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Chapter 29 : Metabolomics

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Metabolomics, Page 1 of 2

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Abstract:

The ultimate goal in metabolomics is to achieve unbiased identification and quantification of all the metabolites in a defined biological system. Much of the work in bacterial metabolomics has involved the study of well-established metabolic pathways such as the tricarboxylic acid cycle, glycolysis, and specific metabolic pathways of microorganisms used in industrial applications. In contrast, the field of metabolomics is very much in its infancy, and considering the lack of information on many of the novel glycoconjugate biosynthesis pathways in , there is much scope to use targeted metabolomics approaches to further define the substrates and genes involved in these metabolic pathways. The main challenges associated with the study of sugar nucleotide metabolites by nuclear magnetic resonance (NMR) have been the instability of the sugar nucleotides and their presence at low concentrations within the bacterial cells. UDP-α-D-QuiNAc4NAc is an important metabolite in the 2,4-diacetamido-bacillosamine biosynthesis pathway, and its accumulation in had not been expected because it has been thought that the inactivation of would lead to an accumulation of a novel precursor directly related to Pse5Ac7Ac biosynthesis. The focused metabolomics studies of flagellin glycosylation in 81-176 and VC167 were extensive and examined unknown gene functions, characterized novel biosynthetic substrates and novel flagellar glycans, and elucidated poorly understood metabolic pathways.

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29

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Campylobacter coli
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Campylobacter jejuni
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Figures

Image of Figure 1.
Figure 1.

Prokaryotic biosynthetic pathway of N-acetylneuraminic acid (Neu5Ac) and the corresponding putative biosynthetic pathway of pseudaminic acid (Pse5Ac7Ac).

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 2.
Figure 2.

CE-ESMS and precursor ion scanning for fragments related to CMP ( 322) or UDP ( 385) activated sugars in cell lysates. (a) Wild-type 81-176. (b) Isogenic mutant . (c) Isogenic mutant .

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 3.
Figure 3.

Comparison of the ratio of signal to noise (S/N) for a UDP-6-deoxy-α--GlcNAc4NAc metabolite sample isolated from 81-176 showing the advantages of the use of a higher-field NMR spectrometer and cold probe. (a) H NMR spectrum acquired at 600 MHz using a cold probe (S/N = 100:1). (b) H NMR spectrum acquired at 500 MHz using a conventional 3-mm probe (S/N = 39:1). For (a) and (b), the metabolite sample was analyzed in a 3-mm tube (200 μl 99% DO) with 128 scans.

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 4.
Figure 4.

NMR spectroscopy of CMP-5-acetamido-7-acetamidino-3,5,7,9-tetradeoxy---nonulosonic acid (CMP-Pse5-NAc7Am, I) purified from cell lysates. (a) H NMR spectrum (256 transients). (b) One-dimensional TOCSY of I H3ax (80 ms). (c) One-dimensional TOCSY of I H7 (80 ms). (d) One-dimensional TOCSY of I H9 (80 ms). (e) One-dimensional TOCSY of I NAc NH (30 ms). (f) One-dimensional TOCSY of I Am NH (30 ms). (g) The 13C HSQC spectrum (165 transients, 128 increments, 1C,H_150 Hz, 24 h). From .

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 5.
Figure 5.

HILIC-MS and precursor ion scanning for fragment ions related to CMP ( 322). (a) Cell lysate from VC167. (b) Cell lysate from 81-176. (c) Isogenic mutant Peak 1, CMP-Leg5Ac7Ac; peak 2, CMP-Pse5Ac7Ac; peak 3, CMP-Leg5AmNMe7Ac; peak 4, CMP-Leg5Am7Ac; peak 5, CMP-Neu5Ac; peak 6, CMP-Pse5Ac7Am.

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 6.
Figure 6.

First steps of the pseudaminic acid biosynthetic pathway in From . Pyranose rings are shown as their predominant chair conformation determined from nuclear Overhauser effects (NOEs) and (H,H) coupling constants. Step 1, UDP-α--GlcNAc; step 2, UDP-2-acetamido-2,6-dideoxy-β--hexos-4-ulose; step 2′, -diol form of 2; 3, UDP-2-acetamido-2,6-dideoxy-α--hexos-4-ulose; step 3′, -diol form of 3 (from ); step 4, CMP-Pse5Ac7Ac.

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 7.
Figure 7.

PseB reaction monitored directly with H NMR spectroscopy (500 MHz, H) in aqueous reaction buffer (25°C, 10% DO, 25 mM UDP-α--GlcNAc, 225 μg of PseB, 25 mM NaPO, 50 mM NaCl, pH 7.2). From . (a) Integrals for anomeric protons plotted over time. (b, c) H NMR spectra of the PseB reaction showing the anomeric region acquired at 0.08 and 6 h, respectively (from ).

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 8.
Figure 8.

Comparison of -linked protein glycosylation in (a) eukaryotes and (b) the bacterium, . In the eukaryotic system, the oligosaccharide is assembled on the cytoplasmic face of the endoplasmic reticulum (ER) on the polyprenyl carrier dolichol phosphate. It is then flipped to the luminal side of the ER, where it is transferred to acceptor proteins with the Ser/Thr-X-Asn sequon by the oligosaccharytl transferase (OST) complex. In , the heptasaccharide is assembled on the cytoplasmic face of the cytoplasmic membrane on the polyprenyl carrier undecaprenyl phosphate. The completed heptasaccharide is then flipped to the periplasmic face of the membrane by PglK, where it is transferred to acceptor proteins with the extended sequon Ser/Thr-XpAsn-Glu/Asp by PglB.

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Image of Figure 9.
Figure 9.

Metabolomic analysis of the -linked protein glycosylation pathway in . (a) CE-MS precursor ion scans for undecaprenyl-phosphate (Und-P-HO, 907.6) of affinity-captured lipid extracts of indicating accumulation of Und-PP-heptasaccharide 1. (b) CE-MS-MS analysis of 1168.0 in the negative ion mode, confirming that the -glycan heptasaccharide is assembled on undecaprenyl-phosphate. (c) CE-MS spectrum demonstrating accumulation of UDP-diacetamido-trideoxyhexose ( 631.5) in cell lysates.

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
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Tables

Generic image for table
Table 1.

Metabolomic analysis of mutants of Neu5Ac biosynthesis gene homologues in 81-176

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29
Generic image for table
Table 2.

Results of -glycan intermediate analyses in

Citation: Soo E, McNally D, Brisson J, Reid C. 2008. Metabolomics, p 523-542. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch29

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