L-Alanine Prototrophic Suppressors Emerge from L-Alanine Auxotroph through Stress-Induced Mutagenesis in Escherichia coli

In Escherichia coli, L-alanine is synthesized by three isozymes: YfbQ, YfdZ, and AvtA. When an E. coli L-alanine auxotrophic isogenic mutant lacking the three isozymes was grown on L-alanine-deficient minimal agar medium, L-alanine prototrophic mutants emerged considerably more frequently than by spontaneous mutation; the emergence frequency increased over time, and, in an L-alanine-supplemented minimal medium, correlated inversely with L-alanine concentration, indicating that the mutants were derived through stress-induced mutagenesis. Whole-genome analysis of 40 independent L-alanine prototrophic mutants identified 16 and 18 clones harboring point mutation(s) in pyruvate dehydrogenase complex and phosphotransacetylase-acetate kinase pathway, which respectively produce acetyl coenzyme A and acetate from pyruvate. When two point mutations identified in L-alanine prototrophic mutants, in pta (D656A) and aceE (G147D), were individually introduced into the original L-alanine auxotroph, the isogenic mutants exhibited almost identical growth recovery as the respective cognate mutants. Each original- and isogenic-clone pair carrying the pta or aceE mutation showed extremely low phosphotransacetylase or pyruvate dehydrogenase activity, respectively. Lastly, extracellularly-added pyruvate, which dose-dependently supported L-alanine auxotroph growth, relieved the L-alanine starvation stress, preventing the emergence of L-alanine prototrophic mutants. Thus, L-alanine starvation-provoked stress-induced mutagenesis in the L-alanine auxotroph could lead to intracellular pyruvate increase, which eventually induces L-alanine prototrophy.

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Dihydrolipoamide Dehydrogenase Mutation Alters the NADH Sensitivity of Pyruvate Dehydrogenase Complex of Escherichia coli K-12

Journal of Bacteriology ◽

10.1128/jb.00104-08 ◽

2008 ◽

Vol 190 (11) ◽

pp. 3851-3858 ◽

Cited By ~ 76

Author(s):

Youngnyun Kim ◽

L. O. Ingram ◽

K. T. Shanmugam

Keyword(s):

Escherichia Coli ◽

Pyruvate Dehydrogenase ◽

Double Mutant ◽

Pyruvate Dehydrogenase Complex ◽

Anaerobic Growth ◽

Lower Sensitivity ◽

Dihydrolipoamide Dehydrogenase ◽

Fermentation Products ◽

E Coli ◽

K 12

ABSTRACT Under anaerobic growth conditions, an active pyruvate dehydrogenase (PDH) is expected to create a redox imbalance in wild-type Escherichia coli due to increased production of NADH (>2 NADH molecules/glucose molecule) that could lead to growth inhibition. However, the additional NADH produced by PDH can be used for conversion of acetyl coenzyme A into reduced fermentation products, like alcohols, during metabolic engineering of the bacterium. E. coli mutants that produced ethanol as the main fermentation product were recently isolated as derivatives of an ldhA pflB double mutant. In all six mutants tested, the mutation was in the lpd gene encoding dihydrolipoamide dehydrogenase (LPD), a component of PDH. Three of the LPD mutants carried an H322Y mutation (lpd102), while the other mutants carried an E354K mutation (lpd101). Genetic and physiological analysis revealed that the mutation in either allele supported anaerobic growth and homoethanol fermentation in an ldhA pflB double mutant. Enzyme kinetic studies revealed that the LPD(E354K) enzyme was significantly less sensitive to NADH inhibition than the native LPD. This reduced NADH sensitivity of the mutated LPD was translated into lower sensitivity of the appropriate PDH complex to NADH inhibition. The mutated forms of the PDH had a 10-fold-higher Ki for NADH than the native PDH. The lower sensitivity of PDH to NADH inhibition apparently increased PDH activity in anaerobic E. coli cultures and created the new ethanologenic fermentation pathway in this bacterium. Analogous mutations in the LPD of other bacteria may also significantly influence the growth and physiology of the organisms in a similar fashion.

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Expression and lipoylation in Escherichia coli of the inner lipoyl domain of the E2 component of the human pyruvate dehydrogenase complex

Biochemical Journal ◽

10.1042/bj2890081 ◽

1993 ◽

Vol 289 (1) ◽

pp. 81-85 ◽

Cited By ~ 35

Author(s):

J Quinn ◽

A G Diamond ◽

A K Masters ◽

D E Brookfield ◽

N G Wallis ◽

...

Keyword(s):

Escherichia Coli ◽

Pyruvate Dehydrogenase ◽

Pyruvate Dehydrogenase Complex ◽

Structural Studies ◽

Gene Encoding ◽

E Coli ◽

Inner Lipoyl Domain ◽

Dehydrogenase Complex ◽

Lipoyl Domain

The dihydrolipoamide acetyltransferase subunit (E2p) of mammalian pyruvate dehydrogenase complex has two highly conserved lipoyl domains each modified with a lipoyl cofactor bound in amide linkage to a specific lysine residue. A sub-gene encoding the inner lipoyl domain of human E2p has been over-expressed in Escherichia coli. Two forms of the domain have been purified, corresponding to lipoylated and non-lipoylated species. The apo-domain can be lipoylated in vitro with partially purified E. coli lipoate protein ligase, and the lipoylated domain can be reductively acetylated by human E1p (pyruvate dehydrogenase). Availability of the two forms will now allow detailed biochemical and structural studies of the human lipoyl domains.

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Escherichia coli Pyruvate Dehydrogenase Complex Is an Important Component of CXCL10-Mediated Antimicrobial Activity

Infection and Immunity ◽

10.1128/iai.00552-15 ◽

2015 ◽

Vol 84 (1) ◽

pp. 320-328 ◽

Cited By ~ 14

Author(s):

Kirsten M. Schutte ◽

Debra J. Fisher ◽

Marie D. Burdick ◽

Borna Mehrad ◽

Amy J. Mathers ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Activity ◽

Cell Surface ◽

Pyruvate Dehydrogenase ◽

Pyruvate Dehydrogenase Complex ◽

Gene Encoding ◽

Content Type ◽

E Coli ◽

Novel Therapeutic Strategies ◽

Dehydrogenase Complex

Chemokines are best recognized for their role within the innate immune system as chemotactic cytokines, signaling and recruiting host immune cells to sites of infection. Certain chemokines, such as CXCL10, have been found to play an additional role in innate immunity, mediating CXCR3-independent killing of a diverse array of pathogenic microorganisms. While this is still not clearly understood, elucidating the mechanisms underlying chemokine-mediated antimicrobial activity may facilitate the development of novel therapeutic strategies effective against antibiotic-resistant Gram-negative pathogens. Here, we show that CXCL10 exerts antibacterial effects on clinical and laboratory strains ofEscherichia coliand report that disruption of pyruvate dehydrogenase complex (PDHc), which converts pyruvate to acetyl coenzyme A, enablesE. colito resist these antimicrobial effects. Through generation and screening of a transposon mutant library, we identified two mutants with increased resistance to CXCL10, both with unique disruptions of the gene encoding the E1 subunit of PDHc,aceE. Resistance to CXCL10 also occurred following deletion of eitheraceForlpdA, genes that encode the remaining two subunits of PDHc. Although PDHc resides within the bacterial cytosol, electron microscopy revealed localization of immunogold-labeled CXCL10 to the bacterial cell surface in both theE. coliparent andaceEdeletion mutant strains. Taken together, our findings suggest that while CXCL10 interacts with an as-yet-unidentified component on the cell surface, PDHc is an important mediator of killing by CXCL10. To our knowledge, this is the first description of PDHc as a key bacterial component involved in the antibacterial effect of a chemokine.

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Design, synthesis, biological evaluation and molecular docking of amide and sulfamide derivatives as Escherichia coli pyruvate dehydrogenase complex E1 inhibitors

RSC Advances ◽

10.1039/c5ra22573f ◽

2016 ◽

Vol 6 (6) ◽

pp. 4310-4320 ◽

Cited By ~ 7

Author(s):

Haifeng He ◽

Jiangtao Feng ◽

Junbo He ◽

Qin Xia ◽

Yanliang Ren ◽

...

Keyword(s):

Escherichia Coli ◽

Molecular Docking ◽

Pyruvate Dehydrogenase ◽

Pyruvate Dehydrogenase Complex ◽

Binding Mode ◽

Biological Evaluation ◽

Design Synthesis ◽

E Coli ◽

Dehydrogenase Complex

Optimal binding mode of novel E. coli PDHc E1 inhibitor 9d.

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Isolation and characterization of lipoylated and unlipoylated domains of the E2p subunit of the pyruvate dehydrogenase complex of Escherichia coli

Biochemical Journal ◽

10.1042/bj2710139 ◽

1990 ◽

Vol 271 (1) ◽

pp. 139-145 ◽

Cited By ~ 32

Author(s):

S T Ali ◽

J R Guest

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Pyruvate Dehydrogenase ◽

Pyruvate Dehydrogenase Complex ◽

Amino Acid Residues ◽

E Coli ◽

Isolation And Characterization ◽

Lysine Residues ◽

Dehydrogenase Complex ◽

Lipoyl Domain

The dihydrolipoamide acetyltransferase subunit (E2p) of the pyruvate dehydrogenase complex of Escherichia coli has three highly conserved and tandemly repeated lipoyl domains, each containing approx. 80 amino acid residues. These domains are covalently modified with lipoyl groups bound in amide linkage to the N6-amino groups of specific lysine residues, and the cofactors perform essential roles in the formation and transfer of acetyl groups by the dehydrogenase (E1p) and acetyltransferase (E2p) subunits. A subgene encoding a hybrid lipoyl domain was previously shown to generate two products when overexpressed, whereas a mutant subgene, in which the lipoyl-lysine codon is replaced by a glutamine codon, expresses only one product. A method has been devised for purifying the three types of independently folded domain from crude extracts of E. coli, based on their pH-(and heat-)stabilities. The domains were characterized by: amino acid and N-terminal sequence analysis, lipoic acid content, acetylation by E1p, tryptic peptide analysis and immunochemical activity. This has shown that the two forms of domain expressed from the parental subgene are lipoylated (L203) and unlipoylated (U203) derivatives of the hybrid lipoyl domain, whereas the mutant subgene produces a single unlipoylatable domain (204) containing the Lys-244----Gln substitution.

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A Dynamic Loop at the Active Center of the Escherichia coli Pyruvate Dehydrogenase Complex E1 Component Modulates Substrate Utilization and Chemical Communication with the E2 Component

Journal of Biological Chemistry ◽

10.1074/jbc.m704326200 ◽

2007 ◽

Vol 282 (38) ◽

pp. 28106-28116 ◽

Cited By ~ 32

Author(s):

Sachin Kale ◽

Palaniappa Arjunan ◽

William Furey ◽

Frank Jordan

Keyword(s):

Escherichia Coli ◽

Active Center ◽

Pyruvate Dehydrogenase ◽

Active Site ◽

Pyruvate Dehydrogenase Complex ◽

Side Reactions ◽

Thiamin Diphosphate ◽

E Coli ◽

Covalent Intermediate ◽

Dehydrogenase Complex

Our crystallographic studies have shown that two active center loops (an inner loop formed by residues 401-413 and outer loop formed by residues 541-557) of the E1 component of the Escherichia coli pyruvate dehydrogenase complex become organized only on binding a substrate analog that is capable of forming a stable thiamin diphosphate-bound covalent intermediate. We showed that residue His-407 on the inner loop has a key role in the mechanism, especially in the reductive acetylation of the E. coli dihydrolipoamide transacetylase component, whereas crystallographic results showed a role of this residue in a disorder-order transformation of these two loops, and the ordered conformation gives rise to numerous new contacts between the inner loop and the active center. We present mapping of the conserved residues on the inner loop. Kinetic, spectroscopic, and crystallographic studies on some inner loop variants led us to conclude that charged residues flanking His-407 are important for stabilization/ordering of the inner loop thereby facilitating completion of the active site. The results further suggest that a disorder to order transition of the dynamic inner loop is essential for substrate entry to the active site, for sequestering active site chemistry from undesirable side reactions, as well as for communication between the E1 and E2 components of the E. coli pyruvate dehydrogenase multienzyme complex.

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