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Methods in Enzymology

Bradley S Moore
No abstract text is available yet for this article.
2018: Methods in Enzymology
Giuliana d'Ippolito, Genoveffa Nuzzo, Angela Sardo, Emiliano Manzo, Carmela Gallo, Angelo Fontana
Marine diatoms negatively affect reproduction and later larval development of dominant zooplankton grazers such as copepods, thereby lowering the recruitment of the next generations of these small crustaceans that are a major food source for larval fish species. The phenomenon has been explained in terms of chemical defense due to grazer-induced synthesis of oxylipins, lipoxygenase-derived oxygenated fatty acid derivatives. Since this first report, studies about diatom oxylipins have multiplied and broadened toward other aspects concerning bloom dynamics, cell growth, and cell differentiation...
2018: Methods in Enzymology
Martin Tresguerres, Cristina Salmerón
The enzyme soluble adenylyl cyclase (sAC) is the most recently identified source of the messenger molecule cyclic adenosine monophosphate. sAC is evolutionarily conserved from cyanobacteria to human, is directly stimulated by [Formula: see text] ions, and can act as a sensor of environmental and metabolic CO2 , pH, and [Formula: see text] levels. sAC genes tend to have multiple alternative promoters, undergo extensive alternative splicing, be translated into low mRNA levels, and the numerous sAC protein isoforms may be present in various subcellular localizations...
2018: Methods in Enzymology
Alan R Brash
Catalase-related allene oxide synthase (cAOS) is a hemoprotein that converts a specific fatty acid hydroperoxide to an unstable allene oxide intermediate at turnover rates in the order of 1000 per second. Fatty acid allene oxides are intermediates in the formation of cyclopentenone or hydrolytic products in marine systems, most notably the prostanoid-related clavulones. Although the key catalytic amino acid residues around the active site of cAOS are the same as in true catalases, cAOS does not react with hydrogen peroxide...
2018: Methods in Enzymology
Akira Inoue
Alginate, an anionic heteropolysaccharide extracted from natural brown algae, has useful properties for the food, chemical, medical, and agricultural industries. Degradation of alginate by alginate lyase is a key process to produce unsaturated oligoalginate and unsaturated monosaccharide 4-deoxy-l-erythro-5-hexoseulose uronic acid. Alginate lyases belonging to the polysaccharide lyase family 7 have been found in, and isolated from, organisms thriving in various environments. Furthermore, research on their function and structure has also progressed well...
2018: Methods in Enzymology
Takao Ojima, Mohammad M Rahman, Yuya Kumagai, Ryuji Nishiyama, Joemark Narsico, Akira Inoue
Seaweed polysaccharides have been widely used as viscosifier, gelling agents, and stabilizer in the various application fields, e.g., food, pharmaceutical, nutraceutical, and chemical industries. Applications of seaweed polysaccharides are further expanding to versatile directions, e.g., biofuels, bioactive compounds, and functional materials for medical and basic researches. Production of functional oligo- and monosaccharides by the use of specific enzymes is also expected to improve the value of seaweed polysaccharides...
2018: Methods in Enzymology
Katsuhiko Shimizu, Daniel E Morse
Silicatein, a silica-synthesizing, catalytic triad hydrolase, was discovered in the silica spicules comprising the skeletons of certain marine sponges. Sequence similarity is closest to that of the mammalian cathepsin L, a catalytic triad hydrolase and protease. Genetic substitutions of residues in the catalytic triad, the predictive activities of polymeric and small-molecule analogs of the enzyme, and the wide range of structures accepted as substrates all support a reaction mechanism closely analogous to that established for the classical catalytic triad hydrolases...
2018: Methods in Enzymology
Emily C Ulrich, Siddhesh S Kamat, Bjarne Hove-Jensen, David L Zechel
Inorganic phosphate is essential for all life forms, yet microbes in marine environments are in near constant deprivation of this important nutrient. Organophosphonic acids can serve as an alternative source of inorganic phosphate if microbes possess the appropriate biochemical pathways that allow cleavage of the stable carbon-phosphorus bond that defines this class of molecule. One prominent source of inorganic phosphate is methylphosphonic acid, which is found as a constituent of marine-dissolved organic matter...
2018: Methods in Enzymology
Soo Y Ro, Amy C Rosenzweig
Methanotrophic bacteria utilize methane as their sole carbon and energy source. Studies of the model Type II methanotroph Methylosinus trichosporium OB3b have provided insight into multiple aspects of methanotrophy, including methane assimilation, copper accumulation, and metal-dependent gene expression. Development of genetic tools for chromosomal editing was crucial for advancing these studies. Recent interest in methanotroph metabolic engineering has led to new protocols for genetic manipulation of methanotrophs that are effective and simple to use...
2018: Methods in Enzymology
Nathaniel C Gilbert, David B Neau, Marcia E Newcomer
Methods are presented for the use of the coral 8R-lipoxygenase from the Caribbean sea whip coral Plexaura homomalla as a model enzyme for structural studies of animal lipoxygenases. The 8R-lipoxygenase is remarkably stable and can be stored at 4°C for 3 months with virtually no loss of activity. In addition, an engineered "pseudo wild-type" enzyme is soluble in the absence of detergents, which helps facilitate the preparation of enzyme:substrate complexes.
2018: Methods in Enzymology
Christopher R Reisch
Dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide. This enzyme has been purified and characterized from two marine bacteria from different ecological niches. Both enzymes were confirmed to catalyze the tetrahydrofolate-dependent demethylation of DMSP and possessed similar properties...
2018: Methods in Enzymology
Marco N Allemann, Eric E Allen
The long-chain omega-3 polyunsaturated fatty acids (n-3 LC-PUFAs) EPA (20:5n-3) and DHA (22:6n-3) are widely recognized as beneficial to human health and development. Select lineages of cosmopolitan marine prokaryotic and eukaryotic microorganisms synthesize these compounds via a unique fatty acid synthase/polyketide synthase mechanism that is distinct from the canonical desaturase/elongase-mediated pathway employed by the majority of eukaryotic single-cell microorganisms and metazoans. This "Pfa synthase" mechanism is highly efficient and has been co-opted for the large-scale industrial production of n-3 LC-PUFAs for commercial applications...
2018: Methods in Enzymology
Mishtu Dey, Adam E Brummett
The organosulfur metabolite dimethylsulfoniopropionate (DMSP) and its enzymatic breakdown product dimethyl sulfide (DMS) have important implications in the global sulfur cycle and in marine microbial food webs. Enormous amounts of DMSP are produced in marine environments where microbial communities import and catabolize it via either the demethylation or the cleavage pathways. The enzymes that cleave DMSP are termed "DMSP lyases" and generate acrylate or hydroxypropionate, and ~107 tons of DMS annually...
2018: Methods in Enzymology
Lei Lei, Uria Alcolombri, Dan S Tawfik
Dimethyl sulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms release DMS via cleavage of dimethylsulfoniopropionate (DMSP). DMSP lyases have been identified in various organisms, including bacteria, coral, and algae, thus comprising a range of gene families putatively assigned as DMSP lyases. Metagenomics may therefore provide insight regarding the presence of DMSP lyases in various marine environments, thereby promoting a better understanding of global DMS emission...
2018: Methods in Enzymology
Jonathan R Chekan, Bradley S Moore
While halogenases have been studied for decades, the first natural product dehalogenase was only recently described. This bacterial enzyme, Bmp8, catalyzes the reductive debromination of 2,3,4,5-tetrabromopyrrole to form 2,3,4-tribromopyrrole as part of the biosynthesis of pentabromopseudilin, a marine natural product. Bmp8 is hypothesized to utilize a catalytic mechanism analogous to the important human thyroid hormone deiodinase enzyme family, potentially enabling Bmp8 to serve as model system to study this conserved mechanism...
2018: Methods in Enzymology
Antonin Kunka, Jiri Damborsky, Zbynek Prokop
Haloalkane dehalogenases degrade halogenated compounds to corresponding alcohols by a hydrolytic mechanism. These enzymes are being intensively investigated as model systems in experimental and in silico studies of enzyme mechanism and evolution, but also hold importance as useful biocatalysts for a number of biotechnological applications. Haloalkane dehalogenases originate from various organisms including bacteria (degraders, symbionts, or pathogens), eukaryotes, and archaea. Several members of this enzyme family have been found in marine organisms...
2018: Methods in Enzymology
Ron Wever, Bea E Krenn, Rokus Renirie
Vanadium-dependent haloperoxidases in seaweeds, cyanobacteria, fungi, and possibly phytoplankton play an important role in the release of halogenated volatile compounds in the environment. These halocarbons have effects on atmospheric chemistry since they cause ozone depletion. In this chapter, a survey is given of the different sources of these enzymes, some of their properties, the various methods to isolate them, and the bottlenecks in purification. The assays to detect and quantify haloperoxidase activity are described as well as their kinetic properties...
2018: Methods in Enzymology
Carmela Gallo, Genoveffa Nuzzo, Giuliana d'Ippolito, Emiliano Manzo, Angela Sardo, Angelo Fontana
Sterol sulfates are widely occurring molecules in marine organisms. Their importance has been so far underestimated although many of these compounds are crucial mediators of physiological and ecological functions in other organisms. Biosynthesis of sterol sulfates is controlled by cytosolic sulfotransferases (SULTs), a varied family of enzymes that catalyze the transfer of a sulfo residue (-SO3 H) from the universal donor 3'-phosphoadenosine-5'-phosphosulfate to the hydroxyl function at C-3 of the steroid skeleton...
2018: Methods in Enzymology
Bradley S Moore
No abstract text is available yet for this article.
2018: Methods in Enzymology
Xuejun Zhu, Wenjun Zhang
The terminal alkyne is a readily derivatized functionality valued for its diverse applications in material synthesis, pharmaceutical science, and chemical biology. The synthetic biology routes to terminal alkynes are highly desired and yet underexplored. Some marine natural products contain a terminal alkyne functionality, and the discovery of the biosynthetic gene clusters for jamaicamide B and carmabin A marked the beginning of a new era in the understanding and engineering of terminal alkyne biosynthesis...
2018: Methods in Enzymology
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