Gene_locus Report for: psepu-PHAC1

The nucleotide composition of key enzymes involved in medium-chain-length polyhydroxyalkanoates (mcl-PHA) synthesis was analyzed in two newly isolated strains of Pseudomonas. The isolated strains were tested for their abilities to synthesize polyhydroxyalkanoates using three different substrates as a carbon source: sodium octanoate, oleic acid, and sodium gluconate. Both analyzed strains were able to accumulate mcl-PHA in a range from 2.07 to 21.40%, which depended on the substrate used. Potential nitrogen-dependent regulation of mcl-PHA synthesis was analyzed by cell cultivation in nitrogen-limiting and non-limiting conditions. The analyzed strains demonstrated an incremental increase of mcl-PHAs in response to nitrogen starvation when oleic acid and sodium gluconate were applied as the carbon source. The transcriptional analysis showed that the induction of gene coding for PHA synthases was correlated with an increment in mcl-PHAs content. Both analyzed strains revealed differences in terms of the studied gene's expression, showing a dependence on the carbon source used.

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.

Novel biodegradable bacterial plastics, made up of units of 3-hydroxy-n-phenylalkanoic acids, are accumulated intracellularly by Pseudomonas putida U due to the existence in this bacterium of (i) an acyl-CoA synthetase (encoded by the fadD gene) that activates the aryl-precursors; (ii) a beta-oxidation pathway that affords 3-OH-aryl-CoAs, and (iii) a polymerization-depolymerization system (encoded in the pha locus) integrated by two polymerases (PhaC1 and PhaC2) and a depolymerase (PhaZ). The complete assimilation of these compounds requires two additional routes that specifically catabolize the phenylacetyl-CoA or the benzoyl-CoA generated from these polyesters through beta-oxidation. Genetic studies have allowed the cloning, sequencing, and disruption of the genes included in the pha locus (phaC1, phaC2, and phaZ) as well as those related to the biosynthesis of precursors (fadD) or to the catabolism of their derivatives (acuA, fadA, and paa genes). Additional experiments showed that the blockade of either fadD or phaC1 hindered the synthesis and accumulation of plastic polymers. Disruption of phaC2 reduced the quantity of stored polymers by two-thirds. The blockade of phaZ hampered the mobilization of the polymer and decreased its production. Mutations in the paa genes, encoding the phenylacetic acid catabolic enzymes, did not affect the synthesis or catabolism of polymers containing either 3-hydroxyaliphatic acids or 3-hydroxy-n-phenylalkanoic acids with an odd number of carbon atoms as monomers, whereas the production of polyesters containing units of 3-hydroxy-n-phenylalkanoic acids with an even number of carbon atoms was greatly reduced in these bacteria. Yield-improving studies revealed that mutants defective in the glyoxylic acid cycle (isocitrate lyase(-)) or in the beta-oxidation pathway (fadA), stored a higher amount of plastic polymers (1.4- and 2-fold, respectively), suggesting that genetic manipulation of these pathways could be useful for isolating overproducer strains. The analysis of the organization and function of the pha locus and its relationship with the core of the phenylacetyl-CoA catabolon is reported and discussed.

Poly(3-hydroxydodecanoate) [P(3HDD)], a medium-chain-length polyhydroxyalkanoate (PHA), is expected to be used as a novel type of bioplastic characterized by a soft and transparent nature. In this study, to achieve a high yield of P(3HDD), PHA synthase was modified through random mutagenesis of a region of the PHA synthase 1 gene from Pseudomonas putida KT2440 (phaC1(Pp)). Screening of the mutant library using a beta-oxidation-deficient Escherichia coli LSBJ was performed. As a result, four mutants, designated w10, w14, w309, and w311, were selected from 10,000 mutants. The w311 mutant had two amino acid replacements (E358G and N398S), and showed the highest production of P(3HDD) with increased polymer molecular weights when compared to the native enzyme. Saturation mutagenesis at the N398 position, which was found to be highly conserved among Pseudomonas PhaCs, revealed that amino acids with hydrophobic and smaller residues either retained or increased P(3HDD) production. This study demonstrates the benefit of using the PHA synthase mutants to enhance the production of P(3HDD).

In order to diversify the number of applications for poly[(R)-3-hydroxyalkanoates] (PHAs), methods must be developed to alter their physical properties so they are not limited to aliphatic polyesters. Recently we developed Escherichia coli LSBJ as a living biocatalyst with the ability to control the repeating unit composition of PHA polymers, including the ability to incorporate unsaturated repeating units into the PHA polymer at specific ratios. The incorporation of repeating units with terminal alkenes in the side chain of the polymer allowed for the production of random PHA copolymers with defined repeating unit ratios that can be chemically modified for the purpose of tailoring the physical properties of these materials beyond what are available in current PHAs. In this study, unsaturated PHA copolymers were chemically modified via thiol-ene click chemistry to contain an assortment of new functional groups, and the mechanical and thermal properties of these materials were measured. Results showed that cross-linking the copolymer resulted in a unique combination of improved strength and pliability and that the addition of polar functional groups increased the tensile strength, Young's modulus, and hydrophilic profile of the materials. This work demonstrates that unsaturated PHAs can be chemically modified to extend their physical properties to distinguish them from currently available PHA polymers.

We report the complete sequence of the 5.7-Mbp genome of Pseudomonas putida BIRD-1, a metabolically versatile plant growth-promoting rhizobacterium that is highly tolerant to desiccation and capable of solubilizing inorganic phosphate and iron and of synthesizing phytohormones that stimulate seed germination and plant growth.

The nucleotide composition of key enzymes involved in medium-chain-length polyhydroxyalkanoates (mcl-PHA) synthesis was analyzed in two newly isolated strains of Pseudomonas. The isolated strains were tested for their abilities to synthesize polyhydroxyalkanoates using three different substrates as a carbon source: sodium octanoate, oleic acid, and sodium gluconate. Both analyzed strains were able to accumulate mcl-PHA in a range from 2.07 to 21.40%, which depended on the substrate used. Potential nitrogen-dependent regulation of mcl-PHA synthesis was analyzed by cell cultivation in nitrogen-limiting and non-limiting conditions. The analyzed strains demonstrated an incremental increase of mcl-PHAs in response to nitrogen starvation when oleic acid and sodium gluconate were applied as the carbon source. The transcriptional analysis showed that the induction of gene coding for PHA synthases was correlated with an increment in mcl-PHAs content. Both analyzed strains revealed differences in terms of the studied gene's expression, showing a dependence on the carbon source used.

High substrate costs decrease the profitability of polyhydroxyalkanoates (PHAs) production, and thus low-cost carbon substrates coming from agricultural and industrial residuals are tested for the production of these biopolymers. Among them crude glycerol, formed as a byproduct during biodiesel production, seems to be the most promising source of carbon. The object of this study was to characterize the mixed population responsible for the conversion of crude glycerol into PHAs by the cultivation-dependent and -independent methods. Enrichment of the microbial community was monitored by applying the Ribosomal Intergenic Spacer Analysis (RISA) and the identification of community members was based on 16S rRNA gene sequencing of cultivable species. Molecular analysis revealed that mixed populations consist of microorganisms affiliated with four bacterial lineages: alpha, gamma- Proteobacteria, Actinobacteria and Bacteroides. Among them, three Pseudomonas strains and Rhodobacter sp. possessed genes coding for polyhydroxyalkanoates synthase. Comparative analysis revealed that most of the microorganisms detected by direct molecular analysis were obtained by the traditional culturing method.

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.

Novel biodegradable bacterial plastics, made up of units of 3-hydroxy-n-phenylalkanoic acids, are accumulated intracellularly by Pseudomonas putida U due to the existence in this bacterium of (i) an acyl-CoA synthetase (encoded by the fadD gene) that activates the aryl-precursors; (ii) a beta-oxidation pathway that affords 3-OH-aryl-CoAs, and (iii) a polymerization-depolymerization system (encoded in the pha locus) integrated by two polymerases (PhaC1 and PhaC2) and a depolymerase (PhaZ). The complete assimilation of these compounds requires two additional routes that specifically catabolize the phenylacetyl-CoA or the benzoyl-CoA generated from these polyesters through beta-oxidation. Genetic studies have allowed the cloning, sequencing, and disruption of the genes included in the pha locus (phaC1, phaC2, and phaZ) as well as those related to the biosynthesis of precursors (fadD) or to the catabolism of their derivatives (acuA, fadA, and paa genes). Additional experiments showed that the blockade of either fadD or phaC1 hindered the synthesis and accumulation of plastic polymers. Disruption of phaC2 reduced the quantity of stored polymers by two-thirds. The blockade of phaZ hampered the mobilization of the polymer and decreased its production. Mutations in the paa genes, encoding the phenylacetic acid catabolic enzymes, did not affect the synthesis or catabolism of polymers containing either 3-hydroxyaliphatic acids or 3-hydroxy-n-phenylalkanoic acids with an odd number of carbon atoms as monomers, whereas the production of polyesters containing units of 3-hydroxy-n-phenylalkanoic acids with an even number of carbon atoms was greatly reduced in these bacteria. Yield-improving studies revealed that mutants defective in the glyoxylic acid cycle (isocitrate lyase(-)) or in the beta-oxidation pathway (fadA), stored a higher amount of plastic polymers (1.4- and 2-fold, respectively), suggesting that genetic manipulation of these pathways could be useful for isolating overproducer strains. The analysis of the organization and function of the pha locus and its relationship with the core of the phenylacetyl-CoA catabolon is reported and discussed.