Cloning and sequencing of the leu C and npr M genes and a putative spo IV gene from Bacillus megaterium DSM319

A Bacillus megaterium System for the Production of Recombinant Proteins and Protein Complexes

For many years the Gram-positive bacterium Bacillus megaterium has been used for the production and secretion of recombinant proteins. For this purpose it was systematically optimized. Plasmids with different inducible promoter systems, with different compatible origins, with small tags for protein purification and with various specific signals for protein secretion were combined with genetically improved host strains. Finally, the development of appropriate cultivation conditions for the production strains established this organism as a bacterial cell factory even for large proteins. Along with the overproduction of individual proteins the organism is now also used for the simultaneous coproduction of up to 14 recombinant proteins, multiple subsequently interacting or forming protein complexes. Some of these recombinant strains are successfully used for bioconversion or the biosynthesis of valuable components including vitamins. The titers in the g per liter scale for the intra- and extracellular recombinant protein production prove the high potential of B. megaterium for industrial applications. It is currently further enhanced for the production of recombinant proteins and multi-subunit protein complexes using directed genetic engineering approaches based on transcriptome, proteome, metabolome and fluxome data.

yneA mRNA instability is involved in temporary inhibition of cell division during the SOS response of Bacillus megaterium

The SOS response, a mechanism enabling bacteria to cope with DNA damage, is strictly regulated by the two major players, RecA and LexA (Bacillus homologue DinR). Genetic stress provokes formation of ssDNA-RecA nucleoprotein filaments, the coprotease activity of which mediates the autocatalytic cleavage of the transcriptional repressor DinR and ensures the expression of a set of din (damage-inducible) genes, which encode proteins that enhance repair capacity, accelerate mutagenesis rate and cause inhibition of cell division (ICD). In Bacillus subtilis, the transcriptional activation of the yneAB-ynzC operon is part of the SOS response, with YneA being responsible for the ICD. Pointing to its cellular function in Bacillus megaterium, overexpression of homologous YneA led to filamentous growth, while ICD was temporary during the SOS response. Genetic knockouts of the individual open reading frames of the yneAB-ynzC operon increased the mutagenic sensitivity, proving - for the first time in a Bacillus species - that each of the three genes is in fact instrumental in coping with genetic stress. Northern- and quantitative real-time PCR analyses revealed - in contrast to other din genes (exemplified for dinR, uvrBA) - transient mRNA-presence of the yneAB-ynzC operon irrespective of persisting SOS-inducing conditions. Promoter test assays and Northern analyses suggest that the decline of the ICD is at least partly due to yneAB-ynzC mRNA instability.

Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus

Bacillus pumilus mutants were generated by targeted deletion of a set of genes eventually facilitating genetic handling and assuring biological containment. The well-defined and stable mutants do not form functional endospores due to the deletion of yqfD, an essential sporulation gene; they are affected in DNA repair, as ΔuvrBA rendered them UV hypersensitive and, thus, biologically contained; they are deficient for the uracil phosphoribosyl-transferase (Δupp), allowing for 5-fluorouracil-based counterselection facilitating rapid allelic exchanges; and they are readily transformable due to the deletion of the restrictase encoding locus (ΔhsdR) of a type I restriction modification system. Vegetative growth as well as extracellular enzyme production and secretion are in no case affected. The combination of such gene deletions allows for development of B. pumilus strains suited for industrial use and further improvements.

Transcriptome profiling of degU expression reveals unexpected regulatory patterns in Bacillus megaterium and discloses new targets for optimizing expression

The first whole transcriptome assessment of a Bacillus megaterium strain provides unanticipated insights into the degSU regulon considered to be of central importance for exo-enzyme production. Regulatory patterns as well as the transcription of degSU itself deviate from the model organism Bacillus subtilis; the number of DegU-regulated secretory enzymes is rather small. Targets for productivity optimization, besides degSU itself, arise from the unexpected DegU-dependent induction of the transition-state regulator AbrB during exponential growth. Induction of secretion-assisting factors, such as the translocase subunit SecY or the signal peptidase SipM, promote hypersecretion. B. megaterium DegSU transcriptional control is advantageous for production purposes, since the degU32 constitutively active mutant conferred hypersecretion of a heterologous Bacillus amyloliquefaciens amylase without the detrimental rise, as for B. subtilis and Bacillus licheniformis, in extracellular proteolytic activities.

An improved transconjugation protocol for Bacillus megaterium facilitating a direct genetic knockout

We provide a simple but very efficient transconjugation protocol for Bacillus megaterium. By combining utile attributes of known transconjugation methods (small size of the transferred DNA, close physical contact between donor and recipient cells, and heat treatment of the latter) and by determining the appropriate donor/recipient ratio, mating approaches yielded 5 x 10(-5) transconjugants/recipient. Counter-selection for eliminating Escherichia coli donor cells from the mating mixture was possible by pasteurization in case a wild type sporulation proficient B. megaterium served as the mating partner. For nonsporulating mutants, the sacB gene from Bacillus subtilis coding for levansucrase was successfully employed to select against the E. coli donor. The transfer efficiency, up to 15,000 transconjugants acquirable in a single experiment, sufficed--for the first time in this species--to directly select a gene (uvrA) knockout in a one-step procedure. By making use of a mobilizable B. megaterium suicide vector, ten out of the 40 sampled putative transconjugants displayed the expected UV sensitivity and were found to harbor the suicide vector at the anticipated position. Along with the soon available information arising from current B. megaterium sequencing projects, the possibility to quickly inactivate genetic loci will considerably speed up genetic work with this biotechnologically relevant species.

Bacillus megaterium—from simple soil bacterium to industrial protein production host

Bacillus megaterium has been industrially employed for more than 50 years, as it possesses some very useful and unusual enzymes and a high capacity for the production of exoenzymes. It is also a desirable cloning host for the production of intact proteins, as it does not possess external alkaline proteases and can stably maintain a variety of plasmid vectors. Genetic tools for this species include transducing phages and several hundred mutants covering the processes of biosynthesis, catabolism, division, sporulation, germination, antibiotic resistance, and recombination. The seven plasmids of B. megaterium strain QM B1551 contain several unusual metabolic genes that may be useful in bioremediation. Recently, several recombinant shuttle vectors carrying different strong inducible promoters and various combinations of affinity tags for simple protein purification have been constructed. Leader sequences-mediated export of affinity-tagged proteins into the growth medium was made possible. These plasmids are commercially available. For a broader application of B. megaterium in industry, sporulation and protease-deficient as well as UV-sensitive mutants were constructed. The genome sequence of two different strains, plasmidless DSM319 and QM B1551 carrying seven natural plasmids, is now available. These sequences allow for a systems biotechnology optimization of the production host B. megaterium. Altogether, a "toolbox" of hundreds of genetically characterized strains, genetic methods, vectors, hosts, and genomic sequences make B. megaterium an ideal organism for industrial, environmental, and experimental applications.

Strain development in Bacillus licheniformis: construction of biologically contained mutants deficient in sporulation and DNA repair

By introducing defined deletions in recA and an essential sporulation gene (spoIV), stable mutant strains of Bacillus licheniformis were obtained which are totally asporogenous and severely affected in DNA repair, and thus being UV-hypersensitive. Studies on growth in various liquid media as well as on amylase production revealed no differences of the mutants when compared to the wild type. Hence, such genes appear to be suitable disruption targets for achieving passive biological containment in this industrially exploited species.

Test systems to study transcriptional regulation and promoter activity in Bacillus megaterium

Plasmid-located (multi-copy) and chromosomally located (single-copy) promoter test systems were developed for Bacillus megaterium by making use of the homologous beta-galactosidase-encoding bgaM gene. The multi-copy system facilitates rapid promoter analyses and promoter trapping, whereas the single-copy system, integrated into the chromosome, allows investigation of tightly regulated promoters. As a prerequisite for both the multi- and the single-copy systems, a beta-galactosidase-deficient B. megaterium strain was generated by deletion mutagenesis. Both test systems were verified using the promoter of the xylose operon (P( xylA )) from B. megaterium along with its repressor (XylR). As expected, expression levels in the two systems differed significantly, although expression of the bgaM reporter gene was induced by xylose in both cases, thereby proving the functionality of both the multi- and the single-copy system.

Evidence for two recA genes mediating DNA repair in Bacillus megaterium

Isolation and subsequent knockout of arecA-homologous gene inBacillus megateriumDSM 319 resulted in a mutant displaying increased sensitivity to mitomycin C. However, this mutant did not exhibit UV hypersensitivity, a finding which eventually led to identification of a second functionalrecAgene. Evidence forrecAduplicates was also obtained for two otherB. megateriumstrains. In agreement with potential DinR boxes located within their promoter regions, expression of both genes (recA1andrecA2) was found to be damage-inducible. Transcription from therecA2promoter was significantly higher than that ofrecA1. Since arecA2knockout could not be achieved, functional complementation studies were performed inEscherichia coli. Heterologous expression in a RecA null mutant resulted in increased survival after UV irradiation and mitomycin C treatment, proving bothrecAgene products to be functional in DNA repair. Thus, there is evidence for an SOS-like pathway inB. megateriumthat differs from that ofBacillus subtilis.

Identification of theAnabaenasp. Strain PCC7120 Cyanophycin Synthetase as Suitable Enzyme for Production of Cyanophycin in Gram-Negative Bacteria LikePseudomonasputidaandRalstoniaeutropha

The cyanophycin synthetase gene cphA1 encoding the major cyanophycin synthetase (CphA) of Anabaena sp. strain PCC7120 was expressed in Escherichia coli conferring so far the highest specific CphA activity to E. coli (6.7 nmol arginine per min and mg protein). CphA1 and cphA genes of Synechocystis sp. strains PCC6803 and PCC6308 and Synechococcus strain MA19 were also expressed in wild types and polyhydroxyalkanoate-negative (PHA) mutants of Pseudomonas putida and Ralstonia eutropha. Recombinant strains of these bacteria expressing cphA1 accumulated generally more cyanophycin (23.0 and 20.0% of cellular dry matter, CDM, respectively) than recombinants expressing any other cphA (6.8, 9.0, or 15.8% of CDM for P. putida strains and 7.3, 12.6, or 14.1% of CDM for R. eutropha). Furthermore, PHA-negative mutants of P. putida (9.7, 10.0, 17.5, or 24.0% of CDM) and R. eutropha (8.9, 13.8, 16.0, or 22.0% of CDM) accumulated generally more cyanophycin than the corresponding PHA-positive parent strains (6.8, 9.0, 15.8, and 23.0% of CDM for P. putida strains and 7.3, 12.6, 14.1, or 20.0% of CDM for R. eutropha strains). Recombinant strains of Gram-positive bacteria (Bacillus megaterium, Corynebacterium glutamicum) were not suitable for cyanophycin production due to accumulation of less cyanophycin and retarded release of cyanophycin. PHA-negative mutants of P. putida and R. eutropha expressing cphA1 of Anabaena sp. strain PCC7120 are therefore preferred candidates for industrial production of cyanophycin.

Kluyveromyces lactis cytoplasmic plasmid pGKL2: heterologous expression of Orf3p and proof of guanylyltransferase and mRNA-triphosphatase activities

The predicted ORF3 polypeptide (Orf3p) of the linear genetic element pGKL2 from Kluyveromyces lactis was expressed in Bacillus megaterium as a fusion protein with a His(6X)-tag at the C-terminus for isolation by Ni-affinity chromatography. This is the first time that a yeast cytoplasmic gene product has been expressed heterologously as a functional protein in a bacterial system. The purified protein was found to display both RNA 5'-triphosphatase and guanylyltransferase activities. When the lysine residue present at position 177 of the protein within the sequence motif (KXDG), highly conserved in capping enzymes and other nucleotidyl transferases, was substituted by alanine, the guanylyltransferase activity was lost, thereby proving an important role for the transfer of GMP from GTP to the 5'-diphosphate end of the mRNA. Our in vitro data provides the first direct evidence that the polypeptide encoded by ORF3 of the cytoplasmic yeast plasmid pGKL2 functions as a plasmid-specific capping enzyme. Since genes equivalent to ORF3 of pGKL2 have been identified in all autonomous cytoplasmic yeast DNA elements investigated so far, our findings are of general significance for these widely distributed yeast extranuclear genetic elements.

Bacterial community analysis of Indonesian hot springs

We report the first attempts to describe thermophilic bacterial communities in Indonesia's thermal springs using molecular phylogenetic analyses. 16S rRNA genes from laboratory cultures and DNA directly amplified from three hot springs in West Java were sequenced. The 22 sequences obtained were assignable to the taxa Proteobacteria, Bacillus and Flavobacterium, including a number of clades not normally associated with thermophily.

Regulation of beta-galactosidase expression in Bacillus megaterium DSM319 by a XylS/AraC-type transcriptional activator

The beta-galactosidase-encoding bgaM gene of Bacillus megaterium DSM319 and the divergently orientated bgaR operon were isolated and sequenced. Both traits are subject to catabolite repression. A set of single-gene replacement mutants was generated and used to analyze gene function. BgaR was found to be a XylS/AraC-type positive transcriptional regulator of bgaM; a potential regulator binding site overlaps the bgaM promoter. A mechanism for regulation of beta-galactosidase expression in B. megaterium is proposed.

Molecular characterization of the operon comprising the spoIV gene of Bacillus megaterium DSM319 and generation of a deletion mutant

According to sequence analysis, the spoIV-locus of Bacillus megaterium DSM 319 is 1,185 bp long; it is the second gene of a sporulation operon, which altogether contains three open reading frames. The ORF preceding spoIV encodes a putative polypeptide with 94 amino acids; the 3rd ORF of the operon has 972 bp corresponding to 324 amino acids. The operon is flanked on both sides by palindromic sequences, probably representing Rho-independent terminators. A primer extension analysis revealed that mRNA synthesis starts immediately downstream of a promoter, which is similar to the consensus sequence of Bacillus subtilis sigma(E) dependent promoters. Both the -35 and the -10 region are within the terminator region of the preceding operon. Gene knockout experiments and reporter gene assays with a newly developed system based on the heterologous Paenibacillus macerans glucanase gene (bgl) confirmed sigma(E)-dependent transcription. Two open reading frames of a further upstream operon were also identified. Northern analysis revealed that transcription of these ORFs comes about in late sporulation phases. The genetic organization of the spoIV comprising operon and adjacent loci clearly resembles that of the B. subtilis yqfa-phoH gene cluster. Thus our findings are of general significance for endospore-forming bacteria.

Cloning and sequencing of the LEU2 homologue gene of Schwanniomyces occidentalis

A gene that complements the leu2 mutation of Saccharomyces cerevisiae has been cloned from Schwanniomyces occidentalis. The gene codes for a protein of 379 amino acids. As expected for a Schwanniomyces gene, it has a high AT content, which is also reflected in the codon usage. The sequence homology with other known leu2 complementing genes is low.

Inactivation of the major extracellular protease from Bacillus megaterium DSM319 by gene replacement

An efficient method for gene replacement in Bacillus megaterium was developed and used to inactivate the chromosomal neutral protease gene (nprM) from strain DSM319. A temperature-dependant suicide vector was constructed to allow replacement of the normal chromosomal copy with an altered version of the nprM gene. One mutant B. megaterium MS941 was selected for further characterization. Measurement of extracellular protease activity from strain MS941 indicated the existence of an additional minor extracellular protease in B. megaterium. Inhibitor studies revealed that this minor protease, comprising only 1.4% of the wild-type total extracellular protease activities, is a serine-type enzyme.