobacteria is unclear. Hanson and Tabita (2001) reported that C. tepidum RLP, included in RLP group , is involved in sulphur oxidation and oxidative stress, suggesting that this RLP functions in other biological process.
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Evolutionary and functional linkage between RLP and photosynthetic RuBisCO |
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Evolutionary and functional linkage between RLP and photosynthetic RuBisCO has attracted interest. It is concluded 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 for RuBisCO from the photosynthetic bacterium R. rubrum rescued 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 photosynthetic 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 photosynthetic 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 Gupta's hypothesis, RLP in the methionine salvage pathway might have evolved earlier than photosynthetic RuBisCO. Furthermore, photosynthetic 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 metabolic pathways. 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 ancestral metabolic pathway of the methionine salvage pathway might have been involved in some form of ribose metabolism, incorporating the sequential reactions catalysed by the methionine-salvaging enzymes. In other words, an ancestral RLP protein might be an enolase enzyme that functioned in ancient ribose metabolism.
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Concluding remarks |
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Many genome projects have revealed that Bacteria and Archaea possess genes for RLPs that cannot catalyse either the carboxylase or the oxygenase reactions of photosynthetic 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 the enolase enzyme functioning in the methionine salvage pathway. In addition, RLPs from the cyanobacterium, M. aeruginosa, and G. kaustophilis catalyse the enolase reaction 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 similar structure 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. Furthermore, considering the molecular evolution of RuBisCO based on Gupta's evolutionary hypothesis of micro-organisms, the hypothesis is proposed that RLP, functioning 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 RuBisCO is 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 provide important information on the structure and amino acid residues involved in carboxylase or oxygenase reactions.
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Acknowledgements |
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The authors thank Drs Naotake Ogasawara and Kazuo Kobayashi for help and discussion in molecular manipulation of Bacillus. We are grateful to Dr Chojiro Kojima for 1H-NMR analysis. This work was supported partly by a Grant in Aid (17208031 and 18688021) for Scientific Research from the Japan Society for the Promotion of Science (JSPS), partly by a grant (FY2004-2006) for General Science and Technology from the Asahi Glass Foundation, and partly by a grant (FY2005-2007) from the Nissan Science Foundation.
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