Biosynthesis of Various Amino Acids | Microbiology

In this article we will discuss about the biosynthesis of various amino acids:- 1. Glutamic Acid Family 2. Aspartic Acid Family 3. α-Alanine, Serine, Glycine and Cysteine 4. Valine and leucine 5. Aromatic Amino Acids: Tyrosine, Phenylalanine, Tryptophan 6. Histidine.

1. Glutamic Acid Family:

Glutamic acid is the main pathway for assimilation of ammonia by reductive amination of α-keto glutaric acid catalysed by glutamic acid dehydrogenase using NADPH₂ as reductant:

Several other amino acids of this family may be formed by specific transaminases which use pyridoxal phosphate (PAL) as coenzyme. The amino group of glutamic acid is transferred to PAL forming pyridoxamine phosphate (PAM). The latter reacts with a keto acid, like oxalacetic acid to produce aspartic acid. 

Apart from amino acids produced by transamination, three other amino acids belonging to the glutamic acid family are synthesized in other ways.

These are:

Glutamine (an amide), proline and

Arginine.

(i) Glutamine:

Glutamine is synthesized by the enzyme glutamine synthetase which requires ATP. An enzyme- bound glutamyl phosphate acts as an intermediate which reacts with ammonia to produce glutamine.

(ii) Proline:

Proline is a heterocyclic amino acid. It is synthesized via the intermediates, glutamic acid semi-aldehyde and pyrroline 5-carboxylic acid. Glutamic acid is reduced by an NADH₂-linked dehydrogenase to glutamic acid semi-aldehyde which undergoes spontaneous cyclization to form pyrroline 5-carboxylic acid.

The latter is reduced by an NADPH₂-linked dehydrogenase yielding proline:

(iii) Arginine:

Arginine biosynthetic pathway is more complex. It is synthesized from glutamic acid via two non-­protein amino acids — ornithine and citrulline. The steps from glutamic acid to ornithine, from ornithine to citrulline and from citrulline to orginine are described separately.

It can be seen that ornithin differs from glutamic acid in having an extra amino (NH₂^–) group attached to the y-carbon atom. This amino group is donated by another molecule of glutamic acid which is thereby deaminated to α-ketoglutaric acid.

The first step consists of condensation of acetyl CoA and glutamic acid forming N-acetyl glutamic acid with release of free coenzyme A. In the next two steps, phosphorylation by ATP and reduction occur to yield N-acetyl glutamyl semi-aldehyde which by amination forms N-acetyl ornithine. In the last step, N-acetyl ornithine yields ornithine by removal of acetic acid and addition of water.

Ornithine produced by the above pathway next reacts with carbamyl phosphate to produce citrulline. In bacteria, carbamyl phosphate is synthesized from CO₂, NH₃ and ATP by the enzyme carbamyl phosphate synthetase.

The reactions are:

Finally, citrulline is converted to arginine in two steps. The first step consists of condensation of citrulline with aspartic acid requiring ATP to form arginine succinic acid. The reaction is catalysed by arginine-succinate synthetize. ATP supplies the energy for condensation and is hydrolysed to AMP and pyrophosphate.

The product of the synthetase reaction is next cleaved into arginine and fumaric acid:

2. Aspartic Acid Family:

This family includes besides aspartic acid several other amino acids, like asparagine, threonine, isoleucine, methionine, lysine and diaminopimelic acid. Except the last one, others are protein amino acids. Diaminopimelic acid is found in bacterial cell wall. Besides these amino acids, carbon skeleton of aspartic acid is incorporated into pyrimidine’s.

In many bacteria, aspartic itself is produced by transamination of oxalacetic acid, an intermediate of the TCA cycle, the amino donor being glutamic acid. Another possible route of aspartic acid formation is by amination of fumaric acid catalysed by aspartase.

Biosynthetic pathways of the amino acids belonging to this family are branched as shown in a simplified manner in Fig. 8.74:

(i) Asparagine:

Like glutamine, asparagine is also an amide. It is formed from aspartic acid by addition of NH₃ in a reaction that is similar to formation of glutamine.

Another route of asparagine formation is by transfer of the amido amino group of glutamine to aspartic acid:

(ii) Conversion of aspartic acid to aspartyl semi-aldehyde:

It can be seen from Fig. 8.74 that the protein amino acids of the aspartic acid family (except asparagine) originate from aspartyl β- semi-aldehyde which is produced from aspartic acid through an intermediate, β-aspartyl phosphate.

Conversion of aspartic acid to β-aspartyl phosphate is catalysed by an important enzyme, aspartokinase, phosphate group being donated by ATP. Next, β-aspartyl phosphate is dehydrogenated by aspartyl β-semi-aldehyde dehydrogenase to the key intermediate aspartyl β-semi-aldehyde. In this reaction NADPH₂ acts as H-donor and inorganic phosphate is released.

From Fig. 8.74, it can be seen that from the key intermediate, aspartyl β-semi-aldehyde, two different biosynthetic pathways originate. One of these leads to lysine and the other to homoserine. The latter, though not a protein amino acid, is a key intermediate in the biosynthesis of methionine, threonine and isoleucine.

(iii) Lysine:

Lysine is an important amino acid, because it is essential for all animal organisms which must get it from an external source. Lysine is synthesized in plants and bacteria by one pathway, and by a different pathway in fungi. In plants and bacteria, the immediate precursor of lysine is diaminopimelic acid and hence it is called diaminopimelic acid pathway. For similar reasons, the fungal route is called aminoadipic acid pathway. The diaminopimelic acid pathway is described here in details.

Lysine biosynthesis branches off from aspartyl β-semi-aldehyde. The latter is condensed with pyruvic acid by aldol condensation and the product is dehydrated to yield a heterocyclic compound, dihydroxydipicolinic acid. It is then dehydrogenated to tetrahydrodipiolinic acid which combines with a succinyl group donated by succinyl-CoA to form an open chain compound which receives an amino group from glutamic acid.

The resulting compound is succinyl diamino pimelic acid. By removal of the succinyl group as succinic acid, diaminopimelic acid is produced which is the immediate precursor of lysine. Lysine is produced by decarboxylation of meso-diaminopimelic acid. An enzyme diaminopimelic acid racemase can reversibly convert L-diaminopimelic acid to its meso-form.

The reactions are:

In fungi, a different pathway exists for lysine biosynthesis which is briefly shown:

(iv) Methionine:

It can be seen from Fig. 8.74 that methionine, threonine and isoleucine are synthesized from a common intermediate, homoserine. Homoserine is produced by reduction of aspartyl β-semi-aldehyde.

As H-donor for this reduction acts either NADH₂ or NADPH₂ and the enzyme is homoserine dehydrogenase:

Homoserine is converted to O-succinyl homoserine by transfer of the succinyl group from succinyl-CoA. At the next step, a molecule of cysteine is added with release of succinic acid resulting in the formation of cystathionine which is cleaved in the next step to eliminate pyruvic acid and NH₃ to yield homocysteine.

In the final step, the methyl group of methyl-tetrahydrofolate is added to homocysteine to produce methionine. Methionine is a sulfur-containing amino acid and its sulfur atom originates from cysteine.

The reactions from homoserine to methionine are:

(v) Threonine:

Threonine is synthesised from homoserine via an intermediate, phosphohomoserine. The conversion of homoserine to threonine consists essentially of the transfer of the hydroxyl group from y-position to β-position. The second step is catalysed by threonine synthetase which requires pyridoxal phosphate as coenzyme. Inorganic phosphate is released from phosphohomoserine.

Although apparently simple, the reaction is actually quite complex:

(vi) Isoleucine:

Isoleucine is an isomer of leucine, but the two amino acids are synthesized by different pathways. It can be seen from Fig. 8.74 that isoleucine is synthesized from threonine. At first, threonine is deaminated to α-keto butyric acid by the action of threonine deaminase. TPP-linked active acetaldehyde is then added to α-keto butyric acid to form α-acetohydroxy butyric acid. It is next reduced by an NADH₂-linked dehydrogenase to yield α, β-dihydroxy β-methyl valeric acid. The latter is dehydrated to α-keto β-methyl valeric acid. In the final step, an amino group is added by transamination to α-keto β-methyl valeric acid to yield isoleucine.

The reactions from threonine to isoleucine are:

3. Biosynthesis of α-Alanine, Serine, Glycine and Cysteine:

(i) α-Alanine:

In most organisms, α-alanine is produced through transamination of pyruvic acid by glutamic acid catalysed by a transaminase using pyridoxal phosphate as coenzyme. In bacteria, besides glutamic acid, other amino acids, like valine or leucine, may act as an amino donor. In Bacillus subtilis, α-alanine is synthesized by direct amination of pyruvic acid catalysed by an NADPH₂-linked enzyme.

Reactions involved in α-alanine synthesis are:

(ii) Serine:

Precursor of serine is 3-phosphoglyceric acid (3-PGA) which is an intermediate of the glycolytic pathway. Biosynthesis of serine starts with reduction of 3-PGA to 3-phospho-hydroxy pyruvic acid. At the next step, an amino group is added to 3-phospho-hydroxy pyruvic acid by transamination to yield 3-phosphoserine. In the final step, 3-phospho-serine undergoes hydrolysis to yield serine and inorganic phosphate.

The reactions are:

(iii) Glycine:

Glycine is produced from serine in a single step in which the hydroxymethyl group (-CH₂OH) of serine is transferred to tetrahydrofolate (THF) through the action of the enzyme serine hydroxy-methylase. The enzyme requires, in addition to THF, pyridoxal phosphate.

The reaction is reversible and the two amino acids are inter-convertible:

(iv) Cysteine:

Cysteine is a sulfur-containing amino acid which differs from serine in having a sulfhydryl (-SH) group instead of the hydroxyl group. Cystine is a dimer of cysteine joined by a disulfide (-S-S-) bond.

In yeast, cysteine is produced from serine by addition of a sulfide (H₂S).

The reaction is catalysed by serine sulfhydrase and requires ATP:

However, cysteine synthesis in other organisms — including mammals — takes place by a complicated pathway starting from methionine and the immediate precursor of cysteine is cystathionine. In fact, in this pathway of cysteine biosynthesis, some of the steps of methionine biosynthesis are reversed.

The synthesis begins with formation of S-adenosyl methionine from methionine through addition of the adenosyl group from ATP leaving behind a pyrophosphate and orthophosphate. S-adenosyl methionine then loses its methyl group to an acceptor producing S-adenosyl homocysteine.

This compound then undergoes hydrolytic cleavage to produce homocysteine and adenosine. Homocysteine then combines with serine to yield cystathionine. Finally, cystathionine is cleaved by the enzyme cystathionase to produce cysteine and α-ketobutryic acid + NH₃. Thus, in this pathway also, serine provides the backbone of cysteine though the sulfur atom originates from methionine, instead of H₂S as found in case of yeast.

The pathway is shown:

4. Biosynthesis of Valine and Leucine:

Valine and leucine are both branched chain neutral amino acids and they are synthesized up to a point by a common pathway. The immediate precursors of valine and leucine are α-keto iso-valeric acid and α-keto iso-caproic acid, respectively.

The synthetic pathway starts with condensation of pyruvic acid with a TPP-linked acetaldehyde group donated by another molecule of pyruvic acid to form α-acetolactate. This compound is next reduced by an NADH₂-linked dehydrogenase to dihydroxy isovaleric acid which, by a dehydration reaction, yields α-keto isovaleric acid. This compound receives an amino group from an amino-donor by transamination reaction to produce valine.

The pathway of leucine branches off from α-keto isovaleric acid of the valine pathway. α-Keto isovaleric acid condenses with an acetyl (CH₃-CO-) group donated by acetyl-CoA to form isopropyl malic acid. This compound through a step of dehydration followed by a step of rehydration forms α-hydroxy β-carboxy isocaproic acid.

The latter, by another two steps of dehydrogenation and decarboxylation reactions, yields α-keto isocaproic acid which by addition of an amino group through a transamination reaction, forms leucine.

The reactions of valine synthesis and leucine synthesis are:

5. Biosynthesis of Aromatic Amino Acids:

Among the protein amino acids, there are three which are aromatic. These are phenylalanine, tyrosine and tryptophan. Biosynthesis of these amino acids is interlinked and has a common key intermediate, shikimic acid. This compound is the first six-carbon ring structure produced from aliphatic precursors. So, formation of shikimic acid is considered first, before dealing with individual amino acids.

The aliphatic compounds that give rise to shikimic acid are erythrose 4-phosphate and phosphoenol pyruvic acid. The two compounds react to give rise to a seven-carbon keto-compound—, deoxyarabino-heptulosonic acid 7-phosphate. This cyclizes to form the six-carbon ring structure of 5-dehydroquinic acid. At the next step, 5-dehydroquinic acid is reduced to shikimic acid.

The reactions are:

Another key intermediate of this biosynthetic pathway is chorismic acid. Shikimic acid is phosphorylated by ATP to form shikimic acid phosphate to which another molecule of phosphoenol pyruvic acid (PEP) is added to yield enolpyruvyl shikimic acid phosphate. By elimination of the phosphate group, chorismic acid is produced. From chorismic acid, phenylalanine and tyrosine are synthesized via prephenic acid in one direction and tryptophan in another branch.

Formation of chorismic acid from shikimic acid is shown:

(i) Formation of phenylalanine:

Phenylalanine and tyrosine are both produced from prephenic acid which originates from chorismic acid by shifting the position of pyruvic acid. Prephenic acid by decarboxylation yields phenyl pyruvic acid which is then trans-aminated to produce phenylalanine.

(ii) Formation of tyrosine:

Tyrosine, which is para-hydro-xyphenylalanine, may be formed by direct addition of a hydroxyl group to phenylalanine, or, alternatively, from prephenic acid via parahydroxyphenyl pyruvic acid.

(iii) Formation of tryptophan:

Tryptophan pathway branches off from chorismic acid and proceeds via anthranilic acid. This compound is produced by aromatization of chorismic acid accompanied by elimination of phosphoenol pyruvic acid and addition of an amino group to the aromatic ring. Anthranilic acid adds a phosphoribosyl moiety donated by phosphoribosyl pyrophosphate (PRPP) to produce N-phosphoribosyl anthranilic acid.

This compound is then decarboxylated to form indole 3-glycerol phosphate. Thus a new five-membered heterocyclic ring is added to the aromatic ring. In the last step, glyceraldehyde 3-phosphate is eliminated and a serine molecule is added to yield tryptophan which is chemically indolylalanine.

6. Biosynthesis of Histidine:

Chemically, histidine is imidazolyl alanine. The five-membered heterocyclic imidazole ring is formed partly from phosphoribosyl pyrophosphate (PRPP) and partly from ATP, while one of the N-atoms is contributed by glutamine.

Some reactions of the biosynthetic pathway of histidine are quite complex:

The first step consists of a reaction between 5-phosphoribosyl 1-pyrophosphate (PRPP) and ATP involving elimination of pyrophosphate (PP) and joining of the phosphoribosyl moiety with the purine ring of ATP through its nitrogen atom (N-l) producing N-phosphoribosyl-ATP.

In the next step, this compound loses the pyrophosphate group of ATP to yield N-phosphoribosyl-AMP. The adenine ring of AMP then opens between N-l and C-6. The resulting compound, by elimination of water and the amido imidazole carboxamide ribose 5-phosphate moiety, and addition of a N-atom from glutamine, produces imidazole glycerol phosphate through two steps of complex reactions.

From imidazole glycerol phosphate, by transamination, histidinol phosphate is produced which, by elimination of the phosphate group produces histidinol. The latter, by oxidation through NAD/NADP, yields histidine. The main reactions are shown above. The origin of different parts of the histidine molecule is shown in the box.