# Patent

## Title
Compositions and methods for using NADH oxidases

## Abstract

The present disclosure relates generally to bacterial NADH oxidases and, more particularly, to novel NADH oxidases obtained from Lactobacillus plantarum, and derivatives thereof that demonstrate enzymatic activity for NADH, NADPH, or both NADH and NADPH. The compositions comprising an NADH oxidase obtained from L. plantarum or derivatives thereof include: isolated enzymes; recombinantly produced enzymes and derivatives thereof, as well as catalytically active portions thereof; nucleic acids encoding an NADH oxidase obtained from L. plantarum, derivatives thereof, and portions thereof. The methods of the present invention include isolation of NADH oxidases obtained from L. plantarum, derivatives thereof, and portions thereof, and methods for enzymatic reactions comprising NADH oxidase obtained from L. plantarum, including the production of enantiomer-enriched organic compounds.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims, under 35 U.S.C. §119(e), the benefit of U.S. Provisional Application Ser. No. 61/265,915, filed 2 Dec. 2009, and U.S. Provisional Application Ser. No. 61/383,858, filed 17 Sep. 2010, the entire contents and substance of which are hereby incorporated by reference as if fully set forth below.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
This invention was made with U.S. Government support under Grant No. 2 R44AI65127-02 awarded by the National Institutes of Health. The U.S. Government has certain rights in the invention.


BACKGROUND OF THE INVENTION
1. Technical Field
The various embodiments of the present disclosure relate generally to bacterial NADH oxidases and, more particularly, to NADH oxidases obtained from Lactobacillus plantarum, and derivatives thereof that demonstrate enzymatic activity for NADH, NADPH, or both NADH and NADPH.
2. Description of Related Art
Enantiomerically pure compounds (EPCs), especially amino and hydroxy acids as well as alcohols, amines, and lactones are increasingly useful in the pharmaceutical, food, and crop protection industries as building blocks for novel compounds not accessible through fermentation as well as for asymmetric synthesis templates. For example, interest in the production of L-nucleosides such as L-ribose, L-mannose and L-glucose has arisen for a number of L-nucleoside-based pharmaceutical compounds. Emtricitabine and Clevudine are some examples of pharmaceutical compounds that are based on L-nucleosides, and a number of these pharmaceuticals are currently approved or in clinical trials.
One advantageous route to a wide variety of EPCs is the use of dehydrogenases, to afford either reduction of keto compounds or oxidation of alcohol or amine groups. The repertoire of dehydrogenases useful for synthesis of EPCs encompasses alcohol dehydrogenases (ADHs), D- and L-lactate dehydrogenases (LDHs), D- or L-hydroxyisocaproate dehydrogenases (D- or L-HicDHs), or amino acid dehydrogenases such as leucine dehydrogenase (LeuDH), phenylalanine dehydrogenase (PheDH), or glutamate dehydrogenase (GluDH). Monooxygenases have been used to synthesize, regio- and enantioselectively, lactones from cyclic ketones useful in the flavor and fragrance industries.
Dehydrogenases and monooxygenases require nicotinamide-based cofactors, such as NAD+ and NADP+ or their reduced equivalents, NADH and NADPH, to function. Economic use of dehydrogenases and cofactor necessitates cofactor regeneration. Cofactor costs, for example, $31 per gram for NAD+ and $232 per gram of NADP+, have to be considered and having cofactors regenerated would cut costs by the turnover number for such cofactors, between 100 and up to 600,000.
Cofactor regeneration with alcohol dehydrogenases can be performed by using the same enzyme for in-situ substrate conversion and cofactor regeneration, usually employing isopropanol as co-substrate, as demonstrated with (S)-ADH from Thermoanaerobium brockii for both NADH and NADPH and with (R)-ADH from L. brevis for NADPH; this coupled-substrate approach, however, suffers from equilibrium limitations. The more common coupled-system approach, employing a separate second enzyme for regeneration, has been developed for reducing oxidized cofactors, NAD+ or NADP+, to NADH or NADPH. By far the most successful regeneration enzyme is formate dehydrogenase (FDH) for regeneration to either NADPH or NADH, the latter even up to industrial scale. Other options include the use of glucose 6-phosphate dehydrogenase (to NADPH only) or of glucose dehydrogenase, GluDH. For the opposite direction of regeneration, however, from NADPH to oxidized cofactors NAD+ or NADP+, no universally accepted system exists.
For reductive reactions with dehydrogenases or for monooxygenases, NADPH has to be regenerated from NADP+. For this problem, the system formate dehydrogenase (FDH)/formate is now used almost universally, which is shown below:

HCOOH+NAD+→NADH+H++CO2  (1)

FDH functions as a universal regeneration enzyme in tandem with dehydrogenases catalyzing extremely enantioselective reduction reactions.

There are some currently known NADH oxidases that are able to oxidize NADH to NAD+ with simultaneous reduction of O2 to either H2O2 or H2O. Four-electron reduction to benign H2O is preferred over two-electron reduction to H2O2, which, even in small amounts, can deactivate either enzyme of the production-regeneration cycle. Addition of catalase as a possible remedy, to degrade the H2O2, increases complexity of the system to the point where three enzymes have to be coupled and adjusted as to their activity over time.
For oxidative reactions requiring regeneration of NADP+ from NADPH, prior to the present invention, no universal cofactor regeneration system was known. Alcohol dehydrogenase (ADH) itself can be utilized to catalyze both the oxidative production reaction as well as the reductive regeneration reaction by adding isopropanol which is oxidized to acetone, but such a scheme tends to be equilibrium-limited and plagued by deactivation of ADH. Both the ADH and the lactate dehydrogenase (LDH) systems cannot take NADPH, in contrast to glutamate dehydrogenase (GluDH), which has been utilized to reduce α-ketoglutarate to L-glutamate. NADH oxidases from thermophiles have been employed which regenerate NAD+ from NADH by reducing O2 to H2O2.
What is needed are enzymes that regenerate NADH and NADPH to oxidized cofactors NAD+ and NADP+ and synthesis methods that employ such enzymes alone or in coupled reactions. What is also needed are enzymes that perform the oxidation of NADH to NAD+ with the concomitant reduction of molecular oxygen to water as a solution to the cofactor regeneration problem from NADH to NAD+. Further, what is needed are methods for efficiently isolating the enzymes.
BRIEF SUMMARY OF THE INVENTION
Various embodiments of the present invention are directed to bacterial NADH oxidases and, more particularly, to NADH oxidases obtained from Lactobacillus plantarum, and derivatives thereof that demonstrate enzymatic activity for NADH, NADPH, or both NADH and NADPH. A composition of the present invention comprises an isolated bacterial NADH oxidase, which is obtained from Lactobacillus plantarum. This isolated bacterial NADH oxidase can comprise the amino acid sequence of SEQ ID NO: 1, which is encoded by a nucleic acid sequence comprising SEQ ID NO: 2. Such a nucleic acid sequence can be incorporated into a vector, which may in turn be introduced into a host cell.
In one embodiment of the present invention, isolated bacterial NADH oxidases obtained from Lactobacillus plantarum can regenerate NAD+. In another embodiment of the present invention, isolated bacterial NADH oxidases derived from Lactobacillus plantarum can regenerate NADP+. In yet another embodiment of the present invention, isolated bacterial NADH oxidases derived from Lactobacillus plantarum can regenerate both NADP+ and NAD+.
For example, an isolated bacterial NADH oxidases derived from Lactobacillus plantarum, which regenerates NADP+ or both NADP+ and NAD+, comprises SEQ ID NO: 1, wherein SEQ ID NO: 1 comprises at least one amino acid mutation that facilitates enzymatic activity towards NADPH. A nucleic acid sequence that encodes a NADH oxidases derived from Lactobacillus plantarum, which regenerates NADP+ or both NADP+ and NAD+ can hybridize under stringent conditions to the nucleic acid comprising SEQ ID NO: 2.
An isolated bacterial NADH oxidases derived from Lactobacillus plantarum, which regenerates NADP+ or both NADP+ and NAD+, can comprise an amino acid sequence selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO: 17. In an exemplary embodiment, an isolated bacterial NADH oxidases derived from Lactobacillus plantarum, which regenerates NADP+ or both NADP+ and NAD+, can comprise an amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 16
Examples of nucleic acid sequences that encode a NADH oxidases derived from Lactobacillus plantarum, which regenerates NADP+ or both NADP+ and NAD+ that can hybridize under stringent conditions to the nucleic acid comprising SEQ ID NO: 2, include, but are not limited to nucleic acid sequences selected from the group consisting of SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 13, and SEQ ID NO: 18. In an exemplary embodiment, an isolated bacterial NADH oxidases derived from Lactobacillus plantarum, which regenerates NADP+ or both NADP+ and NAD+, can be encoded by a nucleic acid sequence comprising SEQ ID NO: 10 or SEQ ID NO: 18.
Another aspect of the present invention comprises a method of producing an enantiomer-enriched organic compound, comprising: reacting a substrate with a first enzyme selective for producing an enantiomer, wherein the first enzyme requires a oxidized nicotinamide-based cofactor for catalytic activity; producing the enantiomer, its oxidized counterpart, and a reduced nicotinamide-based cofactor; and oxidizing the reduced nicotinamide-based cofactor with a second enzyme selective for a nicotinamide-based cofactor. In one embodiment of the present invention, the enantiomer comprises an L-nucleoside, and the second enzyme selective for a nicotinamide-based cofactor comprises a NADH oxidase obtained from Lactobacillus plantarum. In another embodiment of the present invention, the second enzyme selective for a nicotinamide-based cofactor can catalyze more than 113,000 turnovers per active site. In yet another embodiment of the present invention, the second enzyme selective for a nicotinamide-based cofactor can catalyze more than 100,000 turnovers per active site in the absence of an externally added reducing agent.
In this method, the NADH oxidase obtained from Lactobacillus plantarum can comprise SEQ ID NO: 1. In one embodiment of the present invention, isolated bacterial NADH oxidases obtained from Lactobacillus plantarum can regenerate NAD+. In another embodiment of the present invention, isolated bacterial NADH oxidases derived from Lactobacillus plantarum can regenerate NADP+. In yet another embodiment of the present invention, isolated bacterial NADH oxidases derived from Lactobacillus plantarum can regenerate both NADP+ and NAD+. The isolated bacterial NADH oxidases derived from Lactobacillus plantarum, which regenerates NADP+ and NAD+, can comprise an amino acid sequence selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17. In an exemplary embodiment, the second enzyme selective for a nicotinamide-based cofactor comprises SEQ ID NO: 8 or SEQ ID NO: 18.
Other aspects and features of embodiments of the present invention will become apparent to those of ordinary skill in the art, upon reviewing the following description of specific, exemplary embodiments of the present invention in conjunction with the accompanying figures.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 is a schematic illustrating the conversion of ribitol to L-ribose through mannitol-1-dehydrogenase from Apium graveolens complemented with NADH cofactor regeneration using NADH oxidase.
FIG. 2 illustrates the activity profile of NADH oxidase from Lactobacillus plantarum V (NOX5) at different pHs.
FIG. 3 illustrates the activity profile of NOX5 at various temperatures.
FIG. 4 is a T5030 plot that demonstrates stability of NOX5 by incubating at different temperatures.
FIG. 5 is a plot of kinetics using different models: non-linear Michaelis-Menten, Lineweaver-Burk, Eadie-Hofstee, and Hanes-Woolf.
FIG. 6 graphically depicts a Hanes-Woolf plot of NAD+ inhibition pattern of NOX5.



DETAILED DESCRIPTION OF THE INVENTION
Throughout this description, various components can be identified as having specific values or parameters, however, these items are provided as exemplary embodiments. Indeed, the exemplary embodiments do not limit the various aspects and concepts of the present invention as many comparable parameters, sizes, ranges, and/or values can be implemented. The terms “first,” “second,” and the like, “primary,” “secondary,” and the like, do not denote any order, quantity, or importance, but rather are used to distinguish one element from another. Further, the terms “a,” “an,” and “the” do not denote a limitation of quantity, but rather denote the presence of “at least one” of the referenced item.
In general, NADH oxidases (E.C. 1.6.-.-) catalyze the oxidation of NADH by simultaneously reducing molecular O2 to either hydrogen peroxide, H2O2, in a two-electron reduction (reaction 2), or directly to water in a four-electron reduction (reaction 3).

NADH+O2+H+→NAD++H2O2  (2)

2NADH+O2+2H+→2NAD++2H2O  (3)

NADH oxidases contain a second cofactor, presumably covalently bound FAD, as evidenced by the consensus sequence GXT(H/S)AG near the N-terminus, and are widespread among different, evolutionary distinct organisms, such as humans, vertebrates, plants, Drosophila and different strains of bacteria. Bacteria harbor both H2O2-forming and H2O-forming NADH-oxidases. Owing to the deactivation of almost all proteins upon the exposure to H2O2, the H2O-forming enzymes are superior as biocatalysts. Addition of catalase could potentially destroy the H2O2 formed, however, catalase itself features a very high KM-value of 1.1 M, so that the enzyme is not particularly active at low H2O2 concentrations. Thermophilic bacteria usually only feature peroxide-producing NADH oxidases, which, despite their superior stability, render them unfavorable for catalytic purposes. Water-producing NADH-oxidases can be found in various organisms, such as Streptococcus, Enterococcus, Lactobacillus, Mycobacterium, Methanococcus, or Leuconostoc. These organisms can contain both water- as well as peroxide-producing enzymes.

The various embodiments of the present invention provide novel bacterial NADH oxidases. More specifically, the various embodiment of the present invention provide an NADH oxidase obtained from Lactobacillus plantarum, and derivatives thereof that demonstrate enzymatic activity for NADH, NADPH, or for both NADH and NADPH. The compositions comprising an NADH oxidase obtained from L. plantarum or derivatives thereof include: isolated enzymes; recombinantly produced enzymes and derivatives thereof, as well as catalytically active portions thereof; nucleic acids encoding an NADH oxidase obtained from L. plantarum, derivatives thereof, and portions thereof; vectors and plasmids comprising an NADH oxidase obtained from L. plantarum, derivatives thereof, and portions thereof; cells (i.e., prokaryotic or eukaryotic) comprising enzymes or nucleic acids encoding an NADH oxidase obtained from L. plantarum, derivatives thereof, and portions thereof. Compositions also include products made in enzymatic reactions in which an NADH oxidase obtained or derived from L. plantarum regenerates nicotinamide-based cofactors in the production of enantiomer-enriched organic compounds. The methods of the present invention include isolation of NADH oxidase obtained from L. plantarum, derivatives thereof, and portions thereof, and methods for enzymatic reactions comprising NADH oxidase obtained from L. plantarum. 
As used herein, the term “NADH oxidase, which is obtained from L. plantarum” is understood to include the NADH oxidases isolated from L. plantarum, which are capable of oxidizing (sometimes referred to as “regenerating”) NADH. An example of such an isolated NADH oxidase obtained from L. plantarum is illustrated by SEQ ID NO: 1. The term “NADH oxidase, which is obtained from L. plantarum” also encompasses an amino acid sequence that encodes an enzyme exhibiting oxidase activity for NADH that has substantial homology to SEQ ID NO 1. As used herein, the term “substantial homology” of an amino acid sequence means that an amino acid sequence includes a sequence that has at least 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, or 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, or 79%, preferably at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, more preferably at least 90%, 91%, 92%, 93%, or 94%, and most preferably at least 95%, 96%, 97%, 98%, or 99% sequence identity, as compared to a reference sequence (e.g., SEQ ID NO: 1), provided that the enzymatic activity is retained or the purpose of the sequence is retained, e.g. coding for a protein having a specific enzymatic activity or a protein fragment having a particular binding capability or immunogenic capability.
An NADH oxidase obtained from L. plantarum can be encoded by a nucleic acid sequence that encodes an enzyme with oxidase activity for NADH, such as that described in SEQ ID NO: 2. The purified nucleic acid sequence encoding an enzyme exhibiting oxidase activity has substantial homology to SEQ ID NO 2. As used herein, the term “substantial homology” of a nucleic acid sequence means that a nucleic acid sequence includes a sequence that has at least 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, or 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, or 79%, preferably at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, more preferably at least 90%, 91%, 92%, 93%, or 94%, and most preferably at least 95%, 96%, 97%, 98%, or 99% sequence identity, as compared to a reference sequence (e.g., SEQ ID NO: 2).
As used herein, the term “NADH oxidase, which is derived from L. plantarum” is understood to include derivatives of a NADH oxidase isolated from L. plantarum that are capable of oxidizing NADH, NADPH, or both NADH and NADPH. NADH oxidases derived from L. plantarum include recombinant nucleic acid sequences derived from the bacterial oxidases of L. plantarum, recombinant proteins and peptides expressed by those sequences in heterologous hosts, and any nucleic acid or amino acid variants, mutants, or portions thereof (e.g., catalytically active portions) of bacterial oxidases from L. plantarum that are capable of oxidizing NADH, NADPH, or both NADH and NADPH. Thus, NADH oxidases, which are derived from L. plantarum, can include proteins and recombinant constructs having altered sequences obtained by mutational methods. Embodiments of mutations of the sequences and resulting proteins disclosed herein also include, but are not limited to, substitutions, insertions, deletions, additions, reversions, changes due to recombination, and other mutations known to those skilled in the art.
In one embodiment of the present invention, an NADH oxidase that is derived from L. plantarum can comprise SEQ ID NO: 1, wherein SEQ ID NO: 1 comprises at least one amino acid mutation that facilitates enzymatic activity towards NADPH. In another embodiment, an NADH oxidase that is derived from L. plantarum can comprise SEQ ID NO: 1, wherein SEQ ID NO: 1 comprises more than one amino acid mutation that facilitates enzymatic activity towards NADPH. One or more mutations to the amino acid sequence for an NADH oxidase that is derived from L. plantarum can confer enzyme activity to only NADH, to only NADPH, or to both NADH and NADPH.
In one embodiment, an NADH oxidase that is derived from L. plantarum may include amino acid mutations to accommodate the negative charge associated with the phosphate moiety of NADPH so as to confer enzymatic activity for NADPH. Basic amino acids, such as arginine, lysine, and histidine, are preferred residues for substitution at amino acid residue 178, which is a glycine in the native enzyme, and amino acid residue 179, which is a leucine in the native enzyme. Consequently, amino acid residues 178 and 179 may be mutated to any one basic amino acid and various combinations therebetween. Examples of such NADH oxidase derivatives include G178K (SEQ ID NO: 3), G178R (SEQ ID NO: 4), L179K (SEQ ID NO: 6), L179R (SEQ ID NO: 8), L179H (SEQ ID NO: 9), G178K/L179K (SEQ ID NO: 11), G178R/L179K (SEQ ID NO: 12), G178K/L179R (SEQ ID NO: 14), G178K/L179H (SEQ ID NO: 15), G178R/L179R (SEQ ID NO: 16), and G178R/L179H (SEQ ID NO: 17). These NADH oxidase derivatives are encoded by nucleic acids including G178K/R (SEQ ID NO: 5), L179K (SEQ ID NO: 7), L179R/H (SEQ ID NO: 10), G178K/R/L179K (SEQ ID NO: 13), and G178K/R/L179R/H (SEQ ID NO: 18).
The present invention also comprises nucleic acids that hybridize under stringent conditions with the single-stranded nucleic acids or their complementary single stranded nucleic acids of the present invention. Stringent conditions are well known to those skilled in the art; see Sambrook et al., (Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press (1989), 1.101-1.104). Stringent conditions are established by conditions such as salt concentrations, temperature and amount of time for washing of the hybridized nucleic acids. For example, conditions include washing of hybridized nucleic acids in 0.1% S DS and 1.0× to 0.2×SSC, at temperatures from 50° C. to 68° C., for times of 0.5 to 1.0 hours.
The nucleic acids of the present invention can be incorporated into a vector. The term “vector” as used herein can refer to a cloning vector or an expression vector. A cloning vector refers to a plasmid, phage DNA, a cosmid, or other DNA molecule that is able to replicate autonomously in a host cell. A cloning vector is characterized by one or a number of restriction endonuclease recognition sites at which such DNA sequences may be cut in a determinable fashion without loss of an essential biological function of the vector, and into which a DNA fragment (e.g., SEQ ID NO: 2) may be spliced in order to bring about its replication and cloning. The cloning vector may further contain a marker suitable for use in the identification of cells transformed with the cloning vector (e.g., an antibiotic resistance marker).
An expression vector is similar to a cloning vector but is capable of expressing a gene which has been cloned into it, after transformation into a host. The cloned gene is usually placed under the control of (i.e., operably linked to) a variety of elements for controlling expression of the gene, including promoter sequences, transcription initiation sequences, enhancer sequences, selectable elements, and reporter genes. Examples of suitable expression vectors include, but are not limited to, plasmids, phagemids, cosmids, artificial chromosomes, such as a yeast artificial chromosome (YAC), a bacterial artificial chromosome (BAC), or a P1-derived artificial chromosome (PAC), and bacteriophages, such as lambda phage or M13 phage.
The present invention comprises compositions comprising NADH oxidases obtained or derived from derived from L. plantarum and methods of making and using such oxidases, wherein the oxidases regenerate NAD+, NADP+, or NAD+ and NADP+. The ability of an oxidase to oxidize one or both of these cofactors renders it an extremely useful catalyst for coupled enzymatically-catalyzed oxidations. Thus, the present invention comprises bacterial oxidases that regenerate both NADP+ and NAD+. The present invention also comprises novel NADH oxidases that reduce oxygen directly to water, which also makes such enzymes useful in coupled enzymatic reactions.
The NADH oxidases of the present invention participate in enzymatic reactions where there is a conversion of a substrate into a product. In a particularly preferred embodiment of the present invention, the product comprises an enantiomer-enriched organic compound. Consequently, the substrate can include a racemic mixture, such as an alcohol to a ketone, and upon enzymatic reaction will result in a highly enantiomer-enriched unreacted optical antipode of the original molecule, such as an alcohol. Dehydrogenases are capable of very specific enantiomeric selection and are used to prepare enantiomerically pure alcohols, hydroxy acids and amino acids as well as the corresponding ketones and keto acids. The dehydrogenase reaction requires the regeneration of the NADH or NADPH for cofactor activity, and thus, the NADH oxidases of the present invention have utility in coupled reactions with dehydrogenases including, but not limited to, alcohol dehydrogenase, lactate dehydrogenase and amino acid dehydrogenase. Products from such reactions include the resolution of racemic mixtures, such resolution dependent on the selectivity of the dehydrogenase used, and resulting in the unreacted racemate from the original racemic mixture, and the product of the enzyme reaction. For example, from a racemic mixture of an R/S-alcohol, in a reaction with an S-alcohol dehydrogenase, the resulting products are the unreacted enantiomer, the R-alcohol, and the resulting product, e.g., a ketone.
The NADH oxidases of the present invention are involved in synthesis methods comprising enzyme reactions where the substrates have one or more chiral centers. An embodiment of the present invention comprises a method of producing an enantiomer-enriched organic compound, comprising: reacting a substrate with a first enzyme selective for producing an enantiomer, wherein the first enzyme requires an oxidized nicotinamide-based cofactor for catalytic activity; producing the enantiomer and a reduced nicotinamide-based cofactor; and oxidizing the reduced nicotinamide-based cofactor with a second enzyme selective for a nicotinamide-based cofactor. In such methods, the second enzyme selective for a nicotinamide-based cofactor comprises a NADH oxidase obtained or derived from L. plantarum. The oxidized nicotinamide-based cofactors can include NAD+, NADP+, or both NAD+ and NADP+. Embodiments of the present invention comprise isolated bacterial oxidases derived from L. plantarum that use NADH and NADPH as a cofactor. In a preferred embodiment, isolated bacterial oxidases derived from L. plantarum that use NADH and NADPH as a cofactor include SEQ ID NO: 8 or SEQ ID NO: 16.
The compositions of the present invention also comprise combinations of all or a portion of one or more of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 13, and SEQ ID NO: 18 with other nucleic acid sequences to encode chimera proteins, or the nucleic acids of NADH oxidases combined with proteins or attached to solid supports such as beads. Such chimera proteins or other combinations may or may not retain the enzyme activity of NADH oxidases. For example, a nucleic acid construct that codes for a chimera protein is constructed from SEQ. ID NO: 2 and sequences for an antibody protein or binding fragment thereof. Such a chimera can be used in antibody labeling experiments.
The present invention also comprises compositions comprising the NADH oxidases disclosed herein that include immobilization of the enzymes on heterogeneous substrates. For example, the enzymes may be immobilized or attached to other proteins, through methods such as chemical linking of the proteins, attached to inert substrates such as microtiter plates, chromatography materials, balls, beads or other substances. The invention contemplates the use of such immobilized enzymes in methods of synthesis, measurement, analysis or other methods wherein enzymes are used. These methods for immobilizing and using such immobilized enzymes are known to those skilled in the art.
The compositions of the present invention also comprise antibodies and other specific binding partners, such as substrates, of NADH oxidases, and immunogenic epitopes thereof. Such antibodies may be polyclonal or monoclonal, and include fragments such as Fab, FC, heavy chains, light chains, constant, variable, or hypervariable fragments or regions, and any type of antibody include but are not limited to IgM, IgG, IgA, IgD, and IgE.
The compositions of the present invention also contemplate the inclusion of any cofactors, metals or other compounds or molecules necessary for activity or stability of the NADH oxidases of the present invention. However, it should be noted that the NADH oxidases of the present invention demonstrate stability in the absence of an exogenous reducing agent, such as dithiothreitol (DTT) or β-mercaptoethanol.
The present invention also comprises host cells comprising the nucleic acids disclosed herein, particularly SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 13, and SEQ ID NO: 18. Examples of such host cells include, but are not limited to, prokaryotes or eukaryotes, such as Pseudomonas, Streptomyces, Arthrobacter, Bacillus, Staphylococcus, Enterococcus, especially Escherichia coli, Candida, Hansenula, Pichia and various eukaryotic cells using for example viral-based expression systems. The host cells in which the nucleic acids are cloned are useful for propagation and production of a sufficient amount of the recombinant enzyme or enzymes. The methods for cloning, propagating and producing recombinant proteins in cellular systems are well known in the art.
The nucleic acids disclosed herein that code for the NADH oxidases as described herein, are preferably suitable for the production of whole-cell catalysts. The invention provides a whole-cell catalyst containing a cloned gene for a first enzyme selective for producing an enantiomer (e.g., a dehydrogenase) and a cloned gene for a NADH oxidase, as disclosed herein. The whole-cell catalyst according to one embodiment of the invention can comprise a NADH oxidase, preferably a bacterial oxidase obtained or derived from L. plantarum that can regenerate NAD+, NADP+, or both NAD+ and NADP+. More preferably, the NADH oxidase is one or more of the NADH oxidases disclosed herein and encoded for by SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 13, and SEQ ID NO: 18. The production of such an organism is known to the person skilled in the art as disclosed in PCT/EP00/08473 and PCT/US00/08159, which are hereby incorporated by reference.
The advantage of such an organism is the simultaneous expression of at least two different enzymes, and as a result the whole cell catalyst recombinant organism is only used for the enzymatic reaction. In order to match the expression of the enzymes with respect to their reaction rates, the coding nucleic acids may be cloned into various plasmids having different copy numbers and/or promoters of different strengths. In one embodiment, the enzymes are encoded on plasmids with similar copy numbers in a host cell and/or under the control of promoters of similar strength. With enzyme systems matched in this way there is advantageously no accumulation of a possible inhibiting intermediate compound(s), and the reaction under consideration may proceed at an optimal overall rate.
Methods of the present invention comprise methods for growing and isolating bacterial NADH oxidases, particularly bacterial oxidases obtained or derived from L. plantarum capable of regenerating NAD+, NADP+, or both NAD+ and NADP+. One embodiment comprises growing host organisms, such as Lactobacillus plantarum, and isolating the NADH oxidases by methods known to those skilled in the art, such as ammonium or acid precipitation, chromatography methods, and other protein purification techniques.
The nucleic acids according to the invention can be used for the production of recombinant NADH oxidases, which is include NADH oxidases obtained or derived from L. plantarum. Recombinant techniques known in the art can be used to produce the enzymes described herein in an amount sufficient for an industrial process from host cells carrying the nucleic acids encoding the enzyme of interest. The production of the recombinant enzymes according to the invention is carried out by genetic engineering processes as described in, for example, Sambrook supra, Balbas P & Bolivar F. 1990; Design and construction of expression plasmid vectors in E. coli, Methods Enzymology 185, 14-37; Vectors: A Survey of Molecular Cloning Vectors and Their Uses. R. L. Rodriguez & D. T. Denhardt, Eds: 205-225). With regard to the general procedure (PCR and fusion PCR, inverse PCR, cloning, expression etc.), reference may be made to the following literature and the references cited therein: Riley J, Butler R, Finniear R, Jenner D, Powell S, Anand R, Smith J C, Markham A F (1990). A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucl Acids Res. 18, 8186; Triglia T, Peterson M G, Kemp D J (1988). A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16, 8186; Sambrook J, Fritsch E F, Maniatis T (1989). Molecular Cloning. Cold Spring Harbour Laboratory Press; Vectors: A Survey of Molecular Cloning Vectors and Their Uses. R. L. Rodriguez & D. T. Denhardt, II.
The bacterial oxidase enzymes described herein may be used in the free form as homogeneously purified compounds, or as enzymes produced by recombinant technology. Furthermore the enzymes may also be employed as a constituent of an intact host organism or in conjunction with the macerated cell mass of the host organism purified to an arbitrarily high degree. It is also possible to use the enzymes in immobilized form (Bhavender P. Sharma, Lorraine F. Bailey and Ralph A. Messing, “Immobilisierte Biomaterialien—Techniken and Anwendungen”, Angew. Chem. 1982, 94, 836-852). The immobilization is preferably carried out by lyophilisation (Dordick et al. J. Am. Chem. Soc. 194, 116, 5009-5010; Okahata et al. Tetrahedron Lett. 1997, 38, 1971-1974; Adlercreutz et al. Biocatalysis 1992, 6, 291-305). It is most particularly preferred to carry out the lyophilisation in the presence of surfactants such as aerosol OT, polyvinylpyrrolidone, polyethylene glycol (PEG) or Brij 52 (diethyleneglycolmonocetyl ether) (Goto et al. Biotechnol. Techniques 1997, 11, 375-378). The use as CLECs is also possible (St Clair et al. Angew Chem Int Ed Engl 2000 January, 39(2), 380-383).
The present invention also comprises using NADH oxidases obtained or derived from L. plantarum having NAD+, NADP+, or both NAD+ and NADP+ regeneration activity (e.g., G178K (SEQ ID NO: 3), G178R (SEQ ID NO: 4), L179K (SEQ ID NO: 6), L179R (SEQ ID NO: 8), L179H (SEQ ID NO: 9), G178K/L179K (SEQ ID NO: 11), G178R/L179K (SEQ ID NO: 12), G178K/L179R (SEQ ID NO: 14), G178K/L179H (SEQ ID NO: 15), G178R/L179R (SEQ ID NO: 16), and G178R/L179H (SEQ ID NO: 17). These NADH oxidase derivatives are encoded by nucleic acids including G178K/R (SEQ ID NO: 5), L179K (SEQ ID NO: 7), L179R/H (SEQ ID NO: 10), G178K/R/L179K (SEQ ID NO: 13), and G178K/R/L179R/H (SEQ ID NO: 18)) and any mutations thereof, for the production of chiral enantiomer-enriched organic compounds such as, for example, alcohols, amino acids, or nucleosides, in coupled enzymatic reactions. Such compounds are useful in pharmaceutical preparations, in agricultural uses, for food, and crop protection industries as well as building blocks for novel compounds not accessible through fermentation and for asymmetric synthesis templates. For example, compounds are produced that are effective in treatment of humans and other animals for hypertension, diabetes, cardiovascular disease, cancer, infectious disease, and conditions involving the brain, eyes, heart, lungs, liver, immune system, urinary organs, reproductive organs, integumentary system, nervous system and other conditions where pharmaceutical agents are effective.
All patents, patent applications, and references included herein are specifically incorporated by reference in their entireties.
It should be understood, of course, that the foregoing relates only to exemplary embodiments of the present invention and that numerous modifications or alterations may be made therein without departing from the spirit and the scope of the invention as set forth in this disclosure. Therefore, while embodiments of this invention have been described in detail with particular reference to exemplary embodiments, those skilled in the art will understand that variations and modifications can be effected within the scope of the invention as defined in the appended claims. Accordingly, the scope of the various embodiments of the present invention should not be limited to the above discussed embodiments, and should only be defined by the following claims and all equivalents.
The present invention is further illustrated by way of the examples contained herein, which are provided for clarity of understanding. The exemplary embodiments should not to be construed in any way as imposing limitations upon the scope thereof. On the contrary, it is to be clearly understood that resort may be had to various other embodiments, modifications, and equivalents thereof which, after reading the description herein, may suggest themselves to those skilled in the art without departing from the spirit of the present invention or the scope of the appended claims.
EXAMPLES
Example 1
NADH Oxidase Isolated from Lactobacillus plantarum 
Among the different systems that can be chosen for cofactor regeneration, the use of NADPH oxidases standout with a number of advantages. NADPH oxidases utilize NADPH and oxygen as co-substrates, both which would not needed to be added externally for a regeneration system. (FIG. 1). This would prevent complication of the system by introducing additional substrates. The reaction would either produce water or hydrogen peroxide as final products, and the latter can be easily eliminated through the use of catalases.
Overoxidation of the catalytically active cysteine residue has been shown to be a limitation in production for previous NADPH oxidases. All of the previously discovered NADPH oxidases have shown to have a cysteine residue that is catalytically active. This thiol is oxidized to sulfenic acid and reduced back to the thiol as a part of the NADPH reduction mechanism. Studies have also shown that during this redox cycle the cysteine can also be overoxidized, producing a sulfinic or sulfonic acid, killing the enzymatic activity. This has been overcome to some extent by using reducing agents such as dithiothreitol (DTT) and β-mercaptoethanol. These reducing agents have shown to prevent overoxidation, thus elongating the catalytically active enzyme lifetime.
As demonstrated in this Example, NADH oxidase from Lactobacillus plantarum V is different in that it has a higher productivity indicated by its total turnover number (TTN) and is more stable against overoxidation as compared to its predecessors. While the native enzyme only showed activity on NADH, mutations in the substrate binding pocket were introduced to change its specificity and to accommodate NADPH.
Materials and Methods
Cloning and Site-Directed Mutagenesis.
The gene encoding NADH oxidase from Lactobacillus plantarum V was cloned out from the original plasmid through PCR using the following primers: forward primer (SEQ ID NO: 19) (5′-TGCATGCATGCCATGGTTATGAAAGTTATTGTAATTGGTTGTACCCA-3′) and reverse primer (SEQ ID NO: 20) (5′-CCGCCGCCGCCGCTCGAGTTATTCAGTGACAGCTTCGGCC-3′). The PCR product was then gel purified with a Qiagen gel extraction kit and cloned into a pET-28a vector (Novagen, Inc.) using restriction sites NcoI and XhoI. The plasmid was then transformed into BL21(DE3)pLysS for expression.
Single and double mutations were performed on residues G178 and L179 into K, R and K, R, H respectively, through overlap and quikchange PCR using the following forward primers and their complementary reverse primers; G178K/R (SEQ ID NO: 21) (5′-GCAAGGTAAGGAAGTCACACTAATTGATARRTTACCACGGATTTTAAATAAATACT TAGACAA-3′), L179H/R (SEQ ID NO: 22) (5′-AGGTAAGGAAGTCACACTAATTGATGGTCRYCCACGGATTTTAAATAAATACTTAG ACAAAG-3′), L179K (SEQ ID NO: 23) (5′-AGGTAAGGAAGTCACACTAATTGATGGTAAACCACGGATTTTAAATAAATACTTAG ACAAA-3′), G178K/R/L179R/H (SEQ ID NO: 24) (5′-GCAAGGTAAGGAAGTCACACTAATTGATARRCRYCCACGGATTTTAAATAAATACT TAGACAAAG-3′), G178K/R/L179K (SEQ ID NO: 25) (5′-GCAAGGTAAGGAAGTCACACTAATTGATARRAAACCACGGATTTTAAATAAATACT TAGACAAA-3′). Degenerate codons for K/R and H/R were used as ARR and CRY respectively.
Overexpression.
Growth and overexpression was carried out in MagicMediaTM E. coli Expression Medium (Invitrogen) with a final concentration of 30 μg. mL−1 of kanamycin and chloromphenicol. A dual temperature protocol was used for growth, starting out at 30° C. for 6 hours, and then continued at room temperature for an additional 22 hours. Cultures were harvested by centrifugation in a Beckman centrifuge with a JS-5.2 rotor at 4000 rpm for 20 minutes in 50 mL conical tubes. The resulting cell pellet was either frozen, and stored at −80° C. or purified directly.
Enzyme Assay and Protein Determination.
Standard assays were performed at 25° C. in 100 mM TEA buffer (pH 7.5) with 5 mM DTT in cuvettes with either a 1 cm or 1 mm path length, depending on the concentration of substrate. Initial activity was measured by following the absorbance change using a Beckman Coulter DU 800 UV/Vis spectrophotometer at 340 nm. Activity of the enzyme was calculated using an extinction coefficient of NAD(P)H, ε, as 6.22 mM−1 cm−1. Unless otherwise noted, a substrate concentration of 0.2 mM NADPH was used for assays. 1 unit (U) of activity is defined as 1 mol min−1.
The protein concentration was determined by a Bradford assay. BSA was used as standards, and the absorbance was measured on a biophotometer. SDS-page analysis was performed to determine to purity.
Purification.
Purification of NOX5 was carried out at 4° C. or on ice to prevent denaturation of the enzyme. Cell pellets were resuspended in 15 mL of 10 mM Tris-HCl buffer (pH 7.5) with 5 mM DTT (Buffer A) and sonicated at 14 watts for 30 seconds nine times in an ice water bath. Sonicated cells were centrifuged at 15000 rpm in a Beckman J2-21 with a JA-21 rotor for 30 minutes. The clarified cell lysate was transferred to a dialysis membrane and dialyzed against 250 mL of Buffer A with 50% ammonium sulfate for 2 hours. The dialysis membrane was then transferred to fresh buffer and further dialyzed for 2 hours. The solution was then centrifuged at 15000 rpm for 30 minutes. The resulting supernatant was filtered through a 0.8 μM filter and 0.2 μM filter in series. The filtrate was loaded onto a HIPREPTM 16/10 Butyl column on an AKTA. A reverse gradient separation was performed starting from Buffer A with 30% ammonium sulfate to 15%. The fractions with the highest activity were collected and dialyzed against a Buffer A for 2 hours. After exchanging the fresh buffer, the sample was dialyzed for an additional 2 hours. The sample was loaded on a HIPREPTM 16/10 DEAE anionic exchange column on the AKTA. Separation was achieved with Buffer A containing NaCl, a gradient of 150 mM to 250 mM. The resulting fractions were assayed, and the fractions with highest activity were collected as pure protein. The purified protein was either stored in 4° C. or in −20° C. with 25% glycerol.
pH Activity.
Enzyme pH activity profiles were obtained at 25° C. using 100 mM buffers with the following salts: sodium citrate from pH 4.0 to pH 6.5; sodium phosphate from pH 6.0 to pH 8.0; TEA from pH 7.0 to pH 8.0; Tris-HCl from pH 7.0 to pH 9.0; glycine from pH 9.0 to pH 10.0.
Temperature Activity.
Temperature dependent activity was studied by incubating the enzyme at different temperatures. After one minute of incubation, the standard assay was carried out. A temperature range of 10 to 55° C. was chosen for this study.
Temperature Stability.
Temperature stability was studied by incubating the enzyme at various temperatures for 30 minutes. The enzyme solution was then cooled down and assayed at 25° C. This study covered a temperature range of 15° C. to 55° C.
Kinetic Parameters.
Depending on the enzyme, a substrate concentration range from 1.5 μM up to 984 μM was investigated to determine the kcat and KM of NADPH. This was conducted with an excess of oxygen present in the system. The reaction was initiated by mixing two separate 2× solutions of each the substrate and enzyme. The specific activity was measured, and the kinetic parameters were calculated from that data.
Inhibition effects of NAD+ and H2O2 were measured by incubating the enzyme with possible inhibitors for 30 minutes before the assay. For NAD+, 0.2, 0.3, 0.4 and 0.6 mM were chosen and for H2O2, 25, 50, 100 and 200 μM were investigated.
Amplex Red Assay.
An Amplex Red Hydrogen Peroxide/Peroxidase Assay Kit (Invitrogen) was used to determine the amount of hydrogen peroxide (H2O2) produced during turnover. Various amounts of substrates were reacted and assayed to detect the presence of H2O2. The reactions were carried out in the provided 50 mM sodium phosphate buffer (pH 7.4). Standards for the calibration curve were made with the same reaction buffer.
Total Turnover Number (TTN).
Standard kinetic assays were performed with small amounts of enzyme. Assays were carried out for two to three hours until there was no more enzymatic conversion of the substrate.
Results and Discussion
NADH oxidase V from Lactobacillus plantarum (NOX5) consists of 1350 bp and has a predicted size of 49 kDa. Sequencing of the gene (SEQ ID NO. 1) showed a nucleotide mutation of C to T at position 45, but the resulting amino acid sequence (SEQ ID NO. 2) was the same as the predicted sequence.
Purification of NOX5 resulted in a yield of 14% of the total units and a 12.7 fold increase of specific activity. Purified NOX 5 shows a strong band at 49 kDa in SDS-page analysis. Table 1 is a table of purification. “Lysate” refers to clarified lysate; “AS50 dia.” refers to the supernatant from centrifuged sample dialyzed against 50% ammonium sulfate; “Butyl dia.” refers to the fractions collected from HIPREPTM 16/10 Butyl column dialyzed against 100 mM TEA pH 7.5 and 5 mM DTT; and “DEAE” refers to fractions collected from HIPREPTM 16/10 DEAE column.














TABLE 1







Volume
Units
Protein
Sp. ac.
Purification
Yield



(ml)
(U)
(mg)
(U mg−1)
Fold
(%)






















Lysate
20
1843.5
139.3
13.24
1.0
100


AS50
7
930.0
88.5
10.51
0.8
50


dia.


Butyl
37.5
379.3
4.7
80.72
6.1
21


dia.


DEAE
20
261.9
1.6
167.5
12.7
14









Enzyme Activity and Stability.
NADPH oxidases will mostly be used in cofactor regeneration, as water and hydrogen peroxide are not of great interest for final products. As the true value of these enzymes are shown when they are coupled with other enzymes, the study of reaction conditions, especially in terms of pH and temperature, were necessary to maximize activity and stability.
NOX5 showed a rather broad pH activity range. Maximum activity was found at pH 7.5, but the enzyme was fairly active from pH 5.5 to 8.0. (FIG. 2). This is a range that is common for many NADPH oxidases. The upper limit is also compatible with dehydrogenases that are active in alkaline conditions. Although it would be difficult to have a single corresponding maximum for both enzymes, a person of ordinary skill in the art could identify optimal conditions for a dehydrogenase and NOX5.
The temperature activity profile showed that maximum instantaneous activity was found at 40° C., and the activity quickly reached zero beyond that. (FIGS. 3 and 4). Using an Arrhenius model, the activation energy, Ea, was calculated as 32.7 kJ mol−1, and the deactivation energy, Ed, was calculated as −93.6 kJ mol−1. The temperature that exhibited half of the original activity, T5030, was estimated to be 45° C. At 55° C., the enzyme was inactive. Enthalpy of deactivation, ΔH, was calculated to be 4.98 kJ·mol−1.
Kinetic Parameters.
The data was fitted with four different models: non-linear Michaelis-Menten, Lineweaver-Burk, Eadie-Hofstee and Hanes. Through non-linear fitting, kcat and KM of the wild type were measured to be 211.6 s−1 and 50.2 μM, respectively with an R2 of 0.998. (FIG. 5).
Possible product inhibitory effects were investigated by incubating the enzyme with different concentrations of NAD+. NAD+ exhibited a non-competitive inhibition pattern where the Umax mg−1 decreased as the inhibitor concentration increased while KM,app was consistent. Analysis of the different concentrations showed that the KI of NAD+ was 289 μM. (FIG. 6).
To determine whether NOX5 is a water or hydrogen peroxide producing enzyme, an amplex red assay was performed. The presence of H2O2 can be confirmed by incubating the standard assay mixture with amplex red and peroxidase. Produced resorufin can be detected using a fluorescence spectroscopy analysis. NOX5 produced H2O2 at a 2.63% ratio of NADH strongly suggesting that it is a water forming NADPH oxidase.
Total Turnover Number (TTN).
Total turnover number (TTN) is a measurement of catalyst productivity. For biocatalysts, TTN is defined as the total amount of product produced over the lifetime of an enzyme. Calculations of TTN were performed by dividing the change of NADPH concentration by the amount of enzyme that was used for each assay. In the standard assay conditions with the presence of DTT the TTN was found to be about 168,000, consistently, at 25° C. (data not shown).
This experiment was repeated to see if the presence of reducing agents had any effect on the total turnover number. The stock solution of enzyme was dialyzed against 250 mL of 10 mM Tris-HCl (pH 7.5) for two hours. The solution was then exchanged and dialyzed for an additional 2 hours. The TTN was then measured with the dialyzed enzyme with and without reducing agents. DTT and β-mercaptoethanol (β-ME) were used at a concentration of 5 mM. The TTN for the sample with no reducing agents, DTT and β-ME were 128,000, 168,000 and 107,000, respectively. The presence of DTT had a positive effect, but it was not as dramatic compared to the NADH oxidase from Lactobacillus sanfranciscensis. β-ME did not have a positive effect at all and actually decreased the TTN.
To examine TTN limitation possibilities, three properties were investigated: i) thermal stability of enzyme at 25° C.; ii) presence of hydrogen peroxide (H2O2) and stability of enzyme against it; and iii) product (NAD+) inhibition in the system.
Thermal stability at 25° C. was measured by incubating the enzyme for extended periods of time. The enzyme was then assayed to check the remaining activity (data not shown). The thermal stability at 25° C. was investigated in order to show the relevance of thermal degradation during turnover. Through this study, it can be concluded that the enzyme shows to be inactive before it is thermally deactivated.
The effect of H2O2 was studied with a concentration range up to 200 μM, which would be the total amount produced from a standard assay if the enzyme was a hydrogen peroxide producing NADPH oxidase. Even at high concentrations, there was no change found in the initial specific activity (data not shown), thus showing that the enzyme is indeed quite stable against H2O2.
The presence of NAD+ inhibition, and its pattern was known. However, even at high concentrations of NAD+, there was a reasonable amount of activity. So, it would be difficult to conclude that NAD+ had inhibited the reaction completely.
Example 2
Mutation of NADH Oxidase from Lactobacillus plantarum for NADPH Activity
Since the wild type NOX5 had activity exclusively towards NADH, and had little to no activity towards NADPH, mutational options were investigated to introduce NADPH activity. Crystal structure comparisons of NADPH oxidase from Lactobacillus sanfranciscensis and a homology model of NOX5 from Lactobacillus plantarum showed differences in where the 2′-phosphate would be located. The one from L. sanfranciscensis had a histidine, which would be able to accommodate the negative charge but NOX5 only had hydrophobic residues in that area. Based on this knowledge, different basic residues were chosen for mutation in that region.
Single mutations were done on residues G178 and L179 into K, R and K, R, H respectively, and double mutations were also investigated with different combinations of the single mutations. The mutation of G178H was excluded due to the fact that the enzyme would then have two histidines next to each other, creating steric hindrance in the binding pocket. The resulting mutants were expressed on small scale and assayed at the cell lysate level. Table 2 provides the NOX5 mutants and the activity of the mutants at the cell lysate level.
Among the mutants, L179R retained the highest amount of NADH activity, and G178R/L179R had the highest activity for NADPH. Although not wishing to be bound by any particular theory, it is believed that a positive charge is introduced through the mutation at L179R, and the additional mutation at G178R stabilizes the positioning, effectively decreasing the amount of free rotation of L179R through hydrogen bonding. It seems reasonable for arginine to have the largest effect, as it has the most options for hydrogen bonding. The low activity of L179H can be explained by the presence of an adjacent proline causing steric hindrance.











TABLE 2








NADH activity
NADPH activity



Mutant
(U/mg)
(U/mg)




















Wild Type
10.0
0.00



G178K
3.92
0.46



G178R
1.51
0.23



L179K
5.14
1.03



L179R
7.32
1.76



L179H
1.37
0.64



G178K/L179K
0.84
3.11



G178K/L179R
2.00
5.68



G178K/L179H
1.24
3.85



G178R/L179K
0.94
3.56



G178R/L179R
2.64
6.00



G178R/L179H
0.64
0.52










Study of mutants L179R and G178R/L179R. L179R and G178R/L179R were selected for further purification. Table 3 provides kinetic parameters of wild-type (WT) and mutant NADPH oxidases. L179R was not as active as the wild-type having a kcat, NADH of 122.0 s−1. However, the KM, NADH was much lower at 6.56 μM, improving the kcat/KM by more than 4-fold. The mutant also showed NADPH activity but had a very high KM of 489.6 μM. The double mutant G178R/L179R also had the same trend for NADH as L179R but to a larger extent. The kcat, NADH was 34.0 s−1 and the KM, NADH was 34.0 μM, resulting in a kcat/KM of 13.2 μM−1s−1. It also showed a kcat/KM for NADPH at 11.7 μM−1 s−1, where at, NADPH was 114.1 s−1 and the KM, NADPH was 9.76 μM. Overall, both enzymes were improvements over the wild-type, in terms of kcat/KM.










TABLE 3









NADH
NADPH














kcat
KM
kcat/KM
kcat
KM
kcat/KM


enzyme
(s−1)
(μM)
(μM−1 · s−1)
(s−1)
(μM)
(μM−1 · s−1)
















WT
211.6
50.2
4.22
—
—
—


L179R
122.0
6.56
18.6
146.4
489.6
0.30


G178R/
34.0
2.57
13.2
114.1
9.76
11.7


L179R









The TTN of the mutants were measured and the same trend, where the presence of reducing agents did not affect the enzyme to a great extent, was found. The double mutant successfully exhibited NADPH activity, expanding the range of applications where this enzyme could be used.
Example 3
Higher Operational Stability of Lactobacillus plantarum NAD(P)H Oxidase (Higher Total Turnover Number)
Comparison of NADPH oxidases. Table 4 provides a comparison of TTN with and without DTT, for NADH oxidases from L. plantarum, Lactobacillus sanfranciscensis, Lactococcus lactis.










TABLE 4









NADH
NADPH















TTN

TTN





with

with


organism
enzyme
TTN
DTT
TTN
DTT















L. plantarum
NOX5
128,000
168,000
—
—



WT



L179R
181,000
149,000



G178R/
108,000
128,000
105,000
118,000



L179R


L. sanfranciscensis
NOX2
5,000
112,500


L. lactis
NOX2
38,740
78,480
—
—









NOX5 has shown a higher total turnover number with and even without any reducing agents. This is an indication of improved stability against overoxidation at the catalytically active cysteine residue. Since there are known effects of inhibition of DTT on certain rare sugar producing dehydrogenases, such as mannitol dehydrogenase from Apium graveolens, it is preferable for an NADPH oxidase to be is stable without DTT. Also, improved stability without reducing agents would be a advantage in the pharmaceutical industry (or any other area that is related for the matter) where the presence of these reducing agents lack acceptability.

A broad study of NOX5 from Lactobacillus plantarum was conducted to study the possibility of an NADPH oxidase stable against overoxidation. In this study, pH and temperature characteristics were investigated to identify a common ground for enzyme coupled systems. Kinetic parameters were defined and the TTN was studied to discover the advantages compared to previous NADPH oxidases. Through this study, the high stability of this enzyme was proven with and without the presence of reducing agents.
As the wild-type enzyme demonstrates specificity for a NADH substrate, in order to be able to utilize NADPH, mutations were made to change the specificity of the enzyme. By positioning different positively charged residues to interact and accommodate the 2′-phosphate of NADPH, it was possible to find a mutation that would be of this effect. This will broaden the range and usage of this NADPH oxidase, that has higher stability against over oxidation than its predecessors.










SEQUENCE LISTING















SEQ ID NO: 1-NADH Oxidase Obtained from


Lactobacillus plantarum


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDGLPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGPRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 2-NADH Oxidase Obtained from


Lactobacillus plantarum


ATGAAAGTTATTGTAATTGGTTGTACCCATGCCGGCACTGCTGCTGT


TAATCAGATTTTAGCATCAAATCCAGATACTGAAGTGACGATTTATG


AAAGAAATGACAATGTCTCGTTCCTATCCTGTGGGATCGCACTTTAC


CTTGGCGGCCAAGTTGCTGATCCTCAAGGCCTATTTTATTCCAGTCC


TGAACAGTTAGCTAAGTTAGGCGCAACTGTTCATATGCAACATGATG


TGACGGATGTGAATACTGACAAACATGAAATTACGGTTACTGACTTA


AAGACTGGTGAATCTAAGACTGATCACTATGACAAGTTAGTTGTCAC


TACTGGTTCATGGCCTGTTATTCCACCAATTGACGGCATCGATAGTC


CCAATGTCTACTTATGCAAGAACTGGACGCACGCTCAGAATTTATGG


GAAGCAGCCAAACCAGCTAAGCGGGTCATTGTGATCGGTGGCGGTTA


TATCGGTACTGAATTAGTTGAAGCTTACCAGAAGCAAGGTAAGGAAG


TCACACTAATTGATGGTTTACCACGGATTTTAAATAAATACTTAGAC


AAAGAATTCACTGACCGGGTTGAACAAGACTTTGTTGATCACGGTAT


CAAGATGGCTTTGAATCAAATGGTGCAAGGCTTCAGTGATGATGGTA


AAGAAGTTACGGTCAAGACTGACAAGGGCAGCTACACAGCCGACATG


GCGATTCTTTGTGTTGGCTTCCGGCCAAATACCGGCTTACTCAAGGG


CAAGGTCGATATGAACGCTAATGGCTCGATCAAGACCAATGACTACA


TGCAAACTTCTGATCCAGACATTTACGGGGCTGGTGACTCGGTTGCT


GTTCACTATAACCCAACTAAGAAAGATGCTTATATCCCATTAGCAAC


GAATGCGGTTCGCCAAGGAACCTTAGTTGGTTTGAACATCTTCAAGC


CAACGCGGAAGTACATGGGGACACAATCAACTTCTGGGTTAATGTTG


TTCGGCCAAACCATCGTTTCATCTGGGATGACCCTAGAACATGCACA


GGCCGAAAATGTTCCGGCAGCCGCTGTCACTTTTGAAGACAACTACC


GGCCAGAATTTATGCCAACCACTAAGCCTGTTTTAATGCAATTGGTT


TACAATCCTGAAACTCGCGAAATCCTAGGTGCACAATTCATGAGTGA


ACATGATGTTTCGCAATCAGCCAATGTGATTTCAGTGATGATTCAAA


ATCACAATACCATTGACGACTTAGGGTTCGTAGATATGTTCTTCCAA


CCAATTTACGACCGGCCATTTAACTATTTGAACTTACTTGGTCAAGC


AGCGATTGCCCATGCGGCCGAAGCTGTCACTGAATAA


 


SEQ ID NO: 3-NADH Oxidase Derived from


Lactobacillus plantarum, G178K mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDKLPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 4-NADH Oxidase Derived from


Lactobacillus plantarum, G178R mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDRLPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 5-NADH Oxidase Derived from


Lactobacillus plantarum, G178K/R mutants


ATGAAAGTTATTGTAATTGGTTGTACCCATGCCGGCACTGCTGCTGT


TAATCAGATTTTAGCATCAAATCCAGATACTGAAGTGACGATTTATG


AAAGAAATGACAATGTCTCGTTCCTATCCTGTGGGATCGCACTTTAC


CTTGGCGGCCAAGTTGCTGATCCTCAAGGCCTATTTTATTCCAGTCC


TGAACAGTTAGCTAAGTTAGGCGCAACTGTTCATATGCAACATGATG


TGACGGATGTGAATACTGACAAACATGAAATTACGGTTACTGACTTA


AAGACTGGTGAATCTAAGACTGATCACTATGACAAGTTAGTTGTCAC


TACTGGTTCATGGCCTGTTATTCCACCAATTGACGGCATCGATAGTC


CCAATGTCTACTTATGCAAGAACTGGACGCACGCTCAGAATTTATGG


GAAGCAGCCAAACCAGCTAAGCGGGTCATTGTGATCGGTGGCGGTTA


TATCGGTACTGAATTAGTTGAAGCTTACCAGAAGCAAGGTAAGGAAG


TCACACTAATTGATARRTTACCACGGATTTTAAATAAATACTTAGAC


AAAGAATTCACTGACCGGGTTGAACAAGACTTTGTTGATCACGGTAT


CAAGATGGCTTTGAATCAAATGGTGCAAGGCTTCAGTGATGATGGTA


AAGAAGTTACGGTCAAGACTGACAAGGGCAGCTACACAGCCGACATG


GCGATTCTTTGTGTTGGCTTCCGGCCAAATACCGGCTTACTCAAGGG


CAAGGTCGATATGAACGCTAATGGCTCGATCAAGACCAATGACTACA


TGCAAACTTCTGATCCAGACATTTACGGGGCTGGTGACTCGGTTGCT


GTTCACTATAACCCAACTAAGAAAGATGCTTATATCCCATTAGCAAC


GAATGCGGTTCGCCAAGGAACCTTAGTTGGTTTGAACATCTTCAAGC


CAACGCGGAAGTACATGGGGACACAATCAACTTCTGGGTTAATGTTG


TTCGGCCAAACCATCGTTTCATCTGGGATGACCCTAGAACATGCACA


GGCCGAAAATGTTCCGGCAGCCGCTGTCACTTTTGAAGACAACTACC


GGCCAGAATTTATGCCAACCACTAAGCCTGTTTTAATGCAATTGGTT


TACAATCCTGAAACTCGCGAAATCCTAGGTGCACAATTCATGAGTGA


ACATGATGTTTCGCAATCAGCCAATGTGATTTCAGTGATGATTCAAA


ATCACAATACCATTGACGACTTAGGGTTCGTAGATATGTTCTTCCAA


CCAATTTACGACCGGCCATTTAACTATTTGAACTTACTTGGTCAAGC


AGCGATTGCCCATGCGGCCGAAGCTGTCACTGAATAA


 


SEQ ID NO: 6-NADH Oxidase Derived from


Lactobacillus plantarum, L179K mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDGKPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 7-NADH Oxidase Derived from


Lactobacillus plantarum, L179K mutant


ATGAAAGTTATTGTAATTGGTTGTACCCATGCCGGCACTGCTGCTGT


TAATCAGATTTTAGCATCAAATCCAGATACTGAAGTGACGATTTATG


AAAGAAATGACAATGTCTCGTTCCTATCCTGTGGGATCGCACTTTAC


CTTGGCGGCCAAGTTGCTGATCCTCAAGGCCTATTTTATTCCAGTCC


TGAACAGTTAGCTAAGTTAGGCGCAACTGTTCATATGCAACATGATG


TGACGGATGTGAATACTGACAAACATGAAATTACGGTTACTGACTTA


AAGACTGGTGAATCTAAGACTGATCACTATGACAAGTTAGTTGTCAC


TACTGGTTCATGGCCTGTTATTCCACCAATTGACGGCATCGATAGTC


CCAATGTCTACTTATGCAAGAACTGGACGCACGCTCAGAATTTATGG


GAAGCAGCCAAACCAGCTAAGCGGGTCATTGTGATCGGTGGCGGTTA


TATCGGTACTGAATTAGTTGAAGCTTACCAGAAGCAAGGTAAGGAAG


TCACACTAATTGATGGTAAACCACGGATTTTAAATAAATACTTAGAC


AAAGAATTCACTGACCGGGTTGAACAAGACTTTGTTGATCACGGTAT


CAAGATGGCTTTGAATCAAATGGTGCAAGGCTTCAGTGATGATGGTA


AAGAAGTTACGGTCAAGACTGACAAGGGCAGCTACACAGCCGACATG


GCGATTCTTTGTGTTGGCTTCCGGCCAAATACCGGCTTACTCAAGGG


CAAGGTCGATATGAACGCTAATGGCTCGATCAAGACCAATGACTACA


TGCAAACTTCTGATCCAGACATTTACGGGGCTGGTGACTCGGTTGCT


GTTCACTATAACCCAACTAAGAAAGATGCTTATATCCCATTAGCAAC


GAATGCGGTTCGCCAAGGAACCTTAGTTGGTTTGAACATCTTCAAGC


CAACGCGGAAGTACATGGGGACACAATCAACTTCTGGGTTAATGTTG


TTCGGCCAAACCATCGTTTCATCTGGGATGACCCTAGAACATGCACA


GGCCGAAAATGTTCCGGCAGCCGCTGTCACTTTTGAAGACAACTACC


GGCCAGAATTTATGCCAACCACTAAGCCTGTTTTAATGCAATTGGTT


TACAATCCTGAAACTCGCGAAATCCTAGGTGCACAATTCATGAGTGA


ACATGATGTTTCGCAATCAGCCAATGTGATTTCAGTGATGATTCAAA


ATCACAATACCATTGACGACTTAGGGTTCGTAGATATGTTCTTCCAA


CCAATTTACGACCGGCCATTTAACTATTTGAACTTACTTGGTCAAGC


AGCGATTGCCCATGCGGCCGAAGCTGTCACTGAATAA


 


SEQ ID NO: 8-NADH Oxidase Derived from


Lactobacillus plantarum, L179R mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDGRPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 9-NADH Oxidase Derived from


Lactobacillus plantarum, L179H mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDGHPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 10-NADH Oxidase Derived from


Lactobacillus plantarum, L179H/R mutants


ATGAAAGTTATTGTAATTGGTTGTACCCATGCCGGCACTGCTGCTGT


TAATCAGATTTTAGCATCAAATCCAGATACTGAAGTGACGATTTATG


AAAGAAATGACAATGTCTCGTTCCTATCCTGTGGGATCGCACTTTAC


CTTGGCGGCCAAGTTGCTGATCCTCAAGGCCTATTTTATTCCAGTCC


TGAACAGTTAGCTAAGTTAGGCGCAACTGTTCATATGCAACATGATG


TGACGGATGTGAATACTGACAAACATGAAATTACGGTTACTGACTTA


AAGACTGGTGAATCTAAGACTGATCACTATGACAAGTTAGTTGTCAC


TACTGGTTCATGGCCTGTTATTCCACCAATTGACGGCATCGATAGTC


CCAATGTCTACTTATGCAAGAACTGGACGCACGCTCAGAATTTATGG


GAAGCAGCCAAACCAGCTAAGCGGGTCATTGTGATCGGTGGCGGTTA


TATCGGTACTGAATTAGTTGAAGCTTACCAGAAGCAAGGTAAGGAAG


TCACACTAATTGATGGTCRYCCACGGATTTTAAATAAATACTTAGAC


AAAGAATTCACTGACCGGGTTGAACAAGACTTTGTTGATCACGGTAT


CAAGATGGCTTTGAATCAAATGGTGCAAGGCTTCAGTGATGATGGTA


AAGAAGTTACGGTCAAGACTGACAAGGGCAGCTACACAGCCGACATG


GCGATTCTTTGTGTTGGCTTCCGGCCAAATACCGGCTTACTCAAGGG


CAAGGTCGATATGAACGCTAATGGCTCGATCAAGACCAATGACTACA


TGCAAACTTCTGATCCAGACATTTACGGGGCTGGTGACTCGGTTGCT


GTTCACTATAACCCAACTAAGAAAGATGCTTATATCCCATTAGCAAC


GAATGCGGTTCGCCAAGGAACCTTAGTTGGTTTGAACATCTTCAAGC


CAACGCGGAAGTACATGGGGACACAATCAACTTCTGGGTTAATGTTG


TTCGGCCAAACCATCGTTTCATCTGGGATGACCCTAGAACATGCACA


GGCCGAAAATGTTCCGGCAGCCGCTGTCACTTTTGAAGACAACTACC


GGCCAGAATTTATGCCAACCACTAAGCCTGTTTTAATGCAATTGGTT


TACAATCCTGAAACTCGCGAAATCCTAGGTGCACAATTCATGAGTGA


ACATGATGTTTCGCAATCAGCCAATGTGATTTCAGTGATGATTCAAA


ATCACAATACCATTGACGACTTAGGGTTCGTAGATATGTTCTTCCAA


CCAATTTACGACCGGCCATTTAACTATTTGAACTTACTTGGTCAAGC


AGCGATTGCCCATGCGGCCGAAGCTGTCACTGAATAA


 


SEQ ID NO: 11-NADH Oxidase Derived from


Lactobacillus plantarum, G178K/L179K mutants


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDKKPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 12-NADH Oxidase Derived from


Lactobacillus plantarum, G178R/L179K mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDRKPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 13-NADH Oxidase Derived from


Lactobacillus plantarum G178R/K/L179K mutants


ATGAAAGTTATTGTAATTGGTTGTACCCATGCCGGCACTGCTGCTGT


TAATCAGATTTTAGCATCAAATCCAGATACTGAAGTGACGATTTATG


AAAGAAATGACAATGTCTCGTTCCTATCCTGTGGGATCGCACTTTAC


CTTGGCGGCCAAGTTGCTGATCCTCAAGGCCTATTTTATTCCAGTCC


TGAACAGTTAGCTAAGTTAGGCGCAACTGTTCATATGCAACATGATG


TGACGGATGTGAATACTGACAAACATGAAATTACGGTTACTGACTTA


AAGACTGGTGAATCTAAGACTGATCACTATGACAAGTTAGTTGTCAC


TACTGGTTCATGGCCTGTTATTCCACCAATTGACGGCATCGATAGTC


CCAATGTCTACTTATGCAAGAACTGGACGCACGCTCAGAATTTATGG


GAAGCAGCCAAACCAGCTAAGCGGGTCATTGTGATCGGTGGCGGTTA


TATCGGTACTGAATTAGTTGAAGCTTACCAGAAGCAAGGTAAGGAAG


TCACACTAATTGATARRAAACCACGGATTTTAAATAAATACTTAGAC


AAAGAATTCACTGACCGGGTTGAACAAGACTTTGTTGATCACGGTAT


CAAGATGGCTTTGAATCAAATGGTGCAAGGCTTCAGTGATGATGGTA


AAGAAGTTACGGTCAAGACTGACAAGGGCAGCTACACAGCCGACATG


GCGATTCTTTGTGTTGGCTTCCGGCCAAATACCGGCTTACTCAAGGG


CAAGGTCGATATGAACGCTAATGGCTCGATCAAGACCAATGACTACA


TGCAAACTTCTGATCCAGACATTTACGGGGCTGGTGACTCGGTTGCT


GTTCACTATAACCCAACTAAGAAAGATGCTTATATCCCATTAGCAAC


GAATGCGGTTCGCCAAGGAACCTTAGTTGGTTTGAACATCTTCAAGC


CAACGCGGAAGTACATGGGGACACAATCAACTTCTGGGTTAATGTTG


TTCGGCCAAACCATCGTTTCATCTGGGATGACCCTAGAACATGCACA


GGCCGAAAATGTTCCGGCAGCCGCTGTCACTTTTGAAGACAACTACC


GGCCAGAATTTATGCCAACCACTAAGCCTGTTTTAATGCAATTGGTT


TACAATCCTGAAACTCGCGAAATCCTAGGTGCACAATTCATGAGTGA


ACATGATGTTTCGCAATCAGCCAATGTGATTTCAGTGATGATTCAAA


ATCACAATACCATTGACGACTTAGGGTTCGTAGATATGTTCTTCCAA


CCAATTTACGACCGGCCATTTAACTATTTGAACTTACTTGGTCAAGC


AGCGATTGCCCATGCGGCCGAAGCTGTCACTGAATAA


 


SEQ ID NO: 14-NADH Oxidase Derived from


Lactobacillus plantarum, G178K/L179R mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDKRPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 15-NADH Oxidase Derived from


Lactobacillus plantarum, G178K/L179H mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDKHPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEFMPTTKPVLMQLV


YNPETREILGAQFMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 16-NADH Oxidase Derived from


Lactobacillus plantarum, G178R/L179R mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDRRPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEEMPTTKPVLMQLV


YNPETREILGAQEMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 17-NADH Oxidase Derived from


Lactobacillus plantarum, G178R/L179H mutant


MKVIVIGCTHAGTAAVNQILASNPDTEVTIYERNDNVSFLSCGIALY


LGGQVADPQGLFYSSPEQLAKLGATVHMQHDVTDVNTDKHEITVTDL


KTGESKTDHYDKLVVTTGSWPVIPPIDGIDSPNVYLCKNWTHAQNLW


EAAKPAKRVIVIGGGYIGTELVEAYQKQGKEVTLIDRHPRILNKYLD


KEFTDRVEQDFVDHGIKMALNQMVQGFSDDGKEVTVKTDKGSYTADM


AILCVGFRPNTGLLKGKVDMNANGSIKTNDYMQTSDPDIYGAGDSVA


VHYNPTKKDAYIPLATNAVRQGTLVGLNIFKPTRKYMGTQSTSGLML


FGQTIVSSGMTLEHAQAENVPAAAVTFEDNYRPEEMPTTKPVLMQLV


YNPETREILGAQEMSEHDVSQSANVISVMIQNHNTIDDLGFVDMFFQ


PIYDRPFNYLNLLGQAAIAHAAEAVTE


 


SEQ ID NO: 18-NADH Oxidase Derived from


Lactobacillus plantarum, G178K/R /L179R/H


mutants


ATGAAAGTTATTGTAATTGGTTGTACCCATGCCGGCACTGCTGCTGT


TAATCAGATTTTAGCATCAAATCCAGATACTGAAGTGACGATTTATG


AAAGAAATGACAATGTCTCGTTCCTATCCTGTGGGATCGCACTTTAC


CTTGGCGGCCAAGTTGCTGATCCTCAAGGCCTATTTTATTCCAGTCC


TGAACAGTTAGCTAAGTTAGGCGCAACTGTTCATATGCAACATGATG


TGACGGATGTGAATACTGACAAACATGAAATTACGGTTACTGACTTA


AAGACTGGTGAATCTAAGACTGATCACTATGACAAGTTAGTTGTCAC


TACTGGTTCATGGCCTGTTATTCCACCAATTGACGGCATCGATAGTC


CCAATGTCTACTTATGCAAGAACTGGACGCACGCTCAGAATTTATGG


GAAGCAGCCAAACCAGCTAAGCGGGTCATTGTGATCGGTGGCGGTTA


TATCGGTACTGAATTAGTTGAAGCTTACCAGAAGCAAGGTAAGGAAG


TCACACTAATTGATARRCRYCCACGGATTTTAAATAAATACTTAGAC


AAAGAATTCACTGACCGGGTTGAACAAGACTTTGTTGATCACGGTAT


CAAGATGGCTTTGAATCAAATGGTGCAAGGCTTCAGTGATGATGGTA


AAGAAGTTACGGTCAAGACTGACAAGGGCAGCTACACAGCCGACATG


GCGATTCTTTGTGTTGGCTTCCGGCCAAATACCGGCTTACTCAAGGG


CAAGGTCGATATGAACGCTAATGGCTCGATCAAGACCAATGACTACA


TGCAAACTTCTGATCCAGACATTTACGGGGCTGGTGACTCGGTTGCT


GTTCACTATAACCCAACTAAGAAAGATGCTTATATCCCATTAGCAAC


GAATGCGGTTCGCCAAGGAACCTTAGTTGGTTTGAACATCTTCAAGC


CAACGCGGAAGTACATGGGGACACAATCAACTTCTGGGTTAATGTTG


TTCGGCCAAACCATCGTTTCATCTGGGATGACCCTAGAACATGCACA


GGCCGAAAATGTTCCGGCAGCCGCTGTCACTTTTGAAGACAACTACC


GGCCAGAATTTATGCCAACCACTAAGCCTGTTTTAATGCAATTGGTT


TACAATCCTGAAACTCGCGAAATCCTAGGTGCACAATTCATGAGTGA


ACATGATGTTTCGCAATCAGCCAATGTGATTTCAGTGATGATTCAAA


ATCACAATACCATTGACGACTTAGGGTTCGTAGATATGTTCTTCCAA


CCAATTTACGACCGGCCATTTAACTATTTGAACTTACTTGGTCAAGC


AGCGATTGCCCATGCGGCCGAAGCTGTCACTGAATAA


 


SEQ ID NO: 19-Forward Cloning Primer for NADH


Oxidase from Lactobacillus plantarum


TGCATGCATGCCATGGTTATGAAAGTTATTGTAATTGGTTGTACCCA


 


SEQ ID NO: 20-Reverse Cloning Primer for NADH


Oxidase from Lactobacillus plantarum


CCGCCGCCGCCGCTCGAGTTATTCAGTGACAGCTTCGGCC


 


SEQ ID NO: 21-Forward Primer for NADH Oxidase


for Lactobacillus plantarum G178K/R mutants


GCAAGGTAAGGAAGTCACACTAATTGATARRTTACCACGGATTTTAA


ATAAATACTTAGACAA


 


SEQ ID NO: 22-Forward Primer for NADH Oxidase


for Lactobacillus plantarum L179H/R mutants


AGGTAAGGAAGTCACACTAATTGATGGTCRYCCACGGATTTTAAATA


AATACTTAGACAAAG


 


SEQ ID NO: 23-Forward Primer for NADH Oxidase


for Lactobacillus plantarum L179K mutant


AGGTAAGGAAGTCACACTAATTGATGGTAAACCACGGATTTTAAATA


AATACTTAGACAAA


 


SEQ ID NO: 24-Forward Primer for NADH Oxidase


for Lactobacillus plantarum G178K/R/L179R/H


mutants


GCAAGGTAAGGAAGTCACACTAATTGATARRCRYCCACGGATTTTAA


ATAAATACTTAGACAAAG


 


SEQ ID NO: 25-Forward Primer for NADH Oxidase


for Lactobacillus plantarum G178K/R/L179K


mutants


GCAAGGTAAGGAAGTCACACTAATTGATARRAAACCACGGATTTTAA


ATAAATACTTAGACAAA









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## Claims

1. An isolated bacterial NADH oxidase, which is obtained from Lactobacillus plantarum, and regenerates NADP+ and NAD+, comprising
at least one amino acid mutation that facilitates enzymatic activity towards NADPH and comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO: 17.

2. The isolated bacterial NADH oxidase of claim 1, encoded by a nucleic acid sequence, which hybridizes under stringent conditions to the nucleic acid selected from the group consisting of SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 13, and SEQ ID NO: 18.

3. The isolated bacterial NADH oxidase of claim 1, which comprises SEQ ID NO: 8.

4. The isolated bacterial NADH oxidase of claim 3, encoded by a nucleic acid sequence comprising SEQ ID NO: 10.

5. The isolated bacterial NADH oxidase of claim 1, which comprises SEQ ID NO: 16.

6. The isolated bacterial NADH oxidase of claim 5, encoded by a nucleic acid sequence comprising SEQ ID NO: 18.

7. A method of producing an enantiomer-enriched organic compound, comprising:
reacting a substrate with a first enzyme selective for producing an enantiomer, wherein the first enzyme requires a oxidized nicotinamide-based cofactor for catalytic activity;
producing the enantiomer, its oxidized counterpart, and a reduced nicotinamide-based cofactor; and
oxidizing the reduced nicotinamide-based cofactor with a second enzyme selective for a nicotinamide-based cofactor,
wherein the second enzyme selective for a nicotinamide-based cofactor comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17.

8. The method of producing an enantiomer-enriched organic compound of claim 7, wherein the enantiomer comprises an L-nucleoside, and wherein the second enzyme selective for a nicotinamide-based cofactor comprises a NADH oxidase obtained from Lactobacillus plantarum.

9. The method of producing an enantiomer-enriched organic compound of claim 7, wherein the second enzyme selective for a nicotinamide-based cofactor can oxidize NADPH and NADH.

10. The method of producing an enantiomer-enriched organic compound of claim 9, wherein the second enzyme selective for a nicotinamide-based cofactor comprises SEQ ID NO: 8.

11. The method of producing an enantiomer-enriched organic compound of claim 9, wherein the second enzyme selective for a nicotinamide-based cofactor comprises SEQ ID NO: 18.

12. The method of producing an enantiomer-enriched organic compound of claim 7, wherein the second enzyme selective for a nicotinamide-based cofactor can catalyze more than 113,000 turnovers per active site.

13. The method of producing an enantiomer-enriched organic compound of claim 7, wherein the second enzyme selective for a nicotinamide-based cofactor can catalyze more than 100,000 turnovers per active site in the absence of an externally added reducing agent.