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Chapter 14 : Nitrogen Source Utilization and Its Regulation

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Abstract:

In and other gram-positive bacteria, nitrogen metabolism genes are regulated by fundamentally different mechanisms. Three proteins—GlnR, TnrA, and CodY—control gene expression in response to nitrogen availability in . TnrA both activates and represses transcription during nitrogen-limited growth. TnrA-like proteins have been identified by sequence analysis in and . Four nitrogen degradative pathways—arginine, histidine, glutamate and urea—are described in this chapter. By several criteria, glutamine serves as the best nitrogen source for , followed by arginine. The regulation and genetics of several nitrogen catabolite pathways are also discussed in the chapter. has two routes for arginine degradation, the arginase-dependent and arginine deiminase-dependent pathways. Expression of both pathways is induced by arginine and repressed by growth in the presence of glucose. Expression of the histidine-degrading enzymes is induced by histidine and subject to nutritional regulation by CodY and CcpA. The expression of the plasmid-encoded genes found in several strains and the chromosomal genes in are nitrogen regulated. Several low-G+C gram-positive bacteria contain genes encoding NrgA-like ammonium transporters proteins. The second gene in the AB operon encodes a protein that resembles the PII signal transduction protein found in the enteric Ntr nitrogen regulatory system and in cyanobacteria.

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14

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Amino Acids
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Figures

Image of FIGURE 1
FIGURE 1

Proline and arginine degradative pathways. The proline degradative enzymes are as follows: 1, proline oxidase; 2, pyrroline-5-carboxylate dehydrogenase; 6, glutamate dehydrogenase. The enzymes of the arginase degradative pathway are as follows: 3, arginase; 4, ornithine transaminase; 5, urease. The enzymes of the deiminase pathway are as follows: 7, arginine deiminase; 8, ornithine carbamoyltransferase; 9, carbamate kinase. Glutamate semialdehyde is spontaneously converted to pyrroline 5-carboxylate, the more stable cyclic form of glutamate semialdehyde. Two genes encode pyrroline-5-carboxylate dehydrogenase isozymes in Either RocA or YcgN can function in the degradation of proline and arginine ( ). Although does not contain the arginine deiminase pathway, this bacterium can utilize citrulline as a nitrogen source. Interestingly, citrulline utilization requires ornithine transaminase (RocD), not ornithine transcarbamylase (ArgF), in ( ).

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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Image of FIGURE 2
FIGURE 2

Transcriptional organization of the operon. The element (located between +203 and +216) and DNA region required for CodY binding are indicated ( ). The stem-loop structure between and indicates a transcriptional terminator, encodes a regulatory protein required for transcriptional antitermination at this transcriptional terminator ( ).

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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Image of FIGURE 3
FIGURE 3

Probable isoleucine and valine degradative pathway. The isoleucine and valine degradative enzymes in are as follows: leucine dehydrogenase branched-chain α-keto acid dehydrogenase phosphate butyryl-CoA transferase and butyrate kinase The branched-chain α-keto acid dehydrogenase enzyme is also required for the synthesis of branched-chain fatty acids, which are major acyl components of the cell membrane in ( ).

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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Image of FIGURE 4
FIGURE 4

Probable threonine degradative pathway. The putative threonine degradative enzymes in are as follows: threonine dehydrogenase 2-amino-3-ketobutyrate CoA ligase glycine cleavage system serine hydroxymethyltransferase and serine deaminase

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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Image of FIGURE 5
FIGURE 5

Transcriptional organization of the . ABC operon. The three ABC promoters are indicated ( ). The P1 and P3 promoters are SigA-dependent promoters. The P2 promoter is a SigH-dependent promoter. CodY represses transcription of both the P3 and P2 promoters. P3 transcription is repressed by GlnR and activated by TnrA.

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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Image of FIGURE 6
FIGURE 6

Purine degradative pathway. The purine degradative enzymes in are as follows: adenine deaminase guanine deaminase xanthine dehydrogenase (pucABCDE), uricase allantoinase (pucH), and urease (ureABC). The enzymes that convert allantoic acid to urea (reviewed in reference ) have not yet been identified in .

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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Image of FIGURE 7
FIGURE 7

Transcriptional organization of the region. The two σ-dependent promoters (−24 −12) and the RocR binding sites (UAS/DAS) are indicated. Expression of the rocG and promoters is activated by RocR and AhrC. RocR binds to the UAS/DAS sequence and activates transcription of the and rocABC promoters ( ). AhrC has been shown to bind to a site located between -20 and +1 in the rocA promoter region ( ). CcpA negatively regulates rocG expression by binding to a cre element located between +39 and +52 in the promoter region ( ).

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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Tables

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TABLE 1

Nitrogen compounds utilized as sole nitrogen sources by

Gene products and their corresponding genes involved in nitrogen source utilization are indicated. Proteins whose function was identified only by sequence analysis are indicated with a superscript asterisk (*). Genes encoding permeases identified only by sequence analysis have not been included in this table unless the permease gene is cotranscribed with gene(s) encoding degradative enzyme(s).

Regulatory proteins known to control gene expression are indicated on the same line. +, positive regulation; —, negative regulation.

At neutral pH where ammonium is primarily present as NH, analysis of ammonium acquisition in enteric bacteria and yeasts showed that diffusion of NH across biological membranes is sufficient to support good growth. At acidic pH, where the charged species NH predominates, ammonium transport proteins are required for optimal growth on low levels of ammonium ( ).

Asparaginase converts L-asparagine to L-aspartate and NH . L-Aspartate can either be degraded to NH and rumarate by aspartase or be further metabolized by the aspartate-glutamate transaminase AspB. Since aspartase mutant grow very slowly with L-aspartate as a sole nitrogen source, aspartase is the major pathway for aspartate metabolism in Residual growth with aspartate seen in the mutants results from AspB-dependent transamination, because the double mutant cannot grow with aspartate as a nitrogen source ( ).

Because a double mutant grows as well as wild-type cells with glutamate as sole nitrogen source ( ), additional enzymes (most likely transaminases) participate in glutamate utilization.

In wild-type cells, the gene is cryptic owing to a 9-bp insertion in the coding region ( ).

mutants grow as well as wild-type cells with glutamine as sole nitrogen source, indicating that additional enzymes such as glutaminases participate in glutamine metabolism ( ).

The expression of is subject to (i) negative autoregulation and (ii) activation by TnrA ( ).

In the common laboratory 168 strain, the operon is cryptic owing to a frameshift mutation in ( ).

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14
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TABLE 2

Nitrogen degradative pathways in low-G+C gram-positive bacteria

Presence of various enzymes or transporter proteins involved in the utilization of selected nitrogen sources, as determined by biochemical or genetic analysis or by searching genomic databases (as of June 2, 2000). Databases were searched using the gene encoding the indicated protein or the arginine deiminase () gene.

Citation: Fisher S, Débarbouillé M. 2002. Nitrogen Source Utilization and Its Regulation, p 181-191. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch14

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