# Patent

## Title
Producing methionine without N-acyl-methionine

## Abstract

The present invention relates to a method for the production of methionine or its derivatives by culturing a microorganism in an appropriate culture medium comprising a source of carbon and a source of sulphur. The microorganism and/or the culture medium and/or the process parameters were modified in a way that the accumulation of the by-product N-acyl-methionine (NAM) is reduced. The isolation of methionine or its derivatives from the fermentation medium is also claimed.

## Background
FIELD OF THE INVENTION
The present invention relates to a method for the production of methionine or its derivatives by culturing a microorganism in an appropriate culture medium comprising a source of carbon and a source of sulphur. The microorganism and/or the culture medium and/or the process parameters were modified in a way that the accumulation of the by-product N-acyl-methionine (NAM) is reduced. The isolation of methionine or its derivatives from the fermentation medium is also claimed.
INTRODUCTION
Sulphur-containing compounds such as cysteine, homocysteine, methionine or S-adenosylmethionine are critical to cellular metabolism and are produced industrially to be used as food or feed additives and pharmaceuticals. In particular, methionine, an essential amino acid, which cannot be synthesized by animals, plays an important role in many body functions. Currently D,L-methionine is produced by chemical synthesis from acrolein, methyl mercaptan and hydrogen cyanide. Increasing prices for petrol-derived precursors acrolein and methyl mercaptan coupled to the increasing methionine demand render microbial production of methionine attractive.
The pathway for L-methionine synthesis is well known in many microorganisms (reviewed in Figge R M (2006), ed Wendisch V F, Microbiol Monogr (5) Amino acid biosynthesis p164-185). E. coli and C. glutamicum methionine producer strains have been described in patent applications WO2005/111202, WO2007/077041, WO2007/012078 and WO2007/135188.
Methionine produced by fermentation needs to be purified from the fermentation broth. Cost-efficient purification of methionine relies on producer strains and production processes that minimize the amount of by-products in the fermentation broth. “By-products” originate from methionine transforming and/or degrading pathways. In particular these products are S-adenosyl-methionine (SAM), thio-methyl-ribose and the N-acyl-methionines (NAM) such as N-acetyl-methionine and N-propionyl-methionine. As shown in patent application PCT/EP2007/060433, E. coli methionine producer strains produce N-acetyl-methionine. E. coli also produces N-propionyl-methionine.
The production of NAM is not desirable, since it reduces methionine yield and renders purification of methionine more difficult. NAM can be transformed to methionine and acetate by the addition of NAM acylases at the end of the fermentation run, but this drastically increases the cost of the product. Therefore, it is necessary to reduce or eliminate the accumulation of NAM during the fermentation run. This requires a good understanding of the reactions that are responsible for the accumulation of NAM.
N-terminal acetylation of methionine as a co-translational process is one of the most common protein modifications in eukaryotes. Nevertheless, it is unlikely that N-acetyl-methionine is produced by N-terminal acetylases (for review see Polevoda & Sherman 2000 JBC 275, 47, pp 36479-36482), since methionine seems to be acetylated as a free amino acid in methionine producing bacteria and methionine acetylation as a co-translational process is rare in prokaryotes (Driessen et al. 1985, CRC Crit. Rev. Biochem. 18, 281-325). N-acetyl-methionine is most likely obtained by acetylating free L-methionine. N-acetylating enzymes, which possibly could acetylate methionine, have been described. For example, ArgA encodes an N-acetyl-glutamate synthase in E. coli (Marvil & Leisinger 1977 JBC 252, 10 pp. 3295-3303).
Up to now, enzymes able to catalyze the biosynthetic production of N-acetyl-methionine, N-propionyl-methionine or other methionine derivatives with longer acyl chains were unknown. Identification of the major methionine-N-acyl transferase activities and their attenuation in methionine producing microorganisms is thus crucial for the reduction of NAM production.
NAM accumulation may also be reduced by deacetylating the accumulated NAM to obtain methionine. Deacetylation of N-acyl groups from amino acids has been demonstrated in bacteria. For example, ArgE encoded N-acetylornithine deacetylase has a broad substrate spectrum and deacetylates efficiently N-acetylmethionine (Javid-Majd & Blanchard 2000 Biochemistry 39, 1285-93). Thus, overexpression of argE or other amino acid deacetylases, such as rat kidney acylase I (Giardina et al 2000 Eur. J. Biochem. 267, 6249-55), amino acid acylase from Aspergillus niger or pig kidney (Gentzen et al. 1980 Z. Naturforsch 35 c, 544-50) may reduce the accumulation of NAM.
Since NAM is exported into the extracellular space, the export of NAM acylases into the periplasm or extracellular space can be an advantage. Several export systems are known in E. coli that permit the export into the periplasm, for example systems TAT and Sec (reviewed in Manting & Driessen 2000 Mol Microbiol 37, 226-38, Choi & Lee 2004 Appl. Microbiol. Biotechnol. 64, 625-635). Export via the TAT or Sec pathway requires the presence of specific signal peptides. If export into the extracellular space is favoured, the protein of interest may be fused to carrier proteins that are normally exported into the medium, such as OmpF or hemolysin (Choi & Lee 2004 Appl. Microbiol. Biotechnol. 64, 625-635). The protein can also be exported into the medium or displayed on the cell surface by fusing it to protein domains that are required for the export of autotransporter proteins, such as IgA1 from N. gonorrhoeae or AIDA-I from E. coli. Proteins may also be exported via the two-partner pathway or phage display (Jacob-Dubuisson et al. 2004 Biochim et Biophys Act 1694 235-257, Jose & Meyer 2007 Microbiol and Molecul Biol Rev 71, 600-19). Process design has also been shown to impact on the export of certain proteins (Shokri et al 2003 Appl Microbiol Biotechnol 60, 654-64).
SUMMARY
The applicants have solved the problem of reducing the accumulation of the by-product N-acyl-methionine (NAM) in methionine producer strains.
The inventors have identified the major methionine N-acyltransferase activity (MNAT), which catalyzes the conversion of methionine to NAM, to be encoded by the gene yncA in E. coli. 
A modified microorganism presenting an attenuation of the expression of the gene yncA, and therefore a reduced production of NAM, is here disclosed.
The inventors also showed that the overexpression of deacylating enzymes, such as Aspergillus oryzae amino acid acylase or pig kidney amino acid acylase, that convert NAM to methionine, lead to a decreased amount of NAM. Preferentially said deacylating enzymes are exported into the periplasm or into the extracellular space.
In another aspect, the culture conditions were adapted to obtain a reduction of the production and/or accumulation of NAM.
These three means to reduce the accumulation of NAM were applied individually or in combination, to reduce the accumulation of NAM.
Glucose is used as a model substrate and recombinant E. coli as model organism, but the invention is not limited to these features.
Accordingly, the object of the present invention is to provide a microorganism in which the expression of major MNAT (Methionine N-Acyl-Transferase) encoding genes have been attenuated, preferentially the corresponding genes deleted, and/or homologous or heterologous NAM deacylating enzymes have been overexpressed, to reduce the accumulation of NAM.
This microorganism with decreased NAM production and/or accumulation shows an improved methionine production/carbon source yield.


DETAILED DESCRIPTION OF THE INVENTION
The invention relates to a method for the production of methionine, its derivatives, or precursors in a fermentative process comprising the following steps:

    
    
        culturing a modified microorganism in an appropriate culture medium comprising a source of carbon, a source of sulphur and a source of nitrogen, and
        recovering methionine and/or its derivatives from the culture medium,

wherein compared to a non-modified microorganism or method, the microorganism or the method has been modified to reduce the accumulation of the by-product N-acyl methionine.

    
    


In a particular aspect of the invention, the N-acyl methionine whose accumulation is reduced is chosen among the following group: N-acetyl-methionine, N-propionyl-methionine, N-butyryl-methionine, and combinations thereof.
The accumulation of the by-product N-acyl methionine can be obtained by at least one of the following modifications:

    
    
        The attenuation of the expression of at least one methionine N-acyl transferase (i.e. transacylases) in the microorganism, and/or
        The expression (or enhancement of expression) of at least one methionine specific amino acylases in the microorganism; and/or
        The variation of culture conditions such as pH, oxygenation temperature, and/or addition of a NAM acylase into the culture medium,

and combinations thereof.

    
    


According to the invention the terms ‘culture’, “fermentation” or “fermentative process” are used interchangeably to denote the growth of bacteria on an appropriate growth medium containing a simple carbon source.
An “appropriate culture medium” is a medium appropriate for the culture and growth of the microorganism. Such media are well known in the art of microorganisms fermentation, depending upon the microorganism to be cultured.
The phrase “recovering methionine and/or its derivatives from the culture medium” designates the action of recovering methionine, and possibly SAM and NAM and all other derivatives that may be useful.
The term “microorganism” designates a bacterium, yeast or fungus. Preferentially, the microorganism is selected among Enterobacteriaceae, Bacillaceae, Streptomycetaceae and Coynebacteriaceae. More preferentially, the microorganism is a species of Escherichia, Klebsiella, Pantoea, Salmonella or Corynebacterium. Even more preferentially, the microorganism is either the species Escherichia coli or Corynebacterium glutamicum. 
The term “modified microorganism” denotes a microorganism that has been genetically modified with the goal to reduce the accumulation of NAM in the fermentation broth. The man skilled in the art knows how to modulate the expression of specific genes. Usual modifications include transforming microorganisms with genetic elements, including deletions of genes, gene replacements, modification of promoters, and introduction of vectors for the expression of heterologous genes.
The inventors have shown that NAM is formed by acylation of methionine and have identified the gene yncA as the major NAM producing enzyme. yncA also known as E. coli gene b1448 has been mentioned in patent application WO2001070776. It is part of a group of genes induced by the regulator Mar, involved in multidrug resistance.
Amino acid acylase enzymes (EC 3.5.1.14), also called deacetylases, catalyze the hydrolytic cleavage of an acyl amino acid to produce the free amino acid and the carbonic acid corresponding to the acyl rest. More specifically N-acyl methionine acylases catalyze the reaction of NAM to methionine and the corresponding carboxy acid.
The term “N-acyl methionine” designates N-formyl-methionine, N-acetyl-methionine, N-propionyl-methionine, N-butyryl methionine and in general, any methionine derivative comprising a functional group derived from any carboxylic acid that lacks the hydroxyl function.
To measure the accumulation of N-acetyl-methionine, the amount of N-acetyl-methionine is determined in the fermentation broth using refractometric HPLC using N-acetyl-methionine (Sigma, Ref 01310) as a standard. N-propionyl-methionine is determined in the fermentation broth by GC-MS using N-acetyl-methionine as a standard.
The accumulation of NAM should be reduced at least by 20% preferentially 50%, more preferentially 80% and even more preferentially 95% of the amount accumulated in a process with the non-modified organism or in the non-modified process.
The term ‘carbon source’ according to the present invention denotes any source of carbon that can be used by those skilled in the art to support the normal growth of a microorganism, which can be hexoses (such as glucose, galactose or lactose), pentoses, monosaccharides, disaccharides (such as sucrose, cellobiose or maltose), oligosaccharides, molasses, starch or its derivatives, hemicelluloses, glycerol and combinations thereof. An especially preferred carbon source is glucose. Another preferred carbon source is sucrose.
In a particular embodiment of the invention, the carbon source is derived from renewable feed-stock. Renewable feed-stock is defined as raw material required for certain industrial processes that can be regenerated within a brief delay and in sufficient amount to permit its transformation into the desired product.
The term nitrogen source corresponds to either an ammonium salt or ammoniac gas. The nitrogen source is supplied in the form of ammonium or ammoniac.
The sulphur source used for the fermentative production of L-methionine, its precursors or compounds derived thereof, may be any of the following: sulfate, thiosulfate, hydrogen sulfide, dithionate, dithionite, sulfite, methylmercaptan, dimethyldisulfide or a combination thereof.
In a preferred embodiment of the invention, the sulphur source is sulfate and/or thiosulfate.
The fermentation is generally conducted in fermenters with an appropriate culture medium adapted to the microorganism being used, containing at least one simple carbon source, and if necessary co-substrates for the production of metabolites.
Those skilled in the art are able to define the culture conditions for the microorganisms according to the invention. In particular the bacteria are fermented at a temperature between 20° C. and 55° C., preferentially between 25° C. and 40° C., and more specifically about 30° C. for C. glutamicum and about 37° C. for E. coli. 
As an example of known culture medium for E. coli, the culture medium can be of identical or similar composition to an M9 medium (Anderson, 1946, Proc. Natl. Acad. Sci. USA 32:120-128), an M63 medium (Miller, 1992; A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) or a medium such as defined by Schaefer et al. (1999, Anal. Biochem. 270: 88-96).
As an example of known culture mefium for C. glutamicum, the culture medium can be of identical or similar composition to BMCG medium (Liebl et al., 1989, Appl. Microbiol. Biotechnol. 32: 205-210) or to a medium such as described by Riedel et al. (2001, J. Mol. Microbiol. Biotechnol. 3: 573-583).
In a specific embodiment of the invention, the production of N-acyl-methionine is reduced by attenuating at least one of the methionine transacylases. Methionine transacylases are also called methionine N-acyltransferase (MNAT). argA encodes an enzymes with putative methionine transacetylase activity. The inventors have purified MNAT activity from an E. coli strain with an argA deletion, sequenced the purified protein and shown that the purified protein, YncA has MNAT activity (patent application PCT/EP2008/060999). Attenuation of the expression of the gene yncA eliminates a large amount of the residual MNAT activity, leading to a dramatic reduction of NAM production, especially of compounds N-acetyl-methionine and N-propionyl-methionine. In a preferred embodiment of the invention, YncA is entirely deleted from the E. coli genome.
Other N-acyltransferases with a lower activity have been identified, that permit to obtain a reduced NAM production when attenuated; these enzymes are encoded by the following genes:, yjdJ, yfaP, yedL, yjhQ. Any of the described methionine N-acyl transferases may be attenuated individually or in combination with the others.
Terms “attenuating a gene” or ‘attenuation of the expression of a gene’ according to the invention denotes the partial or complete suppression of the expression of a gene, which is then said to be ‘attenuated’. This suppression of expression can be either an inhibition of the expression of the gene, an insertion into or a deletion of all or part of the promoter region necessary for gene expression, a deletion or insertion in the coding region of the gene, or the exchange of the wildtype promoter by a weaker natural or synthetic promoter. Preferentially, the attenuation of a gene is essentially the complete deletion of that gene, which can be replaced by a selection marker gene that facilitates the identification, isolation and purification of the strains according to the invention. A gene is inactivated preferentially by the technique of homologous recombination (Datsenko, K. A. & Wanner, B. L. (2000) “One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products”. Proc. Natl. Acad. Sci. USA 97: 6640-6645).
In another specific embodiment of the invention, the accumulation of N-acyl-methionine may be reduced by expressing into the microorganism native or heterologous methionine specific amino acylase enzymes, such as:

    
    
        Aspergillus N-acylamino acid acylase
        Pig N-acylamino acid acylase
        E. coli argE encoding acetylornithine deacetylase, acting also on N-acetylmethionine.
    
    


Increased expression of methionine specific amino acylases increases the conversion rate of NAM into methionine with the concomitant production of one molecule of the corresponding carboxy acid, such as acetate, priopionate or butyrate. Favouring the consumption of acetate by overexpressing the genes acs, pta-ackA or genes coding for the glyoxylate shunt is also part of the invention.
The terms “enhanced” or “overexpressed” in this context describe the increase in the intracellular activity of an enzymatic activity which is encoded by the corresponding DNA, for example by increasing the number of copies of the gene, using a stronger promoter or using an allele with increased activity and possibly combining these measures.
The terms “increased expression” “enhanced expression” or “overexpression” are used interchangeably in the text and have similar meaning.
To increase the expression of a gene it may be encoded chromosomally or extrachromosomally. Chromosomally there may be one or several copies on the genome that can be introduced by methods of recombination known to the expert in the field.
Extrachromosomally genes may be carried by different types of plasmids that differ with respect to their origin of replication and thus their copy number in the cell. They may be present as 1-5 copies, about 20 or up to 500 copies, corresponding to low copy number plasmids with tight replication (pSC101, RK2), low copy number plasmids (pACYC, pRSF1010) or high copy number plasmids (pSK bluescript II).
In a preferred embodiment of the invention, the gene may be expressed using promoters with different strength, which may be inducible. These promoters may be homologous or heterologous. The man skilled in the art knows which promoters are the most convenient, for example, promoters Ptrc, Ptac, Plac or the lambda promoter cI are widely used.
Expression of the enzymes may be boosted or reduced by elements stabilizing or destabilizing the corresponding messenger RNA (Carrier and Keasling (1998) Biotechnol. Prog. 15, 58-64) or the proteins (e.g. GST tags, Amersham Biosciences).
The present invention also relates to microorganisms that contain one or several alleles of the gene to be enhanced according to the invention.
All techniques for transforming the microorganisms, and regulatory elements used for enhancing the production of the protein of the invention are well known in the art and available in the literature, including applicant's own patent applications on modification of biosynthesis pathways in various microorganisms, including WO2008/052973, WO2008/052595, WO2008/040387, WO2007/144346, WO2007/141316, WO2007/077041, WO2007/017710, WO2006/082254, WO2006/082252, WO2005/111202, WO2005/073364, WO2005/047498, WO2004/076659, the content of which is incorporated herein by reference.
N-acyl-methionine acylase enzymes will be expressed in the intracellular space and may remain in the intracellular space or be exported into the periplasm or be exported into the extracellular space. The expert in the field will be able to identify means to target the protein to the periplasm. Export may also be based on fusing the N-acetyl-methionine acylases to proteins like OmpF, by phage display or by using protein export systems such as two-partner pathway or autotransport. In a preferred embodiment of the invention NAM acylase enzymes are exported into the periplasm or the extracellular compartment to avoid futile cycling between NAM and methionine.
In another embodiment of this invention, the inventors have adapted the parameters of the fermentation process, i.e. the culture conditions, to reduce the production of NAM. This is accomplished by changing the pH of the fermentation broth, modifying oxygenation or substrate feeding parameters. Another option is to add into the culture medium a NAM specific acylase.
In one embodiment, the change of the fermentation parameters does not include the starving of the microorganism for an inorganic substrate such as phosphate, potassium, magnesium.
These three means to modulate the accumulation of NAM can be used alone or combined with one or two of the other means.
Accordingly, the attenuation of the MNAT activity is obtained by attenuating the expression of the following genes: yncA and/or argA and/or, yjdJ, yfaP, yedL, yjhQ, these genes encoding enzymes with methionine-N-acyltransferases. This attenuation may be combined with the increased expression of the N-acyl-methionine deacylase enzymes, such as Aspergillus N-amino acid acylase, pig N-amino acid acylase or acetylornithine deacetylase encoded by the argE gene.
Similarly, the attenuation of at least one MNAT enzymes, as described above, may be combined with the adaptation of the process parameters, such as pH, oxygenation, temperature and/or by adding NAM acylase to the fermentation broth, permitting together a reduction of the accumulation of NAM.
Similarly, the expression of the NAM acylase enzymes may be combined with the adaptation of the process. Details of both means have been described above.
Finally, all three means may be combined: the attenuation of the MNAT activity, the increased expression of the NAM acylase enzymes and the adaptation of the process conditions.
In the description of the present invention, genes and proteins are identified using the denominations of the corresponding genes in E. coli. However, and unless specified otherwise, use of these denominations has a more general meaning according to the invention and covers all the corresponding genes and proteins in other organisms, more particularly microorganisms.
PFAM (protein families database of alignments and hidden Markov models) represents a large collection of protein sequence alignments. Each PFAM makes it possible to visualize multiple alignments, see protein domains, evaluate distribution among organisms, gain access to other databases, and visualize known protein structures.
COGs (clusters of orthologous groups of proteins are obtained by comparing protein sequences from fully sequenced genomes representing major phylogenic lines. Each COG is defined from at least three lines, which permits the identification of former conserved domains.
The means of identifying homologous sequences and their percentage homologies are well known to those skilled in the art, and include in particular the BLAST programs. The sequences obtained can then be exploited (e.g., aligned) using, for example, the programs CLUSTALW or MULTALIN, with the default parameters indicated on those websites.
Using the references given in GenBank for known genes, those skilled in the art are able to determine the equivalent genes in other organisms, bacterial strains, yeasts, fungi, mammals, plants, etc. This routine work is advantageously done using consensus sequences that can be determined by carrying out sequence alignments with genes derived from other microorganisms, and designing degenerate probes to clone the corresponding gene in another organism. These routine methods of molecular biology are well known to those skilled in the art, and are claimed, for example, in Sambrook et al. (1989 Molecular Cloning: a Laboratory Manual. 2nd ed. Cold Spring Harbor Lab., Cold Spring Harbor, N.Y.).
The present invention is also related to a microorganism such as described above. A microorganism with a reduced accumulation and/or production of N-acyl methionine is in particular useful for producing methionine with high yield. Preferentially, the microorganism according to the invention is already a high-producer of methionine before being used in the process according to the invention.
Efficient production of methionine requires the optimisation of the methionine specific pathway and several precursor-providing pathways. Methionine producing strains have been described in patent applications WO 2005/111202, WO2007/077041 and PCT/EP2007/060433 and are incorporated as reference into this application.
A methionine producing strain that overexpresses homoserine succinyltransferase alleles with reduced feed-back sensitivity to its inhibitors SAM and methionine is described in patent application WO 2005/111202. This application describes also combination of these alleles with a deletion of the methionine repressor MetJ (GenBank 1790373), responsible for the down-regulation of the methionine regulon as was suggested in patent application JP 2000/157267. In addition, combinations of the two modifications with the overexpression of aspartokinase/homoserine dehydrogenase are described in patent application WO 2005/111202.
The overexpression of the genes cysE, metH and metF has been suggested in WO 2007/077041.
Production of methionine may be further increased by using an altered metB allele that uses preferentially or exclusively H2S and thus produces homocysteine from O-succinyl-homoserine as has been described in the patent application WO 2004/076659 that is incorporated herein by reference.
Further increase in methionine production may be obtained by deleting the genes pykA, pykF and/or purU as described in patent application PCT/EP2007/060433. This application also describes methionine-producing strains in which the operons cysPUWAM, cysJIH and gcvTHP and the genes serA, serB, serC, lpd and glyA are overexpressed.
In E. coli, other enzymes may be increased in their activity to increase the production of methionine (followed by accession numbers and function of the corresponding polypeptide):
The expression of the genes involved in sulphur assimilation may be increased:















gene
accession number
function









cysK
1788754
cysteine synthase



CysZ
g1788753
ORF upstream of cysK



cysN
g1789108
ATP sulfurylase



cysD
g1789109
sulfate adenylyltransferase



cysC
g1789107
adenylylsulfate kinase



cysZ
1788753
sulfate transport



sbp
1790351
Periplasmic sulfate-binding protein










Anaplerotic reactions may be boosted by expressing

















ppc
1790393
phosphoenolpyruvate carboxylase



pps
1787994
phosphoenolpyruvate synthase










Acetate consuming reactions may be boosted by over expressing acs 1790505 acetyl-CoA synthetase
Furthermore expression of genes in pathways degrading methionine (see list below) or deviating from the methionine production pathway may be attenuated or the genes may be deleted.
Attenuation in this context describes the reduction of the intracellular activity of an enzyme by measures such as reducing its expression, reducing the stability of the enzyme, increasing its degradation and/or other solutions known to the expert in the field.












Gene
Genbank entry
activity







ackA
1788633
acetate kinase


pta
1788635
phosphotransacetylase


aceE
1786304
pyruvate deydrogenase E1


aceF
1786305
pyruvate deydrogenase E2


lpd
1786307
pyruvate deydrogenase E3


sucC
1786948
succinyl-CoA synthetase, beta subunit


sucD
1786949
succinyl-CoA synthetase, alpha subunit


pck
1789807
phosphoenolpyruvate carboxykinase


poxB
1787096
pyruvate oxidase


ilvB
1790104
acetohydroxy acid synthase I, large subunit


ilvN
1790103
acetohydroxy acid synthase I, small subunit


ilvG
1790202
acetohydroxy acid synthase II, large subunit



1790203


ilvM
1790204
acetohydroxy acid synthase II, small subunit


ilvI
1786265
acetohydroxy acid synthase III, large subunit


ilvH
1786266
acetohydroxy acid synthase III, small subunit


aroF
1788953
DAHP synthetase


aroG
1786969
DAHP synthetase


aroH
1787996
DAHP synthetase


thrB
1786184
homoserine kinase


thrC
1786185
threonine synthase


sdaA
1788116
serine deaminase


sdaB
1789161
serine deaminase


speD
g1786311
S-Adenosylmethionine decarboxylase


speC
g1789337
Ornithine decarboxylase


astA
g1788043
Arginine succinyltransferase


dapA
g1788823
Dihydrodipicolinate synthase









The invention also concerns the process for the production of L-methionine, its precursors or compounds derived thereof, comprising the fermentation of the methionine producing microorganism described above, the concentration of methionine, its precursors or derivatives and the isolation of the desired product(s) of the fermentation broth.
Those skilled in the art are able to define the culture conditions for the microorganisms according to the invention. In particular the bacteria are fermented at a temperature between 20° C. and 55° C., preferentially between 25° C. and 40° C., and more specifically about 30° C. for C. glutamicum and about 37° C. for E. coli. 
The fermentation is generally conducted in fermenters with an inorganic culture medium of known defined composition adapted to the bacteria used, containing at least one simple carbon source, and if necessary a co-substrate necessary for the production of the metabolite.
In particular, the inorganic culture medium for E. coli can be of identical or similar composition to an M9 medium (Anderson, 1946, Proc. Natl. Acad. Sci. USA 32:120-128), an M63 medium (Miller, 1992; A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) or a medium such as defined by Schaefer et al. (1999, Anal. Biochem. 270: 88-96).
Analogously, the inorganic culture medium for C. glutamicum can be of identical or similar composition to BMCG medium (Liebl et al., 1989, Appl. Microbiol. Biotechnol. 32: 205-210) or to a medium such as described by Riedel et al. (2001, J. Mol. Microbiol. Biotechnol. 3: 573-583). The media can be supplemented to compensate for auxotrophies introduced by mutations.
After fermentation, L-methionine, its precursors or compounds derived thereof, is/are recovered and purified if necessary. The methods for the recovery and purification of the produced compound such as methionine in the culture media are well known to those skilled in the art.
Optionally, from 0 to 100%, preferentially at least 90%, more preferentially 95%, even more preferentially at least 99% of the biomass may be eliminated during the purification of the fermentation product.
In a preferred embodiment of the invention, the method for the production of methionine comprises a step of isolation of the desired amino acids/constituents of the fermentation broth and/or the biomass optionally remaining in portions or in the total amount (0-100%) in the end product.
Means of reducing the amount of NAM may be combined with limitation or starvation for phosphate and/or potassium. The expert in the field will be able to determine the amounts of phosphate or potassium necessary for growth of the chosen organism.
“Subjecting an organism to a limitation of an inorganic substrate” defines a condition under which growth of the microorganisms is governed by the quantity of an inorganic chemical supplied that still permits weak growth. Examples for these substrates are phosphate, potassium, magnesium or a combination of these.
Starving a microorganism for an inorganic substrate defines the condition under which growth of the microorganism stops completely due to the absence of the inorganic substrate. Examples for these substrates are phosphate, potassium, magnesium or a combination of these.
The invention also relates to a microorganism such as described previously that is optimized for the fermentative production of methionine with a reduced accumulation of NAM, i.e. accumulating lower amounts of NAM compared to a non-modified microorganism, and the microorganism that comprises the genetic modifications described above.
EXAMPLES
Example 1
Construction of Strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH ΔpykA ΔpykF Ptrc09-gcvTHP ΔpurU ΔyncA::Km (pME101-thrA*1-cysE-PgapA-metA*11) (pCC1BAC-serB-serA-serC)
To delete the putative acyltransferase yncA gene in a methionine producer strain, we used the Escherichia coli BW25113 ΔyncA::Km strain of the Keio mutant collection (Baba et al., 2006). The ΔyncA::Km deletion was transferred by P1 phage transduction (see below) from the BW25113 ΔyncA::Km strain to strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU (described in PCT/EP2007/060433). Kanamycine resistant transformants were selected and the insertion of the resistance cassette was verified by PCR analysis with the oligonucleotides YncAF and YncAR defined below (reference sequence on the website ecogene.org/). The strain retained was designated MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA::Km.
YncAF: GTTTGCCGATTTGCCCCACCG (homologous to the yncA region from 1517564 to 1517544) (SEQ ID NO 01)
YncAR: CGCCCATCACGGTCGCAAGC (homologous to the yncA region from 1515827 to 1515846) (SEQ ID NO 02)
Then, the plasmids pME101-thrA*1-cysE-PgapA-metA*11 and pCC1BAC-serB-serA-serC were introduced into the strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA::Km, giving rise to MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA::Km (pME101-thrA* 1-cysE-PgapA-metA*11) (pCC1BAC-serB-serA-serC).
Preparation of Phase Lysate P1:


    
    
        Inoculation of 10 mL LB supplemented with kanamycin (50 μg/mL), glucose (0.2%) and CaCl2 (5 mM) with 100 μL overnight culture of the strain BW25113 ΔyncA::Km Incubation for 30 min at 37° C. with shaking
        Addition of 100 μL of phage lysate P1 prepared on the strain BW25113 ΔyncA::Km (about 1.109 phage/mL)
        Shaking at 37° C. for 3 hours until all cells were lysed
        Addition of 200 μL chloroform and vortexing
        Centrifugation for 10 min at 4500 g to eliminate cell debris
        Transfer of the supernatant to a sterile tube and addition of 200 μL chloroform
        Storage of lysate at 4° C.

Transduction:

        Centrifugation for 10 min at 1500 g of 5 mL over-night culture of the strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU in LB medium
        Suspension of the cell pellet in 2.5 mL 10 mM of MgSO4, 5 mM CaCl2 
        Control tubes: 100 μL cells
        
            100 μL phages P1 of strain BW25113 ΔyncA::Km
        
        
        Test tubes: 100 μL cells +100 μphages P1 of strain BW25113 ΔyncA::Km
        Incubation for 30 min at 30° C. without shaking
        Addition of 100 μL 1 M sodium citrate to each tube and vortexing
        Addition of 1 mL LB
        Incubation for 1 hour at 37° C. with shaking
        Spreading on LB petri dishes supplemented with kanamycin (50 μg/mL) after centrifuging of tubes for 3 min at 7000 rpm
        Incubation at 37° C. overnight

Verification of Strain:

    
    


Kanamycin resistant transformants were selected and the presence of the ΔyncA::Km modification was verified by PCR analysis with the oligonucleotides YncAF and YncAR defined above.
Construction of Strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH ΔpykA ΔpykF Ptrc09-gcvTHP ΔpurU ΔyncA::Km ΔargA::Cm
To inactive the amino-acid acetyltransferase argA gene, the homologous recombination strategy described by Datsenko & Wanner (2000) was used. This strategy allows the insertion of a chloramphenicol resistance cassette, while deleting most of the gene concerned. For this purpose, two oligonucleotides, DargAF and DargAR, were used (reference sequence on the website ecogene.org/):







DargAF


(SEQ ID NO 03)


gtggtaaaggaacgtaaaaccgagttggtcgagggattccgccattcggt


 


tccctatatcaatacccaccggggaaaaacgTGTAGGCTGGAGCTGCTTC


 


G






with

    
    
        a region (lower case) homologous to the argA region from 2947264 to 2947344,
        a region (upper case) for the amplification of the chloramphenicol resistance cassette (reference sequence in Datsenko, K. A. & Wanner, B. L., 2000, PNAS, 97: 6640-6645)
    
    









DargAR


(SEQ ID NO 04)


ccctaaatccgccatcaacactttggatttacgctggtagttgtacaact


 


gctttttgctctcgggcagtaaatcaatatccCATATGAATATCCTCCTT


 


AG






with

    
    
        a region (lower case) homologous to the argA region from 2948592 to 2948511,
        a region (upper case) for the amplification of the chloramphenicol resistance cassette (reference sequence in Datsenko, K. A. & Wanner, B. L., 2000, PNAS, 97: 6640-6645).
    
    


The oligonucleotides DargAF and DargAR were used to amplify the chloramphenicol resistance cassette from the plasmid pKD3. The PCR product obtained was introduced by electroporation into the strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA::Km (pKD46) in which the expressed Red recombinase enzyme permitted the homologous recombination. Chloramphenicol resistant transformants were selected and the insertion of the resistance cassette was verified by PCR analysis with the oligonucleotides ArgAF and ArgAR defined below (reference sequence on the website ecogene.org/). The strain retained was designated MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA::Km ΔargA::Cm.
ArgAF: cagctgacgatttgattcc (homologous to the argA region from 2946859 to 2946877) (SEQ ID NO 05)
ArgAR: gggttgtttaatggcgatatcgg (homologous to the argA region from 2949010 to 2948988) (SEQ ID NO 06)
Construction of Strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH ΔpykA ΔpykF Ptrc09-gcvTHP ΔpurU ΔyncA ΔargA
To eliminate the chloramphenicol and kanamycin resistance cassettes, the pCP20 plasmid, carrying recombinase FLP acting on the FRT sites of the chloramphenicol and kanamycin resistance cassettes, is introduced into the recombinant strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA::Km ΔargA::Cm by electroporation. After a series of cultures at 42° C., the loss of the chloramphenicol and kanamycin resistance cassettes is verified by PCR analysis with the oligonucleotides described above, YncAF/YncAR and ArgAF/ArgAR. The strain retained is designated MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH ΔpykA ΔpykF Ptrc09-gcvTHP ΔpurU ΔyncA ΔargA.
Construction of Strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH ΔpykA ΔpykF Ptrc09-gcvTHP ΔpurU ΔyncA ΔargA (pME101-thrA*1-cysE-PgapA-metA*11) (pCC1BAC-serB-serA-serC)
The plasmids pME101-thrA*1-cysE-PgapA-metA*11 and pCC1BAC-serB-serA-serC are introduced into strain MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA ΔargA giving rise to MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH Ptrc09-gcvTHP ΔpykA ΔpykF ΔpurU ΔyncA ΔargA (pME101-thrA*1-cysE-PgapA-metA*11) (pCC1BAC-serB-serA-serC).
Construction of Synthetic Genes Expressing Amino Acid Acylase Activity
To transform NAM into methionine, NAM acylases (amino acid acylases) were expressed in the methionine producing microorganism.
For this purpose synthetic genes of the pig and Aspergillus acyl amino acid acylase genes were prepared by the company Codon Devices. The codon usage and GC content of the genes was adapted to E. coli according to the supplier matrix. All sequences with the optimized codon usage are shown below. Expression of the synthetic genes was driven by Ptrc promoters controlled by operator sequences. Transcriptional terminators were added downstream of the genes. The constructs were cloned into pUC19 vectors and verified by sequencing, before transforming them into the methionine producer strains.
Aspergillus Acyl Aminoacylase
Promoter and Operator Sequence







(SEQ ID NO 07)


Gagctgttgacaattaatcatccggctcgtataatgtgtggaattgtgag


cggataacaatttcatgacacaggaaacagacc


 


Aspergillus acyl aminoacylase sequence


(XP_001827519.1)


(SEQ ID NO 8)


Mttstvvsllsslmqtqstseheqelahflddhltnlgytverlpiaegs


trenvyaylgtqrktrvcltshldtvppyiplriegstiygrgacddkgp


maaqicaleelraegavkegdvgllfvvgeekggpgmiaanhqdlsfegv


ifgeptegklvvghkghlvfeligegkachsgypqhgvnanfalietlsd


fvqtefpsssllgpstfnvgkieggvsynivpetskalcavrvatdmagi


kkivsdtvarhsnvrlefkfeypetlldhdvegsfnvrsccymnrsilva


hgdneqieidelmegvraykkltmhalnsar


 


(SEQ ID NO 9)


atgaccacgtcgactgtcgtttctctgctgagttcactgatgcagacaca


atccacctcggaacacgagcaggaactggcgcactttctggatgaccatc


tgacaaacctgggatatactgtcgagcgtctgccgattgcagaagggtcc


actcgcgagaacgtctacgcatatctggggacccaacgtaaaacgcgtgt


atgtctgacctctcacctggatactgttccgccgtacatcccgctgcgta


ttgagggcagtacaatctatggtcgcggggcttgtgacgataagggcccg


atggctgcacagatctgcgctctggaagagctgcgtgctgaaggtgcggt


caaagaaggcgacgtaggtctgctgttcgtcgttggggaggaaaaaggcg


gtccgggcatgatcgcagcgaaccaccaggatctgtcttttgaaggggtt


atttttggggaaccgacggaaggcaagctggtagtaggtcacaaagggca


cctggtttttgagctgatcggtgagggaaaggcttgtcactccggctacc


cgcaacacggtgtgaacgcgaatttcgccctgattgagacactgtcggat


tttgtccagacggagtttcctagctctagtctgctggggccgtcaacatt


taacgttggcaagatcgaaggtggcgtatcctataatattgtgccggaaa


cgtcgaaagccctgtgtgcagtgcgcgttgcgacggacatggccggtatc


aaaaagattgtgagcgataccgtagcacgtcactctaacgtccgcctgga


gttcaagtttgaatatccagagacactgctggaccatgatgttgaaggga


gttttaatgtgcgttcctgctgttatatgaaccgctccatcctggttgcc


cacggagacaatgagcaaattgaaatcgatgaactgatggagggagtacg


cgcctataaaaagctgacaatgcacgccctgaactcagcccgctaa






Transcriptional terminator sequence: (ref: Harrington K. J., Laughlin R. B. and Liang S. Proc Natl Acad Sci USA. 2001 Apr. 24; 98(9):5019-24.)








Tcacactggctcaccttcgggtgggcctttctgc
(SEQ ID NO 10)






Pig Acyl Aminoacylase

Promoter and Operator Sequence








(SEQ ID NO 11)


Gagctgttgacaattaatcatccggctcgtataatgtgtggaattgtgag


cggataacaatttcatgacacaggaaacagaac


 


Pig acyl aminoacylase sequence (NP_999061.1)


(SEQ ID NO 12)


Maskgregehpsvtlfrqylrirtvqpepdygaavafleerarqlglgcq


kvevvpghvvtvltwpgtnptlssillnshtdvvpvfkehwshdpfegfk


dadgyiygrgaqdmkcvsiqyleavrrlkveghhfprtihmtfvpdeevg


ghqgmelfvkrpefqalragfaldeglasptdaftvfyserspwwlrvts


tgkpghgsrfiedtaaeklhkvinsilafrekekqrlqsnqlkpgavtsv


nltmleggvaynvvpatmsacfdfrvapdvdlkafeeqlqswcqaagegv


tfefvqkwmetqvtsddsdpwwaafsgvfkkmklaleleicpastdaryi


raagvpalgfspmnhtpvllhdhderlheavflrgvdiytqllsalasvp


alpses


 


(SEQ ID NO 13)


atggcgagcaaaggccgtgaaggtgagcatccgtctgtgaccctgtttcg


ccagtatctgcgtattcgcacggttcagcctgaaccggattacggagcag


ctgtggctttcctggaggaacgcgctcgtcagctgggtctgggttgccaa


aaggtagaagttgtcccagggcacgtcgtaactgtactgacttggcctgg


aacgaatccgaccctgagttcaatcctgctgaactcccatacagatgtag


tgccagtgttcaaggaacattggagtcacgaccctttcgaagggtttaaa


gatgccgatggctatatttacggtcgtggggcacaggacatgaagtgtgt


atccattcaatatctggaagctgttcgccgtctgaaagttgaagggcacc


actttccacgcactattcacatgactttcgtgcctgacgaggaagtcggg


ggtcaccaaggtatggaactgttcgtaaaacgccctgagtttcaggcact


gcgtgcgggttttgctctggacgagggtctggcgagcccgacagacgcgt


ttaccgtgttttacagtgaacgttcgccttggtggctgcgcgttacttcc


acaggtaagccggggcacggctcgcgtttcatcgaggatacagccgctga


aaagctgcacaaagttattaatagcatcctggcctttcgcgagaaggaaa


agcaacgtctgcagagcaaccagctgaaaccgggtgcggtcactagcgtg


aatctgactatgctggaggggggtgtcgcctataacgttgtgccggcaac


tatgagcgcatgcttcgactttcgcgtagctccggatgttgacctgaaag


ccttcgaagaacaactgcagagctggtgtcaagcagcgggagaaggtgta


acctttgagttcgtccagaaatggatggaaacacaggttacctcgactga


tgatagcgatccttggtgggcagccttttctggtgtgttcaaagatatga


agctggcgctggaactggaaatctgcccagcgagtacagacgctcgttac


atccgcgccgcaggcgtaccagccctgggtttttcaccgatgaatcacac


gccggtcctgctgcatgatcacgatgagcgcctgcatgaggcagttttcc


tgcgcggcgtcgacatttatacccaactgctgagtgcactggcttctgtt


cctgcgctgccatcggaatca






Transcriptional terminator sequence: (ref: Harrington K. J., Laughlin R. B. and Liang S. Proc Natl Acad Sci USA. 2001 Apr. 24; 98(9):5019-24.)








Tcacactggctcaccttcgggtgggcctttctgc
(SEQ ID NO 10)






Example 2
Methionine Production under Fermentation Conditions
Strains that produced substantial amounts of metabolites of interest were tested under production conditions in 2.5 L fermentors (Pierre Guerin) using a fed-batch strategy with phosphate starvation.
To stop growth at a cellular concentration of 30 g·L−1, phosphate was added to 28.7 mM to the mineral medium B1b. The fedbatch medium F1 was phosphate free. Briefly, an 8 hour culture grown in 10 mL LB medium with 2.5 g·L−1 glucose was used to inoculate a 24 h preculture in minimal medium B1a. These cultures were grown in 500 mL baffled flasks containing 50 mL of minimal medium (B1a) in a rotary shaker (200 RPM) at 37° C.







TABLE 1







Culture batch mineral medium compositions (B1a and B1b).











Concentration


Compound
Concentration (g · L−1) B1a
(g · L−1) B1b












Zn(CH3COO)2•2H2O
0.0130
0.0130


CuCl2•2H2O
0.0015
0.0015


MnCl2•4H2O
0.0150
0.0150


CoCl2•6H2O
0.0025
0.0025


H3BO3
0.0030
0.0030


Na2MoO4•2H2O
0.0025
0.0025


MgSO4•7H2O
1.00
1.00


CaCl2•2H2O
0.08
0.08


Citric acid
1.70
1.70


KH2PO4
2.50
2.50


K2HPO4•3H2O
1.38
1.38


(NH4)2HPO4
0.6040
0.6040


Fe(III) citrate H2O
0.11
0.11


(NH4)2S2O3
3.70
3.70


EDTA
0.0080
0.0080


Thiamine
0.01
0.01


Glucose
15.00
20.00


Vitamin B12
0.01
0.01


NaOH 8 N
Adjusted to pH 6.8
Adjusted to pH 6.8


IPTG
0.0024
0.0024


MOPS
5.00
0.00
















TABLE 2







Culture Fed batch medium composition (F1).










Compound
Concentration (g · L−1)














Zn(CH3COO)2,2H2O
0.0104



CuCl2,2H2O
0.0012



MnCl2,4H2O
0.0120



CoCl2•6H2O
0.0020



H3BO3
0.0024



Na2MoO4•2H2O
0.0020



Fe(III) citrate H2O
0.0524



MgSO4
5.00



(NH4)2S2O3
44.10



EDTA
0.0067



Thiamine
0.01



Glucose
500.00



Vitamin B12
0.01



IPTG
0.0190










Subsequently 2.5L fermentors (Pierre Guerin) were filled with 600 mL of minimal medium (B1b) and were inoculated to a biomass concentration of 0.1 g·L−1 with a preculture volume ranging from 25 to 45 mL.
The culture temperature was maintained constant at 37° C. and pH was maintained to the working value (6.8) by automatic addition of NH4OH solutions (NH4OH 10% for 10 hours and 24% until the culture end). The initial agitation rate was set at 200 rpm during the batch phase and was increased to up to 1200 rpm during the fed-batch phase. The initial airflow rate was set at 40 NL·h−1 during the batch phase and was increased to 100 NL·h−1 at the beginning of the fed-batch phase. Dissolved oxygen concentration was maintained at values between 20 and 40%, preferentially 30% saturation by increasing the agitation.
When the cell mass reached a concentration close to 5 g·L−1, the fed-batch was started with an initial flow rate of 5 mL·h−1. Feeding solution was injected with a sigmoid profile with an increasing flow rate that reached 21 mL·h−1 after 21 hours. The precise feeding conditions were calculated by the equation:




  
    Q
    ⁡
    
      (
      t
      )
    
  
  =
  
    
      p
      ⁢
      
        
      
      ⁢
      1
    
    +
    
      
        p
        ⁢
        
          
        
        ⁢
        2
      
      
        1
        +
        
          e
          
            
              -
              p
            
            ⁢
            
              
            
            ⁢
            3
            ⁢
            
              (
              
                t
                -
                
                  p
                  ⁢
                  
                    
                  
                  ⁢
                  4
                
              
              )
            
          
        
      
    
  




where Q(t) is the feeding flow rate in mL·h−1 for a batch volume of 600 mL with p1=1.15, p2=18.32, p3=0.270, p4=5.

After 21 hours fedbatch, the cellular concentration attained 30 g·L−1, phosphate was depleted from the medium and cells entered in phosphate starvation. At that point, injection of feeding solution was increased to a constant value of 37 mL·h−1 for 4 hours. Then, the constant flow rate was decreased to 10 mL·h−1 and this flow value was maintained until the end of the fedbatch (50 hours).
Table 3: Maximum methionine/glucose yield (Ymet), methionine+N-acyl-methionine+N-propionyl-methionine/glucose yield (Ymet+NAM), N-acetyl-methionine/glucose yield and N-propionyl-methionine/glucose yield (N-acetyl-methionine and N-propionyl-methionine were counted as methionine, % g/g see below) obtained in fed-batch fermentations of strains described above. For the precise definition of yields see below. Mean values of three fermentation runs are shown for the reference strain 1 and of two fedbatch runs for strain 1 DyncA. Strain1 corresponds to MG1655 metA*11 ΔmetJ Ptrc-metH Ptrc36-ARNmst17-metF PtrcF-cysPUWAM PtrcF-cysJIH ΔpykA ΔpykF Ptrc09-gcvTHP ΔpurU (pME101-thrA*1-cysE-PgapA-metA*11) (pCC1BAC-serB-serA-serC).
















Ymet+NAM
YN-acetyl-methionine
YN-propionyl methionine


Strain
Ymet (% g · g−1)
(% g · g−1)
(% g · g−1)
(% g · g−1)







Reference strain (Strain 1)
16.97 ± 1.00
20.03 ± 0.83
2.65 ± 0.17
0.41 ± 0.13


Strain 1 DyncA
18.33 ± 1.37
18.62 ± 1.24
0.27 ± 0.15
0.02 ± 0.01









Determination of Methionine/Glucose Yield (Ymet)

Extracellular methionine concentration was quantified by HPLC after OPA/FMOC derivatization. The N-acetyl-methionine and residual glucose concentrations were analyzed using HPLC with refractometric detection. The N-propionyl methionine concentration was determinated by GC-MS after silylation, it was expressed as N-acetyl-methionine equivalent.
The fermentor volume was calculated by adding to the initial volume the amount of solutions added to regulate the pH and to feed the culture and by subtracting the volume used for sampling and lost by evaporation.
The fedbatch volume was followed continuously by weighing the feeding stock. The amount of injected glucose was then calculated on the basis of the injected weight, the density of the solution and the glucose concentration controlled by the method of Brix ([Glucose]). The methionine yield was expressed as followed:




  
    Y
    met
  
  =
  
    
      
        
          
            Methionine
            t
          
          *
          
            V
            t
          
        
        -
        
          
            Methionine
            0
          
          *
          
            V
            0
          
        
      
      
        Consummed
        ⁢
        
          
        
        ⁢
        
          glucose
          t
        
      
    
    *
    100
  




With Methionine0 and Methioninet respectively the initial and methionine concentrations at time (t) and V0 and Vt the initial and the instant t volumes.

The YN-acetyl-methionine was calculated as followed:




  
    
      Y
      
        N
        ⁢
        
          -
        
        ⁢
        acetyl
        ⁢
        
          
        
        ⁢
        methionine
      
    
    =
    
      
        
          N
          ⁢
          
            -
          
          ⁢
          acetyl
          ⁢
          
            
          
          ⁢
          
            methionine
            t
          
          *
          
            V
            t
          
        
        
          Consummed
          ⁢
          
            
          
          ⁢
          
            glucose
            t
          
        
      
      *
      100
      *
      0.1492
    
  
  ,




with N-acetyl-methioninet, the concentration in mmol per liter at the instant t.

The YN-propionyl methionine was calculated as followed:




  
    Y
    
      N
      ⁢
      
        -
      
      ⁢
      propionyl
      ⁢
      
        
      
      ⁢
      methionine
    
  
  =
  
    
      
        N
        ⁢
        
          -
        
        ⁢
        propionyl
        ⁢
        
          
        
        ⁢
        
          methionine
          t
        
        *
        
          V
          t
        
      
      
        Consummed
        ⁢
        
          
        
        ⁢
        
          glucose
          t
        
      
    
    *
    100
    *
    0.1492
  




with N-propionyl methioninet, the concentration in mmol per liter at the instant t.

The YMet+N-acetyl-methionine+N-propionyl-methionine (YMet+NAM) was calculated as follows:




  
    Y
    
      Met
      +
      NAM
    
  
  =
  
    
      
        
          
            
              
                
                  Methionine
                  t
                
                *
                
                  V
                  t
                
              
              +
              
                N
                ⁢
                
                  -
                
                ⁢
                acetyl
                ⁢
                
                  -
                
                ⁢
                
                  methionine
                  t
                
                *
                
                  V
                  t
                
                *
              
            
          
        
        
          
            
              
                0
                ,
                1492
              
              +
              
                N
                ⁢
                
                  -
                
                ⁢
                propionyl
                ⁢
                
                  -
                
                ⁢
                methionine
                *
                
                  V
                  t
                
                *
                0
                ,
                1492
              
            
          
        
      
      
        Consummed
        ⁢
        
          
        
        ⁢
        
          glucose
          t
        
      
    
    *
    100
  




With Methioninet the methionine concentration in g per liter, N-acetyl-methioninet and N-propionyl-methioninet, the respective concentrations in mmol per liter at the instant t.

The consumed glucose was calculated as follows:



  
    
      fed
      ⁢
      
        
      
      ⁢
      
        volume
        t
      
    
    =
    
      
        
          fed
          ⁢
          
            
          
          ⁢
          
            weight
            0
          
        
        -
        
          fed
          ⁢
          
            
          
          ⁢
          
            weight
            t
          
        
      
      
        density
        ⁢
        
          
        
        ⁢
        fed
        ⁢
        
          
        
        ⁢
        solution
      
    
  




  
    
      Injected
      ⁢
      
        
      
      ⁢
      
        Glucose
        t
      
    
    =
    
      fed
      ⁢
      
        
      
      ⁢
      
        volume
        t
      
      *
      
        [
        Glucose
        ]
      
    
  




  
    
      Consumed
      ⁢
      
        
      
      ⁢
      
        glucose
        t
      
    
    =
    
      
        
          
            [
            Glucose
            ]
          
          0
        
        *
        
          V
          0
        
      
      +
      
        Injected
        ⁢
        
          
        
        ⁢
        Glucose
      
      -
      
        
          
            [
            Glucose
            ]
          
          residual
        
        *
        
          V
          t
        
      
    
  



With [Glucose]0, [Glucose], [Glucose]residual respectively the initial, the fed and the residual glucose concentrations.

Example 3
Adapting Culture Conditions by Adding Amino Acid Acylase to the Fermentation Medium
To transform N-acetyl-methionine into methionine and acetate 160 U of N-amino acid acylase (porcine kidney, Sigma) were added to 200 μl fermentation broth after the fermentation run of strain 1 (performed as described above). The reaction mixture was incubated at 37° C. for 2 h. Subsequently methionine and N-acetyl-methionine concentrations were determined as described above. 75-95% of N-acetyl-methionine was transformed into methionine by this enzymatic treatment.
Non-Patent References


    
    
        Figge R M (2006), ed Wendisch V F, Microbiol Monogr (5) Amino acid biosynthesis p164-185,
        Polevoda & Sherman 2000 JBC 275, 47, pp 36479-36482,
        Driessen et al. 1985, CRC Crit. Rev. Biochem. 18, 281-325,
        Marvil & Leisinger 1977 JBC 252, 10 pp. 3295-3303,
        Javid-Majd & Blanchard 2000 Biochemistry 39, 1285-93,
        Giardina et al 2000 Eur. J. Biochem. 267, 6249-55,
        Gentzen et al. 1980 Z. Naturforsch 35 c, 544-50,
        Manting & Driessen 2000 Mol Microbiol 37, 226-38,
        Choi & Lee 2004 Appl. Microbiol. Biotechnol. 64, 625-635,
        Jacob-Dubuisson et al. 2004 Biochim et Biophys Act 1694 235-257,
        José & Meyer 2007 Microbiol and Molecul Biol Rev 71, 600-19,
        Shokri et al 2003 Appl Microbiol Biotechnol 60, 654-64,
        Anderson, 1946, Proc. Natl. Acad. Sci. USA 32:120-128,
        Miller, 1992; A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,
        Schaefer et al. (1999, Anal. Biochem. 270: 88-96),
        Liebl et al., 1989, Appl. Microbiol. Biotechnol. 32: 205-210,
        Riedel et al. (2001, J. Mol. Microbiol. Biotechnol. 3: 573-583),
        Datsenko, K. A. & Wanner, B. L. (2000) “One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products”. Proc. Natl. Acad. Sci. USA 97: 6640-6645,
        Carrier and Keasling (1998) Biotechnol. Prog. 15, 58-64,
        Sambrook et al. (1989 Molecular Cloning: a Laboratory Manual. 2nd ed. Cold Spring Harbor Lab., Cold Spring Harbor, N.Y.).

## Claims

1. A method for the production of methionine and/or its derivatives, in a fermentative process comprising the following steps:
culturing a modified E. coli cell in an appropriate culture medium comprising a source of carbon, a source of sulphur and a source of nitrogen; and
recovering methionine and/or its derivatives from the culture medium,
wherein the accumulation of N-acyl methionine in the culture medium is reduced compared to a corresponding E. coli cell that produces methionine, wherein the corresponding E. coli cell comprises a deletion in the endogenous metJ gene and overexpresses a gene encoding a serine acetyltransferase (cysA) and a gene encoding a methionine synthase (metH), by increasing the number of copies of the genes and/or using a stronger promoter, and wherein the modified E. coli cell comprises a deletion in the endogenous metJ gene, overexpresses said gene encoding the serine acetyltransferase and said gene encoding the methionine synthase by increasing the number of copies of the genes and/or using a stronger promoter, and comprises a disruption in an endogenous yncA, argA, yjdJ, yfaP, yedL, and/or yjhQ gene.

2. The method of claim 1, wherein the modified E. coli cell comprises a disruption in the endogenous yncA gene.

3. The method of claim 1, wherein the modified E. coli cell comprises a disruption in the endogenous argA gene.

4. The method of claim 1, wherein the modified E. coli cell comprises a disruption in the endogenous yjdJ, yfaP, yedL, and yjhQ genes.

5. The method of claim 2, wherein the modified E. coli cell comprises a disruption in the endogenous argA gene.

6. The method of claim 1, wherein the N-acyl methionine whose accumulation is reduced is N-acetyl-methionine and/or N-propionyl-methionine.

7. The method of claim 1, wherein the modified E. coli cell further overexpresses a homoserine succinyltransferase allele encoding a homoserine succinyltransferase with reduced feedback sensitivity to its inhibitors S-adenosyl-methionine (SAM) and methionine by increasing the number of copies of the allele and/or using a stronger promoter.

8. The method of claim 1, wherein the modified E. coli cell further overexpresses a gene encoding a methylenetetrahydrofolate reductase (metF) by increasing the number of copies of the gene and/or using a stronger promoter.

9. The method of claim 1, wherein the source of sulphur in the culture medium is sulfate, thiosulfate, hydrogen sulfide, dithionate, dithionite, sulfite, methylmercaptan, dimethyldisulfide or a combination thereof.

10. The method of claim 1, wherein the source of sulphur in the culture medium is sulfate, thiosulfate, or a mixture thereof.

11. The method of claim 1, wherein the source of carbon is derived from renewable feed-stock.

12. The method of claim 1, wherein the source of carbon is glucose or sucrose.

13. The method of claim 1, wherein the source of nitrogen is supplied in the form of ammonium (NH4+) or ammonia (NH3).

14. The method of claim 1, wherein the recovering comprises isolating methionine.

15. The method of claim 1, wherein the modified E. coli cell is limited or starved for phosphate and/or potassium.

16. The method of claim 1, wherein the production of N-acyl-methionine is reduced by expressing at least one native or heterologous N-acyl-L-amino-acid amidohydrolase enzyme in the modified E. coli cell, wherein said N-acyl-L-amino-acid amidohydrolase enzyme is selected from the group consisting of an Aspergillus N-acylamino acid acylase, a pig N-acylamino acid acylase, and an acetylornithine deacetylase (argE).

17. The method of claim 1, wherein the production of N-acyl-methionine is reduced by adapting the culture conditions selected among pH, oxygenation and/or temperature, or by adding a N-acyl amino acid acylase into the medium.