Discovery of bacterial polyhydroxyalkanoate synthase (PhaC)-encoding genes from seasonal Baltic Sea ice and cold estuarine waters

High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741T and in silico analyses of the genus specific PhaC2 polymerase variant

BACKGROUND

Several members of the bacterial Halomonadacea family are natural producers of polyhydroxyalkanoates (PHA), which are promising materials for use as biodegradable bioplastics. Type-strain species of Cobetia are designated PHA positive, and recent studies have demonstrated relatively high PHA production for a few strains within this genus. Industrially relevant PHA producers may therefore be present among uncharacterized or less explored members. In this study, we characterized PHA production in two marine Cobetia strains. We further analyzed their genomes to elucidate pha genes and metabolic pathways which may facilitate future optimization of PHA production in these strains.

RESULTS

Cobetia sp. MC34 and Cobetia marina DSM 4741T were mesophilic, halotolerant, and produced PHA from four pure substrates. Sodium acetate with- and without co-supplementation of sodium valerate resulted in high PHA production titers, with production of up to 2.5 g poly(3-hydroxybutyrate) (PHB)/L and 2.1 g poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/L in Cobetia sp. MC34, while C. marina DSM 4741T produced 2.4 g PHB/L and 3.7 g PHBV/L. Cobetia marina DSM 4741T also showed production of 2.5 g PHB/L from glycerol. The genome of Cobetia sp. MC34 was sequenced and phylogenetic analyses revealed closest relationship to Cobetia amphilecti. PHA biosynthesis genes were located at separate loci similar to the arrangement in other Halomonadacea. Further genome analyses revealed some differences in acetate- and propanoate metabolism genes between the two strains. Interestingly, only a single PHA polymerase gene (phaC2) was found in Cobetia sp. MC34, in contrast to two copies (phaC1 and phaC2) in C. marina DSM 4741T. In silico analyses based on phaC genes show that the PhaC2 variant is conserved in Cobetia and contains an extended C-terminus with a high isoelectric point and putative DNA-binding domains.

CONCLUSIONS

Cobetia sp. MC34 and C. marina DSM 4741T are natural producers of PHB and PHBV from industrially relevant pure substrates including acetate. However, further scale up, optimization of growth conditions, or use of metabolic engineering is required to obtain industrially relevant PHA production titers. The putative role of the Cobetia PhaC2 variant in DNA-binding and the potential implications remains to be addressed by in vitro- or in vivo methods.

Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkaonoic Acid (PHA) Storage Polymers at Low Temperature

Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, Halomonas sp. 363 and Paracoccus sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of Halomonas sp. 363 carries three phaC synthase genes and transcribes genes along three PHA pathways (I to III), whereas Paracoccus sp. 392 carries only one phaC gene and transcribes genes along one pathway (I). Thus, Halomonas sp. 363 has a versatile repertoire of phaC genes and pathways enabling production of both short- and medium-chain-length PHA products. IMPORTANCE Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, Halomonas sp. 363 and Paracoccus sp. 392, are able to produce various types of PHA from inexpensive carbon sources. Halomonas sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.

The underexplored role of diverse stress factors in microbial biopolymer synthesis

Polyhydroxyalkanoates (PHA) are microbial polyesters which, apart from their primary storage role, enhance the stress robustness of PHA accumulating cells against various stressors. PHA also represent interesting alternatives to petrochemical polymers, which can be produced from renewable resources employing approaches of microbial biotechnology. During biotechnological processes, bacterial cells are exposed to various stressor factors such as fluctuations in temperature, osmolarity, pH-value, elevated pressure or the presence of microbial inhibitors. This review summarizes how PHA helps microbial cells to cope with biotechnological process-relevant stressors and, vice versa, how various stress conditions can affect PHA production processes. The review suggests a fundamentally new strategy for PHA production: the fine-tuned exposure to selected stressors, which might be used to boost PHA production and even to tailor their structure.

Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods

Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red–PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the Comamonadaceae family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, Microbacteriaceae and Micrococcaceae also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.

Novel unexpected functions of PHA granules

Polyhydroxyalkanoates (PHA), polyesters accumulated by numerous prokaryotes in the form of intracellular granules, have been for decades considered being predominantly storage molecules. However, numerous recent discoveries revealed and emphasized their complex biological role for microbial cells. Most of all, it was repeatedly reported and confirmed that the presence of PHA granules in prokaryotic cells enhances stress resistance and robustness of microbes against various environmental stress factors such as high or low temperature, freezing, oxidative, and osmotic pressure. It seems that protective mechanisms of PHA granules are associated with their extraordinary architecture and biophysical properties as well as with the complex and deeply interconnected nature of PHA metabolism. Therefore, this review aims at describing novel and unexpected properties of PHA granules with respect to their contribution to stress tolerance of various prokaryotes including common mesophilic heterotrophic bacteria, but also extremophiles or photo-autotrophic cyanobacteria. KEY POINTS: • PHA granules present in bacterial cells reveal unique properties and functions. • PHA enhances stress robustness of bacterial cells.

Microbial polyhydroxyalkanoates from extreme niches: Bioprospection status, opportunities and challenges

Extreme niches are offered with unusual physiochemical conditions that impose stress to the life-forms including microbial communities. Microbes have evolved unique physiology and genetics to interact dynamically with extreme environments for their adaptation and survival. Amongst the several adaptive features of microbes in stressed conditions, polyhydroxyalkanoates synthesis is a crucial strategy of many bacteria and archaea to reserve carbon and energy inside the cell. Apart from the relevance of PHA to microbial world, these intracellular polyesters are seen as essential biological macromolecules for the bio-material industry owing to their plastic-like properties, biodegradable and eco-friendly nature. Recently, much attention has been attracted by the microbes of extreme habitats for a new source of industrially suited PHA producers and novel PHA with unique properties. Therefore, the current review is focused on the critical evaluation of microbes from extreme niches for PHA production and opportunities for the development of commercially feasible PHA bioprocess.

Psychrophilic lifestyles: mechanisms of adaptation and biotechnological tools

Cold-adapted microorganisms inhabiting permanently low-temperature environments were initially just a biological curiosity but have emerged as rich sources of numerous valuable tools for application in a broad spectrum of innovative technologies. To overcome the multiple challenges inherent to life in their cold habitats, these microorganisms have developed a diverse array of highly sophisticated synergistic adaptations at all levels within their cells: from cell envelope and enzyme adaptation, to cryoprotectant and chaperone production, and novel metabolic capabilities. Basic research has provided valuable insights into how these microorganisms can thrive in their challenging habitat conditions and into the mechanisms of action of the various adaptive features employed, and such insights have served as a foundation for the knowledge-based development of numerous novel biotechnological tools. In this review, we describe the current knowledge of the adaptation strategies of cold-adapted microorganisms and the biotechnological perspectives and commercial tools emerging from this knowledge. Adaptive features and, where possible, applications, in relation to membrane fatty acids, membrane pigments, the cell wall peptidoglycan layer, the lipopolysaccharide component of the outer cell membrane, compatible solutes, antifreeze and ice-nucleating proteins, extracellular polymeric substances, biosurfactants, chaperones, storage materials such as polyhydroxyalkanoates and cyanophycins and metabolic adjustments are presented and discussed.

Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico

Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.

Reporting Key Features in Cold-Adapted Bacteria

It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold. Most of these works are focused on characteristics traditionally involved in cold adaptation, such as the structural adjustment of enzymes, maintenance of membrane fluidity, expression of cold shock proteins and presence of compatible solutes. Recent works based mainly on novel "omic" technologies have presented evidence of the presence of other important features to thrive in cold. In this work, we analyze cold-adapted bacteria, looking for strategies involving novel features, and/or activation of non-classical metabolisms for a cold lifestyle. Metabolic traits related to energy generation, compounds and mechanisms involved in stress resistance and cold adaptation, as well as characteristics of the cell envelope, are analyzed in heterotrophic cold-adapted bacteria. In addition, metagenomic, metatranscriptomic and metaproteomic data are used to detect key functions in bacterial communities inhabiting cold environments.

Novel polyhydroxyalkanoate copolymers produced in Pseudomonas putida by metagenomic polyhydroxyalkanoate synthases

Bacterially produced biodegradable polyhydroxyalkanoates (PHAs) with versatile properties can be achieved using different PHA synthases (PhaCs). This work aims to expand the diversity of known PhaCs via functional metagenomics and demonstrates the use of these novel enzymes in PHA production. Complementation of a PHA synthesis-deficient Pseudomonas putida strain with a soil metagenomic cosmid library retrieved 27 clones expressing either class I, class II, or unclassified PHA synthases, and many did not have close sequence matches to known PhaCs. The composition of PHA produced by these clones was dependent on both the supplied growth substrates and the nature of the PHA synthase, with various combinations of short-chain-length (SCL) and medium-chain-length (MCL) PHA. These data demonstrate the ability to isolate diverse genes for PHA synthesis by functional metagenomics and their use for the production of a variety of PHA polymer and copolymer mixtures.

The composition analysis and preliminary cultivation optimization of a PHA-producing microbial consortium with xylose as a sole carbon source

This work aimed at using xylose as sole substrate, and combining feast-famine process with Nile blue staining as well as denaturing gradient gel electrophoresis (DGGE) analysis to screen polyhydroxyalkanoate (PHA)-producing bacteria from waste activated sludge (WAS). Composition changes of the microbial consortium during domestication were analyzed by DGGE, and the results indicated that there were mainly four classes of bacteria in the final stable system, which were γ-Proteobacteria, Cellvibrio sp., an uncultured bacterium and Pseudomonas sp., respectively. After preliminary optimization, the optimal conditions for the microbial consortium to produce PHA were also obtained as follows: temperature 33°C, pH 8, xylose concentration 2.4g/L, C/N ratio 160 and C/P ratio 125. The final PHA accumulation was up to 31% of dry cell weight (DCW), compared to 23.8% of the original consortia. Though our process is at the very beginning and the PHA yield is relatively low, producing PHA from xylose by using microbial consortia is a promising way to save the PHA production cost.

Overexpression of succinyl-CoA synthase for poly (3-hydroxybutyrate-co-3-hydroxyvalerate) production in engineered Escherichia coli BL21(DE3)

AIM

This study aims to increase the 3-hydroxyvalerate (3HV) fraction in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(HB-co-HV)] using succinyl-CoA synthase.

METHODS AND RESULTS

Escherichia coli YH090, a polyhydroxyalkonate (PHA)-producing strain, was further engineered for overexpression of succinyl-CoA synthase genes (sucCD), and examined for P(HB-co-HV) copolymer production in the presence of various precursor molecules using mixture analysis. Glycerol, succinate and propionate were screened as important factors for controlling intracellular PHA accumulation and monomer composition. Glycerol concentrations exerted the greatest influence on the overall biomass concentration and the intracellular PHA content, while propionate concentrations in the presence of succinate influenced the 3HV content of the copolymer. Mixture analysis also demonstrated that the engineered strain has the capacity to accumulate up to 80% of its cell dry weight (CDW) as PHA with a variable fraction of 3HV monomer (maximum of 72 wt %) depending on the controlled conditions.

CONCLUSIONS

Propionate is the principal precursor for 3HV monomer in P(HB-co-HV) biopolymer and its utilization requires conversion to propionyl-CoA. Engineered E. coli YHY99, overexpressing sucCD genes, leads to an increase of the succinyl-CoA pool, which enhances the conversion rate of propionate by providing a CoA supply to other acyltransferase enzymes that have a role in propionate utilization.

SIGNIFICANCE AND IMPACT OF THE STUDY

Engineered E. coli YHY99 was able to utilize propionate with a 4·5-fold increase in rate, as compared to the control strain, and resulted in the synthesis of a copolymer with high 3HV monomer content.

Polyhydroxyalkanoates: Much More than Biodegradable Plastics

Bacterial polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in central metabolism, as they act as dynamic reservoirs of carbon and reducing equivalents. These polymers have a number of technical applications since they exhibit thermoplastic and elastomeric properties, making them attractive as a replacement of oil-derived materials. PHAs are accumulated under conditions of nutritional imbalance (usually an excess of carbon source with respect to a limiting nutrient, such as nitrogen or phosphorus). The cycle of PHA synthesis and degradation has been recognized as an important physiological feature when these biochemical pathways were originally described, yet its role in bacterial processes as diverse as global regulation and cell survival is just starting to be appreciated in full. In the present revision, the complex regulation of PHA synthesis and degradation at the transcriptional, translational, and metabolic levels are explored by analyzing examples in natural producer bacteria, such as Pseudomonas species, as well as in recombinant Escherichia coli strains. The ecological role of PHAs, together with the interrelations with other polymers and extracellular substances, is also discussed, along with their importance in cell survival, resistance to several types of environmental stress, and planktonic-versus-biofilm lifestyle. Finally, bioremediation and plant growth promotion are presented as examples of environmental applications in which PHA accumulation has successfully been exploited.