Nucleotide sequence of the lysA gene of Corynebacterium glutamicum and possible mechanisms for modulation of its expression

Improved production of L-lysine by over-expression of Meso-diaminopimelate decarboxylase enzyme of Corynebacterium glutamicum in Escherichia coli

The aim of this study is over-expression of Meso-diaminopimelate decarboxylase enzyme (EC 4.1.1.20) and enhancement of L-lysine production rate. The C. glutamicum LysA gene which encodes a Meso-diaminopimelate decarboxylase was cloned in E. coli. The cloned gene was sequenced; it encodes a 445 amino acids protein with molecular weight of 47 kD. Expression of the LysA gene in E. coli resulted in an increase in Meso-diaminopimelate decarboxylase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamid gels of a clear protein band that corresponds to this enzyme. The induction of cloned gene by IPTG has been shown to have an inhibitory effect on cell growth due to over-expression of the cloned gene. A two fold increase in lysine production rate was observed after introduction of the cloned gene into E. coli.

Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway

BACKGROUND

Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. An efficient transposon mutagenesis system for the completely sequenced type strain ATCC 13032 would significantly advance functional genome analysis in this bacterium.

RESULTS

A comprehensive transposon mutant library comprising 10,080 independent clones was constructed by electrotransformation of the restriction-deficient derivative of strain ATCC 13032, C. glutamicum RES167, with an IS6100-containing non-replicative plasmid. Transposon mutants had stable cointegrates between the transposon vector and the chromosome. Altogether 172 transposon integration sites have been determined by sequencing of the chromosomal inserts, revealing that each integration occurred at a different locus. Statistical target site analyses revealed an apparent absence of a target site preference. From the library, auxotrophic mutants were obtained with a frequency of 2.9%. By auxanography analyses nearly two thirds of the auxotrophs were further characterized, including mutants with single, double and alternative nutritional requirements. In most cases the nutritional requirement observed could be correlated to the annotation of the mutated gene involved in the biosynthesis of an amino acid, a nucleotide or a vitamin. One notable exception was a clone mutagenized by transposition into the gene cg0910, which exhibited an auxotrophy for histidine. The protein sequence deduced from cg0910 showed high sequence similarities to inositol-1(or 4)-monophosphatases (EC 3.1.3.25). Subsequent genetic deletion of cg0910 delivered the same histidine-auxotrophic phenotype. Genetic complementation of the mutants as well as supplementation by histidinol suggests that cg0910 encodes the hitherto unknown essential L-histidinol-phosphate phosphatase (EC 3.1.3.15) in C. glutamicum. The cg0910 gene, renamed hisN, and its encoded enzyme have putative orthologs in almost all Actinobacteria, including mycobacteria and streptomycetes.

CONCLUSION

The absence of regional and sequence preferences of IS6100-transposition demonstrate that the established system is suitable for efficient genome-scale random mutagenesis in the sequenced type strain C.glutamicum ATCC 13032. The identification of the hisN gene encoding histidinol-phosphate phosphatase in C. glutamicum closed the last gap in histidine synthesis in the Actinobacteria. The system might be a valuable genetic tool also in other bacteria due to the broad host-spectrum of IS6100.

The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins

The complete genomic sequence of Corynebacterium glutamicum ATCC 13032, well-known in industry for the production of amino acids, e.g. of L-glutamate and L-lysine was determined. The C. glutamicum genome was found to consist of a single circular chromosome comprising 3282708 base pairs. Several DNA regions of unusual composition were identified that were potentially acquired by horizontal gene transfer, e.g. a segment of DNA from C. diphtheriae and a prophage-containing region. After automated and manual annotation, 3002 protein-coding genes have been identified, and to 2489 of these, functions were assigned by homologies to known proteins. These analyses confirm the taxonomic position of C. glutamicum as related to Mycobacteria and show a broad metabolic diversity as expected for a bacterium living in the soil. As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate.

Enzymology of bacterial lysine biosynthesis

Bacteria have evolved three strategies for the synthesis of lysine from aspartate via formation of the intermediate diaminopimelate (DAP), a metabolite that is also involved in peptidoglycan formation. The objectives of this chapter are descriptions of mechanistic studies on the reactions catalyzed by dihydrodipicolinate synthase, dihydrodopicolinate reductase, tetrahydrodipicolinate N-succinyl-transferase, N-succinyl-L,L-DAP aminotransferase, N-succinyl-L,L-DAP desuccinylase, L,L-DAP epimerase, L,L-DAP decarboxylase, and DAP dehydrogenase. These enzymes are discussed in terms of kinetic, isotopic, and X-ray crystallographic data that allow one to infer the nature of interactions of each of these enzymes with its substrate(s), coenzymes, and inhibitors.

Molecular control mechanisms of lysine and threonine biosynthesis in amino acid-producing corynebacteria: redirecting carbon flow

Threonine and lysine are two of the economically most important essential amino acids. They are produced industrially by species of the genera Corynebacterium and Brevibacterium. The branched biosynthetic pathway of these amino acids in corynebacteria is unusual in gene organization and in the control of key enzymatic steps with respect to other microorganisms. This article reviews the molecular control mechanisms of the biosynthetic pathways leading to threonine and lysine in corynebacteria, and their implications in the production of these amino acids. Carbon flux can be redirected at branch points by gene disruption of the competing pathways for lysine or threonine. Removal of bottlenecks has been achieved by amplification of genes which encode feedback resistant aspartokinase and homoserine dehydrogenase (obtained by in vitro directed mutagenesis).

A physical and genetic map of the Corynebacterium glutamicum ATCC 13032 chromosome

A combined physical and genetic map of the Corynebacterium glutamicum ATCC 13032 chromosome was constructed using pulsed-field gel electrophoresis (PFGE) and hybridizations with cloned gene probes. Total genomic DNA was digested with the meganucleases SwaI (5'-ATTTAAAT-3'), PacI (5'-TTAATTAA-3'), and PmeI (5'-GTTTAAAC-3') yielding 26,27, and 23 fragments, respectively. The chromosomal restriction fragments were then separated by PFGE. By summing up the lengths of the fragments generated with each of the three enzymes, a genome size of 3082 +/- 20 kb was determined. To identify adjacent SwaI fragments, a genomic cosmid library of C.glutamicum was screened for chromosomal inserts containing SwaI sites. Southern blots of the PFGE gels were hybridized with these linking clones to connect the SwaI fragments in their natural order. By this method, about 90% of the genome could be ordered into three contigs. Two of the remaining gaps were closed by cross-hybridization of blotted SwaI digests using as probes PacI and PmeI fragments isolated from PFGE gels. The last gap in the chromosomal map was closed by hybridization experiments using partial SwaI digestions, thereby proving the circularity of the chromosome. By hybridization of gene probes to SwaI fragments separated by PFGE about 30 genes, including rRNA operons, IS element and transposon insertions were localized on the physical map.

Recent advances in the physiology and genetics of amino acid-producing bacteria

Corynebacterium glutamicum and its close relatives, C. flavum and C. lactofermentum, have been used for over 3 decades in the industrial production of amino acids by fermentation. Since 1984, several research groups have started programs to develop metabolic engineering principles for amino acid-producing Corynebacterium strains. Initially, the programs concentrated on the isolation of genes encoding (deregulated) biosynthetic enzymes and the development of general molecular biology tools such as cloning vectors and DNA transfer methods. With most of the genes and tools now available, recombinant DNA technology can be applied in strain improvement. To accomplish these improvements, it is critical and advantageous to understand the mechanisms of gene expression and regulation as well as the biochemistry and physiology of the species being engineered. This review explores the advances made in the understanding and application of amino acid-producing bacteria in the early 1990s.

Molecular aspects of lysine, threonine, and isoleucine biosynthesis in Corynebacterium glutamicum

The Gram-positive bacterium Corynebacterium glutamicum is used for the industrial production of amino acids, e.g. of L-glutamate and L-lysine. In the last ten years genetic engineering methods were developed for C. glutamicum and consequently, recombinant DNA technology was employed to study the biosynthetic pathways and to improve the amino acid productivity by manipulation of enzymatic, transport and regulatory functions of this bacterium. The present review summarizes the current knowledge on the synthesis and over-production of the aspartate derived amino acids L-lysine, L-threonine and L-isoleucine in C. glutamicum. A special feature of C. glutamicum is its ability to convert the lysine intermediate piperideine2,6-dicarboxylate to diaminopimelate by two different routes, i.e. by reactions involving succinylated intermediates or by the single reaction of diaminopimelate dehydrogenase. The flux distribution over the two pathways is regulated by the ammonium availability. The overall carbon flux from aspartate to lysine, however, is governed by feedback-control of the aspartate kinase and by the level of dihydrodipicolinate synthase. Consequently, expression of lysCFBR encoding a deregulated aspartate kinase and/or the overexpression of dapA encoding dihydrodipicolinate synthase led to overproduction of lysine. As a further specific feature C. glutamicum possesses a specific lysine export carrier which shows high activity in lysine overproducing mutants. Threonine biosynthesis is in addition to control by the aspartate kinase tightly regulated at the level of homoserine dehydrogenase which is subject to feedback-inhibition and to repression. C. glutamicum strains possessing a deregulated aspartate kinase and a deregulated homoserine dehydrogenase produce lysine and threonine. Amplification of deregulated homoserine dehydrogenase in such strains led to an almost complete redirection of the carbon flux to threonine. For a further flux from threonine to isoleucine the allosteric control of threonine dehydratase and of the acetohydroxy acid synthase are important. The expression of the genes encoding the latter enzyme is additionally regulated at the transcriptional level. By addition of 2-oxobutyrate as precursor and by bypassing the expression control of the acetohydroxy acid synthase genes high isoleucine overproduction can be obtained.

A gene encoding arginyl-tRNA synthetase is located in the upstream region of the lysA gene in Brevibacterium lactofermentum: regulation of argS-lysA cluster expression by arginine

The Brevibacterium lactofermentum argS gene, which encodes an arginyl-tRNA synthetase, was identified in the upstream region of the lysA gene. The cloned gene was sequenced; it encodes a 550-amino-acid protein with an M(r) of 59,797. The deduced amino acid sequence showed 28% identical and 49% similar residues when compared with the sequence of the Escherichia coli arginyl-tRNA synthetase. The B. lactofermentum enzyme showed the highly conserved motifs of class I aminoacyl-tRNA synthetases. Expression of the argS gene in B. lactofermentum and E. coli resulted in an increase in aminoacyl-tRNA synthetase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamide gels of a clear protein band that corresponds to this enzyme. One single transcript of about 3,000 nucleotides and corresponding to the B. lactofermentum argS-lysA operon was identified. The transcription of these genes is repressed by lysine and induced by arginine, showing an interesting pattern of biosynthetic interlock between the pathways of both amino acids in corynebacteria.

Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes

The lysA gene of Bacillus methanolicus MGA3 was cloned by complementation of an auxotrophic Escherichia coli lysA22 mutant with a genomic library of B. methanolicus MGA3 chromosomal DNA. Subcloning localized the B. methanolicus MGA3 lysA gene into a 2.3-kb SmaI-SstI fragment. Sequence analysis of the 2.3-kb fragment indicated an open reading frame encoding a protein of 48,223 Da, which was similar to the meso-diaminopimelate (DAP) decarboxylase amino acid sequences of Bacillus subtilis (62%) and Corynebacterium glutamicum (40%). Amino acid sequence analysis indicated several regions of conservation among bacterial DAP decarboxylases, eukaryotic ornithine decarboxylases, and arginine decarboxylases, suggesting a common structural arrangement for positioning of substrate and the cofactor pyridoxal 5'-phosphate. The B. methanolicus MGA3 DAP decarboxylase was shown to be a dimer (M(r) 86,000) with a subunit molecular mass of approximately 50,000 Da. This decarboxylase is inhibited by lysine (Ki = 0.93 mM) with a Km of 0.8 mM for DAP. The inhibition pattern suggests that the activity of this enzyme in lysine-overproducing strains of B. methanolicus MGA3 may limit lysine synthesis.

Cloning of the lysA gene from Mycobacterium tuberculosis

The lysA and proC genes of Mycobacterium tuberculosis were cloned by screening of a recombinant lambda gt11 M. tuberculosis DNA library for phages able to complement lysA and proC Escherichia coli mutants. The lysA gene encodes diaminopimelic acid decarboxylase which catalyzes the conversion of diaminopimelic acid (DAP) to lysine. The lysA gene from M. tuberculosis encodes a 44-kDa protein, as determined by maxicell experiments. The nucleotide sequence of the structural gene was established. The deduced amino acid sequence was found to exhibit significant homology (from 55% to 73% similarity, and from 27% to 53% identity) to DAP decarboxylase sequences from other bacterial species.

Molecular analysis of the Corynebacterium glutamicum lysl gene involved in lysine uptake

Two Corynebacterium glutamicum mutants defective in lysine uptake were identified by analysing mutants resistant to S-(2-aminoethyl)-cysteine (AEC). A 5.6 kb genomic DNA fragment restoring AEC sensitivity and lysine uptake was isolated. A 4.2 kb subfragment was sequenced and three open reading frames were identified. Subcloning and gene disruption experiments showed that only the first open reading frame, termed lysl, is involved in lysine uptake. Lysl consists of 501 amino acids with a Mr of 53600. The hydrophobicity profile suggests that the lysl gene product is an integral membrane protein with 13 transmembrane segments. The amino acid sequence of lysl displays strong homology to that of the arcD gene product of Pseudomonas aeruginosa, which is proposed to act as an arginine-ornithine antiporter. Investigation of the influence of the lysl gene on lysine secretion suggests the existence of a separate lysine efflux system in C. glutamicum.

Manipulation of Corynebacterium glutamicum by gene disruption and replacement

We have developed a system for the genetic manipulation of the amino acid-producing Corynebacterium glutamicum. Gene disruption and replacement were achieved by introducing, via conjugation, Escherichia coli vector plasmids carrying manipulated C. glutamicum DNA fragments. We obtained stable mutants in which the chromosomal lysA gene, encoding meso-diaminopimelate decarboxylase, was interrupted by a chloramphenicol resistance cartridge, or in which an essential internal part of the lysA gene was deleted. The deletion mutants retain neither antibiotic resistance markers nor vector sequences. This strategy is generally applicable to the construction of industrial strains to be used in fermentation processes.

A functionally split pathway for lysine synthesis in Corynebacterium glutamicium

Three different pathways of D,L-diaminopimelate and L-lysine synthesis are known in procaryotes. Determinations of the corresponding enzyme activities in Escherichia coli, Bacillus subtilis, and Bacillus sphaericus verified the fact that in each of these bacteria only one of the possible pathways operates. However, in Corynebacterium glutamicum activities are present which allow in principle the use of the dehydrogenase variant and succinylase variant of lysine synthesis together. Applying gene-directed mutagenesis, various C. glutamicum strains were constructed with interrupted ddh gene. These mutants have an inactive dehydrogenase pathway but are still prototrophic, which is proof that the succinylase pathway of D,L-diaminopimelate synthesis can be utilized. In strains with an increased flow of precursors to D,L-diaminopimelate, however, the inactivation of the dehydrogenase pathway resulted in a reduced formation of lysine, with concomitant accumulation of N-succinyl-diaminopimelate in the cytosol up to a concentration of 25 mM. These data show (i) that both pathways can operate in C. glutamicum for D,L-diaminopimelate and L-lysine synthesis, (ii) that the dehydrogenase pathway is not essential, and (iii) that the dehydrogenase pathway is a prerequisite for handling an increased flow of metabolites to D,L-diaminopimelate.

Control of the Lysine Biosynthesis Sequence in Corynebacterium glutamicum as Analyzed by Overexpression of the Individual Corresponding Genes

The gene cluster that codes for feedback-resistant aspartate kinase (lysCalpha and lysCbeta) and aspartate semialdehyde dehydrogenase (asd) was cloned from a mutant strain of Corynebacterium glutamicum. Its functional analysis by subcloning, enzyme assays, and type of aspartate kinase regulation enabled the isolation of a fragment for separate expression of the feedback-resistant kinase without aspartate semialdehyde dehydrogenase expression. This was used together with other clones constructed (J. Cremer, L. Eggeling, and H. Sahm, Mol. Gen. Genet. 220:478-480, 1990) to overexpress individually each of the six genes that convert aspartate to lysine. Analysis of lysine formation revealed that overexpression of the feedback-resistant kinase alone suffices to achieve lysine formation (38 mM). Also, sole overexpression of wild-type dihydrodipicolinate synthase resulted in lysine formation but in a lower amount (11 mM). The other four enzymes had no effect on lysine secretion. With a plasmid overexpressing both relevant enzymes together, a further increase in lysine yield was obtained. This shows that of the six enzymes that convert aspartate to lysine the kinase and the synthase are responsible for flow control in the wild-type background and can be useful for construction of lysine-producing strains.

Nucleotide sequence and organization of the upstream region of the Corynebacterium glutamicum lysA gene

Maximum expression of the Corynebacterium glutamicum lysA gene is dependent upon the presence of a 2.3 kb region immediately 5' of the lysA reading frame. Subcloning and functional analysis of the upstream region implied that this region contained the lysA promoter. Sequence determination of the upstream region revealed a single open reading frame, orfX, in the same orientation as lysA. The orfX coding sequence exhibited all the sequence characteristics of a gene with the potential for a 550-amino-acid polypeptide product. Expression of lysA is coupled to that of orfX via a common promoter located immediately 5' of orfX. The RNA start site has been determined by S1 nuclease mapping. Both the orfX and the lysA gene are expressed as a single 3.0 kb RNA transcript. These data indicate that orfX and lysA are genes within a two-gene operon. Expression of the lysA gene is not subject to regulation by lysine. The orfX gene product was shown not to be directly linked to the lysine biosynthetic pathway, nor is it the enzyme incorporating DAP into the peptidoglycan precursor.

Molecular cloning, nucleotide sequence and fine-structural analysis of the Corynebacterium glutamicum fda gene: structural comparison of C. glutamicum fructose-1,6-biphosphate aldolase to class I and class II aldolases

The Corynebacterium glutamicum fda gene encoding fructose-1,6-biphosphate (FBP) aldolase has been isolated by complementation of an Escherichia coli mutant. The nucleotide sequence of a 3371 bp chromosomal fragment containing the C. glutamicum fda gene was determined. The N-terminal amino acid sequence of C. glutamicum FBP aldolase identified the correct initiation site for the fda gene, and a molecular weight of 37,092 was predicted for the fda polypeptide. S1 nuclease mapping identified the transcriptional start site, and Northern hybridization analysis indicated that the fda gene encodes a single 1.3 kb transcript. The primary structure of C. glutamicum FBP aldolase shows strong homology to class II FBP aldolases. Conservation of primary structure was observed between class I and class II aldolases, but several residues essential for catalytic activity in class I aldolases were absent from class II aldolases.

The phosphoenolpyruvate carboxylase gene of Corynebacterium glutamicum: molecular cloning, nucleotide sequence, and expression

The ppc gene of Corynebacterium glutamicum encoding phosphoenolpyruvate (PEP) carboxylase was isolated by complementation of a ppc mutant of Escherichia coli using a cosmid gene bank of chromosomal C. glutamicum DNA. By subsequent subcloning into the plasmid pUC8 and deletion analysis, the ppc gene could be located on a 3.3 kb SalI fragment. This fragment was able to complement the E. coli ppc mutant and conferred PEP carboxylase activity to the mutant. The complete nucleotide sequence of the ppc gene including 5' and 3' flanking regions has been determined and the primary structure of PEP carboxylase was deduced. The sequence predicts a 919 residue protein product (molecular weight of 103 154) which shows 34% similarity with the respective E. coli enzyme.

General organization of the genes specifically involved in the diaminopimelate-lysine biosynthetic pathway of Corynebacterium glutamicum

We utilized diaminopimelate-lysine mutants of Escherichia coli K12 to clone the genes specifically involved in the Corynebacterium glutamicum diaminopimelate-lysine anabolic pathway. From a cosmid genomic bank of C. glutamicum strain AS019, we isolated cosmids pSM71, pSM61 and pSM531, that are respectively able to complement dapA/dapB, dapD, and lysA mutants of E. coli. DNA hybridization analysis indicates that these complementing genes are located on the chromosome of C. glutamicum in at least three separate transcription units. Subcloning of parental cosmids in dapA, dapD, and lysA mutants of E. coli localized these genes, respectively, within 1.4, 3.4, and 1.8 kb fragments, cloned in an E. coli/C. glutamicum shuttle vector. Enzymatic analysis in C. glutamicum identified the dapA-complementing gene as L-2,3-dihydrodipicolinate synthetase (dapA), and the lysA-complementing gene as meso-diaminopimelate decarboxylase (lysA). In contrast, complementation of E. coli dapD8, presumably lacking L-delta 1-tetrahydrodipicolinate synthetase (dapD), led us to clone a diaminopimelate-lysine anabolic gene of C. glutamicum which does not exist in E. coli: meso-diaminopimelate dehydrogenase. Although meso-diaminopimelate is crucial in lysine formation and in cell wall biosynthesis, expression of the genomic copies of the cloned genes, which encode activities involved at key branching points of the diaminopimelate-lysine pathway of C. glutamicum, appears constitutive with regard to the addition of diaminopimelate and/or lysine during cell growth.