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Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB.

Latham JA, Chen D, Allen KN, Dunaway-Mariano D - Biochemistry (2014)

Bottom Line: These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function.YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate.Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry & Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States.

ABSTRACT
The work described in this paper, and its companion paper (Wu, R., Latham, J. A., Chen, D., Farelli, J., Zhao, H., Matthews, K. Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry, DOI: 10.1021/bi500334v), focuses on the evolution of a pair of paralogous hotdog-fold superfamily thioesterases of E. coli, YbdB and YdiI, which share a high level of sequence identity but perform different biological functions (viz., proofreader of 2,3-dihydroxybenzoyl-holoEntB in the enterobactin biosynthetic pathway and catalyst of the 1,4-dihydoxynapthoyl-CoA hydrolysis step in the menaquinone biosynthetic pathway, respectively). In vitro substrate activity screening of a library of thioester metabolites showed that YbdB displays high activity with benzoyl-holoEntB and benzoyl-CoA substrates, marginal activity with acyl-CoA thioesters, and no activity with 1,4-dihydoxynapthoyl-CoA. YdiI, on the other hand, showed a high level of activity with its physiological substrate, significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB. These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function. YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate. Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs. The divergence in YbdB and YdiI substrate specificity detailed in this paper set the stage for their structural analyses reported in the companion paper.

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E. coliydiI gene neighborhood(top) and the menaquinone pathway gene cluster (bottom). The arrowsindicate the direction of gene transcription.
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fig5: E. coliydiI gene neighborhood(top) and the menaquinone pathway gene cluster (bottom). The arrowsindicate the direction of gene transcription.

Mentions: Oddly, thegenes encoding the menaquinone pathway in E. coli are not colocated with ydiI (Figure 5). Instead, located downstream of the YdiI gene is a gene(ydiJ in E. coli) which encodesa large (1018 amino acids) multidomain protein annotated in EcoGeneas a FAD-linked, 4Fe-4S cluster-containing oxidoreductase of unknownfunction. Located upstream is the suf operon, theprotein products of which function in Fe-S cluster assembly underconditions of iron starvation or oxidative stress33 (Figure 5). This gene context islargely conserved within Enterobacteriaceae;e however, outside this taxonomic group, the gene context is highlyvaried, and numerous examples can be found where YdiI and the menaquinonepathway genes are colocated (see Figure 2 andFigures SI2 and SI4 of the Supporting Information).


Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB.

Latham JA, Chen D, Allen KN, Dunaway-Mariano D - Biochemistry (2014)

E. coliydiI gene neighborhood(top) and the menaquinone pathway gene cluster (bottom). The arrowsindicate the direction of gene transcription.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4116150&req=5

fig5: E. coliydiI gene neighborhood(top) and the menaquinone pathway gene cluster (bottom). The arrowsindicate the direction of gene transcription.
Mentions: Oddly, thegenes encoding the menaquinone pathway in E. coli are not colocated with ydiI (Figure 5). Instead, located downstream of the YdiI gene is a gene(ydiJ in E. coli) which encodesa large (1018 amino acids) multidomain protein annotated in EcoGeneas a FAD-linked, 4Fe-4S cluster-containing oxidoreductase of unknownfunction. Located upstream is the suf operon, theprotein products of which function in Fe-S cluster assembly underconditions of iron starvation or oxidative stress33 (Figure 5). This gene context islargely conserved within Enterobacteriaceae;e however, outside this taxonomic group, the gene context is highlyvaried, and numerous examples can be found where YdiI and the menaquinonepathway genes are colocated (see Figure 2 andFigures SI2 and SI4 of the Supporting Information).

Bottom Line: These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function.YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate.Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry & Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States.

ABSTRACT
The work described in this paper, and its companion paper (Wu, R., Latham, J. A., Chen, D., Farelli, J., Zhao, H., Matthews, K. Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry, DOI: 10.1021/bi500334v), focuses on the evolution of a pair of paralogous hotdog-fold superfamily thioesterases of E. coli, YbdB and YdiI, which share a high level of sequence identity but perform different biological functions (viz., proofreader of 2,3-dihydroxybenzoyl-holoEntB in the enterobactin biosynthetic pathway and catalyst of the 1,4-dihydoxynapthoyl-CoA hydrolysis step in the menaquinone biosynthetic pathway, respectively). In vitro substrate activity screening of a library of thioester metabolites showed that YbdB displays high activity with benzoyl-holoEntB and benzoyl-CoA substrates, marginal activity with acyl-CoA thioesters, and no activity with 1,4-dihydoxynapthoyl-CoA. YdiI, on the other hand, showed a high level of activity with its physiological substrate, significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB. These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function. YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate. Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs. The divergence in YbdB and YdiI substrate specificity detailed in this paper set the stage for their structural analyses reported in the companion paper.

Show MeSH
Related in: MedlinePlus