Engineered Alcohol Dehydrogenase Methanol Conversion

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Solution Overview

Problem

Current alcohol dehydrogenases, such as methanol dehydrogenases, have limited efficiency in converting methanol to formaldehyde or acetaldehyde, which hinders the utilization of methanol as a sole carbon source and increases production costs, reducing product yields and requiring additional carbon sources like glucose.

Innovation Solution

Engineered non-natural NAD+-dependent alcohol dehydrogenases with specific amino acid substitutions, particularly in the MDH 2315A template, exhibit at least two-fold greater conversion rates of methanol or ethanol to formaldehyde or acetaldehyde, enhancing substrate conversion efficiency and enabling improved methanol utilization.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If wild-type alcohol dehydrogenase is used, then the enzyme structure is simple and easy to manufacture, but the conversion rate of methanol to formaldehyde is low

Engineering Contradiction:
Improveconversion rate of methanol to formaldehydeVSAvoidenzyme structure complexity
Core Design Contradiction:
ProductivityVSDevice complexity

Solution Approach 1:

The patent applies parameter changes by modifying specific amino acid residues in the alcohol dehydrogenase sequence. Mutations at positions corresponding to 145, 146, 147, 148, 149, 150, 161, 162, and 163 in the MDH 2315A sequence are designed to improve catalytic activity. These parameter changes at the molecular level result in at least 2-fold increase in conversion rate while maintaining the overall enzyme structure.

Inventive Principle:
Principle #35Parameter changes

Solution Approach 2:

The patent implements local quality by making targeted mutations at specific positions within the enzyme sequence rather than changing the entire structure. The mutations are localized to regions that interact with substrate or cofactor, such as positions affecting NAD+ binding or catalytic activity. This allows improvement in conversion rate while keeping the rest of the enzyme structure simple and unchanged.

Inventive Principle:
Principle #3Local quality

2Ease of manufacture

If wild-type alcohol dehydrogenase is used, then production costs are higher due to need for additional carbon sources, but enzyme engineering is more complex

Engineering Contradiction:
Improveproduction costVSAvoidenzyme engineering complexity
Core Design Contradiction:
Ease of manufactureVSDevice complexity

Solution Approach 1:

The patent uses parameter changes to improve methanol utilization efficiency, enabling the engineered enzymes to function effectively with methanol as a sole or primary carbon source. This eliminates or reduces the need for expensive additional carbon sources like glucose, thereby lowering production costs. The mutations are designed to optimize substrate binding and catalytic efficiency for cost-effective manufacturing.

Inventive Principle:
Principle #35Parameter changes

Solution Approach 2:

The engineered alcohol dehydrogenases enable the production system to be self-sufficient by using methanol as the primary or sole carbon source. The enzyme mutations improve methanol conversion efficiency to the point where additional expensive carbon sources are no longer needed, making the system self-service and reducing dependency on external supplements.

Inventive Principle:
Principle #25Self-service

3Productivity

If wild-type alcohol dehydrogenase is used, then product yields are reduced, but enzyme modification increases complexity

Engineering Contradiction:
Improveproduct yieldVSAvoidenzyme sequence modification
Core Design Contradiction:
ProductivityVSDevice complexity

Solution Approach 1:

The patent applies parameter changes by mutating specific amino acid positions to enhance catalytic efficiency and product yield. The mutations at defined positions in the enzyme sequence result in at least 2-fold increase in conversion rate and product yield. The changes are limited to specific residues that directly affect catalytic function, maintaining overall structural simplicity.

Inventive Principle:
Principle #35Parameter changes

Solution Approach 2:

The patent implements local quality by making targeted mutations at specific positions that directly influence product yield, such as residues involved in substrate binding, catalysis, or product release. This localized modification approach improves product yield without requiring complex global restructuring of the enzyme, thereby limiting the increase in overall complexity.

Inventive Principle:
Principle #3Local quality

4Productivity

If methanol dehydrogenase activity is increased, then methanol utilization improves, but enzyme engineering complexity increases

Engineering Contradiction:
Improvemethanol utilization rateVSAvoidenzyme engineering complexity
Core Design Contradiction:
ProductivityVSDevice complexity

Solution Approach 1:

The patent applies parameter changes by systematically mutating amino acid residues at positions known to affect methanol dehydrogenase activity. The mutations are designed to enhance substrate binding affinity, catalytic turnover, or cofactor interaction. These parameter changes result in at least 2-fold increase in methanol conversion rate while maintaining reasonable engineering complexity through focused modifications.

Inventive Principle:
Principle #35Parameter changes

Solution Approach 2:

The patent implements local quality by targeting specific residues that directly influence methanol utilization, such as those in the active site or substrate binding pocket. By making localized mutations rather than global changes, the patent achieves improved methanol utilization with minimal increase in overall enzyme engineering complexity.

Inventive Principle:
Principle #3Local quality

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

The engineered enzymes increase methanol conversion rates, reducing the need for additional carbon sources, decreasing production costs, and enhancing product yields by promoting the production of valuable compounds like 1,4-butanediol and other intermediates.

Implementation Method 1

Alcohol dehydrogenases (ADHs; EC 1.1.1.1) promote the conversion of alcohols to and aldehydes or ketones

Methodology Applied
Scientific EffectEnzyme catalysis: Enzyme

Implementation Method 2

MDHs, converts methanol (MeOH) to formaldehyde (Fald)

Methodology Applied
Scientific EffectOxidation: Oxidation

Implementation Method 3

typically along with the reduction of nicotinamide adenine dinucleotide (NAD+ to NADH)

Methodology Applied
Scientific EffectRedox reactions: Redox Reactions

Data Source

PatentUS11384340B2Alcohol dehydrogenase variants
Publication Date: 2022.07.12 GENOMATICA INC
  • US11384340B2 patent drawing
  • US11384340B2 patent drawing
  • US11384340B2 patent drawing

AI summary

Described herein are non-natural NAD+-dependent alcohol dehydrogenases (ADHs) capable of at least two fold greater conversion of methanol or ethanol to formaldehyde or acetaldehyde, respectively, as compared to its unmodified counterpart. Nucleic acids encoding the non-natural alcohol dehydrogenases, as well as expression constructs including the nucleic acids, and engineered cells comprising the nucleic acids or expression constructs are described. Also described are engineered cells expressing a non-natural NAD+-dependent alcohol dehydrogenase, optionally include one or more additional metabolic pathway transgene(s), methanol metabolic pathway genes, target product pathway genes, cell culture compositions including the cells, methods for promoting production of the target product or intermediate thereof from the cells, compositions including the target product or intermediate, and products made from the target product or intermediate.