Amino acid synthesis

Amino acid biosynthesis is the set of

The α-ketoglutarate family of amino acid synthesis (synthesis of glutamate, glutamine, proline and arginine) begins with α-ketoglutarate, an intermediate in the Citric Acid Cycle. The concentration of α-ketoglutarate is dependent on the activity and metabolism within the cell along with the regulation of enzymatic activity. In E. coli citrate synthase, the enzyme involved in the condensation reaction initiating the Citric Acid Cycle is strongly inhibited by α-ketoglutarate feedback inhibition and can be inhibited by DPNH as well high concentrations of ATP.^[2] This is one of the initial regulations of the α-ketoglutarate family of amino acid synthesis.

The regulation of the synthesis of

The regulation of proline biosynthesis can depend on the initial controlling step through negative feedback inhibition.^[4] In E. coli, proline allosterically inhibits Glutamate 5-kinase which catalyzes the reaction from L-glutamate to an unstable intermediate L-γ-Glutamyl phosphate.^[4]

Tyrosine and phenylalanine are biosynthesized from

Tryptophan biosynthesis involves conversion of chorismate to anthranilate using

Oxaloacetate/aspartate: lysine, asparagine, methionine, threonine, and isoleucine

The oxaloacetate/aspartate family of amino acids is composed of

The associated enzymes are subject to regulation via feedback inhibition and/or repression at the genetic level. As is typical in highly branched metabolic pathways, additional regulation at each branch point of the pathway. This type of regulatory scheme allows control over the total flux of the aspartate pathway in addition to the total flux of individual amino acids. The aspartate pathway uses L-aspartic acid as the precursor for the biosynthesis of one-fourth of the building block amino acids.

Aspartate

The biosynthesis of aspartate frequently involves the transamination of oxaloacetate.

The enzyme

Two asparagine synthetases are found in bacteria. Both are referred to as the AsnC protein. They are coded for by the genes AsnA and AsnB. AsnC is autogenously regulated, which is where the product of a structural gene regulates the expression of the operon in which the genes reside. The stimulating effect of AsnC on AsnA transcription is downregulated by asparagine. However, the autoregulation of AsnC is not affected by asparagine.

Methionine

Biosynthesis by the

Methionine biosynthesis is subject to tight regulation. The repressor protein MetJ, in cooperation with the corepressor protein S-adenosyl-methionine, mediates the repression of methionine's biosynthesis. The regulator MetR is required for MetE and MetH gene expression and functions as a transactivator of transcription for these genes. MetR transcriptional activity is regulated by homocystein, which is the metabolic precursor of methionine. It is also known that vitamin B12 can repress MetE gene expression, which is mediated by the MetH holoenzyme.

Threonine

In plants and microorganisms, threonine is synthesized from

The biosynthesis of threonine is regulated via allosteric regulation of its precursor, homoserine, by structurally altering the enzyme homoserine dehydrogenase. This reaction occurs at a key branch point in the pathway, with the substrate homoserine serving as the precursor for the biosynthesis of lysine, methionine, threonin and isoleucine. High levels of threonine result in low levels of homoserine synthesis. The synthesis of aspartate kinase (AK), which catalyzes the phosphorylation of aspartate and initiates its conversion into other amino acids, is feed-back inhibited by lysine, isoleucine, and threonine, which prevents the synthesis of the amino acids derived from aspartate. So, in addition to inhibiting the first enzyme of the aspartate families biosynthetic pathway, threonine also inhibits the activity of the first enzyme after the branch point, i.e. the enzyme that is specific for threonine's own synthesis.

Isoleucine

In plants and microorganisms, isoleucine is biosynthesized from

In terms of regulation, the enzymes threonine deaminase, dihydroxy acid dehydrase, and transaminase are controlled by end-product regulation. i.e. the presence of isoleucine will downregulate threonine biosynthesis. High concentrations of isoleucine also result in the downregulation of aspartate's conversion into the aspartyl-phosphate intermediate, hence halting further biosynthesis of lysine, methionine, threonine, and isoleucine.

Ribose 5-phosphates: histidine

In E. coli, the biosynthesis begins with phosphorylation of 5-phosphoribosyl-pyrophosphate (PRPP), catalyzed by ATP-phosphoribosyl transferase. Phosphoribosyl-ATP converts to phosphoribosyl-AMP (PRAMP). His4 then catalyzes the formation of phosphoribosylformiminoAICAR-phosphate, which is then converted to phosphoribulosylformimino-AICAR-P by the His6 gene product.^[8] His7 splits phosphoribulosylformimino-AICAR-P to form D-erythro-imidazole-glycerol-phosphate. After, His3 forms imidazole acetol-phosphate releasing water. His5 then makes L-histidinol-phosphate, which is then hydrolyzed by His2 making histidinol. His4 catalyzes the oxidation of L-histidinol to form L-histidinal, an amino aldehyde. In the last step, L-histidinal is converted to L-histidine.^[8][9]

In general, the histidine biosynthesis is very similar in plants and microorganisms.^[10][11]

HisG → HisE/HisI → HisA → HisH → HisF → HisB → HisC → HisB → HisD (HisE/I and HisB are both bifunctional enzymes)

The enzymes are coded for on the His operon. This operon has a distinct block of the leader sequence, called block 1:

Met-Thr-Arg-Val-Gln-Phe-Lys-His-His-His-His-His-His-His-Pro-Asp

This leader sequence is important for the regulation of histidine in E. coli. The His operon operates under a system of coordinated regulation where all the gene products will be repressed or depressed equally. The main factor in the repression or derepression of histidine synthesis is the concentration of histidine charged tRNAs. The regulation of histidine is actually quite simple considering the complexity of its biosynthesis pathway and, it closely resembles regulation of

Serine

Serine is the first amino acid in this family to be produced; it is then modified to produce both glycine and cysteine (and many other biologically important molecules). Serine is formed from 3-phosphoglycerate in the following pathway:

3-phosphoglycerate → phosphohydroxyl-pyruvate → phosphoserine → serine

The conversion from 3-phosphoglycerate to phosphohydroxyl-pyruvate is achieved by the enzyme

Glycine is biosynthesized from serine, catalyzed by serine hydroxymethyltransferase (SHMT). The enzyme effectively replaces a hydroxymethyl group with a hydrogen atom.

SHMT is coded by the gene glyA. The regulation of glyA is complex and is known to incorporate serine, glycine, methionine, purines, thymine, and folates, The full mechanism has yet to be elucidated.^[15] The methionine gene product MetR and the methionine intermediate homocysteine are known to positively regulate glyA. Homocysteine is a coactivator of glyA and must act in concert with MetR.^[15][16] On the other hand, PurR, a protein which plays a role in purine synthesis and S-adeno-sylmethionine are known to down regulate glyA. PurR binds directly to the control region of glyA and effectively turns the gene off so that glycine will not be produced by the bacterium.

Cysteine

The genes required for the synthesis of cysteine are coded for on the cys regulon. The integration of sulfur is positively regulated by CysB. Effective inducers of this regulon are N-acetyl-serine (NAS) and very small amounts of reduced sulfur. CysB functions by binding to DNA half sites on the cys regulon. These half sites differ in quantity and arrangement depending on the promoter of interest. There is however one half site that is conserved. It lies just upstream of the -35 site of the promoter. There are also multiple accessory sites depending on the promoter. In the absence of the inducer, NAS, CysB will bind the DNA and cover many of the accessory half sites. Without the accessory half sites the regulon cannot be transcribed and cysteine will not be produced. It is believed that the presence of NAS causes CysB to undergo a conformational change. This conformational change allows CysB to bind properly to all the half sites and causes the recruitment of the RNA polymerase. The RNA polymerase will then transcribe the cys regulon and cysteine will be produced.

Further regulation is required for this pathway, however. CysB can down regulate its own transcription by binding to its own DNA sequence and blocking the RNA polymerase. In this case NAS will act to disallow the binding of CysB to its own DNA sequence. OAS is a precursor of NAS, cysteine itself can inhibit CysE which functions to create OAS. Without the necessary OAS, NAS will not be produced and cysteine will not be produced. There are two other negative regulators of cysteine. These are the molecules sulfide and thiosulfate, they act to bind to CysB and they compete with NAS for the binding of CysB.^[17]

Pyruvate: alanine, valine, and leucine

Pyruvate, the result of glycolysis, can feed into both the TCA cycle and fermentation processes. Reactions beginning with either one or two molecules of pyruvate lead to the synthesis of alanine, valine, and leucine. Feedback inhibition of final products is the main method of inhibition, and, in E. coli, the ilvEDA operon also plays a part in this regulation.

Alanine

Alanine is produced by the transamination of one molecule of pyruvate using two alternate steps: 1) conversion of glutamate to α-ketoglutarate using a glutamate-alanine transaminase, and 2) conversion of valine to α-ketoisovalerate via Transaminase C.

Not much is known about the regulation of alanine synthesis. The only definite method is the bacterium's ability to repress Transaminase C activity by either valine or leucine (see ilvEDA operon). Other than that, alanine biosynthesis does not seem to be regulated.^[18]

Valine

Leucine, like valine, regulates the first step of its pathway by inhibiting the action of the α-Isopropylmalate synthase.[18] Because leucine is synthesized by a diversion from the valine synthetic pathway, the feedback inhibition of valine on its pathway also can inhibit the synthesis of leucine.

ilvEDA operon

The genes that encode both the dihydroxy acid dehydrase used in the creation of α-ketoisovalerate and Transaminase E, as well as other enzymes are encoded on the ilvEDA operon. This operon is bound and inactivated by valine, leucine, and isoleucine. (Isoleucine is not a direct derivative of pyruvate, but is produced by the use of many of the same enzymes used to produce valine and, indirectly, leucine.) When one of these amino acids is limited, the gene furthest from the amino-acid binding site of this operon can be transcribed. When a second of these amino acids is limited, the next-closest gene to the binding site can be transcribed, and so forth.^[18]

Commercial syntheses of amino acids

The commercial production of amino acids usually relies on mutant bacteria that overproduce individual amino acids using glucose as a carbon source. Some amino acids are produced by enzymatic conversions of synthetic intermediates.