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Chapter 16 : Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines

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Abstract:

This chapter provides an overview on biosynthesis of amino acids. Glutamine and glutamate occupy a special place in nitrogen metabolism because virtually all nitrogen-containing groups of biological molecules are derived from these two amino acids, glutamate being the major donor of nitrogen. The major pathway of glutamate synthesis in many bacteria is catalyzed by glutamate synthase (GOGAT or GltAB) through reductive transamidation of a-ketoglutarate. Glutamate can also be generated through degradation of several amino acids (glutamine, arginine, proline, aspartate, ?-aminobutyrate, histidine). The major regulator appears to be the leucine-responsive protein, Lrp, a global transcriptional regulator, that carries out many of its functions in response to leucine or alanine availability. BC and D gene of unknown function is cotranscribed with the A gene and was suggested to be involved in phenylalanine synthesis. Some of the polyamine synthesis genes are organized in two operons, AB and ED. In , proline is synthesized from glutamate in three enzymatic steps. A mutants, defective in γ- glutamyl phosphate reductase, are auxotrophic for proline, indicating that this is the only important pathway of de novo proline biosynthesis. The complex regulation of the genes in stands in sharp contrast with the constitutive expression of the BA and C genes in . The BA-dependent pathway of proline synthesis, similar to that of , is also found in , , , and, as deduced by genome analysis, in most other low-G+C gram-positive bacteria.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16

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Figures

Image of FIGURE 1
FIGURE 1

General scheme of biosynthetic pathways for amino acids of the glutamate and aspartate families, their derivatives, and alanine. See Fig. 4 to 6 , 8 , and 9 for more details. The pathway of methionine biosynthesis is described in chapter 18. Synthesis of D-alanine and D-glutamate is described in chapter 4.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 2
FIGURE 2

The regulatory region. A likely transcription start site and the direction of transcription of the operon are indicated by a right-angle arrow. The −10 and −35 promoter regions are shown as shaded boxes. and are similar dyad-symmetry sequences, separated by two helical turns of DNA, which apparently serve as GlnR-binding sites ( ); overlaps the —35 region. A GlnR dimer binds both sequences in vivo and in vitro ( ). The site can also be bound by another repressor protein, TnrA ( ). Mutations in the regulatory region ( ) and in GlnR ( ), altering regulation of the operon, are available.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 3
FIGURE 3

The intergenic region. The transcription start sites and directions of transcription of the and genes are indicated by right-angle arrows. The −10 and −35 promoter regions of and are shown as shaded boxes above and below the DNA line, respectively. Box I and Box II are the apparent GltC-binding, dyad-symmetry sequences ( ), separated by two helical turns of DNA. Binding of GltC, probably as a dimer, to Box I, immediately downstream of the transcription start site, is virtually constitutive and serves to negatively regulate GltC expression ( ). The ability of another GltC dimer to bind to Box II apparently depends on a conformational change induced by an unidentified effector and on the interaction with a GltC dimer bound to the first site. A TnrA binding sequence is located immediately downstream of the transcription start site ( ). Mutations in the GltC and TnrA binding sites, altering expression from the and promoters, confirm the model of regulation ( ). Mutant forms of GltC, affecting its interaction with the regulatory region, are available ( ).

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 4
FIGURE 4

The pathway of lysine, diaminopimelate, and dipicolinate biosynthesis.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 5
FIGURE 5

The pathway of threonine biosynthesis.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 6
FIGURE 6

The pathway of arginine biosynthesis.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 7
FIGURE 7

The regulatory region. The transcription start site and direction of transcription of the operon are indicated by a right-angle arrow. The −10 and −35 promoter regions are shown as shaded boxes. The binding site of AhrC or its ortholog ArgR overlaps the argC −10 and −35 regions ( ). AhrC/ArgR binding appears to involve arginine- and DN ?-dependent dimerization of two tamers ( ). The consensus sequence for AhrC/ArgR binding is not easily apparent (but see also reference ). A low-affinity site for AhrC is present within the coding region of the gene ( ). AhrC also binds to the promoter (cited in reference ). The three-dimensional structure of ?. ArgR, showing the winged helix-turn-helix motif, has been determined ( ). Mutations in ArgR affecting its DNA-binding properties are available ( ); such mutations were also isolated for licheniformis ArgR ( ).

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 8
FIGURE 8

The pathway of polyamine biosynthesis.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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Image of FIGURE 9
FIGURE 9

The pathway of proline biosynthesis.

Citation: Belitsky B. 2002. Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines, p 203-231. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch16
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