Identification of the intracellular polyhydroxyalkanoate depolymerase gene of Paracoccus denitrificans and some properties of the gene product

Paracoccus denitrificans degraded poly(3-hydroxybutyrate) (PHB) in the cells under carbon source starvation. Intracellular poly(3-hydroxyalkanoate) (PHA) depolymerase gene (phaZ) was identified near the PHA synthase gene (phaC) of P. denitrificans. Cell extract of Escherichia coli carrying lacZ--phaZ fusion gene degraded protease-treated PHB granules. Reaction products were thought to be mainly D(--)-3-hydroxybutyrate (3HB) dimer and 3HB oligomer. Diisopropylfluorophosphonate and Triton X-100 exhibited an inhibitory effect on the degradation of PHB granules. When cell extract of the recombinant E. coli was used, Mg(2+) ion inhibited PHB degradation. However, the inhibitory effect by Mg(2+) ion was not observed using the cell extract of P. denitrificans.     

Structure of the puf operon of the obligately aerobic, bacteriochlorophyll alpha-containing bacterium Roseobacter denitrificans OCh114 and its expression in a Rhodobacter capsulatus puf puc deletion mutant.

Roseobacter denitrificans (Erythrobacter species strain OCh114) synthesizes bacteriochlorophyll a (BChl) and the photosynthetic apparatus only in the presence of oxygen and is unable to carry out primary photosynthetic reactions and to grow photosynthetically under anoxic conditions. The puf operon of R. denitrificans has the same five genes in the same order as in many photosynthetic bacteria, i.e., pufBALMC. PufC, the tetraheme subunit of the reaction center (RC), consists of 352 amino acids (Mr, 39,043); 20 and 34% of the total amino acids are identical to those of PufC of Chloroflexus aurantiacus and Rubrivivax gelatinosus, respectively. The N-terminal hydrophobic domain is probably responsible for anchoring the subunit in the membrane. Four heme-binding domains are homologous to those of PufC in several purple bacteria. Sequences similar to pufQ and pufX of Rhodobacter capsulatus were not detected on the chromosome of R. denitrificans. The puf operon of R. denitrificans was expressed in trans in Escherichia coli, and all gene products were synthesized. The Roseobacter puf operon was also expressed in R. capsulatus CK11, a puf puc double-deletion mutant. For the first time, an RC/light-harvesting complex I core complex was heterologously synthesized. The strongest expression of the R. denitrificans puf operon was observed under the control of the R. capsulatus puf promoter, in the presence of pufQ and pufX and in the absence of pufC. Charge recombination between the primary donor P+ and the primary ubiquinone Q(A)- was observed in the transconjugant, showing that the M and L subunits of the RC were correctly assembled. The transconjugants did not grow photosynthetically under anoxic conditions.     

Cultivation engineering of microbial bioplastics production

Abstract Theoretical yields of poly- d (−)-3-hydroxybutyrate (PHB) from several carbon sources have been estimated from biochemical pathways leading to PHB. In estimating the yields, a special emphasis is made on recycling (or regeneration) of NADP⁺ which is the co-substrate of acetoacetyl-CoA reductase, one of three key enzymes involved in the biosynthesis of PHB. As a NADP⁺-regenerating enzyme, glucose-6-phosphate dehydrogenase or isocitrate dehydrogenase is conceived. Theoretical and observed yields have been compared when polyhydroxyalkanoates (PHA) were synthesized from methanol and from n -amyl alcohol by a methylotroph, Paracoccus denitrificans .
An equation, which predicts the overall yield of PHB when allowance is made for non-PHB biomass formation in actual bacterial PHB production, has been derived as a function of both theoretical yields and PHB content of the total dry cell mass. The ratio of the overall (yield) to be theoretical yield is roughly proportional to the PHB content. A novel specific PHB formation rate on the basis of the residual biomass (total biomass-PHB contained) was proposed. The specific PHB formation rate decreased according to a mono-molecular decay model whose decay constant depended solely on the C/N ratio of the feed solution. From this model, an equation has been derived to calculate the volumetric productivity of PHB on the assumption that the total amount of the residual biomass is unchanged in the nitrogen-deficient PHB formation phase. Also, a graphical procedure has been shown to calculate the volumetric productivity of PHB. A comparison has been made between several data of PHB productivities that have been calculated from the literature.     

Influence of electron acceptor,carbon, nitrogen,and phosphorus on polyhydroxyalkanoate (PHA) production by <Emphasis Type="Italic">Brachymonas</Emphasis> sp. P12

Polyhydroxyalkanoates (PHAs), intracellular carbon and energy reserve compounds in many bacteria, have been used extensively in biodegradable plastics. PHA formation is influenced by nutrient limitations and growth conditions. To characterize the PHA accumulation in a new denitrifying phosphorus-removing bacterium Brachymonas sp. P12, batch experiments were conducted in which the electron acceptor (oxygen or nitrate) was varied and different concentrations of carbon (acetate), nitrogen (NH₄Cl), and phosphorus (KH₂PO₄) were used. Polyhydroxybutyrate (PHB) was the dominant product during PHA formation when acetate was the sole carbon source. The PHB content of aerobically growing cells increased from 431 to 636 mg PHB g⁻¹ biomass, but the PHB concentration of an anoxic culture decreased (−218 mg PHB g⁻¹ biomass), when PHB was utilized simultaneously with acetate as an electron donor for anoxic denitrification. The specific PHB production rate of the carbon-limited batch, 158.2 mg PHB g⁻¹ biomass h⁻¹, was much greater than that of batches with normal or excess carbon. The effects of phosphorus and nitrogen concentrations on PHB accumulation were clearly less than the effect of carbon concentration. According to the correlation between the specific PHB production rate and the specific cell growth rate, PHB accumulation by Brachymonas sp. P12 is enhanced by nutrient limitation, is growth-associated, and provides additional energy for the biosynthesis of non-PHB cell constituents to increase the cell growth rate beyond the usual level.     

Polyhydroxyalkanoates production from carbohydrates by a genetic recombinant Aeromonas sp.

Aims: To develop an Aeromonas strain able to utilize inexpensive carbon sources such as starch for the synthesis of polyhydroxyalkanoates (PHA). Methods and Results: A recombinant Aeromonas sp. (strain KC007‐1) was constructed by introducing the PHB synthesis genes (phaCAB) into the bacterium. Strain KC001‐R1 can not only use carbohydrate (including starch) for growth but also accumulate significant amounts of polyhydroxybutyrate (PHB) in the cells. Conclusions: One of the present focuses on PHA production has been on lowering the production costs. Starch is an example of an inexpensive carbohydrate for use in industrial production of PHA. We have demonstrated that by introducing the phaCAB operon into Aeromonas sp. allowed the bacterium able to accumulated PHB using this substrate. Significance and Impact of the Study: Aeromonas spp. are able to synthesize PHA using fatty acids as carbon source. Although good robust growth results with use of starch as sole carbon source for Aeromonas, PHA synthesis does not occur. Strain KC007‐R1 showed the ability to accumulate PHA in relative high amount with both carbohydrates and fatty acids as carbon source, and can be cultivated to a significant amount of cell mass and hence is a potential strain for further development for industrial applications.     

Peroxisomal polyhydroxyalkanoate biosynthesis is a promising strategy for bioplastic production in high biomass crops

Polyhydroxyalkanoates (PHAs) are bacterial carbon storage polymers with diverse plastic‐like properties. PHA biosynthesis in transgenic plants is being developed as a way to reduce the cost and increase the sustainability of industrial PHA production. The homopolymer polyhydroxybutyrate (PHB) is the simplest form of these biodegradable polyesters. Plant peroxisomes contain the substrate molecules and necessary reducing power for PHB biosynthesis, but peroxisomal PHB production has not been explored in whole soil‐grown transgenic plants to date. We generated transgenic sugarcane (Saccharum sp.) with the three‐enzyme Ralstonia eutropha PHA biosynthetic pathway targeted to peroxisomes. We also introduced the pathway into Arabidopsis thaliana, as a model system for studying and manipulating peroxisomal PHB production. PHB, at levels up to 1.6%–1.8% dry weight, accumulated in sugarcane leaves and A. thaliana seedlings, respectively. In sugarcane, PHB accumulated throughout most leaf cell types in both peroxisomes and vacuoles. A small percentage of total polymer was also identified as the copolymer poly (3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) in both plant species. No obvious deleterious effect was observed on plant growth because of peroxisomal PHA biosynthesis at these levels. This study highlights how using peroxisomal metabolism for PHA biosynthesis could significantly contribute to reaching commercial production levels of PHAs in crop plants.     

Complete amino acid sequence of cytochrome c551 from Erythrobacter species strain OCh 114

The complete amino acid sequence of cytochrome c551 isolated from an aerobic photosynthetic bacterium, Erythrobacter sp. strain OCh 114, was determined. The cytochrome molecule was composed of a total of 119 amino acid residues and its molecular weight including heme was calculated to be 13,235. The sequence was (Sequence: see text). Its molecular weight indicates that this cytochrome is of the L-type. Sequence alignment with other bacterial cytochromes c shows that this cytochrome is similar to cytochromes c of Rhodobacter capsulatus, Rhodobacter sphaeroides, and Paracoccus denitrificans, which were grouped into the alpha-3 subcluster from the 16S rRNA sequence analysis.     

Phage Resistance of a Marine Bacterium, Roseobacter denitrificans OCh114, as Revealed by Comparative Proteomics

Roseobacter is a dominant lineage in the marine environment. This group of bacteria is diverse in terms of both their phylogenetic composition and their physiological potential. Roseobacter denitrificans OCh114 is one of the most studied bacteria of the Roseobacter lineage. Recently, a lytic phage (RDJLΦ1) that infects this bacterium was isolated and a mutant strain (M1) of OCh114 that is resistant to RDJLΦ1 was also obtained. Here, we investigate the mechanisms supporting phage resistance of M1. Our results excluded the possibilities of several phage resistance mechanisms, including abortive infection, lysogeny, and the clustered regularly interspaced short palindromic repeats (CRISPRs) related mechanism. Adsorption kinetics assays revealed that adsorption inhibition might be a potential cause for the phage resistance of M1. Comparative proteomic analysis of M1 and OCh114 revealed significant changes in the membrane protein compliment of these bacteria. Five membrane proteins with important biological functions were significantly down-regulated in the phage-resistant M1. Meanwhile, several outer membrane porins with different modifications and an OmpA family domain protein were markedly up-regulated. We hypothesize that the down-regulated membrane proteins in M1 may serve as the potential phage receptors, whose absence prevented the adsorption of phage RDJLΦ1 to host cells and subsequent infection.     

Growth Characteristics and Substrate Specificity of Aerobic Photosynthetic Bacterium, Erythrobacter Sp. (OCh 114)

Optimal growth conditions and substrate specificity of the aerobicphotosynthetic bacterium, Erythrobacter sp. (OCh 114), wereinvestigated. Erythrobacter utilized 19 out of 26 substratestested, including several sugars and amino acids. Glycerol andlactate were the most effective as electron donors or carbonsources. Maximum growth was obtained at a salinity of about25, pH 8–9 and temperature 28°C in a glycerol-enrichedmedium. A suitable growth medium for Erythrobacter sp. (OCh114) is proposed. (Received October 18, 1985; Accepted January 10, 1986)     

Light-induced changes of carotenoid pigments in anaerobic cells of the aerobic photosynthetic bacterium,Roseobacter denitrificans (Erythrobacter species OCh 114): reduction of spheroidenone to 3,4-dihydrospheroidenone

Roseobacter denitrificans, previously named Erythrobacter species OCh 114, synthesized spheroidenone as a major carotenoid under aerobic dark conditions. When the dark-grown cells were subjected to illumination under anacrobic conditions, many unknown yellow pigments appeared and a considerable amount of spheroidenone disappeared. Absorption maxima of these pigments were blue-shifted from those of spheroidenone. The most abundant of the pigments was isolated, and its chemical structure was determined as 3,4-dihydrospheroidenone on spectroscopic and chemical evidence. Presumably, over-reduction of the photosynthetic apparatus interfered with normal photosynthetic electron transfer and resulted in photoreduction of C=C double bond at the 3,4-position of spheroidenone.     

Polyhydroxyalkanoate (PHA) accumulating bacteria from the gut of higher termite <Emphasis Type="Italic">Macrotermes carbonarius</Emphasis> (Blattodea: Termitidae)

The continuous quest for bacterial strains capable of accumulating polyhydroxyalkanoate (PHA) utilizing cheaper and renewable carbon source prompted us to explore newer and diverse environments like the gut of termites. Among the bacterial strains isolated from the gut of higher termite Macrotermes carbonarius, three strains were found to accumulate PHA, as observed by microscopic studies and PHA production experiments. Among them, strain MC1 with rapid growth and higher PHA accumulation was selected for further studies. API kit-50 CHB and 16S rRNA gene sequence analysis results indicated the strain to have 99% homology with Bacillus megaterium and Bacillus flexus. Bacillus sp. MC1 was able to accumulate PHA during the growth phase utilizing different carbon sources like glucose, fructose, sodium acetate, sodium valerate and 1,4-butanediol. Gas chromatography analysis of the polymer has shown it to be basically composed of poly (3-hydroxybutyrate) (PHB). Growth associated PHB biosynthesis was best in the presence of sodium acetate with 39 wt% after 16 h of cultivation. Though previous studies provided evidence confirming the presence of PHA producing bacteria in termite gut, isolation and characterization of these strains in pure culture has not been documented yet. Presence of other morphotypes in the termite gut with PHA like granular inclusions was evident from the transmission electron microscopy studies. This is a novel report and shows the feasibility of using potent strains capable of utilizing lignocellulosic degradation products as a renewable carbon source for the production of PHA in the future.     

Mutations derived from the thermophilic polyhydroxyalkanoate synthase PhaC enhance the thermostability and activity of PhaC from Cupriavidus necator H16

The thermophile Cupriavidus sp. strain S-6 accumulated polyhydroxybutyrate (PHB) from glucose at 50°C. A 9.0-kbp EcoRI fragment cloned from the genomic DNA of Cupriavidus sp. S-6 enabled Escherichia coli XL1-Blue to synthesize PHB at 45°C. Nucleotide sequence analysis showed a pha locus in the clone. The thermophilic polyhydroxyalkanoate (PHA) synthase (PhaC(Csp)) shared 81% identity with mesophilic PhaC of Cupriavidus necator H16. The diversity between these two strains was found dominantly on their N and C termini, while the middle regions were highly homologous (92% identity). We constructed four chimeras of mesophilic and thermophilic phaC genes to explore the mutations related to its thermostability. Among the chimeras, only PhaC(H16β), which was PhaC(H16) bearing 30 point mutations derived from the middle region of PhaC(Csp), accumulated a high content of PHB (65% [dry weight]) at 45°C. The chimera phaC(H16)(β) and two parental PHA synthase genes were overexpressed in E. coli BLR(DE3) cells and purified. At 30°C, the specific activity of the chimera PhaC(H16β) (172 ± 17.8 U/mg) was 3.45-fold higher than that of the parental enzyme PhaC(H16) (50 ± 5.2 U/mg). At 45°C, the half-life of the chimera PhaC(H16β) (11.2 h) was 127-fold longer than that of PhaC(H16) (5.3 min). Furthermore, the chimera PhaC(H16β) accumulated 1.55-fold (59% [dry weight]) more PHA content than the parental enzyme PhaC(H16) (38% [dry weight]) at 37°C. This study reveals a limited number of point mutations which enhance not only thermostability but also PhaC(H16) activity. The highly thermostable and active PHA synthase will provide advantages for its promising applications to in vitro PHA synthesis and recombinant E. coli PHA fermentation.     

ENHANCED BIOSYNTHESIS OF POLY(3-HYDROXYBUTYRATE) FROM POTATO STARCH BY Bacillus cereus STRAIN 64-INS IN A LABORATORY-SCALE FERMENTER

To decrease the polyhydroxyalkanoate (PHA) production cost by supplying renewable carbon sources has been an important aspect in terms of commercializing this biodegradable polymer. The production of biodegradable poly(3-hydroxyalkanoates) (PHA) from raw potato starch by the Bacillus cereus 64-INS strain isolated from domestic sludge has been studied in a lab-scale fermenter. The bacterium was screened for the degradation of raw potato starch by a starch hydrolysis method and for PHA production by Nile blue A and Sudan black B staining. Shake-flask cultures of the bacterium with glucose [2% (w/v)] or raw potato starch [2% (w/v)] produced PHA of 64.35% and 34.68% of dry cell weight (DCW), respectively. PHA production was also carried out in a 5-L fermenter under control conditions that produced 2.78 g/L of PHA and PHA content of 60.53% after 21 hr of fermentation using potato starch as the sole carbon source. Gas chromatography–mass spectroscopy (GC-MS) analyses confirmed that the extracted PHA contained poly(3-hydroxybutyrate) (PHB) as its major constituent (>99.99%) irrespective of the carbon source used. The article describes, for what we believe to be the first time, PHB production being carried out without any enzymatic or chemical treatment of potato starch at higher levels by fermentation. More work is required to optimize the PHB yield with respect to starch feeding strategies.     

Effect of nutritional supplements on bio-plastics (PHB) production utilizing sugar refinery waste with potential application in food packaging

Abstract

Polyhydroxyalkanoates (PHAs) are intracellular carbon and energy storage reserve material stored by gram-negative bacteria under nutrient limitation. PHAs are best alternative biodegradable plastics (bio-plastics) due to their resemblance to conventional synthetic plastic. The present study investigated the synergistic effect of nutritional supplements (amino acid and vitamin) on the PHA production by Alcaligenes sp. NCIM 5085 utilizing a sugar refinery waste (cane molasses) under submerged fermentation process. Initially, the effect of individual factor on PHA yield was studied by supplementing amino acids (cysteine, isoleucine, and methionine), vitamin (thiamin), and cane molasses at varying concentration in the production medium. Further, the cultivation medium was optimized by varying the levels of cane molasses, methionine and thiamin using response surface methodology to enhance the PHA yield. The maximum PHA yield of 70.89% was obtained under the optimized condition, which was then scaled up on 7.5?L-bioreactor. Batch cultivation in 7.5?L-bioreactor under the optimized condition gave a maximum PHA yield and productivity of 79.26% and 0.312 gL^?1 h^?1, respectively. The PHA produced was subsequently characterized as PHB by FTIR. PHB extracted was of relatively high molecular weight and crystallinity index. DSC analysis gave T_g, T_m, and X_c of 4.2, 179?°C and 66%, respectively. TGA analysis showed thermal stability with maximized degradation occurring at 302?°C, which is above the melting temperature (179?°C) of the purified polymer. The extracted polymer, therefore, possessed desirable material properties to be used in food packaging.     

Production of polyhydroxyalkanoates by Pseudomonas nitroreducens

A strain coded AS 1.2343 was isolated from oil-contaminated soil in an oil-field in North China Tianjian City and it was identified as Pseudomonas nitroreducens. The strain demonstrated some unusual ability to synthesize polyhydroxybutyrate (PHB) homopolymer from medium-chain-length (mcl) fatty acids including hexanoate and octanoate. While polyhydroxyalkanoates (PHA) consisting of mcl hydroxyalkanoate (HA) monomers such as hydroxyoctanoate (HO) and hydroxydecanoate (HD) were the major compositions when butyrate, decanoate, lauric acid and tetradecanoic acid were used as substrates for the cell growth, respectively. PHA was accumulated up to 77% of the cell dry weight when growth was conducted in lauric acid, it appeared that the HA contents in the PHA would not be much affected by the changing of the lauric acid concentration. Varying the concentration ratio of butyrate to octanoate could change the composition of PHA accumulated by the strain. Yet PHB homopolymer was always the only polyester synthesized by the strain, regardless of the octanoate concentration change. Additionally, the ratio of carbon to nitrogen (C/N) in butyrate media was found to have effects on the PHA monomer content, as C/N increased from 2 to 100, content of HB decreased from 100% to 7%. PHA polyester synthesized by cells of Pseudomonas nitroreducens AS 1.2343 was a blend polymers consisting of acetone-insoluble HB and acetone-soluble mcl HA monomers.     

Production of poly-3-hydroxybutyrate by Bacillus sp. JMa5 cultivated in molasses media

A strain of Bacillus sp. coded JMa5 was isolated from molasses contaminated soil. The strain was able to grow at a temperature as high as 45°C and in 250 g/l molasses although the optimal growth temperature was 35–37°C. Cell density reached 30 g/l 8 h after inoculation in a batch culture with an initial concentration of 210 g/l molasses. Under fed-batch conditions, the cells grew to a dry weight of 70 g/l after 30 h of fermentation. The strain accumulated 25–35%, (w/w) polyhydroxybutyrate (PHB) during fermentation. PHB accumulation was a growth-associated process. Factors that normally promote PHB production include high ratios of carbon to nitrogen, and carbon to phosphorus in growth media. Low dissolved oxygen supply resulted in sporulation, which reduced PHB contents and dry weights of the cells. It seems that sporulation induced by reduced supply of nutrients is the reason that PHB content is generally low in the Bacillus strain.     

Polyhydroxybutyrate in <Emphasis Type="Italic">Rhizobium</Emphasis> and <Emphasis Type="Italic">Bradyrhizobium</Emphasis>: quantification and <Emphasis Type="Italic">phbC</Emphasis> gene expression

Polyhydroxyalkanoates (PHAs) are hydroxyalkanoate polymers that are produced and accumulate by many kinds of bacteria. These polymers act as an energy store for bacteria. Polyhydroxybutyrate (PHB) is the most studied polymer in the PHA family. These polymers have awakened interest in the environmental and industrial research areas because they are biodegradable and have thermoplastic qualities, like polypropylene. In this work, we analyzed the PHB production in Bradyrhizobium sp., Rhizobium leguminosarum bv. phaseoli, and Rhizobium huautlense cultured with two different carbon sources. We did biochemical quantification of PHB production during the three phases of growth. Moreover, these samples were used for RNA extraction and phbC gene expression analysis via real-time PCR. The bacteria showed different manner of growth, PHB accumulation and phbC gene expression when different quantity and quality of carbon sources were used. These results showed that under different growth media conditions, the growth and metabolism of different species of bacteria were influenced. These differences reflect the increase or decrease in PHB accumulation.     

Plant original Massilia isolates producing polyhydroxybutyrate, including one exhibiting high yields from glycerol

Aims: The purpose of this study was to isolate new and potentially better polyhydroxyalkanoate (PHA)‐producing bacteria, with a view to obtaining high yields from inexpensive substrates like glycerol, a major by‐product of the biodiesel process. Methods and Results: Eleven new plant original isolates of the genus Massilia, a poorly studied lineage within the Betaproteobacteria, were isolated and characterized. Two isolates, 2C4 and 4D3c, could not be assigned to a validated Massilia species and probably represent new species. Six isolates were found to produce poly‐3‐hydroxybutyrate (P3HB) when cultured with glucose or glycerol as carbon source. Isolate 4D6 accumulated up to 50 wt% of cell mass as polyhydroxybutyrate (PHB) when grown on glycerol. Conclusions: The phyllosphere may be a good source of bacteria unrelated or weakly related to human/animal pathogens for screening for new PHA producers for industrial application. Isolate 4D6 was capable of accumulating particularly high levels of PHB from glycerol. Significance and Impact of the Study: With the increase in biodiesel production, which generates increasing amounts of glycerol as a by‐product, there is a major interest in exploiting this compound as feedstock for the synthesis of interesting products, like biopolymers, such as PHA. The new Massilia sp. 4D6 isolate described in this study may be a useful candidate as a cell factory for the industrial production of PHA from glycerol.     

Bacteriochlorophyll-protein complexes of aerobic bacteria,Erythrobacter longus and Erythrobacter species OCh 114

Bacteriochlorophyll(Bchl)-protein complexes were isolated from obligate aerobic bacteria, Erythrobacter longus and Erythrobacter species OCh 114. The apparent molecular weights, absorption spectra and polypeptide compositions of the light-harvesting complexes were, in general, similar to those of the light-harvesting Bchl-protein complexes of purple photosynthetic bacteria. The reaction center complexes of these bacteria also showed similar properties to those of the purple bacteria except for slightly altered polypeptides. However, the following characteristic features of the light-harvesting systems were found in these aerobic bacteria. Major carotenoids were not bound to the Bchl-protein complex in E. longus. In Erythrobacter sp. OCh 114, a new type of Bchl-protein complex which showed a single absorption band in the near infrared region at 806 nm was obtained. The reaction center of strain OCh 114 was associated with a c-type cytochrome.Abbreviations Bchl bacteriochlorophyll a - RC reaction center - SDS sodium dodecylsulfate - PAGE polyacrylamide gel electrophoresis