# Patent

## Title
Methods for the production of methacrylates

## Abstract

The invention relates to methods for the production of methacrylates using methacrylate tolerant microorganisms.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a § 371 national phase application of PCT Application No. PCT/GB2019/051427, filed on May 23, 2019, which claims priority to British Application No. 1808424.4 filed on May 23, 2018, the entire contents of each of which is incorporated by reference herein.
STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING
A Sequence Listing in ASCII text format, submitted under 37 C.F.R. § 1.821, entitled 1553.8 Sequence_ST25.txt, 97,895 bytes in size, generated on Nov. 2, 2020 and filed via EFS-Web, is provided in lieu of a paper copy. This Sequence Listing is hereby incorporated herein by reference into the specification for its disclosure.
INTRODUCTION
Methyl methacrylate (MMA) is an important monomer in the chemical industry. The principal use of MMA is in the production of plastics for various applications; however, MMA can also be used in bone cements for use in orthopaedic surgery. The most significant polymerisation application is the casting, moulding or extrusion of polymethyl methacrylate (PMMA) to produce high optical clarity plastics. The global consumption of PMMA is estimated at approximately 2.1 million tonnes per annum.
Although the most widely used methacrylate ester is MMA, methacrylic acid or MMA can also be used to produce other methacrylate esters either by direct esterification or by transesterification, respectively. Examples are butyl 2-methylprop-2-enoate (BMA, a methacrylate ester with the chemical formula C8H14O2), isobutyl methacrylate (iBMA), ethyl methacrylate (EMA) and 2-ethylhexyl methacrylate (2EHMA). BMA is produced from the transesterification of MMA with butanol. All of these esters and PMMA have a wide variety of applications, namely in manufacturing textiles, coatings and adhesives, packaging, lubricants, automotive equipment, LCD screens, medical equipment and household goods.
MMA is currently produced solely by chemical means and current methods for the production of MMA include the acetone cyanohydrin (ACH) route and other routes starting from various C2-C4 precursors. One of the most successful methods for producing MMA is the ‘Alpha process’ whereby MMA is obtained from the ester, methyl propionate, by anhydrous reaction with formaldehyde. In the Alpha process, the methyl propionate is produced by the carbonylation of ethylene. This ethylene feedstock is derived from fossil fuels. The Alpha process offers many advantages compared to other processes commonly used in the production of MMA. These advantages include a reduction in the use of hazardous chemicals, much higher product selectivity, and a reduced reliance on crude oil derived feedstocks. However, the pricing of the feedstock is linked to the cost of gasoline. It would therefore be desirable to develop an alternative process for the production of MMA which overcomes these deficiencies.
Microorganisms can be used to produce high value chemicals via fermentation, rather than by chemical synthesis. Recombinant DNA technology and synthetic metabolic engineering of such microorganisms has allowed for the reconstruction of metabolic pathways towards the production of specific chemicals. Several sustainable routes towards the bioproduction of acrylates have recently been undergoing development. These methods have generally focused on the production of acrylates from renewable feedstocks via microbial fermentation. For example, WO2016/185211 describes a process for producing methacrylic acid and/or derivatives thereof using recombinant microorganisms.
However, at certain concentrations, accumulation of acrylates such as MMA and BMA during fermentation is generally toxic to the biocatalysts, inhibiting cell growth and/or resulting in cell death. In particular, higher alkyl methacrylates (such as butyl methacrylate (BMA)) are more toxic than lower alkyl methacrylates such as MMA. This can therefore be a limiting factor for the biological production of alkyl methacrylates using microorganisms, in particular at large industrial scale.
It is known that bacteria are able to adapt to environmental stimuli, in particular by adapting regulatory networks that control gene expression. Several such networks exist, including the oxidative stress response and the multidrug resistance system.
In view of the toxic effect of alkyl methacrylates on microorganisms, and the given disadvantages associated with current chemical processes for producing MMA, it would be advantageous to provide microorganisms with improved tolerance to methacrylates for use in methods for the production of alkyl methacrylates.
It is therefore an object of the present invention to obviate or mitigate one or more of these problems, to provide an improved process for the production of methacrylates, in particular BMA and/or MMA and to provide microorganisms with improved tolerance to methacrylates.
SUMMARY
As further described in the examples, the inventors have employed various strategies to select for microorganisms that have acquired resistance to methacrylates upon exposure to methacrylate in culture. Surprisingly, the inventors were able to isolate bacterial strains that survived in the presence of phase separated methacrylates, at a concentration that is usually toxic to wild type bacteria. The resistant strains were isolated and sequenced to identify genetic mutations compared to the wild type that confer resistance. The resistant strains were also further characterised. Knock in and knock out strains were also developed to further assess the mutations responsible for the observed resistance. The inventors found that the mutations which imparted tolerance resided in certain genes encoding components and regulators of the oxidative stress response and the bacterial multidrug resistance system, amongst others. The inventors also found that a combination of certain mutations could enhance the tolerance effect. Thus, the mutations identified can be used to confer tolerance to bacteria by genetically manipulating wild type bacteria to introduce said mutations.
The inventors have thus surprisingly identified, isolated and characterised bacterial strains that are more resistant to methacrylates than wild type bacteria and which can therefore be used in methods for the production of such compounds. Thus, the inventors have demonstrated that mutations in the oxidative stress response and the bacterial multidrug resistance system and its regulators play a crucial role in mediating resistance to methacrylates. In particular, the inventors have shown that mutants of the Acriflavine resistance regulator (acrR) confer tolerance to methacrylates, in particular when combined with one of the global regulators selected from marR, soxR or rob. The inventors have also identified the components and regulators of the oxidative stress response and the bacterial multidrug resistance system which contribute to the observed resistance thus enabling ways to genetically modify microorganisms to confer increased tolerance to methacrylates. Genetically modified microorganisms with increased tolerance to methacrylates are therefore within the scope of the invention. The inventors have also developed a process for the production of methacrylates using a genetically modified microorganism with increased tolerance to methacrylates.



FIGURES
The invention is further described in the following non-limiting figures.
FIG. 1. Effect of the absence [▪] or presence [●] of 20% (v/v) BMA on the growth of E. coli. E. coli MG1655 (A), E. coli MG1655 soxR(R20H) (B), E. coli MG1655 soxR(R20H)acrR(V29G) (C), E. coli MG1655 soxR(R20H)acrR(T32fs) (D) were grown in MSX medium, in 250 mL shake flasks at 37° C. and 250 rpm shaking. Means of two replicates are shown and error bars are standard deviations.
FIG. 2. Effect of the addition of 20% (v/v) BMA during mid exponential phase on the growth of E. coli strains. Shown growth of (A) E. coli MG1655, (B) E. coli MG1655 soxR(R20H), (C) E. coli MG1655 soxR(R20H)acrR(V29G) and (D) E. coli MG1655 soxR(R20H)acrR(T32fs). All strains were grown in 250 mL shake flasks in MSX medium at 37° C. and 250 rpm. BMA or H2O were added after reaching an OD600 nm of approximately 0.3. Samples were taken at different time intervals to determine the OD600 nm. Means of three replicates are shown and error bars are standard deviations.
FIG. 3. Effect of the absence [●] or presence [▴] of 20% (v/v) BMA added immediately after inoculation on the growth of single deletants. E. coli BW25115 ΔsoxR (A) and E. coli BW25115 ΔacrR (B) were grown in MSX medium in 30 mL vials at 37° C. and 250 rpm shaking. Samples were taken at 0, 8 and 24 h to determine the OD600 nm. Means of two replicates are shown and error bars are standard deviations.
FIG. 4. Effect of the absence [●] or presence [▴] of 20% (v/v) BMA added immediately after inoculation on the growth of single mutation strains. E. coli MG1655 acrR(V29G) (A) and E. coli MG1655 acrR(T32fs) (B) were grown in MSX medium in 30 mL vials at 37° C. and 250 rpm shaking. Samples were taken at 0, 8 and 24 h to determine the OD600 nm. Means of two replicates are shown and error bars are standard deviations.
FIGS. 5a-5k, a) Effect of BMA at low concentrations. Growth of E. coli BW 25113 with BMA at 0% (□), 0.01% (⋄), 0.05% (Δ), and 0.1% (x) v/v in M9 minimal medium at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media. b) Effect of BMA at high concentrations. Growth of E. coli BW 25113 with BMA at 0% (□), 0.5% (⋄), 1.0% (Δ), 5.0% (∘), 10.0% (x), and 20.0% (+) v/v in M9 minimal medium at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media. c) Test for inherent tolerance of E. coli towards BMA. Growth of E. coli BW 25113 with BMA at 0% (□), 0.1% (x), 0.5% (*), 0.1% after subculture (⋄), 0.5% after subculture (Δ) v/v in M9 minimal medium at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media (in triplicates). d) ADE-1. Adaptive evolution in serial batch cultures with sequential increases in BMA concentration. E. coli was grown in M9 minimal medium with 10 g L-1 glucose and BMA at 37° C. and 200 RPM in 50 mL FALCON® tubes with 10 mL media in 3 parallel tubes tube 1 (Solid Line), tube 2 (dotted line), and tube 3 (dashed line). BMA concentration was increased in each sequential transfer at 0.1% BMA (x), 0.5% BMA (□), 1% BMA (⋄), 5% (Δ), 10% (∘), and 20% (+) using the best growing culture as starting culture for each of the 3 tubes. e) ADE-3. Adaptive evolution in serial batch cultures, with 5 serial cultures in each BMA concentration. E. coli was grown in M9 minimal medium with 10 g L-1 glucose and BMA at 37° C. and 200 RPM in 50 mL FALCON® tubes with 10 mL media in 3 parallel tubes tube 1 (Solid Line), tube 2 (dotted line), and tube 3 (dashed line). BMA concentration was increased from 0.1% v/v (x) to 0.5% v/v(□), 1% v/v (⋄), 5% v/v(Δ), 10% v/v (*), and 20% v/v(∘) using each separate tube as starting culture for subsequent transfer. f) ADE-3. Adaptive evolution in serial batch cultures, with 1 serial cultures at 0.1% v/v BMA, 2 serial transfers at 10% v/v BMA, and 45 serial transfer at 20% v/v BMA. E. coli was grown in M9 minimal medium with 10 g L-1 glucose and BMA at 37° C. and 200 RPM in 50 mL FALCON® tubes with 10 mL media in 3 parallel tubes tube 1 (Solid Line), tube 2 (dotted line), and tube 3 (dashed line). BMA concentration was increased from 0.1% v/v (x) to 10% v/v(□) and 20% v/v (⋄) using the best growing culture as starting culture for each of the 3 tubes. g) ADE-4 Adaptive evolution and selection of BMA tolerant E. coli in a chemostat. A Chemostat culture of E. coli in a mini-bioreactor (55 mL working volume) was grown in M9 minimal medium with 1 g L-1 glucose at 37° C. and aeration rate of  ̃0.3 L h-1 with BMA concentration (♦) gradually increased from 0-20% v/v and dilution rate (□) varied from 0 to 0.55 h-1. Cell concentration (●) was reported in cell dry weight g L-1. h) Growth of isolates from ADE-1 and ADE-2 in M9 minimal medium with 20% v/v BMA at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media (triplicates). Isolate 2 (Δ), 3 (⋄), 5 (*), 6 (−), 7 (∘), and Wild type with no BMA (- with dotted line). i) Growth of isolates from ADE-3 in M9 minimal medium with 20% v/v BMA at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media (triplicates). Isolate 14 (□), 15 (⋄), 16 (Δ), 17 (x), 18 (∘), and Wild type with no BMA (- with dotted line). j) Growth of isolates from ADE-4 at dilution rate of 0.33 h-1 in M9 minimal medium with 20% v/v BMA at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media (triplicates). Isolate 8 (□), 9 (⋄), 10 (Δ), and Wild type with no BMA (- with dotted line). k) Growth of isolates from ADE-4 at dilution rate of 0.46 h-1 in M9 minimal medium with 20% v/v BMA at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media (triplicates). Isolate 19 (□), 20 (⋄), 21(Δ), and Wild type with no BMA (- with dotted line).
FIG. 6. Growth of isolates from adaptive evolution study at dilution rate of 0.55 h−1 in M9 minimal medium with 20% v/v BMA at 37° C. and 200 RPM using 250 mL conical flasks with 50 mL media (triplicates). Isolate 22 (⋄), 23 (◯) and Wild type with no BMA (- with dotted line).



DETAILED DESCRIPTION
The present invention will now be further described. In the following passages, different aspects of the invention are defined in more detail. Each aspect so defined may be combined with any other aspect or aspects unless clearly indicated to the contrary. In particular, any feature indicated as being preferred or advantageous may be combined with any other feature or features indicated as being preferred or advantageous.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of microbiology, tissue culture, molecular biology, chemistry, biochemistry and recombinant DNA technology, which are within the skill of the art. Such techniques are explained fully in the literature, for example Green and Sambrook: Molecular Cloning: A Laboratory Manual, 4th edition, 2014.
Methods for Producing a Methacrylate, Conferring Tolerance to a Methacrylate to a Microorganism and Growing Methacrylate Tolerant Microorganisms
In a first aspect, the invention relates to a method for the production of a methacrylate comprising
a) providing a genetically modified microorganism with increased tolerance to a C3-C12 methacrylate ester compared to the wild type microorganism in a fermentation medium and
b) growing the microorganism under conditions whereby a C3-C12 methacrylate ester is produced.
In a second aspect, the invention relates to a method for growing or maintaining a microorganism in the presence of a methacrylate comprising providing a genetically modified microorganism with increased tolerance to a C3-C12 methacrylate ester compared to a wild type microorganism in a fermentation medium under conditions whereby a C3-C12 methacrylate ester is produced.
The invention also relates to a method for conferring or increasing the tolerance of a microorganism to a methacrylate comprising introducing a mutation into a nucleic acid encoding a protein component and/or regulator of the oxidative stress response and the bacterial multidrug resistance systems.
As used herein the terms “tolerance” or “resistance” refer to a microorganism's ability to survive in the presence of a methacrylate, in particular in the presence of a C3-C12 methacrylate ester. In one embodiment, the tolerant microorganism can therefore be maintained at a concentration of a methacrylate which is toxic to a wild type microorganism. For example, the microorganism may survive and grow for at least about 2.5 hours longer, preferably, for at least about 5 hours longer, more preferably, for at least about 10 hours longer, most preferably, for at least about 20 hours longer in the presence of butyl methacrylate compared to the wild type microorganism. The survival and growth of the microorganism may be determined by any suitable method known in the art. Preferably, the survival and growth of the microorganism may be determined by measuring the optical density of the microorganism, more preferably the optical density of the microorganism measured at a wavelength of about 600 nm (OD600). For example, the microorganism of the present invention may have an OD600 of at least 0.5 for 2.5 hours longer, preferably, for at least about 5 hours longer, more preferably, for at least about 10 hours longer, most preferably, for at least about 20 hours longer in the presence of butyl methacrylate compared to the wild type microorganism. In another example, an increase in the OD from 0.01-0.1 to 0.15 to 3.0 indicates that the organism is growing. Suitably, the OD600 is measured in a suitable fermentation medium. It will be appreciated by a person skilled in the art that the optical density of the microorganism may be measured at a different wavelength depending upon the fermentation medium used.
In another embodiment, the tolerant microorganism is able to grow at a concentration of a methacrylate which causes death or growth arrest of a wild type microorganism.
The terms “tolerance” or “resistance” and “tolerant” or “resistant” are used interchangeably herein. A genetically modified organism as described herein is characterised by increased “tolerance” or “resistance” to a methacrylate, in particular a C3-C12 methacrylate ester, compared to the wild type microorganism which does not comprise the genetic modification(s).
In one embodiment of the aspects of the invention, the microorganism is tolerant to at least 10% to 30% v/v, for example 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20% v/v C3-C12 methacrylate ester when grown in a liquid medium at about 37° C. Thus, according to various embodiments, the microorganism can be maintained in the presence of a methacrylate at a concentration of at least 10% to 30% v/v, for example 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20% v/v C3-C12 methacrylate ester.
The terms “increase”, “improve” or “enhance” or “increased”, “improved”, “enhanced” or “increased” are used interchangeably herein.
The term microorganism as used herein refers to a prokaryotic or eukaryotic cell or cells. In one embodiment, the microorganism is a prokaryotic cell. In one embodiment, the microorganism is a bacterium.
In one embodiment, the modified microorganism has a mutation in one or more proteins that regulate or form part of the oxidative stress response and the bacterial multidrug resistance systems, including for example members or regulators of efflux pumps, for example the AcrAB TolC efflux pump complex, and AraC family members identified in E. coli (and nucleic acids encoding such proteins). Components and regulators of the oxidative stress response and the bacterial multidrug resistance systems have been characterised in Escherichia coli and homologous complexes are found in other organisms, including in many Gram-negative species.
In one embodiment, the microorganism is a Gram negative bacterium. In one embodiment the Gram negative bacterium is of the Enterobacteriaceae family.
In one embodiment, examples of suitable bacteria within the scope of the invention includes enterobacteria belonging to proteobacteria of the genus Escherichia, Enterobacter, Pantoea, Klebsiella, Serratia, Erwinia, Salmonella, Morganella, or the like, so-called coryneform bacteria belonging to the genus Brevibacterium, Corynebacterium or Microbacterium and bacteria belonging to the genus Alicyclobacillus, Bacillus, Hydrogenobacter, Methanococcus, Acetobacter, Acinetobacter, Agrobacterium, Axorhizobium, Azotobacter, Anaplasma, Bacteroides, Bartonella, Bordetella, Borrelia, Brucella, Burkholderia, Calymmatobacterium, Campylobacter, Chlamydia, Chlamydophila, Clostridium, Coxiella, Cupriavidus, Ehrlichia, Enterococcus, Francisella, Fusobacterium, Gardnerella, Haemophilus, Helicobacter, Klebsiella, Methanobacterium, Micrococcus, Moraxella, Mycobacterium, Mycoplasma, Neisseria, Pasteurella, Peptostreptococcus, Porphyromonas, Prevotella, Pseudomonas, Rhizobium, Rickettsia, Rochalimaea, Rothia, Shigella, Staphylococcus, Stenotrophomonas, Streptococcus, Treponema, Vibrio, Wolbachia, Yersinia, or the like.
Exemplary bacteria include species selected from Escherichia coli, Klebsiella oxytoca, Anaerobiospirillum succiniciproducens, Actinobacillus succinogenes, Mannheimia succiniciproducens, Rhizobium etli. Bacillus subtilis, Corynebacterium glutamicum, Gluconobacter oxydans, Zymomonas mobilis, Lactococcus lactis, Lactobacillus plantarum, Streptomyces coelicolor, Clostridium acetobutylicum. Pseudomonas fluorescens, Hydrogenobacter thermophilus, Methanococcus jannaschii and Pseudomonas putida. 
Preferably the bacterium is of the genus Escherichia, Corynebacterium or Pseudomonas. Preferably the bacterium is Escherichia coli, Corynebacterium glutamicum. Pseudomonas fluorescens or Pseudomonas putida. 
Exemplary yeasts or fungi include those belonging to the genera Saccharomyces, Schizosaccharomyces, Candida, Kluyveromyces, Aspergillus, Pichia, Crytpococcus, or the like. Exemplary yeast or fungi species include those selected from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces marxianus, Aspergillus terreus, Aspergillus niger, Pichia pastoris or the like.
In one embodiment, suitable microorganisms are selected from the genera Escherichia, Erwinia, Providencia, and Serratia. Within the genus Escherichia, the species Escherichia coli can be used. Exemplary strains include E. coli B, E. coli C, E. coli W, or the like. In one embodiment, the microorganism is E. coli, for example a commercially available and/or fully characterized strain E. coli, such as K-12 MG1655, BW25113 or W3110.
While aspects and embodiments relating to bacterial cells herein typically refer to genes or proteins according to their designation in E. coli, for bacterial cells of another family or species, it is within the level of skill in the art to identify the corresponding gene or protein, e.g., the homolog, ortholog and/or paralog, in the other family or species, typically by identifying sequences having moderate (typically ≥30%) or high (typically ≥50%) identity to the E. coli sequence, preferably taking the function of the protein expressed by the gene and/or the locus of the gene in the genome into account. Tables 1a and b below set out the function of the protein encoded by each specific gene, its locus in the E. coli BW25113 genome and the SEQ ID number of the coding sequence. Sequences of the wild nucleic acids and encoded proteins are provided herein.
A skilled person would thus understand that the various aspects of the invention extend to mutant proteins and nucleic acid sequences in other microorganisms, preferably in bacteria, for example E. coli strains. Thus, reference is also made to regulators and components of the oxidative stress response and the bacterial multidrug resistance system and its regulators that are homologues of the E. coli proteins and nucleic acids. As used herein, a homologue of a nucleic acid sequence or amino acid sequence has at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the wild type nucleic acid or amino acid sequence.
“Identity” is a property of sequences that measures their similarity or relationship. The term “sequence identity” or “identity” as used in the present disclosure means the percentage of pair-wise identical residues—following (homologous) alignment of a sequence of a polypeptide of the disclosure with a sequence in question—with respect to the number of residues in the longer of these two sequences. Sequence identity is measured by dividing the number of identical amino acid residues by the total number of residues and multiplying the product by 100.
The term “homology” is used herein in its usual meaning and includes identical amino acids as well as amino acids which are regarded to be conservative substitutions (for example, exchange of a glutamate residue by an aspartate residue) at equivalent positions in the linear amino acid sequence of a polypeptide of the disclosure.
Suitable homologues or orthologues can be identified by sequence comparisons and identifications of conserved domains using databases such as NCBI and Paint ensemble and alignment programmes known to the skilled person. The percentage of sequence homology or sequence identity can, for example, be determined herein using the program BLASTP.
Alignments can be carried out using suitable computer programs such as BLAST2.0, which stands for Basic Local Alignment Search Tool or ClustalW or any other suitable program which is suitable to generate sequence alignments. Accordingly, a wild-type nucleic acid or amino acid sequence can serve as “subject sequence” or “reference sequence”, while the amino acid sequence of a mutant nucleic acid or amino acid sequence different from the wild-type described herein serves as “query sequence”. The terms “reference sequence” and “wild-type sequence” are used interchangeably herein.
The terms “genetic modification” or “genetic engineering” broadly refer to manipulation of the genome or nucleic acids of a microorganism. Likewise, the term “genetically engineered” or “genetically modified” refers to a microorganism comprising a genome or nucleic acid that is different from the genome or nucleic acid of the wild type microorganism. For example, the genome or nucleic acid may be manipulated using methods of genetic modification such as, heterologous gene expression, gene or promoter insertion or deletion, nucleic acid mutation, altered gene expression or inactivation, enzyme engineering, random mutagenesis methods, gene shuffling, or codon optimization. In one embodiment, the “genetically engineered” or “genetically modified” microorganism refers to an isolated strain, for example of a bacterium, comprising a genome or nucleic acid that is different from the wild type microorganism.
For the purposes of the invention, a “mutant” or “genetically modified” microorganism is a microorganism that has been altered compared to a naturally occurring wild type (WT) microorganism.
As used herein, “mutated” refers to a nucleic acid or protein that is modified in the microorganism of the various aspects of the invention compared to the wild-type microorganism. A mutation in a nucleic acid sequence or amino acid sequence can be a deletion, insertion or substitution of one or more residue. Mutations in a nucleic acid sequence can lead to a missense mutation resulting in the substitution of a single amino acid in the protein. Alternatively, a mutation in a nucleic acid sequence can introduce a premature stop codon resulting in a truncated protein or a change in the subsequent amino acid sequence. A knock out mutation is a mutation that abolishes function of the protein.
A “mutant” or “genetically modified” microorganism are isolated from their natural environment. In one embodiment, a “mutant” or “genetically modified” microorganism is not found in nature.
As used herein, the words “nucleic acid”, “nucleic acid sequence”, “nucleotide”, “nucleic acid molecule” or “polynucleotide” are intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), natural occurring, mutated, synthetic DNA or RNA molecules, and analogs of the DNA or RNA generated using nucleotide analogs. It can be single-stranded or double-stranded. Such nucleic acids or polynucleotides include, but are not limited to, coding sequences of structural genes, anti-sense sequences, and non-coding regulatory sequences that do not encode mRNAs or protein products. These terms also encompass a gene. The term “gene” or “gene sequence” is used broadly to refer to a DNA nucleic acid associated with a biological function. Thus, genes may include introns and exons as in the genomic sequence, or may comprise only a coding sequence as in cDNAs, and/or may include cDNAs in combination with regulatory sequences.
The terms “peptide”, “polypeptide” and “protein” are used interchangeably herein and refer to amino acids in a polymeric form of any length, linked together by peptide bonds.
For the purposes of the invention, “transgenic”, “transgene” or “recombinant” means that with regard to, for example, a nucleic acid sequence, an expression cassette, gene construct or a vector comprising the nucleic acid sequence or a microorganism transformed with a nucleic acid sequence, expression cassette or vector described herein, nucleic acid sequences encoding proteins useful in the methods of the invention are not located in their natural genetic environment or have been modified by recombinant methods. The natural genetic environment is understood as meaning the natural genomic or chromosomal locus in the original microorganism.
The term “heterologous” nucleic acid sequence or gene construct designates a nucleic acid sequence of gene construct that cannot usually be found in the organism.
The mutation in the mutant or modified gene according to the various aspect of the invention may reside in a gene that encodes a protein component or regulator of the oxidative stress response and the bacterial multidrug resistance system and its regulators, for example components or regulators of the AcrAB TolC efflux pump or members of the AraC family of proteins. For example, the mutation in the mutant or modified gene according to the various aspects of the invention may reside in a gene that encodes a protein of the AraC family of transcriptional regulators. In particular, the mutation may reside in a soxR nucleic acid sequence resulting in a mutant SoxR protein, an acrR nucleic acid sequence resulting in a mutant AcrR protein, a rob nucleic acid sequence resulting in a mutant Rob protein and/or a marR nucleic acid sequence resulting in a mutant MarR protein or combinations thereof. In particular, the inventors have shown that mutants of the Acriflavine resistance regulator (acrR) confer tolerance to methacrylates, in particular when combined with one of the global regulators selected from marR, soxR or rob.
Redox-Sensitive Transcriptional Activator (soxR)
In one embodiment, the genetically modified microorganism comprises a mutation in a soxR nucleic acid sequence. Thus, the genetically modified microorganism comprises a mutant soxR nucleic acid sequence compared to a wild type soxR nucleic acid sequence. The mutant soxR nucleic acid sequence encodes a mutant SoxR protein.
soxR encodes a regulator of the MerR family. In the absence of an oxidative stress signal, the SoxR homodimer binds to the promoter region of soxS and prevents enhanced transcription. When the SoxR cluster is oxidised, SoxR becomes an activator of soxS transcription.
The E. coli soxR nucleic acid sequence is shown in SEQ ID NO. 1. This encodes a protein as shown in SEQ ID NO. 2. The 17-kDa SoxR protein is composed of 154 amino acid residues and forms a homodimer, which contains a [2Fe-2S] cluster. It has a DNA binding domain (residues 1-80), a dimerization helix (residues 81-118), and a Fe—S cluster binding domain (residues 119-154). SoxR activation is mediated by oxidation of its Fe—S cluster, which leads to the enhanced transcription of soxS.
In one embodiment, the wild type soxR nucleic acid sequence comprises SEQ ID NO. 1 or a homologue thereof.
The homologue of a soxR nucleic acid sequence or SoxR amino acid sequence has at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the wild type nucleic acid or amino acid sequence represented by SEQ ID NO. 1 and SEQ ID NO. 2 respectively. Preferably, overall sequence identity is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. The overall sequence identity is determined using a global alignment algorithm known in the art, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys).
In one embodiment, the mutation in SoxR facilitates oxidation and/or DNA binding, which consequently increases transcription of the SoxR regulon, including SoxS.
In one embodiment, the microorganism comprises a mutant soxR nucleic acid sequence encoding a mutant SoxR protein with a mutation in the DNA binding domain (residues 1-80) or in the FE-S cluster domain (residues 119-154).
In one embodiment, the mutation in the SoxR protein is selected from one of the following: a substitution of R20 with another amino acid, a substitution of R20 with another amino acid, deletion of residue 146 (deletion of nucleic acid residues 435, 436, 437), or a truncation at residue 139 with reference SEQ ID NO. 2. In one embodiment, substitution of R20 is with H. In one embodiment, substitution of R20 is with L. Also within the scope of the invention are modifications at equivalent positions in homologues of SoxR in microorganisms other than E. coli. 
In one embodiment, the mutation is not a knock out mutation. In one embodiment, the mutation is a gain of function mutation. The altered protein is able to confer tolerance to methacrylate esters.
Acriflavine Resistance Regulator (acrR)
In one embodiment, the genetically modified microorganism comprises a mutation in an acrR nucleic acid sequence. Thus, the genetically modified microorganism comprises a mutant acrR nucleic acid sequence compared to a wild type acrR sequence. The mutant acrR nucleic acid sequence encodes a mutant AcrR protein.
AcrR regulates the expression of the acrRAB genes associated with the AcrAB-TolC multidrug efflux pump. AcrR homodimer acts as a repressor to acrAB operon by binding to its operator region and is released when an activator molecule binds on its C-terminal ligand binding domain, which allows transcription of acrAB. The acrAB operon encodes AcrA and AcrB, which cooperates with TolC to form the major multidrug efflux pump complex AcrAB-TolC.
AcrR is a dimeric two-domain molecule with an entirely helical architecture similar to members of the TetR family of transcriptional regulators. In E. coli, the acrR gene encodes the 215 amino acid AcrR protein, which contains an N-terminal DNA binding domain (residues 7-51) and a C-terminal ligand binding domain (residues 55-204).
In one embodiment, the wild type acrR nucleic acid sequence comprises SEQ ID NO. 3 or a homologue thereof encoding SEQ ID NO. 4.
The homologue of a acrR nucleic acid sequence or AcrR amino acid sequence has at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% 98%, or 99% overall sequence identity to the wild type nucleic acid or amino acid sequence represented by SEQ ID NO. 3 and SEQ ID NO. 4 respectively. Preferably, overall sequence identity is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. The overall sequence identity is determined using a global alignment algorithm known in the art, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys).
In one embodiment, the microorganism comprises a mutant acrR nucleic acid sequence encoding a mutant AcrR protein with a mutation in the DNA binding domain (residues 7-51) or in the ligand binding domain (residues 55-204).
In one embodiment, the mutation in AcrR is selected from one of the following: a substitution of V29 with another amino acid, a frameshift mutation at Y49, a frameshift mutation at A191 or a frameshift mutation at T32 with reference SEQ ID NO:4. In one embodiment, substitution of V29 is with G. Also within the scope of the invention are modifications at equivalent positions in homologues of AcrR in microorganisms other than E. coli. 
In one embodiment, the mutation is not a knock out mutation. In one embodiment, the mutation is a gain of function mutation, i.e. a functional protein with altered function compared to the wild type is produced. The altered protein is able to confer tolerance to methacrylate esters.
Right Origin-Binding (Rob)
In one embodiment, the genetically modified microorganism comprises a mutation in a rob nucleic acid sequence. Thus, the genetically modified microorganism comprises a mutant rob nucleic acid sequence compared to a wild type rob sequence. The mutant rob nucleic acid sequence encodes a mutant Rob protein.
The Rob protein in E. coli consists of 289 amino acids with an N-terminal DNA binding domain (residues 1-120) and C-terminal domain (residues 121-189). The C-terminal domain is considered essential for preventing its degradation by the Lon protease as well as its activation-deactivation mechanism.
In one embodiment, the wild type rob nucleic acid sequence comprises SEQ ID NO. 5 or a homologue thereof encoding a protein having SEQ ID No. 6.
The homologue of a rob nucleic acid sequence or Rob amino acid sequence has at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% 98%, or 99% overall sequence identity to the wild type nucleic acid or amino acid sequence represented by SEQ ID NO. 5 and SEQ ID NO. 6 respectively. Preferably, overall sequence identity is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. The overall sequence identity is determined using a global alignment algorithm known in the art, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys).
The mutations found in the BMA tolerant strains caused amino acid substitutions at amino acid residues 70 and 156, which is distant from the DNA binding site of Rob, but may affect the protein-protein interaction involved in self-sequestration or the specificity for activators. Such mutations would either increase the amount of free/active Rob or increase Rob's affinity towards BMA to allow activation or increase activation by BMA. Increased activity of Rob would then result in increased expression of multidrug resistance genes under its regulatory control that could aid in gaining tolerance towards BMA.
In one embodiment, the microorganism comprises a mutant rob nucleic acid sequence encoding a mutant Rob protein with a mutation in the N-terminal DNA binding domain (residues 1-120) and C-terminal domain (residues 121-189).
In one embodiment, the mutation in Rob is selected from one of the following: a substitution of A70, or a substitution of R156 with another amino acid in Rob with reference to SEQ ID NO. 6. In one embodiment, substitution of A70 is with V or T. In one embodiment, substitution of R156 is with H. Also within the scope of the invention are modifications at equivalent positions in homologues of Rob in microorganisms other than E. coli. 
Multiple Antibiotic Resistance Protein (marR)
In one embodiment, the genetically modified microorganism comprises a mutation in a marR nucleic acid sequence. Thus, the genetically modified microorganism comprises a mutant marR nucleic acid sequence compared to a wild type marR sequence. The mutant marR nucleic acid sequence encodes a mutant MarR protein.
In E. coli, the protein product of the marR gene, MarR, is composed of 144 amino acid residues and contains an N-terminal domain, a C-terminal domain, DNA binding site (residue 55-100), and salicylate binding site (residue 70-86). MarR, as a homodimer, acts as a repressor to the marAB operon by binding to its promoter region. Its DNA binding/repressor activity is suppressed by the presence and binding of small molecules such as salicylate, plumbagin, 2,4-dinitrophenol, and menadione, which allows transcription of marA, marB, and marR.
In one embodiment, the wild type marR nucleic acid sequence comprises SEQ ID NO. 7 or a homologue thereof encoding a protein having SEQ ID No. 8.
The homologue of a marR nucleic acid sequence or MarR amino acid sequence has at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% 98%, or 99% overall sequence identity to the wild type nucleic acid or amino acid sequence represented by SEQ ID NO. 7 and SEQ ID NO. 8 respectively. Preferably, overall sequence identity is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. The overall sequence identity is determined using a global alignment algorithm known in the art, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys).
In one embodiment, the microorganism comprises a mutant marR nucleic acid sequence encoding a mutant MarR protein with a mutation in the DNA binding and salicylate binding domain (residue 55-100). For example, the mutation may result in a reduction in DNA binding affinity and/or enhancement of affinity towards BMA as an activator.
In one embodiment, the mutation in MarR is a substitution of V84 with another amino acid with reference to SEQ ID NO. 8. In one embodiment, substitution of V84 is with G. Also within the scope of the invention are modifications at an equivalent position in homologues of MarR in microorganisms other than E. coli. 
In one embodiment, the microorganism has a mutation in the acrR nucleic acid sequence encoding a mutant AcrR protein, e.g. a protein with a mutation in the DNA binding domain (residues 7-51) or in the ligand binding domain (residues 55-204), in combination with a mutation in the nucleic acid sequence of any one of soxR, rob or marR. For example, the microorganisms may comprise a mutation in a acrR and soxR; acrR and rob or acrR and marR nucleic acid sequence. Further mutations, i.e. in other genes, may or may not be present.
In one embodiment, the microorganism may comprise a mutation in the acrR nucleic acid sequence encoding a mutant AcrR protein with a mutation in the DNA binding domain (residues 7-51) or in the ligand binding domain (residues 55-204), comprising one of a substitution of V29 with another amino acid, a frameshift mutation at Y49, a frameshift mutation at A191, or a frameshift mutation at T32 with reference SEQ ID NO:4, in combination with a mutation in soxR selected from any of the following: a substitution of R20 with another amino acid, a substitution of R20 with another amino acid, deletion of residue 146 (deletion of nucleic acid residues 435, 436, 437), or a truncation at residue 139 with reference SEQ ID NO. 2. In one embodiment, substitution of R20 is with H. In one embodiment, substitution of R20 is with L. For example, the microorganism may comprise nucleic acid sequences comprising one of the following combinations of mutations:

    
    
        acrR(V29) and SoxR(R20 L)
        acrR(Y49fs) and SoxR(R20 L)
        acrR(A191 fs) and SoxR(R20 L)
        acrR(T32fs) and SoxR(R20 L)
        acrR(V29) and SoxR(R20H)
        acrR(Y49fs) and SoxR(R20H)
        acrR(A191 fs) and SoxR(R20H)
        acrR(T32fs) and SoxR(R20H)
        acrR(V29) and SoxR(146 del)
        acrR(Y49fs) and SoxR(146 del)
        acrR(A191 fs) and SoxR(146 del)
        acrR(T32fs) and SoxR(146 del)
        acrR(V29) and SoxR(Leu139X)
        acrR(Y49fs) and SoxR(Leu139X)
        acrR(A191 fs) and SoxR(Leu139X)
        acrR(T32fs) and SoxR(Leu139X)
    
    


In one embodiment, the microorganism may comprise a mutation in the acrR nucleic acid sequence encoding a mutant AcrR protein with a mutation in the DNA binding domain (residues 7-51) or in the ligand binding domain (residues 55-204), comprising one of a substitution of V29 with another amino acid, a frameshift mutation at Y49, a frameshift mutation at A191, or a frameshift mutation at T32 with reference SEQ ID NO:4, in combination with a mutation in marR selected from a substitution of V84 with another amino acid with reference to SEQ ID NO. 8. In one embodiment, substitution of V84 is with G. For example, the microorganism may comprise nucleic acid sequences comprising one of the following combinations of mutations:

    
    
        acrR(V29) and marR(V84G)
        acrR(Y49fs) and marR(V84G)
        acrR(A191fs) and marR(V84G)
        acrR(T32fs) and marR(V84G)
    
    


In one embodiment, the microorganism may comprise mutation in the acrR nucleic acid sequence encoding a mutant AcrR protein with a mutation in the DNA binding domain (residues 7-51) or in the ligand binding domain (residues 55-204), comprising one of a substitution of V29 with another amino acid, a frameshift mutation at Y49, a frameshift mutation at A191, or a frameshift mutation at T32 with reference SEQ ID NO:4, in combination with a mutations in rob selected from any one of the following: a substitution of A70, or a substitution of R156 with another amino acid in Rob with reference to SEQ ID NO. 6. In one embodiment, substitution of A70 is with V or T. In one embodiment, substitution of R156 is with H. For example, the microorganism may comprise nucleic acid sequences comprising one of the following combinations of mutations:

    
    
        acrR(V29) and rob(156H)
        acrR(Y49fs) and rob (156H)
        acrR(A191 fs) and rob (156H)
        acrR(T32fs) and rob (156H)
        acrR(V29) and rob (A70T)
        acrR(Y49fs) and rob (A70T)
        acrR(A191fs) and rob (A70T)
        acrR(T32fs) and rob (A70T)
        acrR(V29) and rob (A70V)
        acrR(Y49fs) and rob (A70V)
        acrR(A191fs) and rob (A70V)
        acrR(T32fs) and rob (A70V)
    
    


For the above embodiments reference is made to certain mutations. As explained herein, these refer to positions in the E. coli protein sequences of the genes/protein mentioned (see SEQ ID Nos 2, 4, 6 and 8 respectively for the protein sequences).
In one embodiment, the microorganism may comprise a combination of two or more of the mutant nucleic acid sequences described above. For example, the microorganism may have a mutation in at least two nucleic acid sequences selected from a soxR, rob, acrR and a marR nucleic acid sequence or a homolog thereof. Thus, the microorganism may comprise a mutation in a soxR and a rob nucleic acid sequence, a soxR and an acrR nucleic acid sequence, a soxR and a marR nucleic acid sequence, a rob and an acrR nucleic acid sequence, a rob and a marR nucleic acid sequence or an acrR and a marR nucleic acid sequence or a homolog thereof.
In another embodiment, the microorganism may comprise a mutation in at least three nucleic acid sequences selected from a soxR, rob, acrR and a marR nucleic acid sequence or a homolog thereof. Thus, the microorganism may comprise a mutation in a soxR, acrR and a rob nucleic acid sequence or a homolog thereof. Thus, the microorganism may comprise a mutation in a soxR, acrR and a marR nucleic acid sequence or a homolog thereof. Thus, the microorganism may comprise a mutation in a rob, acrR and a marR nucleic acid sequence or a homolog thereof.
In another embodiment, the microorganism may comprise a mutation in four nucleic acid sequences selected from a soxR, rob, acrR and a marR nucleic acid sequence or a homolog thereof.
In one embodiment, the microorganism may comprises one or more genetic mutation selected from those shown in table 1a.







TABLE 1a







Mutations conferring increased tolerance to methacrylates












Gene and


Genomic




database


Coordinate in




references


reference

Effect of


SEQ ID Nos


sequence
Nucleotide
Nucleotide


refer to the


(NCBI Reference
Change/
change; Length


wild type gene

Cellular
Sequence:
Mutation
of Amino Acid


sequence
Gene Description
Location
NZ_CP009273.1)
Before → After
Sequence





rob
Right origin binding
Cyt
4624661
C → T
missense -


Nucleic acid
protein



Arg156His ; 289


NCBI Reference







Sequence:







NZ_CP009273.1







Protein







UniProtKB -







P0ACI0







SEQ ID NO. 5







rob
Right origin binding
Cyt
4624919
G → A
missense -


SEQ ID NO. 5
protein



Ala70Val ; 289


rob
Right origin binding
Cyt
4624920
C → T
missense -


SEQ ID NO. 5
(rob) protein



Ala70Thr ; 289


rob
Right origin binding
Cyt
4625592
C → T
silent - Val85Val ;


SEQ ID NO. 1
(rob) protein



289


SoxR
Superoxide
Cyt
4267455
G → T
Missense-


nucleic acid
response regulon



Arg20Leu ; 154


NCBI Reference
activator






Sequence:







NC_000913.3







protein







UniProtKB -







P0ACS2







SEQ ID NO. 1







SOXR
Superoxide
Cyt
4267812
T → A
Truncation- stops


SEQ ID NO. 1
response regulon



at Leu139 ; 154



activator






SOxR
Superoxide
Cyt
4267830
3 bp Deletion
Removal of


SEQ ID NO. 1
response regulon



Ala146 without



activator



changing the







succeeding







sequence ; 154


soxR
Superoxide
Cyt
4267455
G → A
Missense-


SEQ ID NO. 1
response regulon



Arg20His; 154



activator






marR
Multiple antibiotic
Cyt
1613627
G → A
Missense-


SEQ ID NO. 17
resistance (mar)



Val84Gly; 144



operon - repressor







protein






acrR
acriflavine
Cyt
481302
T → G
Missense-


nucleic acid
resistance regulator-



Val29Gly; 215


NCBI Reference
acrAB operon






Sequence:
repressor






NC_000913.3







protein







UniProtKB -







P0ACS9







SEQ ID NO. 3







acrR
acriflavine
Cyt
481310
1 bp deletion
Frameshift and


SEQ ID NO. 3
resistance regulator-



truncation- stops



acrAB operon



at residue 73; 215



repressor






acrR
acriflavine
Cyt

Frameshift
Frameshift at


SEQ ID NO. 3
resistance



position 49 Y



regulator -acrAB







operon repressor






acrR
acriflavine
Cyt

Frameshift
Frameshift at


SEQ ID NO. 3
resistance



residue 191 A



regulator -acrAB







operon repressor









In one embodiment, the microorganism also comprises one or more further mutation, for example in a gene that encodes a protein component of the oxidative stress response or multidrug resistance system. In one embodiment, the mutation is in a rpo nucleic acid sequence, for example rpoB (SEQ ID NO 25) or rpoC (SEQ ID NO. 27), ompR (SEQ ID NO 29), acrB (SEQ ID NO 9), yohJ (SEQ ID NO 11), torY (SEQ ID NO 13), ipxM (SEQ ID NO 15), dnaK (SEQ ID NO 17), grol SEQ ID NO 19), ilvN (SEQ ID NO 21), phop SEQ ID NO 31), ygbK(SEQ ID NO 23) or a homolog thereof. In another embodiment, no further modifications of the protein component or regulator of the oxidative stress response or multidrug resistance system are present.
In one embodiment, the one or more further mutation is selected from a genetic mutation listed in table 1b.












TABLE 1b





Gene and







database







references


Genomic




SEQ ID Nos


Coordinate
Nucleotide
Effect of Nucleotide


refer to the


(NCBI Reference
Change/
change; Length of


wild type gene
Gene
Cellular
Sequence:
Mutation
Amino Acid


sequence
Description
Location
NZ_CP009273.1)
Before → After
Sequence







acrB
Part of the
IM
478518
C → A
missense -


nucleic acid
acrAB-toIC



Val448Leu ; 1049


NCBI Reference
multi-drug






Sequence:
efflux complex






NZ_CP009273.1







protein







UniProtKB -







P31224







SEQ ID NO. 9







acrB SEQ ID
Part of the
IM
477159
C → T
missense - Thr379lle;


NO. 9
acrAB-tolC



1049



multi-drug







efflux complex






yohJ
Membrane
IM
2224428
T → G
missense -


nucleic acid
protein



Leu109Arg; 132


NCBI Reference







Sequence:







NZ_CP009273.1







protein







UniProtKB -







P60632







SEQ ID NO. 11







torY
N-oxide and S-
IM
1952131
C → T
missense - Ala87Thr ; 


nucleic acid
oxide reductase



366


NCBI Reference
subunit






Sequence:







NZ_CP009273.1







protein







UniProtKB -







P52005







SEQ ID NO. 13







IpxM
Myristoyl-acyl
IM
1933628
20 bp
change in amino acid


nucleic acid
carrier protein


deletion
sequence starting at


NCBI Reference
dependent



position 275; 323


Sequence:
acyltransferase






NZ_CP009273.1







protein







UniProtKB- 







P24205SEQ ID







NO. 15







dnak
Molecular
Cyt
13292
T → G
missense -


nucleic acid
chaperone



Val377Gly ; 638


NCBI Reference
(HSP70)






Sequence:







NZ_CP009273.1







protein







UniProtKB -







P0A6Y8







SEQ ID NO. 17







groL
Chaperonin
Cyt
4361677
C → T
missense -


nucleic acid
groEL (HSP60)



Pro279Leu ; 548


NCBI Reference







Sequence:







NZ_CP009273.1







protein







UniProtKB -







P0A6F5







SEQ ID NO. 19







ilvN
Acetolactate
Cyt
3844331
C → T
missense - Cys41Tyr ; 


nucleic acid
synthase



96


NCBI Reference
isozyme 1 small






Sequence:
subunit -






NZ_CP009273.1
Activity






protein
regulator






UniProtKB -







P0ADF8







SEQ ID NO. 21







ygbK
Conserved
Uk
2856574
C → A
missense -


nucleic acid
protein



Ala294Glu ; 388


NCBI Reference
unknown






Sequence:
function






NZ_CP009273.1







protein







UniProtKB -







B7LEF1







SEQ ID NO. 23







rpoB
RNA
Cyt
4174281
A → C
missense -


nucleic acid
polymerase β



Thr1037Pro ; 1342


NCBI Reference
subunit






Sequence:







NZ_CP009273.1







protein







UniProtKB -







P0A8V2







SEQ ID NO. 25







rpoC
RNA
Cyt
4174281
T → G
missense -


NCBI Reference
polymerase β′



Leu361Arg ; 1407


Sequence:
subunit






NZ_CP009273.1







Protein







UniProtKB -







P0A8T7







SEQ ID NO. 27







rpoC
RNA
Cyt
4177637
C → T
missense -


SEQ ID NO. 27
polymerase β′



Ala787Val; 1407



subunit






rpoC
RNA
Cyt
4178500
C → T
missense -


SEQ ID NO. 27
polymerase β′



Arg1075Cys ; 1407



subunit






ompR
Outer
Cyt
3529901
G → T
missense - Arg15Ser ; 


nucleic acid
membrane



239


NCBI Reference
porin protein -






Sequence:
activator






NZ_CP009273.1







protein







UniProtKB -







P0AA16







SEQ ID NO. 29







phoP
Magnesium
Per
1185871
C → A
missense - Leu11Phe ; 


nucleic acid
starvation



223


NCBI Reference
regulon-






Sequence:
regulator






NZ_CP009273.1







protein







UniProtKB -







P23836







SEQ ID NO. 31









In one embodiment, the microorganism is selected from a microorganism having one or more genetic mutation as listed below:

    
    
        rob(R156H)rpoC(L361R)ilvN(C41Y)ygbK(A294E)lpxM(168_185del);
        rob(R156H)ilvN(C41Y) phoP(L11F)acrB(V448 L);
        soxR(Leu139X)580116(G>T);
        ssoxR(A146 del));
        rob(A70V);
        rob(R156H)rpoB(T1037P) torY(A87T) acrR(49Yfs);
        rob(A70T)yohJ(L109R) dnaK(V377G) 927777(C>T) acrR(A191fs);
        marR(V84G)rpoC(R1075C)ompR(R15S) acrB(T379I);
        marR(V84G)rpoC(R1075C)ompR(R15S);
        marR(V84G)rpoC(R1075C) rpoC(A787V)ompR(R15S) acr8(V901I);
        rob(R156H)rpoB(T1037P) groL(P279 L)acrR(49Yfs)1197659(C>A) or
        soxR(R20 L)rpoC(r1075C) 2133236(T>A)3915915(T>G).
    
    


As explained herein, the mutations shown above can be introduced in a wild type organism to confer resistance to methacrylates. The nucleic acids described herein may be mutated by insertion, substitution or deletion of one or more nucleotides.
Techniques for the manipulation, including inactivation or knockout of target genes are well-known in the art. These techniques include gene target using vectors that target the gene of interest and which allow integration allows for integration of transgene at a specific site. The targeting construct is engineered to recombine with the target gene, which is accomplished by incorporating sequences from the gene itself into the construct. Recombination then occurs in the region of that sequence within the gene, resulting in the insertion of a foreign sequence to disrupt the gene. With its sequence interrupted, the altered gene will be translated into a non-functional protein, if it is translated at all. Other techniques include genome editing (targeted genome engineering) as described below. Mutations can also be introduced by exposing the microorganism to a mutagen. The mutagen may be fast neutron irradiation or a chemical mutagen, for example selected from the following non-limiting list: ethyl methanesulfonate (EMS), methylmethane sulfonate (MMS), N-ethyl-N-nitrosurea (ENU), triethylmelamine (1 'EM), N-methyl-N-nitrosourea (MNU), procarbazine, chlorambucil, cyclophosphamide, diethyl sulfate, acrylamide monomer, melphalan, nitrogen mustard, vincristine, dimethylnitosamine, N-methyl-N′-nitro-Nitrosoguanidine (MNNG), nitrosoguanidine, 2-aminopurine, 7, 12 dimethyl-benz(a)anthracene (DMBA), ethylene oxide, hexamethylphosphoramide, bisulfan, diepoxyalkanes (diepoxyoctane (DEO), diepoxybutane (BEB), and the like), 2-methoxy-6-chloro-9 [3-(ethyl-2-chloroethyl)aminopropylamino]acridine dihydrochloride (ICR-170) or formaldehyde.
Recently, genome editing techniques have emerged as alternative methods to conventional mutagenesis methods (such as physical and chemical mutagenesis) or methods using the expression of transgenes in plants to produce mutant plants with improved phenotypes that are important in agriculture. These techniques employ sequence-specific nucleases (SSNs) including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the RNA-guided nuclease Cas9 (CRISPR/Cas9), which generate targeted DNA double-strand breaks (DSBs), which are then repaired mainly by either error-prone non-homologous end joining (NHEJ) or high-fidelity homologous recombination (HR). Targeted genome modification or targeted genome editing is a genome engineering technique that uses targeted DNA double-strand breaks (DSBs) to stimulate genome editing through homologous recombination (HR)-mediated recombination events. To achieve effective genome editing via introduction of site-specific DNA DSBs, four major classes of customizable DNA binding proteins can be used: meganucleases derived from microbial mobile genetic elements, ZF nucleases based on eukaryotic transcription factors, transcription activator-like effectors (TALEs) from Xanthomonas bacteria, and the RNA-guided DNA endonuclease Cas9 from the type II bacterial adaptive immune system CRISPR (clustered regularly interspaced short palindromic repeats). Meganuclease, ZF, and TALE proteins all recognize specific DNA sequences through protein-DNA interactions. Although meganucleases integrate its nuclease and DNA-binding domains, ZF and TALE proteins consist of individual modules targeting 3 or 1 nucleotides (nt) of DNA, respectively. ZFs and TALEs can be assembled in desired combinations and attached to the nuclease domain of FokI to direct nucleolytic activity toward specific genomic loci. Upon delivery into host cells via the bacterial type III secretion system, TAL effectors enter the nucleus, bind to effector-specific sequences in host gene promoters and activate transcription. Their targeting specificity is determined by a central domain of tandem, 33-35 amino acid repeats. This is followed by a single truncated repeat of 20 amino acids. The majority of naturally occurring TAL effectors examined have between 12 and 27 full repeats.
These repeats only differ from each other by two adjacent amino acids, their repeat-variable di-residue (RVD). The RVD that determines which single nucleotide the TAL effector will recognize: one RVD corresponds to one nucleotide, with the four most common RVDs each preferentially associating with one of the four bases. Naturally occurring recognition sites are uniformly preceded by a T that is required for TAL effector activity. TAL effectors can be fused to the catalytic domain of the FokI nuclease to create a TAL effector nuclease (TALEN) which makes targeted DNA double-strand breaks (DSBs) in vivo for genome editing. The use of this technology in genome editing is well described in the art, for example in U.S. Pat. Nos. 8,440,431, 8,440,432 and 8,450,471. Customized plasmids that can be used with the Golden Gate cloning method to assemble multiple DNA fragments. The Golden Gate method uses Type IIS restriction endonucleases, which cleave outside their recognition sites to create unique 4 bp overhangs. Cloning is expedited by digesting and ligating in the same reaction mixture because correct assembly eliminates the enzyme recognition site. Assembly of a custom TALEN or TAL effector construct and involves two steps: (i) assembly of repeat modules into intermediary arrays of 1-10 repeats and (ii) joining of the intermediary arrays into a backbone to make the final construct.
Another genome editing method that can be used according to the various aspects of the invention is CRISPR. The use of this technology in genome editing is well described in the art, for example in U.S. Pat. No. 8,697,359 and references cited herein. In short, CRISPR is a microbial nuclease system involved in defence against invading phages and plasmids. CRISPR loci in microbial hosts contain a combination of CRISPR-associated (Cas) genes as well as non-coding RNA elements capable of programming the specificity of the CRISPR-mediated nucleic acid cleavage (sgRNA). Three types (I-III) of CRISPR systems have been identified across a wide range of bacterial hosts. One key feature of each CRISPR locus is the presence of an array of repetitive sequences (direct repeats) interspaced by short stretches of non-repetitive sequences (spacers). The non-coding CRISPR array is transcribed and cleaved within direct repeats into short crRNAs containing individual spacer sequences, which direct Cas nucleases to the target site (protospacer). The Type II CRISPR is one of the most well characterized systems and carries out targeted DNA double-strand break in four sequential steps. First, two non-coding RNA, the pre-crRNA array and tracrRNA, are transcribed from the CRISPR locus. Second, tracrRNA hybridizes to the repeat regions of the pre-crRNA and mediates the processing of pre-crRNA into mature crRNAs containing individual spacer sequences. Third, the mature crRN A: tracrRNA complex directs Cas9 to the target DNA via Watson-Crick base-pairing between the spacer on the crRNA and the protospacer on the target DNA next to the protospacer adjacent motif (PAM), an additional requirement for target recognition. Finally, Cas9 mediates cleavage of target DNA to create a double-stranded break within the protospacer.
Cas9 is thus the hallmark protein of the type II CRISPR-Cas system, and a large monomeric DNA nuclease guided to a DNA target sequence adjacent to the PAM (protospacer adjacent motif) sequence motif by a complex of two noncoding RNAs: CRIPSR RNA (crRNA) and trans-activating crRNA (tracrRNA). The Cas9 protein contains two nuclease domains homologous to RuvC and HNH nucleases. The HNH nuclease domain cleaves the complementary DNA strand whereas the RuvC-like domain cleaves the non-complementary strand and, as a result, a blunt cut is introduced in the target DNA. Heterologous expression of Cas9 together with an sgRNA can introduce site-specific double strand breaks (DSBs) into genomic DNA of live cells from various organisms. For applications in eukaryotic organisms, codon optimized versions of Cas9, which is originally from the bacterium Streptococcus pyogenes, have been used.
The single guide RNA (sgRNA) is the second component of the CRISPR/Cas system that forms a complex with the Cas9 nuclease. sgRNA is a synthetic RNA chimera created by fusing crRNA with tracrRNA. The sgRNA guide sequence located at its 5′ end confers DNA target specificity. Therefore, by modifying the guide sequence, it is possible to create sgRNAs with different target specificities. The canonical length of the guide sequence is typically 20 bp.
Alternatively, global transcription machinery engineering (gTME) can provide an alternative and useful approach for strain improvement.
In one embodiment, mutants are isolated by selection of resistant mutants from populations of microorganisms by applying selection pressure with BMA. Populations of microorganisms are known to contain spontaneously occurring mutants at low frequencies (<1 in 106), and the application of a selection pressure will result in overgrowth of the fittest mutants. For example, the selection pressure is applied by either gradually increasing the concentration of BMA or by adding high concentrations (10-30%) of BMA from the outset. The selection pressure can include (a) batch culture until growth is observed; (b) sequential batch culture for 2 or more transfers; (c) growth in chemostat culture with increasing concentrations of BMA and increasing dilution rate; (d) growth in pH-auxostat or turbidostat culture with increasing concentrations of BMA.
C3-C12 Methacrylate Esters
By the term C3-C12 methacrylate esters is generally meant a methacrylate comprising a C3-C12 alkyl, hydroxyalkyl, alkenyl, alkylaryl or alkenylaryl group including structural isomers thereof. The C3-C12 group may be cyclic, acyclic, or part cyclic, linear or branched, aliphatic, aromatic or part-aromatic/aliphatic. Preferably the C3-C12 methacrylate esters of the present invention may include, for example, n-propyl, isopropyl, isobutyl, n-butyl, t-butyl, isopentyl, hexyl, cyclohexyl, 2-ethylhexyl, decyl, dodecyl, hydroxyethyl, hydroxypropyl, isobornyl, allyl or cinnamyl methacrylate.
Preferably the C3-C12 methacrylate esters are C3-C12 alkyl methacrylates, more preferably, C3-C8 alkyl methacrylates for example n-propyl, isopropyl, isobutyl, n-butyl, isopentyl, hexyl, cyclohexyl, heptyl, octyl, 2-ethylhexyl, decyl or dodecyl methacrylate.
Preferably, the hydroxyalkyl methacrylates are hydroxyethyl or hydroxypropyl methacrylate.
In embodiments, the C3-C12 methacrylate esters are C3-C12 alkenylaryl methacrylates, for example cinnamyl methacrylate.
The C3-C12 alkyl methacrylates are more preferably C3-C6 alkyl methacrylates, such as the propyl, butyl or hexyl methacrylates, including for example, structural isomers thereof. More preferably, the C3-C6 alkyl methacrylates are propyl or butyl methacrylates, in particular isopropyl or n-butyl methacrylate.
In one embodiment, the C3-C12 methacrylate ester is butyl methacrylate (BMA).
For the production of MMA, the methods described herein may include the additional steps of c) removing the C3-C12 methacrylate ester from the fermentation medium and transesterifying the removed C3-C12 methacrylate ester with methanol, to produce methyl methacrylate.
In aspects and embodiments of the present invention, the microorganism may be genetically modified to produce more C3-C12 methacrylate ester than the wildtype. Thus, the microorganism has a mutation that renders it more tolerant to a methacrylate ester compared to the wild type as described herein and that is a modified to increase production of C3-C12 methacrylate ester compared to the wildtype, for example the microorganism carries a transgenic construct that expresses an enzyme of the C3-C12 methacrylate ester biosynthetic pathway.
Thus, the method for the production of a methacrylate as described herein may comprise a) providing a genetically modified microorganism with increased tolerance to a C3-C12 methacrylate ester compared to the wild type and that is further modified to increase production of C3-C12 methacrylate ester compared to a wild type in a fermentation medium and
b) growing the microorganism under conditions whereby a C3-C12 methacrylate ester is produced.
Enhancing the production of C3-C12 methacrylate ester compared to a wildtype microorganism may include making modifications to existing cellular metabolic processes, nucleic acids and/or proteins by the use of various genetic engineering techniques known in the art. Enhancing the production of C3-C12 methacrylate ester may also include modifying the microorganism/s to express one or more heterologous genes in the microorganism/s. These may include genes encoding enzymes of the desired pathway to C3-C12 methacrylate ester from carbon based feedstocks, or may include other auxiliary genes which act to promote the functioning and expression of the enzymes in such pathways either directly or indirectly. Accordingly, in one embodiment, the microorganism may be modified to enhance production of C3-C12 methacrylate esters. One or more gene/s which may be expressed within the microorganism such that it is modified to produce C3-C12 methacrylate ester, preferably C3-C12 alkyl methacrylate, includes those encoding any of the following enzymes. Heterologous genes may be expressed by transforming the microorganism with a vector comprising the heterologous gene.
In embodiments, the microorganism may express one or more enzymes which can convert isobutyryl-CoA to methacrylyl-CoA, for example an oxidase, dehydrogenase or oxidoreductase.
The oxidase may be an oxidase acting on CH—CH bonds, under EC number 1.3.x.x, more preferably an oxidase acting on CH—CH bonds using oxygen as an electron acceptor, under EC number EC 1.3.3.x. Still more preferably, the oxidase is an acyl-CoA oxidase, suitably under EC number EC 1.3.3.6. More preferably the acyl-CoA oxidase is selected from any of the following enzymes: ACX4 from Arabidopsis thaliana, short chain acyl-CoA oxidase from Arthrobacter nicotianae, peroxisomal acyl-CoA oxidase from Vigna radiata, acyl-CoA oxidase from Candida sp. and acyl-CoA oxidase 4 from Candida tropicalis. Most preferably the acyl-CoA oxidase is ACX4 from Arabidopsis thaliana. 
The oxidoreductase, may be an oxidoreductase under EC group number 1.X.X.X. Preferably, the oxidoreductase is an oxidoreductase acting on the CH—CH group of electron donors, suitably under EC group 1.3.X.X. More preferably, the oxidoreductase acting on the CH—CH group of donors is a FAD dependent oxidoreductase, still more preferably the oxidoreductase is a CoA dehydrogenase under EC group 1.3.8.X. More preferably still, the oxidoreductase is a short chain acyl-CoA dehydrogenase, suitably under EC group 1.3.8.1, an isovaleryl-CoA dehydrogenase, suitably under EC group 1.3.8.4, a 2-methyl-branched-chain acyl-CoA dehydrogenase, suitably under EC group 1.3.8.5 or an acyl-CoA dehydrogenase, suitably under EC group 1.3.8.-, such as an isobutyryl-CoA dehydrogenase. Most preferably the oxidoreductase is selected from any of the following enzymes: short/branched chain acyl-CoA dehydrogenase from Pseudomonas putida, isobutyryl-CoA dehydrogenase from Homo sapiens and isovaleryl-CoA dehydrogenase from Arabidopsis thaliana. 
The CoA dehydrogenase enzymes generally require an associated electron transport system to couple oxidation of the substrate with reduction of ubiquinone, which is then regenerated. Such an electron transport system consists of an electron transfer flavoprotein (ETF), and an electron transfer flavoprotein ubiquinone oxidoreductase (ETFQO). The ETF must be compatible with both the acyl-CoA dehydrogenase enzyme and the ETFQO. Accordingly, in the embodiments where an acyl-CoA dehydrogenase is used, one of the following regeneration systems is preferably employed:

    
    
        a host microorganism expressing an endogenous CoA dehydrogenase, with activity on isobutyryl-CoA, and its associated electron transport system, such as is in the case of, for example, Pseudomonas putida; 
        a host microorganism expressing a heterologous CoA dehydrogenase enzyme accompanied by the proteins of the electron transport system from the same organism as the heterologous CoA dehydrogenase. For example, the CoA dehydrogenase and electron transport system components from Homo sapiens, Pseudomonas putida, Paracoccus denitrificans, or from Arabidopsis thaliana, all expressed in Escherichia coli (or another host organism); or
        a host microorganism expressing a heterologous CoA dehydrogenase enzyme, accompanied by electron transport system components also from different microorganisms, whereby those components are compatible with each other and with the CoA dehydrogenase. For example, the CoA dehydrogenase from Homo sapiens is compatible with the electron transfer flavoprotein of Sus scrota which is in turn compatible with the electron transfer flavoprotein ubiquinone oxidoreductase from Rhodobacter sphaeroides. Alternatively, as the ETF-ubiquinone oxidoreductase of A. thaliana has good sequence homology with the ETF-ubiquinone oxidoreductase of R. sphaeroides, isovaleryl-CoA dehydrogenase and the ETF of A. thaliana could form a functional system with the ETF-ubiquinone oxidoreductase from R. sphaeroides for the oxidation of isobutyryl-CoA. Finally, the ETF and ETF-ubiquinone oxidoreductase from Paracoccus denitrificans are predicted to be compatible with an isobutyryl-CoA dehydrogenase from another source, such as that of H. sapiens or homologues from different organisms, due to the similarity of the P. denitrificans ETF with the human and porcine ETFs.
    
    


In embodiments, the microorganism may express one or more enzymes which can convert methacrylyl-CoA to a C3-C12 methacrylate ester, for example an alcohol acyltransferase.
Preferably, the alcohol acyltransferase acts in the presence of an alcohol, more preferably C3-C12 alcohol, most preferably, a C3-C8 alcohol, still more preferably in the presence of propanol or butanol, such as, n-propanol, isopropanol, n-butanol, isobutanol, sec-butanol, tert-butanol, pentanols, hexanols, heptanols or octanols. Most preferably, the alcohol acyltransferase acts in the presence of isopropanol or n-butanol.
By the term alcohol herein is meant a species having a hydroxyl group (—OH group) and which is capable of forming an ester group with the methacrylate.
Preferably the alcohol acyltransferase is derived from a plant origin, more preferably the plant belongs to any order selected from the group consisting of Zingiberales, Rosales, Ericales, Cucurbitales, Brassicales and Laurales; still more preferably the plant belongs to any family selected from the group consisting of Musaceae, Rosaceae, Ericaceae, Actinidiaceae, Cucurbitaceae, Caricaceae and Lauraceae; still more preferably the plant belongs to any genus selected from the group consisting of Musa, Fragaria, Malus, Prunes, Pyrus, Vaccinium, Actinidia, Cucumis, Carica and Persea; still more preferably the plant is any one selected from the group consisting of banana, strawberry, apple, Prunes mume, Pyrus communis, blueberry, kiwi, melon, papaya and avocado. Most preferably, the alcohol acyltransferase is derived from a fruit origin such as apple, melon or tomato origin, suitably apple origin.
In embodiments of the present invention the microorganism may express an oxidase and an alcohol acyltransferase for converting isobutyryl CoA to a C3-C12 methacrylate ester. Suitable oxidases and alcohol acyltransferases are outlined above. It is particularly preferred if the oxidase is ACX4 from Arabidopsis thaliana. 
In embodiments, the microorganism may express one or more enzymes which can convert 2-ketoisovaleric acid to isobutyryl-CoA. In embodiments, the one or more enzymes may be an enzyme complex such as a branched chain keto acid dehydrogenase enzyme complex, consisting of the alpha subunit component, the lipoamide acyltransferase component and the lipoamide dehydrogenase component. Most preferably, the dehydrogenase is selected from any of the following enzymes: branched chain keto acid dehydrogenase (BCKD) from P. putida, BCKD from Bacillus subtilis, BCKD from P. aeuruginosa, BCKD from A. thaliana, BCKD from Streptomyces coelicolor and BCKD from Thermus thermophilus. 
Alternatively, the conversion of 2-ketoisovaleric acid to isobutyryl-CoA may be catalysed by an oxidoreductase enzyme, suitably under EC group 1.X.X.X, preferably an oxidoreductase acting on the aldehyde or oxo group of donors, suitably under EC group 1.2.X.X, more preferably an oxidoreductase enzyme acting on the aldehyde or oxo group of donors, using an iron-sulfur protein as the electron acceptor, suitably under EC group 1.2.7.X, most preferably a 2-ketoisovalerate ferredoxin reductase (known also as ketovaline ferredoxin oxidoreductases), suitably under EC group number 1.2.7.7, which is a tetramer consisting alpha, beta, gamma and delta subunits. Examples of such enzymes are 2-ketoisovalerate ferredoxin reductase from Pyrococcus furiosis; 2-ketoisovalerate ferredoxin reductase from Pyrococcus sp.; 2-ketoisovalerate ferredoxin reductase from Thermococcus sp2-ketoisovalerate ferredoxin reductase from Thermococcus litoralis; 2-ketoisovalerate ferredoxin reductase from Thermococcus profundus and 2-ketoisovalerate ferredoxin reductase from Methanobacterium thermoautotrophicum. 
Alternatively, the microorganism may express one or more enzymes which can convert isobutyric acid to isobutyryl-CoA, for example a ligase. The ligase is suitably under EC group number 6.X.X.X, preferably a carbon-sulfur bond forming ligase under EC group 6.2.X.X, more preferably an acid-thiol forming ligase under EC group 6.2.1.X, more preferably a GDP-forming, an ADP forming or an AMP forming ligase, such as an AMP forming acetate-CoA ligase, suitably under EC group 6.2.1.1, a butyrate-CoA ligase, suitably under EC group 6.2.1.2, a carboxylic acid-CoA ligase, suitably under EC group 6.2.1.10, an ADP forming acetate-CoA ligase, suitably under EC group 6.2.1.13, a propionate-CoA ligase, suitably under EC group 6.2.1.17 or an acid-thiol ligase in EC group 6.2.1.-. Most preferably the ligase is selected from any of the following enzymes: AcsA from Pseudomonas chlororaphis, butyryl-CoA synthetase from Paecilomyces varioti, butyryl-CoA synthetase from bovine heart mitochondria.
Alternatively, the microorganism may express one or more enzymes which can convert isobutyrate to isobutyryl-CoA. For example, isobutyrate may be converted to isobutyryl-phosphate by a kinase enzyme and isobutyryl-phosphate may be converted to isobutyryl-CoA by a transferase enzyme.
Preferably, the isobutyrate is converted to isobutyryl-phosphate by a kinase enzyme, suitably under EC group number EC 2.X.X.X, preferably under EC 2.7.X.X, more preferably under EC group number EC 2.7.2.X, most preferably an acetate kinase, suitably under EC group 2.7.2.1, a formate kinase under EC 2.7.2.6, a butyrate kinase under EC 2.7.2.7, a branched chain fatty acid kinase under EC 2.7.2.14 or a propionate kinase under EC 2.7.2.15.Most preferably the kinase is selected from any of the following enzymes: branched chain fatty acid kinase from Spirochete MA-2, butyrate kinase from C. butyricum. 
Preferably, the isobutyryl-phosphate is converted to isobutyryl-CoA by the action of a transferase enzyme, under EC group number 2.X.X.X, more preferably by the action of an acyltransferase under EC group number 2.3.X.X, still more preferably by the action of acyltransferase transferring groups other than amino-acyl groups under EC group number 2.3.1.X. Still more preferably a phosphate acetyltransferase or a phosphate butyryltransferase, under EC group numbers 2.3.1.8 and 2.3.1.19, respectively. More preferably the transferase is phosphate butyryltransferase from Clostridium acetobutylicum ATCC824 or phosphate acetyltransferase from Bacillus subtilis, Corynebacterium glutamicum ATCC13032, Thermotoga maritima and Clostridium kluyveri. Other sources of these enzymes include other anaerobic bacteria, especially Clostridium species such as Clostridium pasteurianum or Clostridium beijerinckii. 
The microorganism may express one or more enzymes which can convert isobutyric acid to isobutyryl-CoA, for example a synthetase enzyme, preferably an isobutyryl-CoA synthetase, most preferably isobutyryl-CoA synthetase (AcsA) from P. chloraphis B23.
Suitable modifications and constructs used are also disclosed in WO2016/185211 incorporated herein by reference.
Fermentation Medium and Fermentation
In another aspect, the invention relates to a fermentation medium comprising an isolated genetically modified microorganism with increased tolerance to a methacrylate compared to a wild type microorganism. The genetically modified microorganism with increased tolerance comprises a modification of a protein component or regulator of the oxidative stress response or multidrug resistance system as described above.
In one embodiment, the microorganism(s) are provided in a fermentation medium under conditions in which said microorganism will produce a C3-C12 methacrylate ester.
Various aspects and embodiments of the invention comprise culturing a wild type or genetically modified microorganism in said fermentation medium. Culturing or cultivation suitably requires a carbon based feedstock upon which the microorganism may derive energy and grow. Preferably, therefore, the microorganism/s are cultured on a carbon based feedstock.
The fermentation medium may be a surrounding medium which surrounds the microorganism/s. Preferably a carbon based feedstock is present in the medium, optionally dissolved or suspended in the medium, bubbled through the medium and/or mixed with the medium. Preferably, therefore, the medium comprises the microorganism/s and the carbon based feedstock together with any buffers and salts.
The fermentation medium may be any commercially available medium suitable for the needs of the microorganism. The fermentation medium suitably contains a carbon based feedstock and a nitrogen source, as well as additional compounds required for growth of the microorganism/s and/or the formation of C3-C12 methacrylate ester.
Examples of suitable carbon based feedstocks known in the art include glucose, maltose, maltodextrins, sucrose, hydrolysed starch, starch, lignin, aromatics, syngas or its components, methane, ethane, propane, butane, molasses and oils, carbon dioxide. Preferably the carbon based feedstock is derived from biomass. Mixtures may also be used, as well as wastes, such as municipal waste, food waste and lignocellulosic wastes from food processing, forestry or agriculture.
Examples of suitable nitrogen sources known in the art include soy bean meal, corn steep liquor, yeast extract, ammonia, ammonium salts, nitrate salts, urea, nitrogen gas or other nitrogenous sources.
Examples of additional compounds which may be required for growth of the microorganism/s (and therefore may be present in the fermentation medium) include antibiotics, antifungals, anti-oxidants, buffers, phosphate, sulphate, magnesium salts, trace elements and/or vitamins.
Additional compounds required for growth of the microorganism/s and/or for the production of C3-C12 methacrylate ester, like phosphate, sulphate or trace elements, may be added in amounts that may vary between different classes of microorganisms, i.e. between fungi, yeasts and bacteria. In addition, the amount of additional compound to be added may be determined by what pathways are used to form the C3-C12 methacrylate ester.
The amount of carbon based feedstock and nitrogen source to be added to the medium may vary depending on the needs of the microorganism/s and/or the length of the culturing of the microorganisms. The ratio of the carbon based feedstock to the nitrogen source in the culture medium may vary considerably.
Typically, the amount of each fermentation medium component necessary for growth of a microorganism is determined by measuring the growth yield on the nutrient and further assessed in relation to the amount of carbon based feedstock used in the culturing process, since the amount of biomass formed will be primarily determined by the amount of carbon based feedstock used, and the nutrient limitations imposed during any feeding regime.
In embodiments where the carbon based feedstock is derived from biomass, the biomass preferably comprises a high amount of carbohydrates. Particularly preferable are carbohydrates which are sources of C5 or C6 sugars, carbon based gases, or aromatics, preferably C5 or C6 sugars, more preferably glucose, such as, but not limited to starch, lignin, cellulose, glycogen, arabinoxylan, chitin or pectin.
Alternatively, the biomass may comprise a high amount of fats, particularly preferable are fats or oils which are sources of glycerol and fatty acids, specifically triglycerides. Suitable triglycerides include any oil or fat which is readily available from a plant or animal source. Examples of such oils and fats include palm oil, linseed oil, rapeseed oil, lard, butter, herring oil, coconut oil, vegetable oil, sunflower oil, castor oil, soybean oil, olive oil, cocoa butter, ghee, blubber etc.
The biomass may be composed of one or more different biomass sources. Examples of suitable biomass sources include virgin wood, energy crops, agricultural residues, food waste, municipal waste and industrial waste or co-products.
Virgin wood biomass sources may includes but are not limited to wood chips, bark, brash, logs, sawdust, wood pellets or briquettes.
Energy crop biomass sources may include but are not limited to short rotation coppices or forestry, non-woody grasses such as miscanthus, hemp switchgrass, reeds or rye, agricultural crops such as sugar, starch or oil crops, or aquatic plants such as micro or macroalgae and weeds.
Agricultural residues may include but are not limited to husks, straw, corn stover, flour, grains, poultry litter, manure, slurry, syngas or silage.
Food wastes may include but are not limited to peel/skin, shells, husks, cores, pips/stones, inedible parts of animals or fish, pulp from juice and oil extraction, spent grains or hops from brewing, domestic kitchen waste, lard or oils or fats.
Industrial wastes may include but are not limited to untreated wood including pellets, treated wood, shale gases, wood composites including MDF/OSD, wood laminates, paper pulp/shreddings/waste, textiles including fibre/yarn/effluent, or sewage sludge.
The microorganism may be cultured as a batch, a repeated batch, a fed-batch, a repeated fed-batch or a continuous cultivation (chemostat, turbidostat or auxostat) process.
The culturing process is preferably performed on an industrial scale. An industrial scale process is understood to encompass a culturing process in one or more fermenters of a volume scale which is ≥0.01 m3, preferably ≥0.1 m3, preferably ≥0.5 m3, preferably ≥5 m3, preferably ≥10 m3, more preferably ≥25 m3, more preferably ≥50 m3, more preferably ≥100 m3, most preferably ≥200 m3.
In embodiments, the culturing is performed in a bioreactor. A bioreactor is generally understood to mean a container in which microorganisms are industrially cultured. Bioreactors can be of any size, number and form, and can include inlets for providing nutrients, additional compounds for growth, fresh medium, carbon based feedstocks, additives of gases, such as, but not limited to, air, nitrogen, oxygen or carbon dioxide. Bioreactors may also comprise outlets for removing volumes of the culture medium to collect the C3-C12 methacrylate ester from the fermentation medium. The bioreactor may also have an outlet for sampling of the culture. The bioreactor may have a system for measuring and controlling the pH. This pH control system is used to control medium addition in a pH-auxostat culture. In some embodiments, flask cultures may be used.
The bioreactor can generally be configured to mix the fermentation medium, for example, by stirring, rocking, shaking, inverting, bubbling of gas through the culture etc. Alternatively, some continuous cultures do not require mixing, for example microreactor systems using a plug flow system. Bioreactors are common and well known in the art and examples may be found in standard texts, such as ‘Biotechnology: A Textbook of Industrial Microbiology, Section Edition (1989) Authors: Wulf Cruegar and Annelise Crueger, translated by Thomas D. Brock Sinauer Associates, Inc., Sunderland, Mass.
The invention also relates to a culture medium comprising a genetically modified organism as described herein. Furthermore, the invention relates to a vessel comprising a fermentation or culture medium comprising a genetically modified organism as described herein. Furthermore, the invention relates to a kit comprising a fermentation or culture medium comprising a genetically modified organism as described herein.
Mutant Organisms and Uses Thereof
In another aspect, the invention also relates to an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism for use in the production of a methacrylate, for example a C3-C12 methacrylate ester. Furthermore, the invention relates to the use of an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism in the production of a methacrylate, for example a C3-C12 methacrylate ester. The genetically modified microorganism may be as described in detail above.
In a further aspect, the invention relates to an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism comprising a mutation in marR (SEQ ID NO. 7) wherein said mutant marR nucleic acid encodes a protein with substitution of V84 with another amino acid, for example G, with reference to SEQ ID NO. 8. In a further aspect, the invention relates to an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism comprising a mutation in rob (SEQ ID NO. 5) wherein said mutant Rob nucleic acid encodes a protein with substitution of A70 or a substitution of R156 with another amino acid in Rob with reference to SEQ ID NO. 6. In a further aspect, the invention relates to an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism comprising a mutation in acrR (SEQ ID NO. 3) wherein said mutant acrR nucleic acid encodes a protein with a frameshift mutation at T32 with reference SEQ ID NO:4. In a further aspect, the invention relates to an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism comprising a mutation in soxR (SEQ ID NO. 1) wherein said mutant soxR nucleic acid encodes a protein with a substitution of R20 with another amino acid, deletion of residue 146 or a truncation at residue 139 with reference SEQ ID NO. 2.
In a further aspect, the invention relates to an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism comprising a mutation in two or more nucleic acids selected from the following: a soxR, acrR, marR and/or a rob nucleic acid or a homolog thereof wherein said nucleic acid encodes a mutant protein.
In a further aspect, the invention relates to an isolated methacrylate tolerant, in particular a C3-C12 methacrylate ester tolerant, genetically modified microorganism comprising a mutation in acrR and a mutation in a nucleic acid selected from the following: a soxR, marR or a rob nucleic acid or a homolog thereof wherein said nucleic acid encodes a mutant protein.
According to the various aspects of the invention, the microorganism is as described above and in one embodiment, the microorganism is E. coli. 
In one embodiment, the mutant soxR nucleic acid sequence encodes a mutant SoxR protein with a mutation in the DNA binding domain (residues 1-80) or in the FE-S cluster domain (residues 119-154). In one embodiment, the mutation in SoxR is selected from one of the following: a substitution of R20 with another amino acid, a substitution of R20 with another amino acid, deletion of residue 146, or a truncation at residue 139 with reference SEQ ID NO. 2. In one embodiment, substitution of R20 is with H. In one embodiment, substitution of R20 is with L. Also within the scope of the invention are modifications at equivalent positions in homologues of SoxR in microorganisms other than E. coli. 
In one embodiment, the acrR nucleic acid sequence encodes a mutant AcrR protein with a mutation in the DNA binding domain (residues 7-51) or in the ligand binding domain (residues 55-204). In one embodiment, the mutation in AcrR is selected from one of the following: a substitution of V29 with another amino acid, a frameshift mutation at T32, a frameshift mutation at Y49, a frameshift mutation occurs at A191, a deletion of residue 146, or a truncation at residue 139 with reference SEQ ID NO:3. In one embodiment, substitution of V29 is with G. Also within the scope of the invention are modifications at equivalent positions in homologues of AcrR in microorganisms other than E. coli. 
In one embodiment, the mutant rob nucleic acid sequence encodes a mutant Rob protein with a mutation in the N-terminal DNA binding domain (residues 1-120) and C-terminal domain (residues 121-189). In one embodiment, the mutation in Rob is selected from one of the following: a substitution of A70 or a substitution of R156 with another amino acid in Rob with reference to SEQ ID NO. 6. In one embodiment, substitution of A70 is with V or T. In one embodiment, substitution of R156 is with H. Also within the scope of the invention are modifications at equivalent positions in homologues of Rob in microorganisms other than E. coli. 
In one embodiment, the mutant marR nucleic acid sequence encodes a mutant MarR protein with a mutation in the DNA binding domain (residue 55-100). In one embodiment, the mutation in MarR is a substitution of V84 with another amino acid with reference to SEQ ID NO. 8. In one embodiment, substitution of V84 is with G. Also within the scope of the invention are modifications at an equivalent position in homologues of MarR in microorganisms other than E. coli. 
In one embodiment, two or more mutations as shown in table 1a are present. In one embodiment, the microorganism is selected from a microorganism having genetic mutations as listed below:

    
    
        rob(R156H)rpoC(L361R)ilvN(C41Y)ygbK(A294E)lpxM(168_185del);
        rob(R156H)ilvN(C41Y) phoP(L11F)acrB(V448 L);
        soxR (Leu139X) 580116(G>T);
        soxR(A146del);
        rob(A70V);
        rob(R156H)rpoB(T1037P) torY(A87T) acrR(49Yfs);
        rob(A70T)yohJ(L109R) dnaK(V377G) 927777(C>T) acrR(A191fs);
        marR(V84G)rpoC(R1075C)ompR(R15S) acrB(T379I);
        marR(V84G)rpoC(R1075C)ompR(R15S);
        marR(V84G)rpoC(R1075C) rpoC(A787V)ompR(R15S) acrB(V901I);
        rob(R156H)rpoB(T1037P) groL(P279 L) acrR(49Yfs) 1197659(C>A) or
        soxR(R20 L)rpoC(r1075C) 2133236(T>A)3915915(T>G).
    
    


In one embodiment, a mutation in soxR is combined with a mutation in acrR. As demonstrated in the examples, the inventors have surprisingly found that combining mutations in the two genes leads to an additive tolerance effect. In one embodiment, a mutation in soxR is combined with a mutation in marR. In one embodiment, a mutation in soxR is combined with a mutation in rob.
In one embodiment, the microorganism also comprises one or more further mutation, for example in a gene that encodes a protein component or regulator of the oxidative stress response. In one embodiment, the mutation is in a rpo nucleic acid sequence, for example rpoB (SEQ ID NO 25) or rpoC (SEQ ID NO 27), ompR (SEQ ID NO 29), acrB (SEQ ID NO 9), yohJ (SEQ ID NO 11), torY (SEQ ID NO 13), ipxM (SEQ ID NO 15), dnaK (SEQ ID NO 17), grol SEQ ID NO 19), ilvN (SEQ ID NO 21), phop SEQ ID NO 31), ygbK(SEQ ID NO 23). In another embodiment, no further modifications of the protein component or regulator of the oxidative stress response or multidrug resistance system are present.
In one embodiment, a mutation in acrR is combined with one or more mutations in one of marR, rob or soxR. This is based on the surprising finding that a mutation in acrR was found in combination with marR, rob or soxR (see example 2).
In one embodiment, a mutation in acrR is combined with one or more mutations in marR. In one embodiment, a mutation in acrR is combined with one or more mutations in rob. In one embodiment, the one or more further mutation is selected from a mutation listed in table 1b.
Methods for Making Mutant Organisms
The invention also relates to methods for the isolation of a methacrylate tolerant microorganism comprising:
a) providing a microorganism in a fermentation medium
b) contacting the microorganism with a methacrylate; and
c) isolating the viable microorganism of step (b)
wherein the viable microorganism is tolerant to at least 20% v/v a methacrylate when grown in liquid medium at about 37° C.
The microorganism is selected from a microorganism as described above, such as E. coli. In one embodiment, the method employs an adaptive evolution approach which comprises culturing the organism in a medium that comprises sequentially increasing concentrations of a methacrylate, for example BMA. For example, in a first step, the microorganism is contacted with a methacrylate at a concentration of 0.1%. In subsequent steps, the concentration is increased stepwise from 0.1%, to, for example, 0.5%, 1%, 5%, 10% and 20% and the microorganism is exposed to this concentration of a period of time. In another embodiment, the concentration is increased stepwise to 10% and 20%. Contacting the microorganism with a methacrylate at each concentration may be for about (0.1 h to 144 hours) for 1 to 45 times. In another embodiment, the culturing temperature may be altered during the method. The culturing temperature may be maintained at 4° C. to 50° C. In another embodiment, the method comprises incubating one culture with BMA until growth occurs then isolating mutants.
For example, the adaptive evolution can be carried out in the following way: Adaptive evolution of E. coli in a chemostat can be established at a starting dilution rate of about 0.33 h−1. The BMA concentration is then gradually increased in a step-wise manner from 0 to 20% v/v at a constant dilution rate. After attaining a stable cell concentration at about 20% v/v BMA, the dilution rate of the culture can be adjusted between about 0.33 h−1 and about 0.55 h−1 with the BMA concentration kept constant at about 20% v/v. A further adaptive evolution experiment was achieved with a step-wise increases in temperature from 37° C. to 44° C., while maintaining the BMA concentration at about 20% v/v and initial dilution rate of about 0.41 h−1. Adaptive evolution with the use of a pH-auxostat can be achieved using a pH feedback control system, where the inflow of nutrients, base, and other additives are initiated only when the pH goes below the set value. The acidification of the media in the bioreactor indicates growth of cells in the culture with its rate controlling the addition of nutrients and consequently the dilution rate. The dilution rate adjusts to match the growth rate of the culture under the imposed condition and allows auto-selection, where the rapidly growing strains persist in the bioreactor and slower growing strains being washed out. The evolution experiment of E. coli in the pH-auxostat can be started with no BMA initially added to the bioreactor. The BMA concentration can gradually be increased from 0 to 0.1%, 0.5%, 1.0%, 5.0%, 10%, and 20% v/v.
The microorganism is grown in a suitable fermentation medium as described above at about 37° C., for example at about 200 RPM.
The methacrylate is as described elsewhere herein.
The invention also relates to a microorganism isolated by a method described above.
All documents mentioned in this specification, including all reference to SEQ ID NOs in gene and protein databases are incorporated herein by reference in their entirety. Sequence versions are version 1 unless otherwise specified.
“and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example “A and/or B” is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually herein. Unless context dictates otherwise, the descriptions and definitions of the features set out above are not limited to any particular aspect or embodiment of the invention and apply equally to all aspects and embodiments which are described.
The invention is further described in the following non-limiting examples.
EXAMPLES
Example 1: Isolation and Characterisation of BMA Tolerant Mutant Strains
E. coli K12 MG1655 was used in these experiments. This is a common laboratory strain and the complete genome sequence of this strain is available (NCBI Reference Sequence: NC_000913.3). This strain can, for example, be obtained from the Coli Genetic Stock Center (CGSC) (strain 7636) or ATCC.
We isolated E. coli MG1655 variants that are tolerant to BMA. E. coli MG1655 was grown in MSX medium containing 20% (v/v) BMA for 72 hours, in 30 mL vials at 37° C., 250 rpm. Growth was observed after 72 h. A sample from this culture was streaked out onto LB agar plates and incubated overnight at 37° C. Colonies were then isolated and whole genome deep sequencing analysis using Illumina NGS technology according to the manufacturers' directions was performed to characterise the mutants. Fastq output files were analyzed for variants compared to the MG1655 reference genome (accession number NC_00913.1). Sequencing analysis identified the following mutations:
E. coli MG1655 soxR(R20H)
E. coli MG1655 soxR(R20H)acrR(V29G)
E. coli MG1655 soxR(R20H)acrR(T32fs)
In a subsequent screening experiment, wild type E. coli MG1655 and mutants isolated as described above, (E. coli MG1655 soxR(R20H), E. coli MG1655 soxR(R20H)acrR(V29G), E. coli MG1655 soxR(R20H)acrR(T32fs)) were grown in defined medium (MSX) in the absence or presence of 20% (v/v) BMA added immediately after inoculation (FIG. 1). Cultures were grown in 250 mL shake flasks at 37° C. and 250 rpm. The WT strain was unable to grow in the presence of 20% (v/v) BMA, but all mutants were able to grow in the presence of 20% (v/v) BMA demonstrating that the mutations confer resistance to BMA. We also observed that double mutants E. coli MG1655 soxR(R20H)acrR(V29G) and E. coli MG1655 soxR(R20H)acrR(T32fs) were able to grow better than the single mutant with the soxR mutation, showing that the combination of mutations in soxR and acrR provides an additive effect and enhances the tolerant phenotype.
E. coli MG1655, E. coli MG1655 soxR(R20H), E. coli MG1655 soxR(R20H)acrR(V29G) and E. coli MG1655 soxR(R20H)acrR(T32fs) were then grown in MSX medium with 20% (v/v) BMA added during mid-exponential phase (FIG. 2). Cultures were grown in 250 mL shake flasks at 37° C. and 250 rpm. These results show once again that the mutated genes acrR(V29G) and acrR(T32fs) in combination with soxR(R20H) improve the adaptation of the cells and confer enhanced tolerance to BMA compared to the soxR(R20H) mutation alone.
We then created strains in which soxR and acrR respectively were knocked out using standard protocols. The knock-out strains E. coli BW25113 ΔsoxR and E. coli BW25113 ΔacrR were grown in the absence or presence of 20% (v/v) BMA added immediately after inoculation (FIG. 3). Cultures were grown in MSX medium in 30 mL vials at 37° C. and 250 rpm shaking. Although the knock-out strains were able to grow in the medium with no BMA, all of them were unable to grow in the presence of BMA. This shows that the loss of function of acrR and soxR does not confer BMA tolerance. Hence, soxR(R20H) encodes a functional SoxR, capable of regulating the transcription of other genes. Likewise, the mutated genes acrR(V29G) and acrR(T32fs) may encode functional proteins able to confer BMA tolerance.
Strains with single mutations were prepared to understand if acrR(V29G) and acrR(T32fs) could confer BMA tolerance by themselves and, therefore, encode functional proteins. E. coli MG1655 acrR(V29G) and E. coli MG1655 acrR(T32fs) were then grown with or without 20% (v/v) BMA, added immediately after inoculation (FIG. 4). Cultures were grown in MSX medium in 30 mL vials at 37° C. and 250 rpm shaking E. coli MG1655 acrR(V29G) and E. coli MG1655 acrR(T32fs) were all able to grow in the presence of BMA. This suggests that these mutations encode a functional AcrR, able to act as transcription factor, conferring resistance to BMA.
In summary, the results show that mutations in soxR or acrR confer resistance to BMA compared to wild type E. coli and that double mutants that comprise mutations in both soxR or acrR show enhanced resistance.
Example 2: Isolation and Characterisation of BMA Tolerant Mutant Strains by Adaptive Evolution
We identified BMA tolerant strains using an adaptive evolution approach. In summary, adaptive evolution involves the extended propagation of a microbial strain under the influence of the desired selective pressure. Mutants with enhanced growth rates due to increased tolerance will occasionally arise and expand within the population over time. Enhanced strains are therefore obtained by repeated isolation, characterization, and sequencing of these mutant isolates.
The experiments used E. coli strain BW25113. This is a common laboratory strain and the complete genome sequence of this strain is available (NCBI Reference Sequence: NZ_CP009273.1, see Grenier et al: Complete Genome Sequence of Escherichia coli BW25113, Genome Announc. 2014 September-October; 2(5): e01038-14). This strain can, for example, be obtained from the Coli Genetic Stock Center (CGSC) (strain 7636) or ATCC.
The effect of BMA on its growth was firstly investigated by growing the microorganism in the presence of BMA at a concentration range of 0.01% to 20.0% v/v (FIGS. 5a and 5b). Growth of E. coli at a BMA concentration of 0.01% v/v (FIG. 5.1) was very similar to its growth in the absence of BMA. However, a longer lag phase and lower growth rate was observed as the BMA concentration was increased further to 0.05 and 0.1% v/v (FIG. 5a and Table 2.1). Therefore, BMA inhibits the growth of E. coli at concentrations above 0.05% v/v.
As the BMA concentration was increased further to 20% v/v (FIG. 5b), cell growth was only observed after 24-36 hours of incubation, and growth was inconsistent.







TABLE 2.1







Growth kinetic parameters of E. coli at various BMA concentrations










BMA content 
Max cell 
Growth 
Lag 


(% v/v)
concentration (g L−1)
rate (h−1)
phase (h)





0
1.436 ± 0.213
0.728 ± 0.011
 1


0.01
1.365 ± 0.120
0.617 ± 0.009
 2


0.05
1.269 ± 0.074
0.517 ± 0.014
 4


0.1
1.335 ± 0.074
0.519 ± 0.010
12









Cultures grown with 0.1 and 0.5% v/v BMA were subcultured (FIG. 5.3) to understand the BMA tolerance limit of E. coli. An aliquot was taken from a culture grown with 0.1% v/v BMA, transferred to fresh medium and grown under the same conditions. The growth pattern of the subculture population was very much the same as for the previous culture (FIG. 5c), which suggests that the tolerance observed at 0.1% v/v BMA is likely due to the inherent tolerance of E. coli. On the other hand, the subculture taken from a culture grown at 0.5% v/v BMA exhibited significant growth after only 12 hours of inoculation, which is much earlier compared to the progenitor culture grown under the same conditions (FIG. 5c). The difference in the growth pattern of the original culture and the subculture suggests that the growth of E. coli in the subculture was not due to inherent tolerance but rather acquired after exposure to 0.5% v/v BMA.
The result from the subculture experiments suggested that the inherent tolerance of E. coli towards BMA is at least 0.1% v/v, but no more than 0.5% v/v.
Various adaptive evolution experiments were used to generate BMA tolerant E. coli. In the first experiment (ADE-1; FIG. 5d), three parallel cultures were grown in a 50 mL FALCON® tube containing 10 mL M9 minimal medium with increasing BMA concentration from 0.1% to 0.5%, 1.0%, 5.0%, 10.0%, and 20% v/v, respectively for each sequential transfer. An aliquot of 0.15 mL was used from the previous culture and transferred to the fresh media with higher BMA concentration. The best growing culture was used as the starting culture for the next sequential transfer.
In the second adaptive evolution experiment (ADE-2; FIG. 5e), the cells allowed to undergo five (5) serial transfers at the same BMA concentration prior to increasing the BMA concentration. In this experiment, each of the three cultures were used as a starting culture for the sequential transfer in separate tubes.
A third adaptive evolution experiment (ADE-3; FIG. 5f) was done by growing E. coli once with 0.1% v/v BMA, then twice with 10% v/v BMA, and finally 45 times with 20% v/v BMA.
The fourth adaptive evolution experiment was achieved using a chemostat culture (ADE-4; FIG. 5g). The BMA concentration was gradually increased in a step-wise manner from 0 to 20% v/v at a constant dilution rate. After attaining a stable cell concentration at 20% v/v BMA, the dilution rate of the culture was adjusted between 0.33 h−1 and 0.55 h−1 with the BMA concentration kept constant at 20% v/v.
After the adaptive evolution experiments, an aliquot of the surviving culture was plated into LB agar and a number (at least 6) individual colonies were picked and regrown in liquid media to save stock cultures of each isolated strain. In order to evaluate and compare how BMA affects the growth of each of the isolated strains, their growth kinetics in the presence of 20% v/v BMA were determined. The standard growth conditions used in the determination of strain growth kinetics was a starting optical density (O.D.) of  ̃0.025 in 50 mL of M9 medium containing 10 g L−1 glucose and 20% v/v BMA in a 250 mL conical flasks fitted with suba-seals at 37° C. and 200 rpm using a shaker incubator. Growth was monitored by measuring its O.D. for 36 hours and samples were taken every hour for the first 13-18, 24 and 36 hours after inoculation. A summary of the cell growth kinetic parameters of the isolated strains are listed in Table 2.2. The growth curves of the isolated strains are also shown in FIG. 5.













Strain; % BMA (v/v)
Max cell concentration (g L−1)
Growth rate (h−1)
Lag time (h)







Wild Type; 0
1.436 ± 0.213
0.728 ± 0.011
2


Wild Type; 0.05
1.269 ± 0.074
0.517 ± 0.014
4


Wild Type; 0.1
1.335 ± 0.074
0.519 ± 0.010
12 


2a-rob(R156H) rpoC(L361R)
0.651 ± 0.052
0.532 ± 0.028
6


ilvN(C41Y) ygbK(A294E)





IpxM(168_185del)





3b-rob(R156H) ilvN(C41Y)
0.790 ± 0.076
0.566 ± 0.010
4


phoP(L11F) acrB(V448L)





acrR(indels)





5c-soxR(Leu139X),
0.597 ± 0.096
0.625 ± 0.052
5


580116(G > T)





acrR(indels)





6c-soxR(A146del),
0.588 ± 0.029
0.620 ± 0.029
4


acrR(indels)





7c-rob(A70V)
0.568 ± 0.050
0.613 ± 0.033
4


acrR(indels)





8e-rob(R156H) rpoB(T1037P)
0.435 ± 0.010
0.712 ± 0.015
5


torY(A87T) acrR(49Yfs)





18d-rob(A70T)yohJ(L109R)
1.036 ± 0.046
0.709 ± 0.015
5


dnaK(V377G) 927777(C > T)





acrR(A191fs)





19f-marR(V84G) rpoC(R1075C)
0.653 ± 0.023
0.701 ± 0.007
5


ompR(R15S) acrB(T3791)





acrR(indels)





20f-marR(V84G) rpoC(R1075C)
0.589 ± 0.012
0.719 ± 0.041
5


ompR(R15S)





acrR(indels)





21f-marR(V84G) rpoC(R1075C)
0.438 ± 0.022
0.703 ± 0.030
5


rpoC(A787V) ompR(R15S)





acrB(V901l)





acrR(indels)





22g-rob(R156H) rpoB(T1037P)
0.523 ± 0.024
0.701 ± 0.015
4


groL(P279L) acrR(49Yfs)





1197659(C > A)





23g-soxR(R20L) rpoC(r1075C)
0.529 ± 0.023
0.722 ± 0.019
4


2133236( T> A) 3915915(T > G)





acrR(indels)





Source of strains: a= FIG. 5.2,


b= ADE-1,


c= ADE-2,


d= ADE-3


e= ADE-4.


f to g were taken from ADE-4 at different dilution rates (h1), where f = 0.46 and g = 0.54.


NCBI Reference Sequence: NZ_CP009273.1






The genomic DNA sequences of various BMA tolerant strains generated from ADE-1, ADE-2, ADE-3 and ADE-4 were analysed and compared with reference to the parental strain E. coli BW25113 (Tables 2.3, 2.4, and 2.55). Genomic DNA samples for DNA sequencing were prepared from overnight cultures of selected isolates in LB broth using the GeneEluteTM Bacterial Genomic DNA Kit with Tris-HCl (10 mM; pH=7.5) as the eluent. The DNA sequence was analyzed using MiSeq v2 150PE (Illumina®) to yield at least 11M+11M reads per run. Reads were trimmed to a minimum length of 36 for quality at the 3′ end with a threshold of 30 and adapter sequences of the Nextera XT kit (SEQ ID NO. 33: CTGTCTCTTATA) using Cutadapt version 1.12. Genome alignment and variant calling were undertaken with the Snippy pipeline to identify the difference in genomic DNA sequence between the isolated strains and parental strain/reference genome (Escherichia coli strain BW25113, assembly ASM75055v1, annotation version 34 from Ensembl). Snippy version 3 was used with a minimum of 10 reads covering each position, and 0.9 as the minimum fraction of the reads that must differ from the reference.







TABLE 2.3







Summary of changes in the genomic DNA of the BMA tolerant isolates from various batch culture


adaptive evolution encoding gene expression regulatory proteins.
















Genomic








Coordinate
Nucleotide
Effect of Nucleotide






(NCBI Reference
Mutation
change; Length of




Gene Description
Cellular
Sequence:
Before →
Amino Acid



Gene
(Uniprot)
Location
NZ_CP009273.1)
After
Sequence
Strain
















rpoB
RNA polymerase β
Cyt
4174281
A → C
missense -
 8



subunit



Thr1037Pro ; 1342



rpoC
RNA polymerase β′
Cyt
4174281
T → G
missense -
 2



subunit



Leu361Arg ; 1407



rpoC
RNA polymerase β′
Cyt
4177637
C → T
missense -
21



subunit



Ala787Val; 1407



rpoc
RNA polymerase β′
Cyt
4178500
C → T
missense -
19, 20,



subunit



Arg1075Cys ; 1407
21,23


rob
Right origin binding
Cyt
4624661
C → T
missense -
2, 3,



protein



Arg156His ; 289
8,22


rob
Right origin binding
Cyt
4624919
G → A
missense -
 7



protein



Ala70Val ; 289



rob
Right origin binding
Cyt
4624920
C → T
missense -
18



(rob) protein



Ala70Thr ; 289



rob
Right origin binding
Cyt
4625592
C → T
silent - Val85Val;
18



(rob) protein



289



SOXR
Superoxide
Cyt
4267455
G → T
Missense-
23



response regulon



Arg20Leu; 154




activator







SOXR
Superoxide
Cyt
4267812
T → A
Truncation- stops at
 5



response regulon



Leu139 ; 154




activator







SOXR
Superoxide
Cyt
4267830
3 bp
Removal of Ala146
 6



response regulon


Deletion
without changing the




activator



succeeding








sequence ; 154



marR
Multiple antibiotic
Cyt
1613627
G → A
Missense-Val84Gly ;
19, 20,



resistance (mar)



144
21



operon - repressor








protein







acrR
acriflavine
Cyt
 481361
11 bp
change in amino
 8



resistance regulator-


deletion
acid sequence




acrAB operon



starting at position




repressor



53 ; 215



acrR
acriflavine
Cyt

Frameshift
Frameshift at
8, 22



resistance regulator-



position 49 Y




acrAB operon








repressor







acrR
acriflavine
Cyt

Frameshift
Frameshift at
 8



resistance regulator-



position 191




acrAB operon








repressor







acrR
acriflavine
Cyt

Indels
Unknown
2, 3, 5,



resistance regulator




6, 7,



-acrAB operon




19, 20,



repressor




21,23


ompR
Outer membrane
Cyt
3529901
G → T
missense -
19, 20,



porin protein -



Arg15Ser ; 239
21



activator







phoP
Magnesium
Per
1185871
C → A
missense -
 3,



starvation regulon-



Leu11Phe ; 223




regulator





Notes:


Cellular Location; Cyt- Cytoplasm, Per- Periplasm, IM- Inner Membrane, Uk- Unknown













TABLE 2.4







Summary of changes in the genomic DNA of the BMA tolerant isolates from various


batch culture adaptive evolution encoding non-regulatory functional proteins.


















Effect of






Genomic

Nucleotide






Coordinate
Nucleotide
change;




Gene

(NCBI Reference
Change/
Length of




Description
Cellular
Sequence:
Mutation
Amino Acid



Gene
(Uniprot)
Location
NZ_CP009273.1)
Before → After
Sequence
Strain
















acrB
Part of the
IM
 478518
C → A
missense -
 3



acrAB-tolC



Val448Leu ; 




multi-drug efflux



1049




complex







acrB
Part of the
IM
 477159
C → T
missense -
19, 21



acrAB-tolC



Thr379lle ;




multi-drug efflux



1049




complex







yohJ
Membrane
IM
2224428
T → G
missense -
18



protein



Leu109Arg;








132



tory
N-oxide and 
IM
1952131
C → T
missense -
 8



S-oxide reductase



Ala87Thr ;




subunit



366
 


IpxM
Myristoyl-acyl
IM
1933628
20 bp deletion
change in
2



carrier protein



amino acid




dependent



sequence




acyltransferase



starting at








position 275;








323



dnak
Molecular
Cyt
  13292
T → G
missense -
18



chaperone



Val377Gly ;




(HSP70)



638



groL
Chaperonin
Cyt
4361677
C → T
missense -
22



groEL (HSP60)



Pro279Leu ;








548



ilvN
Acetolactate
Cyt
3844331
C → T
missense -
2,3



synthase



Cys41Tyr ;




isozyme 1 small



96




subunit -








Activity








regulator







ygbK
Conserved
Uk
2856574
C → A
missense -
 2



protein -



Ala294Glu ;




unknown



388




function





Notes:


Cellular Location; Cyt- Cytoplasm, Per- Periplasm, IM- Inner Membrane, Uk- Unknown













TABLE 2.5







Summary of changes in the genomic DNA of the BMA tolerant isolates from various


batch culture adaptive evolution in non-coding regions.


















Effect of






Genomic

Nucleotide






Coordinate
Nucleotide
change;






(NCBI Reference
Change/
Length of




Gene Description
Cellular
Sequence:
Mutation
Amino Acid



Gene
(Genome Viewer)
Location
NZ_CP009273.1)
Before → After
Sequence
Strain





+230
Unknown
Uk
 580116
G → T
unknown
 5


appY








and








+19








ompT








−271
unknown
Uk
 927777
C → T
unknown
18


Irp








and








−274








trxB








+45
Unknown
Uk
1197659
C → A
unknown
22


cohE








and








−120








ymfJ








+4
Unknown
Uk
2133236
T → A
unknown
23


asmA








and








+270








yegH








−115
Unknown
Uk
3915915
T → G
unknown
23


atpl








and








+502








rsmG





Notes:


Cellular Location; Cyt- Cytoplasm, Per- Periplasm, IM- Inner Membrane, Uk- Unknown indels- insertion or deletion






As can be inferred from Table 2.3 and Table 2.4, each strain had a mutation in acrR. Furthermore, each strain further had a mutation in one of soxR, marR or rob.
Example 3—Transcriptomic Data
Transcriptome analysis was carried out to characterize transcriptional activity in mutant microorganisms using standard methods.
RNA Extraction Protocol
Material:

    
    
        RNeasy Protect Bacteria Mini kit (50)—Qiagen 74524
        RNase-Free DNase Set (50)—Qiagen 79254
        RNaseZAP—Cleaning agent for removing Rnase—Sigma-Aldrich R2020-250ML
        RNase free eppenfords and 15 ml falcon tubes
        RNase free tips
    
    


Perform all the extraction in a RNase free “environment”, clean everything with RNaseZAP, always use gloves and change gloves frequently.
1. MSX Medium
To prepare 1 L:
Vishniac Trace Elements
Combine EDTA disodium salt (50 g) with water (800 ml), dissolved by adding KOH pellets (2-3 at a time). Add chemicals in the following order; ZnSO4 (2.2 g), CaCl2 (5.54 g), MnCl2·4H2O (5.06 g), FeSO4·7H2O (5 g), (NH4)6MO7O24·4H2O (1.1 g), CuSO4·5H2O (1.57 g) and CoCl2·6H2O (1.61 g).
Adjust to pH 6 using 1M KOH, make up to 1 L using water and store at 4° C. until use.
MSA


    
    
        KH2PO4 (6 g) and Vishniac trace elements (2 ml) in water (700 ml)
    
    


Adjust to pH 7 using 1M KOH. Make up to 760 ml with water.
MSB


    
    
        NH4Cl (3 g) and MgSO4·7H2O (0.4 g) in water (200 ml).
    
    


Sterilize MSA and MSB, then mix and add 40 mL of a stock solution of 12.5% glucose. To make a total 1 L of MSX.
2. Sample Preparation

    
    
        1) Streak strains onto fresh MSX agar (15 g/L) plates directly from the cryostocks and incubate overnight at 37° C.
        2) Isolate single colonies and inoculate pre-cultures in MSX, using 50 ml shake flasks. Incubate overnight at 37° C. and 250 rpm.
        3) Inoculate cultures in MSX to an initial OD600 of 0.05, using 250 mL pyrex shake flasks with 24/29 neck join. Incubate at 37° C. and 250 rpm. Do 4 biological replicates (3 replicates for sequencing plus one backup)—4 flasks per strain.
        4) Seal shake flasks with sterile Suba seals. To monitor OD, take samples using a sterile syringe and needle after first swabbing the Suba seals with 70% ethanol. Monitor OD.
        5) When OD reaches 0.3, collect first sample for RNA extraction (“before” sample) into a pre-chilled falcon. Keep samples on ice.
        6) Immediately after, add 20% (v/v) BMA. Re-incubate cultures.
        7) Quickly process the samples according to the RNeasy kit protocol, until step 6 of protocol 1. Always keep samples on ice and store it at −80° C. until further use, if possible, flash freeze in liquid nitrogen it before storing.
        8) One hour after the first sample collection/BMA addition, collect the second sample for RNA extraction (“after” sample). Proceed as explained before.
        9) Continue to monitor the OD until the cultures reach 24 h.
        To summarise, each strain tested will have 6 samples to send for sequencing, 3 collected right before the addition and 3 collected one hour after, plus 1 “back-up” for before and after, in case something goes wrong during extraction (8 samples total). Besides the WT strain with the addition of BMA, samples were also collected from a WT culture with no BMA, one hour after reaching OD of 0.3, as a control.
    
    


3. RNA Extraction
Proceed according to the RNeasy kit instructions. Protocol 1 and 7—for Gram-negative bacteria grown on minimal media—plus appendix B “On-Column DNase Digestion Using the RNase-Free DNase Set”.
Separate final sample into 3 aliquots. Use only one aliquot to check concentration and if there are gDNA contaminations. Do not use this aliquot for sequencing, as thawing and freezing the samples can degrade the RNA.
Check RNA Concentration and RIN Numbers Using TapeStation.
Transcription was compared for a double mutant and the wild-type in the presence and absence of BMA relative to the level in the wild type in the absence of BMA. For the avoidance of doubt the level in the table is the ratio of the level in the strain under the BMA exposure relative to the level in the wild type in the absence of added BMA. Levels of transcription of acrA and acrB were enhanced in the absence of BMA, however this was very variable. For the wild type strain, exposure to BMA actually reduces the expression level of the global regulator. This demonstrates that the principal multi drug resistance pump is strongly over expressed in these strains. The results are shown in Table 2.6 below.







TABLE 2.6







acrAB gene expression
















LM 










double






wild



mutant
2
5
18
21
22
23
type





Transcriptomics










without BMA










added vs wild










type










acrA
6.88
2.81
7.54
16.98
0.75
8.31
2.49



acrB
6.89
3.71
7.13
 3.12
2.02
3.81
4.80



Transcriptomics










with added










BMA vs wild










type without










BMA










acrA
5.13
7.33
6.28
 6.47
5.63
7.44
6.50
0.64


acrB
4.99
6.68
7.49
10.12
8.93
7.17
7.66
0.98









The transcription levels of some key genes was enhanced or reduced strongly by BMA. The “top 27” enhancements with BMA relative to BW25113 without BMA exposure are shown in the table 2.7. For comparison, the same genes without exposure to BMA are shown in table 2.8. Transcription was compared for a double mutant and the wild-type in the presence and absence of BMA relative to the level in the wild type in the absence of BMA. For the avoidance of doubt the level in the table is the ratio of the level in the strain under the BMA exposure relative to the level in the wild type in the absence of added BMA.







TABLE 2.7







Transcriptomic data of the double mutant compared with wild-type and 6 other strains, with 


added BMA.














double mutant
2
5
18
21
22
23
wild type


















ibpB
672.54 
84.03
174.50 
158.35 
30.97
107.99 
41.67
0.42


asr
711.06 
95.27
160.42 
74.22
11.63
225.15 
123.20 
0.22


yhjx
 2.32
 7.35
105.59 
251.44 
 3.11
902.70 
596.44 
1.72


ydgU
188.87 
31.80
48.46
28.47
 6.39
94.74
50.45
7.95


narG
 3.23
11.38
47.85
25.46
65.34
61.85
42.52
0.40


ibpA
80.35
20.83
43.39
74.55
29.21
70.31
31.35
0.09


soxS
20.93
 4.10
41.81
 1.17
 1.08
 3.66
30.40
0.24


ynfM
29.92
14.42
40.65
55.40
65.39
61.15
41.92
0.07


nirB
 3.28
 8.77
34.19
23.98
39.43
20.40
25.46
0.06


yibT
43.57
36.87
29.57
83.81
95.47
77.30
42.63
0.09


adiY
10.80
 5.37
24.79
21.13
10.74
23.19
 6.73
0.19


pspA
27.60
15.40
23.32
20.71
21.16
47.39
32.81
0.04


ariR
 8.91
35.30
21.79
25.19
 6.13
12.95
14.82
0.44


spy
99.47
22.92
20.88
 4.36
 1.77
45.77
 4.79
3.91


bssR
 5.47
15.30
20.35
134.14 
198.48 
71.24
71.61
0.46


ybfA
59.92
18.45
20.19
24.95
33.06
36.33
29.99
0.39


raiA
36.36
14.09
20.11
44.16
22.55
52.61
31.13
0.11


ybhG
10.78
 6.87
18.33
18.85
 9.26
21.92
20.82
0.19


IdhA
30.42
11.32
18.24
56.74
20.48
25.80
28.20
0.59


ymgC
11.68
42.36
17.15
12.62
 1.53
5.45
 7.42
6.27


pspB
11.73
11.46
16.87
20.94
14.98
35.43
27.16
0.73


nirD
 3.57
 4.33
16.69
34.98
42.50
26.97
25.17
0.57


pspc
11.09
11.88
16.55
21.37
14.67
39.73
28.45
0.10


ymgA
 9.97
35.59
16.41
11.97
 2.43
 6.44
 8.84
0.16


yohk
19.51
 8.45
16.04
14.54
 7.09
19.75
10.04
0.13


rmf
17.63
 7.05
15.45
20.96
36.77
17.43
 8.80
0.28


ybiH
 7.73
 8.65
15.30
12.75
 7.20
16.75
16.75
0.04


pspD
10.00
11.22
14.10
18.60
14.80
38.90
28.18
0.14
















TABLE 2.8







Transcriptomic data of the double mutant compared with wild-type and 


6 other strains, without added BMA.















double









mutant
2
5
18
21
22
23










Transcriptomics without BMA added vs wild type














ibpB
0.76
0.53
1.12
1.35
0.36
0.81
0.75


asr
1.45
0.89
1.54
1.16
6.45
0.92
0.71


yhjx
0.52
0.66
0.75
0.73
0.59
0.70
1.01


ydgU
0.51

0.86
0.54
1.30
0.44
0.74


narG
6.67
0.84
4.48
25.35 
42.79 
1.06
6.33


ibpA
0.74
0.74
0.86
1.11
0.21
0.58
0.79


soxS
48.09 
0.82
31.44 
0.43
2.23
0.51
32.04 


ynfM
1.43
0.94
1.07
4.08
7.33
1.36
1.23


nirB
13.77 
0.70
5.79
35.54 
24.66 
4.25
10.18 


yibT
0.82
6.72
0.81
1.39
2.51
4.87
0.50


adiY
0.91
0.80
0.96
1.88
2.19
2.11
1.11


pspA
0.27
0.61
0.53
0.11
0.53
0.25
0.47


ariR
0.92
2.82
2.09
2.65
0.21
0.62
0.56


spy
0.42
0.48
0.75
0.42
0.28
0.28
0.40


bssR
2.52
1.08
1.48
4.39
43.23 
4.43
3.69


ybfA
1.27
1.03
1.29
0.91
3.08
1.57
1.27


raiA
1.06
0.77
0.81
1.49
5.91
0.89
0.84


ybhG
1.20
0.83
1.19
0.37
0.78
0.28
0.33


IdhA
1.18
0.78
1.13
0.92
0.90
0.95
1.09


ymgC
0.74
3.06
2.04
1.86
0.26
1.11
0.57


pspB
0.28
0.59
0.47
0.09
0.30
0.25
0.45


nirD
22.13 
0.78
9.18
54.68 
45.97 
3.30
16.04 


pspc
0.29
0.59
0.46
0.08
0.18
0.23
0.44


ymgA
0.57
2.99
2.16
2.47
0.35
0.86
0.74


yohK
1.02
1.20
1.08
0.88
1.94
1.64
0.97


rmf
1.54
1.07
1.31
1.50
4.53
1.14
0.50


ybiH
1.21
0.93
1.05
0.46
0.69
0.54
0.61


pspD
0.28
0.58
0.48
0.08
0.12
0.21
0.40









There was no consistent trends for transcription levels in the case where BMA is not fed. In the presence of BMA, ibpA, ibpB, ynfM, yibT, pspA, bssR, ybfA, raiA, IdhA, pspB pspC and pspD are all enhanced by greater than x10 in the strains, but all are reduced in the wild type strain. In the absence of BMA none of ibpA, ibpB, ynfM, yibT, pspA, bssR, ybfA, raiA, IdhA, pspB and pspC were enhanced in the strains. The functions of these genes are listed in Table 2.9.







TABLE 2.9







functions of the genes that were not enhanced 


when BMA was not fed to cultures.








gene
function





IbpA
heat shock chaperone(ibpA)


IbpB
heat shock chaperone(ibpB)


pspA
regulatory protein for phage-shock-protein operon(pspA)


pspB
Phage shock protein operon transcription co-activator(pspB)


pspc
Phage shock protein operon transcription co-activator(pspC)


pspD
Phage shock protein operon transcription co-activator(pspD)


raiA
cold shock protein associated with 30S ribosomal subunit(raiA)


ynfM
putative arabinose efflux transporter(ynfM)


yibT
uncharacterized protein(yibT)


bssR
repressor of biofilm formation by indole transport regulation



(bssR)


ybfA
DUF2517 family protein(ybfA)


IdhA
fermentative D-lactate dehydrogenase, NAD-dependent(IdhA)

## Claims

1. A method for the production of a methacrylate comprising
a) providing a genetically modified microorganism with increased tolerance to a C3-C12 methacrylate ester compared to the wild type microorganism in a fermentation medium and
b) growing the microorganism under conditions whereby a C3-C12 methacrylate ester is produced;
wherein the microorganism is E coli; 
wherein the genetically modified microorganism comprises a mutation in a wild type soxR nucleic acid sequence;
wherein the wild type soxR nucleic acid sequence comprises SEQ ID NO. 1 or a homologue thereof, and
wherein the mutant soxR nucleic acid sequence encodes a mutant SoxR protein comprising R20 substituted with H.

2. The method according to claim 1 wherein the microorganism is tolerant to at least 20% v/v C3-C12 methacrylate ester when grown in a liquid medium at about 37° C.

3. The method according to claim 1 wherein the genetically modified microorganism further comprises a mutation in one or more of:
an acrR nucleic acid sequence comprising SEQ ID NO. 3 or a homologue thereof, a rob nucleic acid sequence comprising SEQ ID NO. 5 or a homologue thereof, a marR nucleic acid sequence comprising SEQ ID NO. 7 or a homologue thereof.

4. The method according to claim 3, wherein the mutant acrR nucleic acid sequence encodes a mutant AcrR protein, and wherein the mutation is selected from one of the following: a substitution of V29 with another amino acid, a frameshift mutation at T32, A191 or position 49 in AcrR.

5. A method for growing or maintaining a microorganism in the presence of a C3-C12 methacrylate ester comprising providing a genetically modified microorganism with increased tolerance to a C3-C12 methacrylate ester compared to a wild type microorganism in a fermentation medium under conditions whereby a C3-C12 methacrylate ester is produced,
wherein the microorganism is E coli; 
wherein the genetically modified microorganism comprises a mutation is in a wild type soxR nucleic acid sequence;
wherein the wild type soxR nucleic acid sequence comprises SEQ ID NO. 1 or a homologue thereof; and
wherein the mutant soxR nucleic acid sequence encodes a mutant SoxR protein comprising R20 substituted with H.

6. A fermentation medium comprising a C3-C12 methacrylate ester and a genetically modified microorganism with increased tolerance to a C3-C12 methacrylate ester compared to a wild type microorganism;
wherein the microorganism is E. coli; 
wherein the genetically modified microorganism comprises a mutation is in a wild type soxR nucleic acid sequence;
wherein the wild type soxR nucleic acid sequence comprises SEQ ID NO. 1 or a homologue thereof; and
wherein the mutant soxR nucleic acid sequence encodes a mutant SoxR protein comprising R20 substituted with H.

7. A method for the isolation of a methacrylate tolerant microorganism comprising:
a) providing a microorganism in a fermentation medium
b) contacting the microorganism with a methacrylate; and
c) isolating the viable microorganism of step (b)
wherein the viable microorganism is tolerant to at least 20% v/v a methacrylate when grown in liquid medium at about 37° C.
wherein the microorganism is E coli; 
wherein the microorganism comprises a mutation in a wild type soxR nucleic acid sequence;
wherein the wild type soxR nucleic acid sequence comprises SEQ ID NO. 1 or a homologue thereof; and
wherein the mutant soxR nucleic acid sequence encodes a mutant SoxR protein comprising R20 substituted with H.

8. The method according to claim 3, wherein the mutant rob nucleic acid sequence encodes a mutant Rob protein, and wherein the mutation is selected from one of the following: a substitution of A70 or a substitution of R156 with another amino acid in Rob.

9. The method according to claim 3, wherein the mutant marR nucleic acid sequence encodes a mutant MarR protein, and wherein the mutation is a substitution of V84 with another amino acid in MarR.