Subsystem: L-ascorbate utilization (and related gene clusters)

This subsystem's description is:

This Subsystem is an attempt to discern two conserved sets of paralogous protein families based on distinct genome contexts of the corresponding genes. It has been started by MattC and extended by SvetaG.
Two closely related operons have been described in E. coli K12: yjf-sga and yia-sgb (Ibanez et al. 2000; Yew and Gerlt 2002). The yjf-sga operon consists of 6 genes: sgaT, sgaB, ptxA, sgaH, sgaU, and sgaE. The first three genes apparently encode components of a PTS sugar transporter, sgaH encodes 3-keto-L-gulonate 6-phosphate decarboxylase, sgaU - L-xylulose 5-phosphate 3-epimerase (EC 5.1.3.-), and sgaE encodes L-ribulose-5-phosphate 4-epimerase. The second operon (yia-sgb) contains close homologs of sgaH, sgaU, and sgaE with gene order preserved. However, PTS components are missing and a sigar kinase (lyxK) is present in the same cluster.

The yjf-sga operon has been implicated in L-ascorbate utilization in E. coli based on the fact that a knockout mutant missing this entire gene cluster failed to ferment L-ascorbate (Yew and Gerlt 2002). On the other hand, disruption of the yia-sgb operon did not affect fermentation of L-ascorbate (Yew and Gerlt 2002). Specific sugar substrate of the yia-sgb catabolic operon remains unknown.

For more information, please check out the description and the additional notes tabs, below

Literature ReferencesUtilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. Yew WS Journal of bacteriology 2002 Jan11741871
Aerobic L-ascorbate metabolism and associated oxidative stress in Escherichia coli. Campos E Microbiology (Reading, England) 2007 Oct17906139
The yiaKLX1X2PQRS and ulaABCDEFG gene systems are required for the aerobic utilization of L-ascorbate in Klebsiella pneumoniae strain 13882 with L-ascorbate-6-phosphate as the inducer. Campos E Journal of bacteriology 2008 Oct18708499
DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional NotesScenarios 

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3DGDHSgaHSgbHUlaD*regulator*PTSUlaESgaESgbEUlaFSgaUSgbU*kinaseUlaG*RK
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This Subsystem is an attempt to discern two conserved sets of paralogous protein families based on distinct genome contexts of the corresponding genes. It has been started by MattC and extended by SvetaG.
Two closely related operons have been described in E. coli K12: yjf-sga and yia-sgb (Ibanez et al. 2000; Yew and Gerlt 2002). The yjf-sga operon consists of 6 genes: sgaT, sgaB, ptxA, sgaH, sgaU, and sgaE. The first three genes apparently encode components of a PTS sugar transporter, sgaH encodes 3-keto-L-gulonate 6-phosphate decarboxylase, sgaU - L-xylulose 5-phosphate 3-epimerase (EC 5.1.3.-), and sgaE encodes L-ribulose-5-phosphate 4-epimerase. The second operon (yia-sgb) contains close homologs of sgaH, sgaU, and sgaE with gene order preserved. However, PTS components are missing and a sigar kinase (lyxK) is present in the same cluster.

The yjf-sga operon has been implicated in L-ascorbate utilization in E. coli based on the fact that a knockout mutant missing this entire gene cluster failed to ferment L-ascorbate (Yew and Gerlt 2002). On the other hand, disruption of the yia-sgb operon did not affect fermentation of L-ascorbate (Yew and Gerlt 2002). Specific sugar substrate of the yia-sgb catabolic operon remains unknown.
Subsystem analysis allowed projection of the experimental data obtained in E.coli onto other microbial groups. It was indeed possible to accurately identify orthologs of each of the paralogs: sgaH and sgbH, sgaU and sgbU, sgaE and sgbE in many bacterial species based of their conserved clustering on the chromosome (in spite of a high degree of sequence similarity between them). It might also be possible to trace the evolution of these gene clusters as well (has not been attempted yet, but please note Vibrio sp. MED222 - the only genome where the 2 cliusters are next to each other forming inverted repeat! The origin of this chromosomal douplication??). It would be very interesting to test whether or not sugar substrate for each of the two orthologous operons has remained the same in all the species. For the time being - a few observations made during this SS encoding:

1. The yjf-sga operon has counterparts in a large number of diverse microbial species within the following genera: Gamma-proteobacteria (Enterobacteriales, Vibrionales, Pasteurellales) and Firmicutes

2. In addition to the 6 functionally characterized proteins (three PTS components and the SgaH, SgaU, and SgaE proteins) several uncharacterized ORFs often cluster with the yjf-sga operon: Putative transcriptional regulators and Metal-dependent hydrolase (eco:b4192 ortholog). The latter may be a suitable gene candidate for a “missing" role of a hydrolase required for the L-ascorbate ring opening. In Enterobacteriales a Putative DeoR-type transcriptional regulator is a part of the yjf-sga cluster, while Firmicutes contain a different putative regulator instead.

3. Gene clusters orthogous to the yia-sgb operon are present only in Enterobacteriales and Pasteurellales (in addition to yjf-sga), and might have resulted from a relatively recent duplication event(s).

4. Additionally, an interesting version of a yia-sgb-like gene cluster is present and Actinomycetales. In Tropheryma whipplei it contains 2-keto-3-deoxygluconate kinase (EC 2.7.1.45) in place of L-xylulose/3-keto-L-gulonate kinase – possibly indicating involvement of this operon in utilization of mucopolysaccharides, potentially an important source of carbon and energy for this obligate human pathogen.


Variant codes:

-1: no yjf-sga or yia-sgb related gene clusters are present (use "show -1 variants" checkbox to display these genomes)

The FIRST digit describes the presence or absence of the yjf-sga-like gene clusters:
[1_] - full cluster of 8 genes is present in an organism (as in E. coli)
[2_] - cluster is “incomplete”, missing one or more components
[4_] - cluster appears to have split in two sub-clusters. Several (if not all) of such variant are likely due to yet unassembled genome sequences.
[9_] - cluster is missing

The SECOND digit describes the presence or absence of the yia-sgb-like gene clusters:
[_1] - full cluster of 4 genes is present in an organism (as in E. coli)
[_2] - cluster is “incomplete”, missing one or more of these components
[_3] - a putative 2-keto-3-deoxygluconate kinase has replaced L-xylulose/3-keto-L-gulonate kinase (as in Actinomycetales)
[_4] - cluster appears to have split in two sub-clusters. Several (if not all) of such variant are likely due to yet unassembled genome sequences.
[_9] - cluster is missing

Notes:
1. Although it has been reported that E. coli proteins the SgaH and SgbH exhibit sequence similarity to the D-arabino-3-hexulose 6-phosphate formaldehyde lyase (HPS) of M. aminofaciens (Reizer et al. 1997), no HPS activity could be detected for either of the sgaH and sgbH gene products in direct enzymatic assay (Yasueda et al. 1999; Taylor et al. 2004). Furthermore, no HPS activity could be detected in extracts of E. coli cells cultured under several stresses, including formaldehyde exposure (Yasueda et al. 1999). See SS: Formaldehyde assimilation: Ribulose monophosphate pathway

2. The presence of L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) in the absence of all other sga or sgb genes (Variant code -1) is due to involvement of this Role also in L-Arabinose utilization (see the corresponding SS). In such cases this epimerase is often clustered with Ribulokinase (EC 2.7.1.16). The latter Role has been included in this SS as AUX to point to the presence of L-Arabinose utilization pathway in an organism.

==========References:===================================

Campos E, de la Riva L, Garces F, Giménez R, Aguilar J, Baldoma L, Badia J. The yiaKLX1X2PQRS and ulaABCDEFG gene systems are required for the aerobic utilization of L-ascorbate in Klebsiella pneumoniae strain 13882 with L-ascorbate-6-phosphate as the inducer. J Bacteriol. 2008 Oct;190(20):6615-24. Epub 2008 Aug 15.PMID: 18708499

Campos E, Montella C, Garces F, Baldoma L, Aguilar J, Badia J. Aerobic L-ascorbate metabolism and associated oxidative stress in Escherichia coli. Microbiology. 2007 Oct;153(Pt 10):3399-408.PMID: 17906139

Yew WS, Gerlt JA. Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. J Bacteriol. 2002 Jan;184(1):302-6.PMID: 11741871

Ibanez, E., R. Gimenez, et al. (2000). "Role of the yiaR and yiaS genes of Escherichia coli in metabolism of endogenously formed L-xylulose." J Bacteriol 182(16): 4625-7.

Reizer, J., A. Reizer, et al. (1997). "Is the ribulose monophosphate pathway widely distributed in bacteria?" Microbiology 143 (Pt 8): 2519-20.

Taylor, E. J., N. L. Smith, et al. (2004). "The gene encoding the ribulose monophosphate pathway enzyme, 3-hexulose-6-phosphate synthase, from Aminomonas aminovorus C2A1 is adjacent to coding sequences that exhibit similarity to histidine biosynthesis enzymes." Antonie Van Leeuwenhoek 86(2): 167-72.

Yasueda, H., Y. Kawahara, et al. (1999). "Bacillus subtilis yckG and yckF encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckH is required for their expression." J Bacteriol 181(23): 7154-60.

Currently selected organism: Escherichia coli 2731150 (open scenarios overview page for organism)