A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamor... more A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamora</i>) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (<i>Dermestes maculatus</i>) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified capable of growth on lignocellulosic components, including lignin. <i>Cedecea lapagei</i> was selected for further study due to growth on most lignocellulose components. The <i>C. lapagei</i> secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.
A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamor... more A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamora</i>) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (<i>Dermestes maculatus</i>) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified capable of growth on lignocellulosic components, including lignin. <i>Cedecea lapagei</i> was selected for further study due to growth on most lignocellulose components. The <i>C. lapagei</i> secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.
Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. Proteins fr... more Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. Proteins from this hyperthemophile organism are extremely thermostable and are highly resistant to chemical denaturants, organic solvents and proteolytic digestion. This thermostability makes it difficult to apply traditional methods of enzymatically digesting a complex mixture of proteins, commonly a first step in peptide generation in most shotgun proteomics methods. Here, we have developed a simple shotgun proteomics approach for the global identification of the P. furiosus proteome. This methodology uses a detergent-based microwave assisted acid hydrolysis (MAAH) step coupled with an overnight trypsin digest to obtain peptides. Subsequent peptide fractionation by isoelectric focusing in immobilized pH gradients (IPG-IEF), followed by chromatographic separation with reverse phase nano-HPLC and electrospray ionization tandem mass spectrometry (ESI-MS/MS) of peptides enabled the identification of over 900 proteins representing over 44% of the proteome. In most functional classes, over 50% of the predicted proteins were identified, including a number of membrane proteins. This new sample preparation technique will enable extensive proteomics data to be obtained for this organism, thereby enabling the reconstruction of metabolic pathways and promoting a systems biology based understanding of this important extremophile.
While much progress has been made in designing biospheres for optimal plant growth and long term ... more While much progress has been made in designing biospheres for optimal plant growth and long term habitation in space, plant productivity remains a major limiting factor for sustainable bioregenerative life support. To meet these challenges, we propose that plant biologists should work with engineers to redesign plants. For example, the mechanisms that plants engage to sense environmental cues can be replaced or modified to eliminate Earth-based responses no longer needed in space and to add responses that will improve growth in a biosphere. In addition, synthetic approaches can be used to fine tune plant responses to stress by expressing genes from organisms that thrive in extreme environments. Producing extremophilic proteins in crop plants can increase a plant’s tolerance to rapid changes in temperature and improve growth in environments which might otherwise be sensed as stressful. Future efforts to redesign plants provide unlimited promise for developing sustainable bioregenerative life support systems and will lead to new fundamental insights into the regulation of plant growth and development.
Prolidase is a metallopeptidase that is ubiquitous in nature and has been isolated from mammals, ... more Prolidase is a metallopeptidase that is ubiquitous in nature and has been isolated from mammals, bacteria and archaea. Prolidase specifically hydrolyzes dipeptides with a prolyl residue in the carboxy terminus (NH(2)-X-/-Pro-COOH). Currently, the only solved structure of prolidase is from the hyperthermophilic archaeon Pyrococcus furiosus. This enzyme is of particular interest because it can be used in many biotechnological applications. Prolidase is able to degrade toxic organophosphorus (OP) compounds, namely, by cleaving the P-F and P-O bonds in the nerve agents, sarin and soman. Applications using prolidase to detoxify OP nerve agents include its incorporation into fire-fighting foams and as biosensors for OP compound detection. Prolidases are also employed in the cheese-ripening process to improve cheese taste and texture. In humans, prolidase deficiency (PD) is a rare autosomal recessive disorder that affects the connective tissue. Symptoms of PD include skin lesions, mental retardation and recurrent respiratory infections. Enzyme replacement therapies are currently being studied in an effort to optimize enzyme delivery and stability for this application. Previously, prolidase has been linked to collagen metabolism and more recently is being associated with melanoma. Increased prolidase activity in melanoma cell lines has lead investigators to create cancer prodrugs targeting this enzyme. Thus, there are many biotechnological applications using recombinant and native forms of prolidase and this review will describe the biochemical and structural properties of prolidases as well as discuss their most current applications.
A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamor... more A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamora</i>) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (<i>Dermestes maculatus</i>) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified capable of growth on lignocellulosic components, including lignin. <i>Cedecea lapagei</i> was selected for further study due to growth on most lignocellulose components. The <i>C. lapagei</i> secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.
A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamor... more A citizen science project found that the greenhouse camel cricket (<i>Diestrammena asynamora</i>) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (<i>Dermestes maculatus</i>) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified capable of growth on lignocellulosic components, including lignin. <i>Cedecea lapagei</i> was selected for further study due to growth on most lignocellulose components. The <i>C. lapagei</i> secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.
Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. Proteins fr... more Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. Proteins from this hyperthemophile organism are extremely thermostable and are highly resistant to chemical denaturants, organic solvents and proteolytic digestion. This thermostability makes it difficult to apply traditional methods of enzymatically digesting a complex mixture of proteins, commonly a first step in peptide generation in most shotgun proteomics methods. Here, we have developed a simple shotgun proteomics approach for the global identification of the P. furiosus proteome. This methodology uses a detergent-based microwave assisted acid hydrolysis (MAAH) step coupled with an overnight trypsin digest to obtain peptides. Subsequent peptide fractionation by isoelectric focusing in immobilized pH gradients (IPG-IEF), followed by chromatographic separation with reverse phase nano-HPLC and electrospray ionization tandem mass spectrometry (ESI-MS/MS) of peptides enabled the identification of over 900 proteins representing over 44% of the proteome. In most functional classes, over 50% of the predicted proteins were identified, including a number of membrane proteins. This new sample preparation technique will enable extensive proteomics data to be obtained for this organism, thereby enabling the reconstruction of metabolic pathways and promoting a systems biology based understanding of this important extremophile.
While much progress has been made in designing biospheres for optimal plant growth and long term ... more While much progress has been made in designing biospheres for optimal plant growth and long term habitation in space, plant productivity remains a major limiting factor for sustainable bioregenerative life support. To meet these challenges, we propose that plant biologists should work with engineers to redesign plants. For example, the mechanisms that plants engage to sense environmental cues can be replaced or modified to eliminate Earth-based responses no longer needed in space and to add responses that will improve growth in a biosphere. In addition, synthetic approaches can be used to fine tune plant responses to stress by expressing genes from organisms that thrive in extreme environments. Producing extremophilic proteins in crop plants can increase a plant’s tolerance to rapid changes in temperature and improve growth in environments which might otherwise be sensed as stressful. Future efforts to redesign plants provide unlimited promise for developing sustainable bioregenerative life support systems and will lead to new fundamental insights into the regulation of plant growth and development.
Prolidase is a metallopeptidase that is ubiquitous in nature and has been isolated from mammals, ... more Prolidase is a metallopeptidase that is ubiquitous in nature and has been isolated from mammals, bacteria and archaea. Prolidase specifically hydrolyzes dipeptides with a prolyl residue in the carboxy terminus (NH(2)-X-/-Pro-COOH). Currently, the only solved structure of prolidase is from the hyperthermophilic archaeon Pyrococcus furiosus. This enzyme is of particular interest because it can be used in many biotechnological applications. Prolidase is able to degrade toxic organophosphorus (OP) compounds, namely, by cleaving the P-F and P-O bonds in the nerve agents, sarin and soman. Applications using prolidase to detoxify OP nerve agents include its incorporation into fire-fighting foams and as biosensors for OP compound detection. Prolidases are also employed in the cheese-ripening process to improve cheese taste and texture. In humans, prolidase deficiency (PD) is a rare autosomal recessive disorder that affects the connective tissue. Symptoms of PD include skin lesions, mental retardation and recurrent respiratory infections. Enzyme replacement therapies are currently being studied in an effort to optimize enzyme delivery and stability for this application. Previously, prolidase has been linked to collagen metabolism and more recently is being associated with melanoma. Increased prolidase activity in melanoma cell lines has lead investigators to create cancer prodrugs targeting this enzyme. Thus, there are many biotechnological applications using recombinant and native forms of prolidase and this review will describe the biochemical and structural properties of prolidases as well as discuss their most current applications.
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