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

Knöll, Martin; Hamm, Thomas; Wagner, Florian; Martínez, Virginia; Pleiss, Jürgen

doi:10.1186/1471-2105-10-89

Cited by 120 publications

(120 citation statements)

References 46 publications

(33 reference statements)

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“…But in the absence of biological agents (bacteria, algae and fungi) PHAs are practically not subject to mass lost under normal conditions (178) and they are degraded in biological media to form products innocuous to the environment. PHA biodegradation is performed by microorganisms that secrete intra-or extracellular PHA depolymerases, which differ in their molecular organization and substrate specificity (179). While intracellular PHA depolymerases are synthesized by PHA-producing bacteria and are used by them to hydrolyze their own PHA storages, extracellular enzymes are produced by other microorganisms to utilize PHAs usually released into environment after death and cell lysis of PHA-accumulating cells (180).…”

Section: Biodegradability Of Phamentioning

confidence: 99%

Bacterial polyhydroxyalkanoates-eco-friendly next generation plastic: Production, biocompatibility, biodegradation, physical properties and applications

Muhammadi

Shabina

Afzal

et al. 2015

Green Chemistry Letters and Reviews

257

139

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Polyhydroxyalkanoates (PHAs) are intracellular aliphatic polyesters synthesized as energy reserves, in the form of water-insoluble, nano-sized discrete and optically dense granules in cytoplasm by a diverse bacteria and some archae under conditions of limiting nutrients in the presence of excess carbon source. Bacteria synthesize different PHAs from coenzyme A thioesters of respective hydroxyalkanoic acid, and degrade intracellularly for reuse and extracellularly in natural environments by other microorganisms. In vivo, PHAs exist as amorphous mobile liquid and water-insoluble inclusions but in vitro, exhibit material and mechanical properties, ranging from stiff and brittle crystalline to elastomeric and molding, similar to petrochemical thermoplastics. Further, they are hydrophobic, isotactic, biocompatible and exhibit piezoelectric properties. But as commodity plastics their applications are limited by high production cost, low yield, in vivo degradation, complexity of technology and difficulty of extraction. Therefore, to replace the conventional plastic with PHAs, it is prerequisite to standardize the PHA production systems.

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Section: Biodegradability Of Phamentioning

confidence: 99%

Bacterial polyhydroxyalkanoates-eco-friendly next generation plastic: Production, biocompatibility, biodegradation, physical properties and applications

Muhammadi

Shabina

Afzal

et al. 2015

Green Chemistry Letters and Reviews

257

139

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“…The ability to degrade extracellular scl-PHA is more widespread among bacteria than the ability to degrade mcl-PHA. Thus, many extracellular scl-PHA depolymerases have been characterized in depth over the last decade, and a considerable number of genes have been identified (1,3,4,24,26,29,40). The prototype of extracellular mcl-PHA depolymerases is that of Pseudomonas fluorescens GK13 (here PhaZ GK13 ) (21,26,52).…”

mentioning

confidence: 99%

Identification and Biochemical Evidence of a Medium-Chain-Length Polyhydroxyalkanoate Depolymerase in the Bdellovibrio bacteriovorus Predatory Hydrolytic Arsenal

Martínez

Peña

García-Hidalgo

et al. 2012

Appl Environ Microbiol

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ABSTRACTThe obligate predatorBdellovibrio bacteriovorusHD100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. We present genetic and biochemical evidence that open reading frame (ORF) Bd3709 ofB. bacteriovorusHD100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase (PhaZBd). The primary structure of PhaZBdsuggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical serine hydrolase catalytic triad (serine-histidine-aspartic acid) in agreement with other PHA depolymerases and lipases. PhaZBdhas been extracellularly produced using different hypersecretor Tol-pal mutants ofEscherichia coliandPseudomonas putidaas recombinant hosts. The recombinant PhaZBdhas been characterized, and its biochemical properties have been compared to those of other PHA depolymerases. The enzyme behaves as a serine hydrolase that is inhibited by phenylmethylsulfonyl fluoride. It is also affected by the reducing agent dithiothreitol and nonionic detergents like Tween 80. PhaZBdis an endoexohydrolase that cleaves both large and small PHA molecules, producing mainly dimers but also monomers and trimers. The enzyme specifically degrades mcl-PHA and is inactive toward short-chain-length polyhydroxyalkanoates (scl-PHA) like polyhydroxybutyrate (PHB). These studies shed light on the potentiality of these predators as sources of new biocatalysts, such as an mcl-PHA depolymerase, for the production of enantiopure hydroxyalkanoic acids and oligomers as building blocks for the synthesis of biobased polymers.

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“…There are mainly two types of such microbial degradation-extracellular and intracellular ones (Jendrossek et al, 1996). Besides using the native PHAs degrading strains, an advanced PHAs degrading system may be built up using the SB methods, for instances, better deploymerases or fermenting strains (Knoll et al, 2009). With more knowledge accumulating on the biodegradation of PHAs, we may expect that plastics made from polymers -which are easy to be broken down -will have more applications in the future.…”

Section: Environmental Impacts Of Synthetic Biological Production Of mentioning

confidence: 99%

Conversion of Biomass into Bioplastics and Their Potential Environmental Impacts

Lei¹,

Schmidt²,

Wei³

2011

Biotechnology of Biopolymers

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

Cited by 120 publications

References 46 publications

Bacterial polyhydroxyalkanoates-eco-friendly next generation plastic: Production, biocompatibility, biodegradation, physical properties and applications

Bacterial polyhydroxyalkanoates-eco-friendly next generation plastic: Production, biocompatibility, biodegradation, physical properties and applications

Identification and Biochemical Evidence of a Medium-Chain-Length Polyhydroxyalkanoate Depolymerase in the Bdellovibrio bacteriovorus Predatory Hydrolytic Arsenal

Conversion of Biomass into Bioplastics and Their Potential Environmental Impacts

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