{"title":"Uncoupling chitosanase production from chitosan.","authors":"Ryszard Brzezinski","doi":"10.1186/1475-2859-10-7","DOIUrl":"https://doi.org/10.1186/1475-2859-10-7","url":null,"abstract":"<p><p>There is a growing interest in chitosanases as enzymatic tools to hydrolyze chitosan into bioactive forms: low molecular weight chitosan (LMWC) or chitosan oligosaccharides (CHOS). However chitosanases are still expensive and methods of large-scale production of these enzymes are not yet established. The article reviews the approaches used for chitosanase production in various bacterial hosts, pointing out the difficulties resulting from the necessity to include chitosan into the medium composition. A mutated Streptomyces host allows for the efficient production of several chitosanases originating from actinobacteria in the absence of chitosan as inducer.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 4","pages":"226-9"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1475-2859-10-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30067563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Uncoupling chitosanase production from chitosan","authors":"R. Brzezinski","doi":"10.4161/bbug.2.4.16111","DOIUrl":"https://doi.org/10.4161/bbug.2.4.16111","url":null,"abstract":"There is a growing interest in chitosanases as enzymatic tools to hydrolyze chitosan into bioactive forms: low molecular weight chitosan (LMWC) or chitosan oligosaccharides (CHOS). However chitosanases are still expensive and methods of large-scale production of these enzymes are not yet established. The article reviews the approaches used for chitosanase production in various bacterial hosts, pointing out the difficulties resulting from the necessity to include chitosan into the medium composition. A mutated Streptomyces host allows for the efficient production of several chitosanases originating from actinobacteria in the absence of chitosan as inducer.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"9 1","pages":"226 - 229"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73254721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A new diet for yeast to improve biofuel production.","authors":"Jonathan M Galazka, Jamie H D Cate","doi":"10.4161/bbug.2.4.15624","DOIUrl":"https://doi.org/10.4161/bbug.2.4.15624","url":null,"abstract":"<p><p>In 2010, our group announced the discovery of two cellodextrin transporter families from the cellulolytic fungus, Neurospora crassa. Furthermore, we demonstrated the utility of these transporters in the production of lignocellulosic biofuels. This discovery was made possible by a decision to systematically study cell wall degradation by N. crassa. The identified transport pathway has opened up a new way of thinking about microbial fermentation of hexoses as well as pentoses derived from plant cell walls. Integrating this pathway with the endogenous metabolism and signaling networks of S. cerevisiae is now a major goal of our group.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 4","pages":"199-202"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.4.15624","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bacteriophage-based biocontrol of biological sludge bulking in wastewater","authors":"Jeongdong Choi, Shireen M Kotay, R. Goel","doi":"10.4161/bbug.2.4.16211","DOIUrl":"https://doi.org/10.4161/bbug.2.4.16211","url":null,"abstract":"In a previous paper, the first ever application of lytic bacteriophage (virus)-mediated biocontrol of biomass bulking in the activated sludge process using Haliscomenobacter hydrossis as a model filamentous bacterium was demonstrated. In this work we extended the biocontrol application to another predominant filamentous bacterium, Sphaerotilus natans, notoriously known to cause filamentous bulking in wastewater treatment systems. Very similar to previous study, one lytic bacteriophage was isolated from wastewater that could infect S. natans and cause lysis. Significant reduction in sludge volume index and turbidity of the supernatant was observed in batches containing S. natans biomass following addition of lytic phages. Microscopic examination confirmed that the isolated lytic phage can trigger the bacteriolysis of S. natans. This extended finding further strengthens our hypothesis of bacteriophage-based biocontrol of overgrowth of filamentous bacteria and the possibility of phage application in activated sludge processes, the world's widely used wastewater treatment processes.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"34 1","pages":"214 - 217"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78300031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"E. coli O104:H4: social media and the characterization of an emerging pathogen.","authors":"Pat G Casey, Colin Hill, Cormac Gm Gahan","doi":"10.4161/bbug.2.4.16961","DOIUrl":"https://doi.org/10.4161/bbug.2.4.16961","url":null,"abstract":"<p><p>The 2011 German E. coli O104:H4 outbreak resulted in thousands of cases of enterohaemorrhagic illness, with approximately 25% of these progressing to develop haemolytic uraemic syndrome (HUS). This high rate of progression to HUS was the first indicator that the bacterial cause of illness was not a typical enterohaemorrhagic E. coli (EHEC) strain. Collaborative bioinformatic analysis while the outbreak was still in progress indicated that the O104:H4 strain was in fact an enteroaggregative E. coli (EAEC) strain which had acquired genes for the production of Shiga - like toxin.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 4","pages":"189-93"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.4.16961","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29973333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Engineering host-derived resistance against plant parasites through RNA interference: Challenges and opportunities","authors":"S. Runo","doi":"10.4161/bbug.2.4.15879","DOIUrl":"https://doi.org/10.4161/bbug.2.4.15879","url":null,"abstract":"RNA interference (RNAi) has rapidly advanced to become a powerful genetic tool and holds promise to revolutionizing agriculture by providing a strategy for controlling a wide array of crop pests. Numerous studies document RNAi efficacy in achieving silencing in viruses, insects, nematodes and weeds parasitizing crops. In general, host derived pest resistance through RNAi is achieved by genetically transforming host plants with double stranded RNA constructs targeted at essential parasite genes leading to generation of small interfering RNAs (siRNAs). Small interfering RNAs formed in the host are then delivered to the parasite and transported to target cells. Delivery can be oral – worms and insects, viral infections, viruses – or through a vascular connections – parasitic plants, while delivery to target cells is by cell to cell systemic movement of the silencing signal. Despite the overall optimism in generating pest resistant crops through RNAi-mediated silencing, some hurdles have recently begun to emerge. Presently, the main challenge is delivery of sufficient siRNAs, in the right cells, and at the right time to mount; a strong, durable, and broad-spectrum posttranscriptional gene silencing (PTGS) signal. This review highlights the novel strategies available for improving host derived RNAi resistance in downstream applied agriculture.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"8 1","pages":"208 - 213"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82356963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Escarlata Rodríguez-Carmona, Antonio Villaverde, Elena García-Fruitós
{"title":"How to break recombinant bacteria: does it matter?","authors":"Escarlata Rodríguez-Carmona, Antonio Villaverde, Elena García-Fruitós","doi":"10.4161/bbug.2.4.15778","DOIUrl":"https://doi.org/10.4161/bbug.2.4.15778","url":null,"abstract":"<p><p>Recombinant proteins and other materials of industrial interest produced in Escherichia coli are usually retained within the bacterial cell, in the cytoplasmic space, where they have been produced. Different protocols for cell disruption have been implemented as an initial downstream step, which keeps the biological and mechanical properties of the process products. Being necessarily mild, these approaches often result in 95-99% cell disruption, what is more than acceptable from the yield point of view. However, when the bacterial product are nano or microparticulate entities that tend to co-sediment with entire bacterial cells, the remaining undisrupted bacteria appear as abounding contaminants, making the product not suitable for a spectrum of biomedical applications. Since bacterial inclusion bodies are now seen as bacterial materials valuable in different fields, we have developed an alternative cell disruption protocol that permits obtaining fully bacterial free protein particles, keeping the conformational status of the embedded proteins and the mechanical properties of the full aggregates.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 4","pages":"222-5"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.4.15778","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30065765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Phagosome proteomics: a powerful tool to assess bacteria-mediated immunomodulation.","authors":"Qingbo Li","doi":"10.4161/bbug.2.4.15563","DOIUrl":"https://doi.org/10.4161/bbug.2.4.15563","url":null,"abstract":"<p><p>Bacteria-mediated immunomodulation has important implications in microbial infection and bacterial vaccines. Intraphagosomal bacteria negotiate survival niches with the intracellular environment by modulating the phagosome composition during invasion. The final phagosome composition determines the fate of the intraphagosomal bacterium or the efficacy of a bacterial vaccine. Therefore, the phagosome proteome is a valuable readout to assess the ability of a natural or genetically engineered bacterial strain to modulate the host immune response. Compared to a preparation of latex-bead-containing phagosomes, the preparation of bacterial phagosomes requires additional measures to ensure comparable purity due to their closer density to some other organelles. This bottleneck can be overcome with delicate preparation protocols, proper experimental designs to facilitate bioinformatics based discrimination against contaminating proteins, and the incorporation of stable-isotope labeled internal standards to correct for contaminating fractions of phagosomal proteins. The rapid progress in the proteomics and bioinformatics fields provides an array of techniques that promise to bring about an unprecedented coverage of both known and as yet undiscovered immunomodulation pathways within bacterial phagosome proteomes. A precise portrait of the bacteria-mediated immunomodulation pathways in phagosomes will likely aid in the intelligent design of bioengineered bacterial vaccine strains for important future biomedical applications.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 4","pages":"194-8"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.4.15563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30067561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Revealing the first uridyl peptide antibiotic biosynthetic gene cluster and probing pacidamycin biosynthesis.","authors":"Emma J Rackham, Sabine Grüschow, Rebecca J M Goss","doi":"10.4161/bbug.2.4.15877","DOIUrl":"https://doi.org/10.4161/bbug.2.4.15877","url":null,"abstract":"<p><p>There is an urgent need for new antibiotics with resistance continuing to emerge toward existing classes. The pacidamycin antibiotics possess a novel scaffold and exhibit unexploited bioactivity rendering them attractive research targets. We recently reported the first identification of a biosynthetic cluster encoding uridyl peptide antibiotic assembly and the engineering of pacidamycin biosynthesis into a heterologous host. We report here our methods toward identifying the biosynthetic cluster. Our initial experiments employed conventional methods of probing a cosmid library using PCR and Southern blotting, however it became necessary to adopt a state-of-the-art genome scanning and in silico hybridization approach to pin point the cluster. Here we describe our \"real\" and \"virtual\" probing methods and contrast the benefits and pitfalls of each approach. </p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 4","pages":"218-21"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.4.15877","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30067567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Engineering host-derived resistance against plant parasites through RNA interference: challenges and opportunities.","authors":"Steven Runo","doi":"10.4161/bbug.2.4.16112","DOIUrl":"https://doi.org/10.4161/bbug.2.4.16112","url":null,"abstract":"<p><p>RNA interference (RNAi) has rapidly advanced to become a powerful genetic tool and holds promise to revolutionizing agriculture by providing a strategy for controlling a wide array of crop pests. Numerous studies document RNAi efficacy in achieving silencing in viruses, insects, nematodes and weeds parasitizing crops. In general, host derived pest resistance through RNAi is achieved by genetically transforming host plants with double stranded RNA constructs targeted at essential parasite genes leading to generation of small interfering RNAs (siRNAs). Small interfering RNAs formed in the host are then delivered to the parasite and transported to target cells. Delivery can be oral - worms and insects, viral infections, viruses - or through a vascular connections - parasitic plants, while delivery to target cells is by cell to cell systemic movement of the silencing signal. Despite the overall optimism in generating pest resistant crops through RNAi-mediated silencing, some hurdles have recently begun to emerge. Presently, the main challenge is delivery of sufficient siRNAs, in the right cells, and at the right time to mount; a strong, durable, and broad-spectrum posttranscriptional gene silencing (PTGS) signal. This review highlights the novel strategies available for improving host derived RNAi resistance in downstream applied agriculture.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 4","pages":"208-13"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.4.16112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30067566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}