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The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

Michael Knoll, Thomas M Hamm, Florian Wagner, Virginia Martinez, Jürgen Pleiss
2009 BMC Bioinformatics  
Results: The PHA Depolymerase Engineering Database (DED, has been established as a tool for systematic analysis of this enzyme family.  ...  The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity.  ...  Conclusion The PHA Depolymerase Engineering Database (DED) has been designed to serve as a navigation and analysis tool of PHA depolymerases.  ... 
doi:10.1186/1471-2105-10-89 pmid:19296857 pmcid:PMC2666664 fatcat:lfrfjzvkijbepia2ykvlljo7am

The phylogenetic and global distribution of extracellular bioplastic degrading genes [article]

Veronica R Viljakainen, Laura A Hug
2020 bioRxiv   pre-print
Polyhydroxyalkanoates (PHAs) are a family of microbially-made polyesters that have been commercialized as biodegradable plastics.  ...  Here we used 3,842 metagenomes to analyze the distribution of PHA depolymerase genes in microbial communities from diverse aquatic, terrestrial and waste management systems.  ...  Microbial degradation of polyhydroxyalkanoates. Annual Review of database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases.  ... 
doi:10.1101/2020.05.08.085522 fatcat:n6eqaogyg5bdroai6ua5jsl4fy

Progressing Plastics Circularity: A Review of Mechano-Biocatalytic Approaches for Waste Plastic (Re)valorization

Efstratios Nikolaivits, Brana Pantelic, Muhammad Azeem, George Taxeidis, Ramesh Babu, Evangelos Topakas, Margaret Brennan Fournet, Jasmina Nikodinovic-Runic
2021 Frontiers in Bioengineering and Biotechnology  
The PHA depolymerase engineering database: a systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases.  ...  PHA-depolymerases are specific for the ( R )-configuration of the polymers.  ... 
doi:10.3389/fbioe.2021.696040 fatcat:my5ozxfqwzevriucnpxnxwxrwe

What Has Been Trending in the Research of Polyhydroxyalkanoates? A Systematic Review

Maciej Guzik, Tomasz Witko, Alexander Steinbüchel, Magdalena Wojnarowska, Mariusz Sołtysik, Sławomir Wawak
2020 Frontiers in Bioengineering and Biotechnology  
One of the most prominent families of such biopolymers are bacterially synthesized polyhydroxyalkanoates (PHAs) that have been known since the 1920s.  ...  Our study provides a comprehensive review of these trends and speculates where PHA research is heading.  ...  based only on a systematic review of literature.  ... 
doi:10.3389/fbioe.2020.00959 pmid:33014998 pmcid:PMC7513618 fatcat:xnre5mokzbcy3mpj7hireqqh4y

Engineering Native and Synthetic Pathways in Pseudomonas Putida for the Production of Tailored Polyhydroxyalkanoates ‡

Mariela P. Mezzina, María Tsampika Manoli, M. Auxiliadora Prieto, Pablo I. Nikel
2020 Biotechnology Journal  
Polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in the central metabolism of producer bacteria, as they act as dynamic reservoirs of carbon and reducing equivalents.  ...  The surge of synthetic biology and metabolic engineering approaches in recent years now offers the possibility of exploiting the untapped potential of Pseudomonas-based cell factories for the production  ...  SWEET M.T.M. acknowledges the support of the Novo Nordisk Foundation.  ... 
doi:10.1002/biot.202000165 pmid:33085217 fatcat:356in2g3tbhsdjyv2iig7sidre

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

Ignacio Poblete‐Castro, Christoph Wittmann, Pablo I. Nikel
2019 Microbial Biotechnology  
, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost-effective substrate.  ...  Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value-added products (ranging from simple molecules to structurally complex biopolymers  ...  The funding bodies were not involved in the design, collection, analysis or interpretation of this study.  ... 
doi:10.1111/1751-7915.13400 pmid:30883020 pmcid:PMC6922529 fatcat:bdqgpkp7ybfn7envhgwv74b7qa

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments

Paul J. Janssen, Rob Van Houdt, Hugo Moors, Pieter Monsieurs, Nicolas Morin, Arlette Michaux, Mohammed A. Benotmane, Natalie Leys, Tatiana Vallaeys, Alla Lapidus, Sébastien Monchy, Claudine Médigue (+6 others)
2010 PLoS ONE  
At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons.  ...  species as a result of gene transfer and through the presence of large genomic islands.  ...  Acknowledgments We thank A. D. Woodhead for excellent scientific editing of the manuscript and D. Vallenet and Z.  ... 
doi:10.1371/journal.pone.0010433 pmid:20463976 pmcid:PMC2864759 fatcat:krys5b5lijd4bhp7wiiqcciokm

Sustainable Production of Novel Biomaterials in Escherichia coli

Asif Rahman
The potential to engineer microorganisms for novel applications can have far-reaching implications and benefits for society.  ...  Spider silk is a unique material with high tensile strength and elasticity and thus could have a wide range of potential applications.  ...  Acknowledgements The authors would like to acknowledge the following groups: Environmental References  ... 
doi:10.26076/5a18-eff7 fatcat:3lq67p2bwzhvlebwj4otjn5ney

Vorhersage struktureller und biochemischer Eigenschaften von Cytochrom P450-Monooxygenasen und Laccasen [article]

Demetgül Sirim, Universität Stuttgart, Universität Stuttgart
By means of a systematic analysis of proteins in the context of their entire family of homologous proteins, structural and biochemical properties should be explained.  ...  Therefore, protein family databases for the industrially relevant enzyme classes cytochrome P450 monooxygenases and laccases were established.  ...  We further are grateful for the unknown reviewer's comments which contributed greatly to the improvement of data content and the user interface of the CYPED.  ... 
doi:10.18419/opus-1268 fatcat:ze7bia4ntrblpgjrak47s5o36e

Growth Characterization and Transcriptomics of Methanotrophic Bacteria as Effected by Carbon and Nitrogen Sources

Catherine Tays
The main carbon sources of interest for industry are methane and methanol, the latter also being a common iii industrial byproduct.  ...  This uncertainty can manifest in undesirable outcomes for bioprocesses, including slow or inhibited growth and diversion of cell resources away from desired bioproducts.  ...  We thank Stefanie Van Wychen and Holly Smith (NREL) for contributions to FAME and metabolite analyses, respectively. Mango Materials Inc. generously provided the bacterium Methylocystis sp. WRRC1.  ... 
doi:10.7939/r3-3n30-qf72 fatcat:uv3mqltklra65jud3ma3a6so44

Bio-plastics and technologies for eco-sustainable packaging

Emanuele Simonini
The experiments demonstrate new application areas of mid-IR fiber laser sources for materials processing.  ...  The morphology of the materials and the relations between the laser process conditions and the quality of the seam were investigated by means of optical microscopy.  ...  Their work provided a solid basis for systematic studies of aliphatic polyester forming mechanisms [21] .  ... 
doi:10.48676/unibo/amsdottorato/9698 fatcat:zxv35jtx7bbytlp3op7gglbq74