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However, widely used bacterial expression systems (e.g. <jats:italic>Escherichia coli<\/jats:italic>, <jats:italic>Pseudomonas fluorescens<\/jats:italic>) are not able to secrete soluble proteins directly into the culture medium. This limits yields and increases downstream processing time and costs. In contrast, <jats:italic>Bacillus<\/jats:italic> spp. secrete native enzymes directly into the culture medium at grams\u2010per\u2010litre quantities, although the yields of some recombinant proteins are severely limited. We have engineered the <jats:italic>Bacillus subtilis<\/jats:italic> genome to generate novel strains with precise deletions in the genes encoding ten extracytoplasmic proteases that affect recombinant protein secretion, which lack chromosomal antibiotic resistance genes. The deletion sites and presence of single nucleotide polymorphisms were confirmed by sequencing. The strains are stable and were used in industrial\u2010scale fermenters for the production of the <jats:italic>Bacillus anthracis<\/jats:italic> vaccine protein, protective antigen, the productivity of which is extremely low in the unmodified strain. We also show that the deletion of so\u2010called quality control proteases appears to influence cell\u2010wall synthesis, resulting in the induction of the cell\u2010wall stress regulon that encodes another quality control protease.<\/jats:p>","DOI":"10.1002\/pmic.201300183","type":"journal-article","created":{"date-parts":[[2013,10,11]],"date-time":"2013-10-11T21:25:07Z","timestamp":1381526707000},"page":"3298-3308","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["Proteomic analysis of <i>Bacillus subtilis<\/i> strains engineered for improved production of heterologous proteins"],"prefix":"10.1002","volume":"13","author":[{"given":"Susanne","family":"Pohl","sequence":"first","affiliation":[{"name":"Centre for Bacterial Cell Biology Baddiley\u2010Clark Building Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaurav","family":"Bhavsar","sequence":"additional","affiliation":[{"name":"Cobra Biologics Stephenson Building Keele Science Park  Keele Staffordshire UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne","family":"Hulme","sequence":"additional","affiliation":[{"name":"Cobra Biologics Stephenson Building Keele Science Park  Keele Staffordshire UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra E.","family":"Bloor","sequence":"additional","affiliation":[{"name":"Cobra Biologics Stephenson Building Keele Science Park  Keele Staffordshire UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Goksel","family":"Misirli","sequence":"additional","affiliation":[{"name":"Centre for Bacterial Cell Biology Baddiley\u2010Clark Building Newcastle University  Newcastle upon Tyne UK"},{"name":"Computing Science Claremont Tower Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew W.","family":"Leckenby","sequence":"additional","affiliation":[{"name":"Cobra Biologics Stephenson Building Keele Science Park  Keele Staffordshire UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David S.","family":"Radford","sequence":"additional","affiliation":[{"name":"Cobra Biologics Stephenson Building Keele Science Park  Keele Staffordshire UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendy","family":"Smith","sequence":"additional","affiliation":[{"name":"Centre for Bacterial Cell Biology Baddiley\u2010Clark Building Newcastle University  Newcastle upon Tyne UK"},{"name":"Computing Science Claremont Tower Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anil","family":"Wipat","sequence":"additional","affiliation":[{"name":"Centre for Bacterial Cell Biology Baddiley\u2010Clark Building Newcastle University  Newcastle upon Tyne UK"},{"name":"Computing Science Claremont Tower Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. 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