Escherichia coli YrbH Is a D-Arabinose 5-Phosphate Isomerase

Meredith, Timothy C.; Woodard, Ronald W.

doi:10.1074/jbc.m303661200

Cited by 64 publications

(68 citation statements)

References 38 publications

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“…The labile sugar nucleotide CMP-Kdo is the Kdo donor (40,126,127). The second Kdo unit is incorporated much more rapidly than the first, and therefore the intermediate with a single Kdo residue does not accumulate (Figure 2).…”

Section: Kdo Incorporation and Secondary Acylationmentioning

confidence: 99%

Lipid A Modification Systems in Gram-Negative Bacteria

Raetz

Reynolds

Trent

et al. 2007

Annu. Rev. Biochem.

1,164

1,329

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The lipid A moiety of lipopolysaccharide forms the outer monolayer of the outer membrane of most gram-negative bacteria. Escherichia coli lipid A is synthesized on the cytoplasmic surface of the inner membrane by a conserved pathway of nine constitutive enzymes. Following attachment of the core oligosaccharide, nascent core-lipid A is flipped to the outer surface of the inner membrane by the ABC transporter MsbA, where the O-antigen polymer is attached. Diverse covalent modifications of the lipid A moiety may occur during its transit from the outer surface of the inner membrane to the outer membrane. Lipid A modification enzymes are reporters for lipopolysaccharide trafficking within the bacterial envelope. Modification systems are variable and often regulated by environmental conditions. Although not required for growth, the modification enzymes modulate virulence of some gram-negative pathogens. Heterologous expression of lipid A modification enzymes may enable the development of new vaccines.

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Section: Kdo Incorporation and Secondary Acylationmentioning

confidence: 99%

Lipid A Modification Systems in Gram-Negative Bacteria

Raetz

Reynolds

Trent

et al. 2007

Annu. Rev. Biochem.

1,164

1,329

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“…API activity was determined by the discontinuous cysteinecarbazole colorimetric assay adapted to 96-well microplates as previously described (20). All plates contained internal Ru5P standards and appropriate A5P controls in triplicate.…”

Section: Methodsmentioning

confidence: 99%

“…API is encoded by the kdsD (formerly yrbH) gene in E. coli K-12, though it was speculated that other APIs may exist in E. coli based on homology searches (20). In particular, the last open reading frame of the glucitol operon GutQ has significant homology (45% identity) to KdsD.…”

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confidence: 99%

Identification of GutQ from Escherichia coli as a d -Arabinose 5-Phosphate Isomerase

Meredith¹,

Woodard

2005

J Bacteriol

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The glucitol operon (gutAEBDMRQ) of Escherichia coli encodes a phosphoenolpyruvate:sugar phosphotransferase system that metabolizes the hexitol D-glucitol (sorbitol). The functions for all but the last gene, gutQ, have been previously assigned. The high sequence similarity between GutQ and KdsD, a D-arabinose 5-phosphate isomerase (API) from the 3-deoxy-D-manno-octulosonate (KDO)-lipopolysaccharide (LPS) biosynthetic pathway, suggested a putative activity, but its role within the context of the gut operon remained unclear. Accordingly, the enzyme was cloned, overexpressed, and characterized. Recombinant GutQ was shown to indeed be a second copy of API from the E. coli K-12 genome with biochemical properties similar to those of KdsD, catalyzing the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and Darabinose 5-phosphate (A5P). Genomic disruptions of each API gene were constructed in E. coli K-12. TCM11[(⌬kdsD)] was capable of sustaining essential LPS synthesis at wild-type levels, indicating that GutQ functions as an API inside the cell. The gut operon remained inducible in TCM7[(⌬gutQ)], suggesting that GutQ is not directly involved in D-glucitol catabolism. The conditional mutant TCM15[(⌬gutQ⌬kdsD)] was dependent on exogenous A5P both for LPS synthesis/growth and for upregulation of the gut operon. The phenotype was suppressed by complementation in trans with a plasmid encoding a functional copy of GutQ or by increasing the amount of A5P in the medium. As there is no obvious obligatory role for GutQ in the metabolism of D-glucitol and there is no readily apparent link between D-glucitol metabolism and LPS biosynthesis, it is suggested that A5P is not only a building block for KDO biosynthesis but also may be a regulatory molecule involved in expression of the gut operon.D-Arabinose 5-phosphate isomerase (API) is the first enzyme in the biosynthetic pathway of 3-deoxy-D-manno-octulosonate (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs). Lipopolysaccharides are amphiphilic macromolecules located in the outer leaflet of the outer membrane of gram-negative bacteria, forming an asymmetric lipid bilayer that surrounds the cell. The LPS layer is anchored in the outer membrane by the highly conserved lipid A domain and is followed by an oligosaccharide core region usually containing at least one KDO molecule that connects lipid A to an extended hypervariable repeating polysaccharide chain (O antigen) (25). In addition to providing a measure of intrinsic antibiotic resistance and defense against host responses, LPS (also referred to as endotoxin) is the main mediator of gramnegative bacterial pathogenesis (13, 33). The minimal LPS structure required for viability of Escherichia coli under laboratory conditions is KDO 2 -lipid A, also referred to as Re endotoxin (11,25,31).API catalyzes the reversible 1,2-keto/aldol isomerization of the pentose pathway intermediate ribulose 5-phosphate (Ru5P) to D-arabinose 5-phosphate (A5P) and is the intracellular source of A5P used f...

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“…This system is comprised of three genes, yrbK (encoding a putative TM protein with just one TM segment), yhbN (encoding a putative periplasmic protein), and yhbG (encoding an ABC protein). These genes are located just downstream of the genes encoding two enzymes involved in the biogenesis of the KDO component of LPS, i.e., kdsD (yrbH) and kdsC (yrbI), encoding D-arabinose 5-phosphate isomerase and 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, respectively (311,532 (Fig. 17), these results are consistent with a model in which the LptA/ LptB complex is responsible for conveying newly synthesized LPS through the periplasmic space to the outer membrane.…”

Section: Biogenesis Of Extracellular Polysaccharidesmentioning

confidence: 99%

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

Davidson

Dassa

Orelle

et al. 2008

Microbiol Mol Biol Rev

1,185

1,137

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SUMMARY ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.

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Escherichia coli YrbH Is a D-Arabinose 5-Phosphate Isomerase

Cited by 64 publications

References 38 publications

Lipid A Modification Systems in Gram-Negative Bacteria

Lipid A Modification Systems in Gram-Negative Bacteria

Identification of GutQ from Escherichia coli as a d -Arabinose 5-Phosphate Isomerase

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

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