Introduction

All organisms on Earth use L- amino acids in proteins and D-form nucleotides in nucleic acids. Although each monomeric compound in proteins and nucleotides is homochiral, overall the monomeric compounds are heterochiral to each other, as shown in Fig. 1.

Fig. 1
figure 1

Heterochiral and homochiral monomeric compounds of biopolymers

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L-Amino acids, D-sugars, and D-nucleotides form the polymers proteins, polysaccharides, and polynucleotides. The origin and development of homochirality in biology have been discussed for many years (Avalos et al. 1998; Palyi et al. 2004; Breslow et al. 2010; Pavlov and Klabunovskii 2014). However, most hypotheses are restricted to the chirality of monomeric compounds and do not explain the heterochiral origins of products formed between amino acids and nucleotides as well as the homochirality in biopolymers (Munegumi and Shimoyama 2003), although several research results have been published (Pizzarello and Weber 2004; Tamura and Schimmel 2004). The heterochiral relationship between amino acids and nucleotides has been discussed by Weber (1987); he used the expression ‘chiral pairing’ (Weber 1987) between L and D, as shown in Fig. 2.

Fig. 2
figure 2

Chiral pairing (heterochiral pairing) between L-amino acids and D-nucleotides

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The first step is characterized as ‘the origin of optical activity, either the L-amino acid or D-nucleotide was initially a small excess of enantiomer’ (Weber 1987). The first step includes the enantiomeric resolution of monomeric compounds: L-amino acids or D-amino acids. The second step is characterized as the step in which ‘either the chiral L-amino acids caused the selection of D-nucleotides or, conversely, D-nucleotides brought about the selection of L-amino acids’ (Weber 1987). He explains the selection by the chemical difference between the L-amino acid–D-nucleotide pair and its diastereomers. The second step can lead to stereospecific (Smith and March 2007) condensation to give L-homochiral polypeptides plus D-homochiral polynucleotides or D-homochiral polypeptides plus L-homochiral polynucleotides. Modern terrestrial organisms use homochiral condensation to give polypeptides from heterochiral pairs. Several experimental results of stereospecific condensation reactions have been shown by Profy and Usher (1984) and Weber (1987).

‘Chiral pairing’ seems to be a key expression in solving the puzzle of the heterochiral relationship between amino acids and nucleotides. The chiral pairing that Weber (1987) showed suggests that the heterochiral chiral pairing between L-amino acids and D-nucleotides is a stronger interaction than the homochiral interaction between L and L or D and D. However, we should call the chiral pairing between L and D ‘heterochiral pairing’ because there may be ‘homochiral chiral pairing’ between L and L or D and D (Fig. 2). Because heterochiral pairing is stronger than homochiral pairing, modern organisms use the heterochiral pairing between L-amino acids and D-nucleotides.

As well as the chemical evolution of L-amino acids and D-sugars, the early metabolic pathways for the biosynthesis of those compounds may serve to reinforce heterochiral pairing. I concentrate here on several enzymes, namely transaminase, enolase, and aldolase in the amino acid biosynthesis, the glycolytic, and/or gluconeogenesis, respectively (Say and Fuchs 2010; Voet and Voet 2011). In particular, this research stresses the role of aldolase, which might have played an important role in the origin and development of the heterochiral pairing between amino acids and sugars. I discuss the theme of this paper using the results in the literature and some calculations using molecular modeling software to explore some viewpoints on heterochiral pairing.

Results and Discussion

Chiral Intersections of L-Amino Acids and D-Sugars in the Metabolic Pathways

Figure 3 summarizes the main metabolic pathways involving chirality inversion and retention of amino acids and sugars. Transaminase catalyzes the amino acid formation from pyruvate and its reversible reaction. The enzyme transaminase is composed of L-amino acids, which forms an achiral compound, pyruvate, and L-amino acids.

Fig. 3
figure 3

Metabolic pathways involving chiral inversion and retention in amino acids and sugars

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Enolase catalyzes the interconversion between phosphoenol pyruvate and D-2-phosphateglycerate (D-2PG). One of the reversible pathways is glycolysis and another is gluconeogenesis. Therefore, the transformation of L-amino acids to D-2PG and its reversible reactions are concentrated in these processes in metabolism.

D-2PG is converted to 3-phosphoglycerateate (D-3PG) and then 1,3-bisphosphoglycerate (D-1,3PG), which affords two sugars: glyceraldehyde 3-phosphate (D-GAP) and dihydroxyacetone 3-phosphate (DHP). These two compounds are coupled to give D-fructose 1,6-bisphosphate (D-FBP) by aldolase in gluconeogenesis.

In the pentose phosphate pathway, D-FBP yields ribose-5-phosphate (D-R5P) which is a building block for nucleotide synthesis. Thus, D-polynucleotides play a role of heterochiral pairing with L-amino acids.

In the formation of D-FBP by aldolase, the configuration of D-GAP is retained at the 5-position of D-FBP, which has four chiral centers at the 2-, 3-, 4- and 5-positions, as shown in Fig. 4. The chiral centers at the 2-, 3- and 4-positions are newly formed by aldolase, and the configurations of the three chiral centers are retained during the synthesis of D-G6P in gluconeogenesis. However, in the pentose phosphate pathway, the chiral center at the 3-position of D-G6P is inverted to give D-R5P by ribose-5-phosphate isomerase. The chiral centers at the 4- and 5-positions in D-FBP are retained in the metabolic pathways to D-R5P, as shown in Fig. 4.

Fig. 4
figure 4

Retention of configuration at the 4- and 5-positions of D-FBP

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Moreover, the chiral center at the 1-position of D-R5P is inverted by aminodo-phosphoribosyltransferase during the construction of D-ribonucleotides, in which the chiral center at the 1′-position (Fig. 5) corresponds to the 1-position of D-R5P.

Fig. 5
figure 5

The enzymes that originally introduce chiral centers to the ribose moiety in RNA

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Figure 5 summarizes the chiral retention and inversion reactions during the metabolic pathways from glyceraldehyde 2-phosphate to nucleotides. In the gluconeogenesis and pentose phosphate pathways to the direction of ribose, initially the 4-position has the R configuration, which enolase directly links to the achiral precursor. The chiral centers at the 3′- and 4′-positions are introduced by aldolase and enolase, respectively. The chiral carbon at the 2′-position is introduced by ribose-5-phosphate isomerase in the pentose phosphate pathway. The chiral center at the 1′-position is introduced by amidophosphoribosyltransferase. The reaction is a steric inversion from the original ribose. These chiral centers are retained in RNA. The combination of 4R and 3R determines the direction of the linkage to RNAs.

Table 1 summarizes the configuration change in the metabolic pathways from phosphoenolpyruvate to nucleotides.

Table 1 Configuration of chiral centers of sugars in the metabolic pathways
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As shown in Table 1, carbon (6) in all of the compounds is achiral and the chirality (2R) of carbon (5) in D-2PG is first elaborated by enolase. The chirality (5R) of carbon (5) in D-FBP is retained and the chirality (4S) of carbon (4) is created by aldolase, which forms two more chiral carbons (2S) and (3S) in the reaction of D-GAP and DHP. The configuration of carbons (4S) and (5R) is consistently retained as 3S and 4R in ribose and ribonucleotides. However, other carbon atoms, (2S) and (3S) in D-FBP, are changed in their chirality several times by the enzymes, including ribose-5-phosphate isomerase and amidophosphoribosyltransferase in the pentose phosphate pathway and the de novo biosynthesis of nucleotides.

Enolase produces the D-configuration (2R) of D-2PG from achiral PEP. This fact means that an L-protein generates a D-configuration chirality in a sugar. Furthermore, aldolase produces some more chiral carbon centers using its L-chiral environment and the D-chirality of D-2PG.

The D-chirality (2R) of D-2PG must interact with the active site of enolase as L-protein to accelerate the differentiation reaction for making D-FBP. This is a heterochiral interaction.

Classification of Aldolases

Aldolases have been classified into class I and class II (Voet and Voet 2011). Class I aldolases, which are found in animals and plants, form an imine intermediate in the active site which Asp and Lys catalyze (Dalby et al. 1999; Voet and Voet 2011). Class II aldolases, which are found in fungi, algae, and some bacteria, need zinc and ferrous ions for catalysis and bypass imine formation. However, a different type of aldolase, class IA, has been found (Siebers et al. 2001) in an archaebacterium, and one of the class IA aldolases, found in Thermococcus kadakaraensis KOD1, was characterized using gene cloning (Imanaka et al. 2002). The class I and class IA aldolases are homologous (Lorentzen et al. 2004) in having similar catalytic groups, which are Asp and Lys, to form an imine intermediate. The enzyme class IA aldolase appears to have a common evolutionary origin with class I and class II aldolases (Andreeva et al. 2008; Say and Fuchs 2010) (Fig. 6). The similarity between class I and class IA suggests that the search for the stereo-differentiation reaction mechanism in the well-known class I aldolase may lead to the primordial reactions in class IA aldolase. Aldolase is considered to play a role in gluconeogenesis as well as glycolysis (Ronimus and Morgan 2003). Moreover, an aldolase IA possessing phosphatase activity has recently been found (Say and Fuchs 2010), which may be considered as an ancestral gluconeogenic enzyme.

Fig. 6
figure 6

Classification of aldolases

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Reaction Mechanism of Class I Aldolases

Figure 7 shows a flowchart for the reaction mechanism in the human muscle aldolase (Dalby et al. 1999; Voet and Voet 2011) belonging to class I aldolases. The first stage is imine formation between DHP and the catalytic side chain, Lys229. The imine intermediate reacts with D-GAP, via general base catalysis by Asp33 to afford a hexose imine intermediate, which is hydrolyzed to D-FBP (Voet and Voet 2011). In the formation of the imine of D-FBP, a stereo-differentiation reaction proceeds using an active site composed of L-amino acid residues (including Lys229, Asp33, and the substrate binding site), D-GAP, and DHP. This is thus due to a heterochiral interaction between L-amino acids and D-sugars. The reaction results in two new chiral centers in the linear product. However, these newly formed chiral centers have only one configuration (3S and 4R, respectively). On the other hand, the configuration (2R) of D-GAP is retained (5R) in the product. Furthermore, the final linear product (2S, 3S, 4R, 5R) is cyclized to D-FBP (2S, 3S, 4S, 5R). Although the expression of RS-nomenclature at 4-position between linear and cyclic D-FBP are different, the configuration at this position is retained.

Fig. 7
figure 7

Plausible reaction mechanism (Voet and Voet 2011) of the human muscle aldolase (Dalby et al. 1999) belonging to class I aldolases. Chemical structure of sugars is displayed using Fischer projections; the configuration of chiral centers are shown as RS-nomenclature

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Predicted Products by Aldol Condensation

The catalysis by aldolase is classified into C–C bond formation, which may yield two chiral centers in a cyclic product, as described above. Figure 8 shows the chiral structures of the predicted four diastereomers without aldolase catalysis. However, aldolase produces only one diastereomer, as shown in Fig. 8d. The reaction is a stereo-differentiation reaction.

Fig. 8
figure 8

The four stereoisomers ((a)–(d)) produced by aldol-type condensation without aldolase and their α-D-furanose form. Stereoisomer (d) is D-FBP

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Table 2 shows the heat of formation (ΔH f °) calculated using the semiempirical method MOPAC based on PM6 (Stewart 2007) for the stereoisomers which would be generated without aldolase. Cyclic stereoisomer (d) is the most stable in both vacuum (ΔH f ° = −505.8 kcal/mol) and water (ΔH f ° = −1104.6 kcal/mol). The difference after cyclization of the linear form also shows the highest value, which suggests that stereoisomer (d) is most stabilized by cyclization compared with the isomers (a) to (c). The calculation error of the heat of formation is shown as the averaged value, 4.4 kcal /mol for the subset of 1373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br (Stewart 2007).

Table 2 Heat of formation calculated for D-FBP and its stereoisomers
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The calculated results show that aldolase catalyzes the stereo-differentiating condensation between D-GAP and DHP to give the most stable stereoisomer, D-FBP. The configuration of the two chiral carbons (4S, 5R) in D-FBP is retained through PRPP (3S, 4R) to D-ribonucleotides (3′S, 4′R), which also have heterochiral pairing with L-amino acids in Fig. 3.

The stereochemical relationship between 3′S-carbon and 4′R-carbon in D-ribonucleotides may be most important in the heterochiral pairing between D-RNA and L-amino acids. 4′R-carbon in D-ribonucleotides dictate the steric direction of the 5′-carbon of D-AMP, in which a phosphoric group at the 5′-carbon of a terminal residue links to a carboxyl group of an L-amino acid in aminoacyl-adenylates. A hydroxyl group at the 3′S-carbon of a t-RNA links to an L-amino acid specially selected for the t-RNA to form an aminoacyl–t-RNA. This is the heterochiral pairing for protein synthesis, as shown in Fig. 3.

Conclusions

Chiral pairing may be classified as heterochiral pairing or homochiral pairing. The chiral pairing between L-amino acids and D-nucleotides can be called a heterochiral pairing. The D-configuration of glyceraldehyde formed by enolase is retained through gluconeogenesis, the pentose phosphate pathway, and de novo synthesis of nucleotides. An important heterochiral pairing between L-proteins and D-sugars can be seen in the reaction by aldolase, which conserves the D-configuration resulting from 5R in D-FBP as the product to make the 4S-carbon. The configurations (4S and 5R) are consistently retained by RNAs, which have heterochiral pairing with L-amino acids for protein synthesis. Therefore, aldolase can be considered a chiral intersection between L-amino acids and D-nucleotides. The role of aldolase IA found in archaea also has to be discussed more from the viewpoint of origin and development of homochirality or heterochiral pairing.