Proteases from gram-positive organisms

Details Proteases from gram-positive organisms Proteases from gram-positive organisms

1999-05-14

2001-10-09

Achutamurthy, Ponnathapu (Department: 1652)

Chemistry: molecular biology and microbiology

Enzyme , proenzyme; compositions thereof; process for...

Hydrolase

C435S069100, C435S252310, C435S320100, C435S471000, C435S006120, C536S023200

Reexamination Certificate

active

06300117

ABSTRACT:

FIELD OF THE INVENTION
The present invention relates to metallo-proteases derived from gram-positive microorganisms. The present invention provides nucleic acid and amino acid sequences of a metallo-protease identified in
Bacillus subtilis
. The present invention also provides methods for the production of the protease in host cells as well as the production of heterologous proteins in a host cell having a mutation or deletion of part or all of the proteases of the present invention.
BACKGROUND OF THE INVENTION
Gram-positive microorganisms such as members of the group Bacillus, have been used for large-scale industrial fermentation due, in part, to their ability to secrete their fermentation products into the culture media. In gram-positive bacteria, secreted proteins are exported across a cell membrane and a cell wall, and then are subsequently released into the external media usually maintaining their native conformation.
Various gram-positive microorganisms are known to secrete extracellular and/or intracellular protease at some stage in their life cycles. Many proteases are produced in large quantities for industrial purposes. A negative aspect of the presence of proteases in gram-positive organisms is their contribution to the overall degradation of secreted heterologous or foreign proteins.
The classification of proteases found in microorganisms is based on their catalytic mechanism which results in four groups: the serine proteases; metallo-proteases; cysteine proteases; and aspartic proteases. These categories, in general, can be distinguished by their sensitivity to various inhibitors. For example, the serine proteases are inhibited by phenylmethylsulfonylfluoride (PMSF) and diisopropylfluorophosphate (DIFP); the metallo-proteases by chelating agents; the cysteine enzymes by iodoacetamide and heavy metals and the aspartic proteases by pepstatin. The serine proteases have alkaline pH optima, the metalloproteases are optimally active around neutrality, and the cysteine and aspartic enzymes have acidic pH optima (Biotechnology Handbooks.
Bacilluis
. vol. 2. edited by Harwood, 1989 Plenum Press, New York).
Metallo-proteases form the most diverse of the catalytic types of proteases. Family M23 contains bacterial enzymes such as the &bgr;-lytic endopeptidases of Lysobacter and
Achromobacier and the Pseudomonas LasA protein and have specificity for Gly bonds, especially in Gly-GIy+Xaa-sequences (Methods in Enzymology, vol. 248, Academic Press, Inc. 1994). The enzymes of the M23 family contain zinc and a conserved His-Xaa-His motif
SUMMARY OF THE INVENTION
The present invention relates to the discovery of a heretofore unknown metallo-protease (MP) found in gram positive microorganisms, uses of the MP in industrial applications, and advantageous strain improvements based on genetically engineering such microorganisms to delete, underexpress or overexpress that MP. Due to the overall relatedness of MP with Psezidomonas as lasA protein, including the presence of the motif His-Xaa-His, MP appears to be a member of the metallo-protease family M23.
Applicant's discovery, in addition to providing a new and useful protease and methods, of detecting DNA encoding such proteases in a gram positive microorganism, provides several advantages which may facilitate optimization and/or modification of strains of gram positive microorganisms, such as Bacillus, for expression of desired, e.g. heterologous, proteins. Such optimizations, as described below in detail, allow the construction of strains having decreased proteolytic degradation of desired expression products.
Applicant's invention is further based on the discovery of the presence of MP's in Gram-positive microorganisms. The Gram-positive microorganism may be Bacillus and may also be selected from the group consisting of
Bacillus stblilis, Bacillis stearotherniophilus, Bacillus lichenformis awd Bacillus amyloliqufaciens
. The present invention further relies or the discovery that naturally occurring MP is encoded by nucleic acid found about 2248 kb from the point of origin of
Bacillus subtilis
I-168 strain (Bacillus Genetic Stock Center, accession number 1A1, Columbus, Ohio). The present invention relates to the MP encoded thereby, as well as the nucleic acid and amino acid molecules having the sequences disclosed in
FIGS. 1A-1O
(nucleic acid shown in SEQ ID NO:1; amino acid sequence shown in SEQ ID NO2).
The present invention thus provides methods for detecting gram positive microorganism homologs of
B. stiblilis
MP that comprises hybridizing part or all of the nucleic acid encoding
B. suzblilis
MP with nucleic acid derived from gram-positive organisms, either of genomic or cDNA origin. Accordingly, the present invention provides a method for detecting a gram-positive microorganism MP, comprising the steps of hybridizing gram-positive microorganism nucleic acid under low stringency conditions to a probe, wherein the probe comprises part or all of the nucleic acid sequence shown in
FIGS. 1A-1O
(SEQ ID NO:1); and isolating gram-positive nucleic acid which hybridizes to said probe.
In a preferred embodiment, the Bacillus is selected from the group consisting of
B. licheniformis, B. lenius, B. brevis, B. stearothermophilus, B. alkalophilts, B. amyloliquefaciens, B. coaguilmis, B. circiIlans, B. lautus
and
B. thuringiensis.
The production of desired heterologous proteins or polypeptides in gram-positive microorganisms may be hindered by the presence of one or more proteases, including MP, which degrade the produced heterologous protein or polypeptide. One advantage of the present invention is that it provides methods and expression systems which can be used to prevent that degradation, thereby enhancing yields of the desired heterologous protein or polypeptide. Accordingly, the present invention provides a gram-positive microorganism having a mutation or deletion of part or all of the gene encoding MP, which results in the inactivation of the MP proteolytic activity, either alone or in combination with mutations in other proteases, such as apr, npr, epr, mpr, bpf or isp for example, or other proteases known to those of skill in the art. In one embodiment of the present invention, the gram-positive organism is a member of the genus Bacillhs. In another embodiment, the Bacillus is selected from the group consisting of
B. sitbtilis, B. lichentformis, B. lentizs, B. brevis, B. stearolhermophilus, B. alkalophiltis, B. amyloliquefaciens, B. coagulais, B. circulats, B. lautus
and
Bacillus thuringiensis
. In a further preferred embodiment, the Bacillus is
Bacillus subtilis.
In another aspect, the gram-positive host having one or more metallo-protease deletions or mutations is further genetically engineered to produce a desired protein. In one embodiment of the present invention, the desired protein is heterologous to the gram-positive host cell. In another embodiment, the desired protein is homologous to the host cell. The present invention encompasses a gram-positive host cell having a deletion, mutation or interruption of the nucleic acid encoding the naturally occurring homologous protein, such as a protease, and having nucleic acid encoding the homologous protein re-introduced in a recombinant form. In another embodiment, the host cell produces the homologous protein. Accordingly, the present invention also provides methods and expression systems for reducing degradation of heterologous proteins produced in gram-positive microorganisms. The gram-positive microorganism may be normally sporulating or non-sporulating. In a preferred embodiment, the gram positive host cell is a Bacillus. In another preferred embodiment, the Bacillus host cell is Bacillus. In another embodiment, the Bacillus is selected from the group consisting of
B. subtilis, B. licheniformis, B. lennus, B. brevis, B. stearothermophilis, B. alkalophilus, B. amyloliquefaciens, B. coagulans, B. circulans, B. lautus
and
Bacillus thurgiensis.
Naturally occurring gram positive MP as well as proteolytically active amino acid vanations or

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