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Woo SG, Averesch NJH, Berliner AJ, Deutzmann JS, Pane VE, Chatterjee S, Criddle CS. Isolation and characterization of a Halomonas species for non-axenic growth-associated production of bio-polyesters from sustainable feedstocks. Appl Environ Microbiol 2024; 90:e0060324. [PMID: 39058034 PMCID: PMC11338360 DOI: 10.1128/aem.00603-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Biodegradable plastics are urgently needed to replace petroleum-derived polymeric materials and prevent their accumulation in the environment. To this end, we isolated and characterized a halophilic and alkaliphilic bacterium from the Great Salt Lake in Utah. The isolate was identified as a Halomonas species and designated "CUBES01." Full-genome sequencing and genomic reconstruction revealed the unique genetic traits and metabolic capabilities of the strain, including the common polyhydroxyalkanoate (PHA) biosynthesis pathway. Fluorescence staining identified intracellular polyester granules that accumulated predominantly during the strain's exponential growth, a feature rarely found among natural PHA producers. CUBES01 was found to metabolize a range of renewable carbon feedstocks, including glucosamine and acetyl-glucosamine, as well as sucrose, glucose, fructose, and further glycerol, propionate, and acetate. Depending on the substrate, the strain accumulated up to ~60% of its biomass (dry wt/wt) in poly(3-hydroxybutyrate), while reaching a doubling time of 1.7 h at 30°C and an optimum osmolarity of 1 M sodium chloride and a pH of 8.8. The physiological preferences of the strain may not only enable long-term aseptic cultivation but also facilitate the release of intracellular products through osmolysis. The development of a minimal medium also allowed the estimation of maximum polyhydroxybutyrate production rates, which were projected to exceed 5 g/h. Finally, also, the genetic tractability of the strain was assessed in conjugation experiments: two orthogonal plasmid vectors were stable in the heterologous host, thereby opening the possibility of genetic engineering through the introduction of foreign genes. IMPORTANCE The urgent need for renewable replacements for synthetic materials may be addressed through microbial biotechnology. To simplify the large-scale implementation of such bio-processes, robust cell factories that can utilize sustainable and widely available feedstocks are pivotal. To this end, non-axenic growth-associated production could reduce operational costs and enhance biomass productivity, thereby improving commercial competitiveness. Another major cost factor is downstream processing, especially in the case of intracellular products, such as bio-polyesters. Simplified cell-lysis strategies could also further improve economic viability.
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Affiliation(s)
- Sung-Geun Woo
- Center for the
Utilization of Biological Engineering in Space
(CUBES), Berkeley,
California, USA
- Department of Civil
and Environmental Engineering, Stanford
University, Stanford,
California, USA
| | - Nils J. H. Averesch
- Center for the
Utilization of Biological Engineering in Space
(CUBES), Berkeley,
California, USA
- Department of Civil
and Environmental Engineering, Stanford
University, Stanford,
California, USA
| | - Aaron J. Berliner
- Center for the
Utilization of Biological Engineering in Space
(CUBES), Berkeley,
California, USA
- Department of
Bioengineering, University of
California, Berkeley,
California, USA
| | - Joerg S. Deutzmann
- Department of Civil
and Environmental Engineering, Stanford
University, Stanford,
California, USA
| | - Vince E. Pane
- Center for the
Utilization of Biological Engineering in Space
(CUBES), Berkeley,
California, USA
- Department of
Chemistry, Stanford University,
Stanford, California,
USA
| | - Sulogna Chatterjee
- Center for the
Utilization of Biological Engineering in Space
(CUBES), Berkeley,
California, USA
- Department of Civil
and Environmental Engineering, Stanford
University, Stanford,
California, USA
| | - Craig S. Criddle
- Center for the
Utilization of Biological Engineering in Space
(CUBES), Berkeley,
California, USA
- Department of Civil
and Environmental Engineering, Stanford
University, Stanford,
California, USA
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Baruah N, Haajanen R, Rahman MT, Pirttilä AM, Koskimäki JJ. Biosynthesis of polyhydroxybutyrate by Methylorubrum extorquens DSM13060 is essential for intracellular colonization in plant endosymbiosis. FRONTIERS IN PLANT SCIENCE 2024; 15:1302705. [PMID: 38390299 PMCID: PMC10883064 DOI: 10.3389/fpls.2024.1302705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Methylorubrum extorquens DSM13060 is an endosymbiont that lives in the cells of shoot tip meristems. The bacterium is methylotrophic and consumes plant-derived methanol for the production of polyhydroxybutyrate (PHB). The PHB provides protection against oxidative stress for both host and endosymbiont cells through its fragments, methyl-esterified 3-hydroxybutyrate (ME-3HB) oligomers. We evaluated the role of the genes involved in the production of ME-3HB oligomers in the host colonization by the endosymbiont M. extorquens DSM13060 through targeted genetic mutations. The strains with deletions in PHB synthase (phaC), PHB depolymerase (phaZ1), and a transcription factor (phaR) showed altered PHB granule characteristics, as ΔphaC had a significantly low number of granules, ΔphaR had a significantly increased number of granules, and ΔphaZ1 had significantly large PHB granules in the bacterial cells. When the deletion strains were exposed to oxidative stress, the ΔphaC strain was sensitive to 10 mM HO· and 20 mM H2O2. The colonization of the host, Scots pine (Pinus sylvestris L.), by the deletion strains varied greatly. The deletion strain ΔphaR colonized the host mainly intercellularly, whereas the ΔphaZ1 strain was a slightly poorer colonizer than the control. The deletion strain ΔphaC lacked the colonization potential, living mainly on the surfaces of the epidermis of pine roots and shoots in contrast to the control, which intracellularly colonized all pine tissues within the study period. In earlier studies, deletions within the PHB metabolic pathway have had a minor effect on plant colonization by rhizobia. We have previously shown the association between ME-3HB oligomers, produced by PhaC and PhaZ1, and the ability to alleviate host-generated oxidative stress during plant infection by the endosymbiont M. extorquens DSM13060. Our current results show that the low capacity for PHB synthesis leads to poor tolerance of oxidative stress and loss of colonization potential by the endosymbiont. Altogether, our findings demonstrate that the metabolism of PHB in M. extorquens DSM13060 is an important trait in the non-rhizobial endosymbiosis.
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Affiliation(s)
- Namrata Baruah
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roosa Haajanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mohammad Tanvir Rahman
- Disease Networks, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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Slaninova E, Obruca S, Kocherbitov V, Sedlacek P. On the bioprotective effects of 3-hydroxybutyrate: Thermodynamic study of binary 3HB-water systems. Biophys J 2023; 122:460-469. [PMID: 36617191 PMCID: PMC9941717 DOI: 10.1016/j.bpj.2023.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/22/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Microorganisms must face various inconvenient conditions; therefore, they developed several approaches for protection. Such a strategy also involves the accumulation of compatible solutes, also called osmolytes. It has been proved that the monomer unit 3-hydroxybutyrate (3HB), which is present in sufficient concentration in poly(3-hydroxybutyrate) (PHB)-accumulating cells, serves as a chemical chaperone protecting enzymes against heat and oxidative stress and as a cryoprotectant for enzymes, bacterial cells, and yeast. The stress robustness of the cells is also strongly dependent on the behavior and state of intracellular water, especially during stress exposure. For a better understanding of the protective mechanism and effect of strongly hydrophilic 3HB in solutions at a wide range of temperatures, a binary phase diagram of system sodium 3HB (Na3HB)-water in equilibrium and the state diagrams showing the glass transitions in the system were constructed. To investigate the activity of water in various compositions of the Na3HB/water system, three experimental techniques have been used (dynamic water sorption analysis, water activity measurements, and sorption calorimetry). First, Na3HB proved its hydrophilic nature, which is very comparable with known compatible solutes (trehalose). Results of differential scanning calorimetry demonstrated that Na3HB is also highly effective in depressing the freezing point and generating a large amount of nonfrozen water (1.35 g of water per gram of Na3HB). Therefore, Na3HB represents a very effective cryoprotectant that can be widely used for numerous applications.
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Affiliation(s)
- Eva Slaninova
- Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Stanislav Obruca
- Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Vitaly Kocherbitov
- Biomedical Science, Faculty of Health & Society, Malmö University, Malmö, Sweden.
| | - Petr Sedlacek
- Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic.
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4
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Subfunctionalization probably drives the emergence of plant growth-promoting genes. Symbiosis 2022. [DOI: 10.1007/s13199-022-00872-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Polyhydroxyalkanoates Production by Mixed Microbial Culture under High Salinity. SUSTAINABILITY 2022. [DOI: 10.3390/su14031346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fishing industry produces vast amounts of saline organic side streams that require adequate treatment and disposal. The bioconversion of saline resources into value-added products, such as biodegradable polyhydroxyalkanoates (PHAs), has not yet been fully explored. This study investigated PHA production by mixed microbial cultures under 30 gNaCl/L, the highest NaCl concentration reported for the acclimatization of a PHA-accumulating mixed microbial culture (MMC). The operational conditions used during the culture-selection stage resulted in an enriched PHA-accumulating culture dominated by the Rhodobacteraceae family (95.2%) and capable of storing PHAs up to 84.1% wt. (volatile suspended solids (VSS) basis) for the highest organic loading rate (OLR) applied (120 Cmmol/(L.d)). This culture presented a higher preference for the consumption of valeric acid (0.23 ± 0.03 CmolHVal/(CmolX.h)), and the 3HV monomer polymerization (0.33 ± 0.04 CmmolHV/(CmmolX.h) was higher as well. As result, a P(3HB-co-3HV)) with high HV content (63% wt.) was produced in the accumulation tests conducted at higher OLRs and with 30 gNaCl/L. A global volumetric PHA productivity of 0.77 gPHA/(L.h) and a specific PHA productivity of 0.21 gPHA/(gX.h) were achieved. These results suggested the significant potential of the bioconversion of saline resources into value-added products, such as PHAs.
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Obruča S, Dvořák P, Sedláček P, Koller M, Sedlář K, Pernicová I, Šafránek D. Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics. Biotechnol Adv 2022; 58:107906. [DOI: 10.1016/j.biotechadv.2022.107906] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 01/10/2023]
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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. Appl Environ Microbiol 2021; 87:e0092921. [PMID: 34160268 PMCID: PMC8357295 DOI: 10.1128/aem.00929-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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8
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Frare R, Stritzler M, Pascuan C, Liebrenz K, Galindo-Sotomonte L, Soto G, Nikel PI, Ayub N. Elimination of GlnKAmtB affects serine biosynthesis and improves growth and stress tolerance of Escherichia coli under nutrient-rich conditions. FEMS Microbiol Lett 2021; 367:6006877. [PMID: 33242092 DOI: 10.1093/femsle/fnaa197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Nitrogen is a most important nutrient resource for Escherichia coli and other bacteria that harbor the glnKamtB operon, a high-affinity ammonium uptake system highly interconnected with cellular metabolism. Although this system confers an advantage to bacteria when growing under nitrogen-limiting conditions, little is known about the impact of these genes on microbial fitness under nutrient-rich conditions. Here, the genetically tractable E. coli BW25113 strain and its glnKamtB-null mutant (JW0441) were used to analyze the impact of GlnK-AmtB on growth rates and oxidative stress tolerance. Strain JW0441 showed a shorter initial lag phase, higher growth rate, higher citrate synthase activity, higher oxidative stress tolerance and lower expression of serA than strain BW25113 under nutrient-rich conditions, suggesting a fitness cost to increase metabolic plasticity associated with serine metabolism. The overexpression of serA in strain JW0441 resulted in a decreased growth rate and stress tolerance in nutrient-rich conditions similar to that of strain BW25113, suggesting that the negative influence on bacterial fitness imposed by GlnK-AmtB can be traced to the control of serine biosynthesis. Finally, we discuss the potential applications of glnKamtB mutants in bioproduction processes.
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Affiliation(s)
- Romina Frare
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Karen Liebrenz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Luisa Galindo-Sotomonte
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
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Ghergab A, Mohanan N, Saliga G, Brassinga AKC, Levin D, de Kievit T. The effect of polyhydroxyalkanoates in Pseudomonas chlororaphis PA23 biofilm formation, stress endurance, and interaction with the protozoan predator Acanthamoeba castellanii. Can J Microbiol 2021; 67:476-490. [PMID: 34057367 DOI: 10.1139/cjm-2020-0497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pseudomonas chlororaphis PA23 is a biocontrol agent capable of protecting canola against the fungal pathogen Sclerotinia sclerotiorum. In addition to producing antifungal compounds, this bacterium synthesizes and accumulates polyhydroxyalkanoate (PHA) polymers as carbon and energy storage compounds. Because the role of PHA in PA23 physiology is currently unknown, we investigated the impact of this polymer on stress resistance, adherence to surfaces, and interaction with the protozoan predator Acanthamoeba castellanii. Three PHA biosynthesis mutants were created, PA23phaC1, PA23phaC1ZC2, and PA23phaC1ZC2D, which accumulated reduced PHA. Our phenotypic assays revealed that PA23phaC1ZC2D produced less phenazine (PHZ) compared with the wild type (WT) and the phaC1 and phaC1ZC2 mutants. All three mutants exhibited enhanced sensitivity to UV irradiation, starvation, heat stress, cold stress, and hydrogen peroxide. Moreover, motility, exopolysaccharide production, biofilm formation, and root attachment were increased in strains with reduced PHA levels. Interaction studies with the amoeba A. castellanii revealed that the WT and the phaC1 and phaC1ZC2 mutants were consumed less than the phaC1ZC2D mutant, likely due to decreased PHZ production by the latter. Collectively these findings indicate that PHA accumulation enhances PA23 resistance to a number of stresses in vitro, which could improve the environmental fitness of this bacterium in hostile environments.
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Affiliation(s)
- Akrm Ghergab
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Grace Saliga
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - David Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Teresa de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Kouřilová X, Schwarzerová J, Pernicová I, Sedlář K, Mrázová K, Krzyžánek V, Nebesářová J, Obruča S. The First Insight into Polyhydroxyalkanoates Accumulation in Multi-Extremophilic Rubrobacter xylanophilus and Rubrobacter spartanus. Microorganisms 2021; 9:909. [PMID: 33923216 PMCID: PMC8146576 DOI: 10.3390/microorganisms9050909] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/27/2022] Open
Abstract
Actinobacteria belonging to the genus Rubrobacter are known for their multi-extremophilic growth conditions-they are highly radiation-resistant, halotolerant, thermotolerant or even thermophilic. This work demonstrates that the members of the genus are capable of accumulating polyhydroxyalkanoates (PHA) since PHA-related genes are widely distributed among Rubrobacter spp. whose complete genome sequences are available in public databases. Interestingly, all Rubrobacter strains possess both class I and class III synthases (PhaC). We have experimentally investigated the PHA accumulation in two thermophilic species, R. xylanophilus and R. spartanus. The PHA content in both strains reached up to 50% of the cell dry mass, both bacteria were able to accumulate PHA consisting of 3-hydroxybutyrate and 3-hydroxyvalerate monomeric units, none other monomers were incorporated into the polymer chain. The capability of PHA accumulation likely contributes to the multi-extremophilic characteristics since it is known that PHA substantially enhances the stress robustness of bacteria. Hence, PHA can be considered as extremolytes enabling adaptation to extreme conditions. Furthermore, due to the high PHA content in biomass, a wide range of utilizable substrates, Gram-stain positivity, and thermophilic features, the Rubrobacter species, in particular Rubrobacter xylanophilus, could be also interesting candidates for industrial production of PHA within the concept of Next-Generation Industrial Biotechnology.
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Affiliation(s)
- Xenie Kouřilová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (X.K.); (I.P.)
| | - Jana Schwarzerová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic; (J.S.); (K.S.)
| | - Iva Pernicová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (X.K.); (I.P.)
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic; (J.S.); (K.S.)
| | - Kateřina Mrázová
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Kralovopolska 147, 612 64 Brno, Czech Republic; (K.M.); (V.K.)
| | - Vladislav Krzyžánek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Kralovopolska 147, 612 64 Brno, Czech Republic; (K.M.); (V.K.)
| | - Jana Nebesářová
- Biology Centre, The Czech Academy of Sciences, v.v.i., Branisovska 31, 370 05 Ceske Budejovice, Czech Republic;
- Faculty of Science, Charles University, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - Stanislav Obruča
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (X.K.); (I.P.)
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Obulisamy PK, Mehariya S. Polyhydroxyalkanoates from extremophiles: A review. BIORESOURCE TECHNOLOGY 2021; 325:124653. [PMID: 33465644 DOI: 10.1016/j.biortech.2020.124653] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.
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Affiliation(s)
| | - Sanjeet Mehariya
- Department of Engineering, University of Campania "Luigi Vanvitelli", Real Casa dell'Annunziata, Italy
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12
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Obruca S, Sedlacek P, Koller M. The underexplored role of diverse stress factors in microbial biopolymer synthesis. BIORESOURCE TECHNOLOGY 2021; 326:124767. [PMID: 33540213 DOI: 10.1016/j.biortech.2021.124767] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Stanislav Obruca
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic.
| | - Petr Sedlacek
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - Martin Koller
- Institute of Chemistry, NAWI Graz, University of Graz, Heinrichstrasse 28/VI, 8010 Graz, Austria; ARENA Arbeitsgemeinschaft für Ressourcenschonende & Nachhaltige Technologien, Inffeldgasse 21b, 11 8010 Graz, Austria
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Grape winery waste as a promising feedstock for the production of polyhydroxyalkanoates and other value-added products. FOOD AND BIOPRODUCTS PROCESSING 2020. [DOI: 10.1016/j.fbp.2020.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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3-Hydroxybutyrate Derived from Poly-3-Hydroxybutyrate Mobilization Alleviates Protein Aggregation in Heat-Stressed Herbaspirillum seropedicae SmR1. Appl Environ Microbiol 2020; 86:AEM.01265-20. [PMID: 32631857 DOI: 10.1128/aem.01265-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/26/2020] [Indexed: 12/14/2022] Open
Abstract
Under conditions of carbon starvation or thermal, osmotic, or oxidative shock, mutants affected in the synthesis or mobilization of poly-3-hydroxybutyrate (PHB) are known to survive less well. It is still unclear if the synthesis and accumulation of PHB are sufficient to protect bacteria against stress conditions or if the stored PHB has to be mobilized. Here, we demonstrated that mobilization of PHB in Herbaspirillum seropedicae SmR1 was heat-shock activated at 45°C. In situ proton (1H) nuclear magnetic resonance spectroscopy (i.e., 1H-nuclear magnetic resonance) showed that heat shock increased amounts of 3-hydroxybutyrate (3HB) only in H. seropedicae strains able to synthesize and mobilize PHB. H. seropedicae SmR1 mutants unable to synthesize or mobilize PHB were more susceptible to heat shock and survived less well than the parental strain. When 100 mM 3-hydroxybutyrate was added to the medium, the ΔphaC1 strain (an H. seropedicae mutant unable to synthesize PHB) and the double mutant with deletion of both phaZ1 and phaZ2 (i.e., ΔphaZ1.2) (unable to mobilize PHB) showed partial rescue of heat adaptability (from 0% survival without 3HB to 40% of the initial viable population). Addition of 200 mM 3HB before the imposition of heat shock reduced protein aggregation to 15% in the ΔphaC1 mutant and 12% in the ΔphaZ1.2 mutant. We conclude that H. seropedicae SmR1 is naturally protected by 3HB released by PHB mobilization, while mutants unable to generate large amounts of 3HB under heat shock conditions are less able to cope with heat damage.IMPORTANCE Bacteria are subject to abrupt changes in environmental conditions affecting their growth, requiring rapid adaptation. Increasing the concentration of some metabolites can protect bacteria from hostile conditions that lead to protein denaturation and precipitation, as well as damage to plasma membranes. In this work, we demonstrated that under thermal shock, the bacterium Herbaspirillum seropedicae depolymerized its intracellular stock polymer known as poly-3-hydroxybutyrate (PHB), rapidly increasing the concentration of 3-hydroxybutyrate (3HB) and decreasing protein precipitation by thermal denaturation. Mutant H. seropedicae strains unable to produce or depolymerize PHB suffered irreparable damage during thermal shock, resulting in fast death when incubated at 45°C. Our results will contribute to the development of bacteria better adapted to high temperatures found either in natural conditions or in industrial processes. In the case of H. seropedicae and other bacteria that interact beneficially with plants, the understanding of PHB metabolism can be decisive for the development of more-competitive strains and their application as biofertilizers in agriculture.
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Novel unexpected functions of PHA granules. Appl Microbiol Biotechnol 2020; 104:4795-4810. [PMID: 32303817 DOI: 10.1007/s00253-020-10568-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
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.
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Yancey PH. Cellular responses in marine animals to hydrostatic pressure. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 333:398-420. [DOI: 10.1002/jez.2354] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Paul H. Yancey
- Department of BiologyWhitman CollegeWalla Walla Washington
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Kumar V, Kumar S, Singh D. Microbial polyhydroxyalkanoates from extreme niches: Bioprospection status, opportunities and challenges. Int J Biol Macromol 2019; 147:1255-1267. [PMID: 31739043 DOI: 10.1016/j.ijbiomac.2019.09.253] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/23/2019] [Accepted: 09/30/2019] [Indexed: 01/20/2023]
Abstract
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.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India.
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Coordinated Regulation of the Size and Number of Polyhydroxybutyrate Granules by Core and Accessory Phasins in the Facultative Microsymbiont Sinorhizobium fredii NGR234. Appl Environ Microbiol 2019; 85:AEM.00717-19. [PMID: 31375484 DOI: 10.1128/aem.00717-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
The exact roles of various granule-associated proteins (GAPs) of polyhydroxybutyrate (PHB) are poorly investigated, particularly for bacteria associated with plants. In this study, four structural GAPs, named phasins PhaP1 to PhaP4, were identified and demonstrated as true phasins colocalized with PHB granules in Sinorhizobium fredii NGR234, a facultative microsymbiont of Vigna unguiculata and many other legumes. The conserved PhaP2 dominated in regulation of granule size under both free-living and symbiotic conditions. PhaP1, another conserved phasin, made a higher contribution than accessory phasins PhaP4 and PhaP3 to PHB biosynthesis at stationary phase. PhaP3, with limited phyletic distribution on the symbiosis plasmid of Sinorhizobium, was more important than PhaP1 in regulating PHB biosynthesis in V. unguiculata nodules. Under the test conditions, no significant symbiotic defects were observed for mutants lacking individual or multiple phaP genes. The mutant lacking two PHB synthases showed impaired symbiotic performance, while mutations in individual PHB synthases or a PHB depolymerase yielded no symbiotic defects. This phenomenon is not related to either the number or size of PHB granules in test mutants within nodules. Distinct metabolic profiles and cocktail pools of GAPs of different phaP mutants imply that core and accessory phasins can be differentially involved in regulating other cellular processes in the facultative microsymbiont S. fredii NGR234.IMPORTANCE Polyhydroxybutyrate (PHB) granules are a store of carbon and energy in bacteria and archaea and play an important role in stress adaptation. Recent studies have highlighted distinct roles of several granule-associated proteins (GAPs) in regulating the size, number, and localization of PHB granules in free-living bacteria, though our knowledge of the role of GAPs in bacteria associated with plants is still limited. Here we report distinct roles of core and accessory phasins associated with PHB granules of Sinorhizobium fredii NGR234, a broad-host-range microsymbiont of diverse legumes. Core phasins PhaP2 and PhaP1 are conserved major phasins in free-living cells. PhaP2 and accessory phasin PhaP3, encoded by an auxiliary gene on the symbiosis plasmid, are major phasins in nitrogen-fixing bacteroids in cowpea nodules. GAPs and metabolic profiles can vary in different phaP mutants. Contrasting symbiotic performances between mutants lacking PHB synthases, depolymerase, or phasins were revealed.
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What keeps polyhydroxyalkanoates in bacterial cells amorphous? A derivation from stress exposure experiments. Appl Microbiol Biotechnol 2019; 103:1905-1917. [DOI: 10.1007/s00253-018-09584-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
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Stritzler M, Berini C, Jozefkowicz C, Soto G, Ayub N. Understanding the intracellular-to-extracellular localization switch of polyhydroxybutyrate polymerase in pseudomonas backgrounds as a microevolutionary process. J Theor Biol 2018; 456:29-33. [PMID: 30063924 DOI: 10.1016/j.jtbi.2018.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/19/2018] [Accepted: 07/27/2018] [Indexed: 11/28/2022]
Abstract
After gene duplication, paralogous genes evolve independently, and consequently, the new proteins encoded by these duplicated genes are exposed to changes in their subcellular location. Although there are increasing evidence that phylogenetically related proteins play different functions in different subcellular compartments, the number of evolutionary steps required for the emergence of a novel protein with a novel subcellular localization remains unclear. Regarding this intriguing topic, here we examine in depth our previous reports describing both intracellular and extracellular polyhydroxybutyrate polymerases (PhaC) in the Pseudomonadales group. The recapitulation of the intracellular-to-extracellular localization switch of PhaC in these strains shows a gradual evolution from a simple cytosolic PhaC form to a complex extracellular PhaC form specifically secreted via the type 1 secretion system. This gradual evolution includes several adaptive and pre-adaptive changes at the genomic, genetic and enzymatic levels, which are intimately related to the lifestyle of organisms during the evolution of protein localization. We conclude that the protein localization switch can be an extremely complex process in nature.
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Affiliation(s)
- Margarita Stritzler
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Carolina Berini
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CABA, Argentina
| | - Cintia Jozefkowicz
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Gabriela Soto
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Nicolás Ayub
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina.
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21
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Wang W, Roberts CJ. Protein aggregation – Mechanisms, detection, and control. Int J Pharm 2018; 550:251-268. [DOI: 10.1016/j.ijpharm.2018.08.043] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
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Plant growth-promoting bacterium Pseudomonas fluorescens FR1 secrets a novel type of extracellular polyhydroxybutyrate polymerase involved in abiotic stress response in plants. Biotechnol Lett 2018; 40:1419-1423. [DOI: 10.1007/s10529-018-2576-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/22/2018] [Indexed: 10/16/2022]
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23
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Involvement of polyhydroxyalkanoates in stress resistance of microbial cells: Biotechnological consequences and applications. Biotechnol Adv 2018; 36:856-870. [DOI: 10.1016/j.biotechadv.2017.12.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/24/2017] [Accepted: 12/12/2017] [Indexed: 01/30/2023]
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24
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A Review on Established and Emerging Fermentation Schemes for Microbial Production of Polyhydroxyalkanoate (PHA) Biopolyesters. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4020030] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Obruca S, Sedlacek P, Krzyzanek V, Mravec F, Hrubanova K, Samek O, Kucera D, Benesova P, Marova I. Accumulation of Poly(3-hydroxybutyrate) Helps Bacterial Cells to Survive Freezing. PLoS One 2016; 11:e0157778. [PMID: 27315285 PMCID: PMC4912086 DOI: 10.1371/journal.pone.0157778] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/03/2016] [Indexed: 11/19/2022] Open
Abstract
Accumulation of polyhydroxybutyrate (PHB) seems to be a common metabolic strategy adopted by many bacteria to cope with cold environments. This work aimed at evaluating and understanding the cryoprotective effect of PHB. At first a monomer of PHB, 3-hydroxybutyrate, was identified as a potent cryoprotectant capable of protecting model enzyme (lipase), yeast (Saccharomyces cerevisiae) and bacterial cells (Cupriavidus necator) against the adverse effects of freezing-thawing cycles. Further, the viability of the frozen-thawed PHB accumulating strain of C. necator was compared to that of the PHB non-accumulating mutant. The presence of PHB granules in cells was revealed to be a significant advantage during freezing. This might be attributed to the higher intracellular level of 3-hydroxybutyrate in PHB accumulating cells (due to the action of parallel PHB synthesis and degradation, the so-called PHB cycle), but the cryoprotective effect of PHB granules seems to be more complex. Since intracellular PHB granules retain highly flexible properties even at extremely low temperatures (observed by cryo-SEM), it can be expected that PHB granules protect cells against injury from extracellular ice. Finally, thermal analysis indicates that PHB-containing cells exhibit a higher rate of transmembrane water transport, which protects cells against the formation of intracellular ice which usually has fatal consequences.
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Affiliation(s)
- Stanislav Obruca
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Petr Sedlacek
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Vladislav Krzyzanek
- Institute of Scientific Instruments, Academy of Sciences of The Czech Republic, Vvi, Kralovopolska 147, 612 64, Brno, Czech Republic
| | - Filip Mravec
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Kamila Hrubanova
- Institute of Scientific Instruments, Academy of Sciences of The Czech Republic, Vvi, Kralovopolska 147, 612 64, Brno, Czech Republic
| | - Ota Samek
- Institute of Scientific Instruments, Academy of Sciences of The Czech Republic, Vvi, Kralovopolska 147, 612 64, Brno, Czech Republic
| | - Dan Kucera
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Pavla Benesova
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Ivana Marova
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
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Röthig T, Ochsenkühn MA, Roik A, van der Merwe R, Voolstra CR. Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome. Mol Ecol 2016; 25:1308-23. [PMID: 26840035 PMCID: PMC4804745 DOI: 10.1111/mec.13567] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 01/03/2023]
Abstract
Scleractinian corals are assumed to be stenohaline osmoconformers, although they are frequently subjected to variations in seawater salinity due to precipitation, freshwater run-off and other processes. Observed responses to altered salinity levels include differences in photosynthetic performance, respiration and increased bleaching and mortality of the coral host and its algal symbiont, but a study looking at bacterial community changes is lacking. Here, we exposed the coral Fungia granulosa to strongly increased salinity levels in short- and long-term experiments to disentangle temporal and compartment effects of the coral holobiont (i.e. coral host, symbiotic algae and associated bacteria). Our results show a significant reduction in calcification and photosynthesis, but a stable microbiome after short-term exposure to high-salinity levels. By comparison, long-term exposure yielded unchanged photosynthesis levels and visually healthy coral colonies indicating long-term acclimation to high-salinity levels that were accompanied by a major coral microbiome restructuring. Importantly, a bacterium in the family Rhodobacteraceae was succeeded by Pseudomonas veronii as the numerically most abundant taxon. Further, taxonomy-based functional profiling indicates a shift in the bacterial community towards increased osmolyte production, sulphur oxidation and nitrogen fixation. Our study highlights that bacterial community composition in corals can change within days to weeks under altered environmental conditions, where shifts in the microbiome may enable adjustment of the coral to a more advantageous holobiont composition.
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Affiliation(s)
- Till Röthig
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Michael A Ochsenkühn
- Biological and Organometallic Catalysis Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Anna Roik
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Riaan van der Merwe
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Evaluation of 3-hydroxybutyrate as an enzyme-protective agent against heating and oxidative damage and its potential role in stress response of poly(3-hydroxybutyrate) accumulating cells. Appl Microbiol Biotechnol 2015; 100:1365-1376. [DOI: 10.1007/s00253-015-7162-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 11/02/2015] [Accepted: 11/07/2015] [Indexed: 10/22/2022]
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Exploring the Ancestral Mechanisms of Regulation of Horizontally Acquired Nitrogenases. J Mol Evol 2015; 81:84-9. [PMID: 26374754 DOI: 10.1007/s00239-015-9698-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
Abstract
The vast majority of Pseudomonas species are unable to fix atmospheric nitrogen. Although several studies have demonstrated that some strains belonging to the genus Pseudomonas sensu stricto do have the ability to fix nitrogen by the expression of horizontally acquired nitrogenase, little is known about the mechanisms of nitrogenase adaptation to the new bacterial host. Recently, we transferred the nitrogen fixation island from Pseudomonas stutzeri A1501 to the non-nitrogen-fixing bacterium Pseudomonas protegens Pf-5, and interestingly, the resulting recombinant strain Pf-5 X940 showed an uncommon phenotype of constitutive nitrogenase activity. Here, we integrated evolutionary and functional approaches to elucidate this unusual phenotype. Phylogenetic analysis showed that polyhydroxybutyrate (PHB) biosynthesis genes from natural nitrogen-fixing Pseudomonas strains have been acquired by horizontal transfer. Contrary to Pf-5 X940, its derived PHB-producing strain Pf-5 X940-PHB exhibited the inhibition of nitrogenase activity under nitrogen-excess conditions, and displayed the typical switch-on phenotype observed in natural nitrogen-fixing strains after nitrogen deficiency. This indicates a competition between PHB production and nitrogen fixation. Therefore, we propose that horizontal transfer of PHB biosynthesis genes could be an ancestral mechanism of regulation of horizontally acquired nitrogenases in the genus Pseudomonas.
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Abstract
It is well recognized that protein product development is far more challenging than that for small-molecule drugs. The major challenges include inherent sensitivity to different types of stresses during the drug product manufacturing process, high rate of physical and chemical degradation during long-term storage, and enhanced aggregation and/or viscosity at high protein concentrations. In the past decade, many novel formulation concepts and technologies have been or are being developed to address these product development challenges for proteins. These concepts and technologies include use of uncommon/combination of formulation stabilizers, conjugation or fusion with potential stabilizers, site-specific mutagenesis, and preparation of nontraditional types of dosage forms-semiaqueous solutions, nonfreeze-dried solid formulations, suspensions, and other emerging concepts. No one technology appears to be mature, ideal, and/or adequate to address all the challenges. These gaps will likely remain in the foreseeable future and need significant efforts for ultimate resolution.
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Affiliation(s)
- Wei Wang
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, 700 Chesterfield Parkway West, Chesterfield, MO, 63017.,Wang Biologics, LLC, 907 Wellesley Place, Chesterfield, Missouri, 63017
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30
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Doronina NV, Torgonskaya ML, Fedorov DN, Trotsenko YA. Aerobic methylobacteria as promising objects of modern biotechnology (Review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Ayub ND, Fox AR, García AN, Mozzicafreddo M, Cuccioloni M, Angeletti M, Pagano E, Soto G. Pseudomonas fluorescens Pf-5 genome-wide mutant screen for resistance to the antimicrobial peptide alfalfa snakin-1. FEMS Microbiol Lett 2014; 362:1-6. [PMID: 25670697 DOI: 10.1093/femsle/fnu006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Snakin-1, a peptide produced by higher plants, has broad-spectrum antibiotic activity, inhibiting organisms ranging from Bacteria to Eukaryotes. However, the mode of action against target organisms is poorly understood. As a first step to elucidate the mechanism, we screened a mutation library of Pseudomonas fluorescens Pf-5 in LB and agar medium supplemented with alfalfa snakin-1 (MsSN1). We identified three biofilm formation-related Pseudomonas mutants that showed increased resistance to MsSN1. Genetic, physiological and bioinformatics analysis validated the results of the mutant screens, indicating that bacterial adhesion protein lapA is probably the target of MsSN1. Collectively, these findings suggest that snakin-1 acts on microbial adhesion properties.
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Affiliation(s)
- Nicolás D Ayub
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917, C1033AAJ, Cuidad Autónoma de Buenos Aires, Argentina
| | - Ana R Fox
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917, C1033AAJ, Cuidad Autónoma de Buenos Aires, Argentina
| | - Araceli N García
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina
| | - Matteo Mozzicafreddo
- School of Biosciences and Biotechnology, University of Camerino, 62032 Camerino (MC), Italy
| | | | - Mauro Angeletti
- School of Biosciences and Biotechnology, University of Camerino, 62032 Camerino (MC), Italy
| | - Elba Pagano
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917, C1033AAJ, Cuidad Autónoma de Buenos Aires, Argentina
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Chien CC, Wang LJ, Lin WR. Polyhydroxybutyrate accumulation by a cadmium-resistant strain of Cupriavidus taiwanensis. J Taiwan Inst Chem Eng 2014. [DOI: 10.1016/j.jtice.2014.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Fox AR, Soto G, Mozzicafreddo M, Garcia AN, Cuccioloni M, Angeletti M, Salerno JC, Ayub ND. Understanding the function of bacterial and eukaryotic thiolases II by integrating evolutionary and functional approaches. Gene 2013; 533:5-10. [PMID: 24120621 DOI: 10.1016/j.gene.2013.09.096] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/26/2013] [Indexed: 10/26/2022]
Abstract
Acetoacetyl-CoA thiolase (EC 2.3.1.9), commonly named thiolase II, condenses two molecules of acetyl-CoA to give acetoacetyl-CoA and CoA. This enzyme acts in anabolic processes as the first step in the biosynthesis of isoprenoids and polyhydroxybutyrate in eukaryotes and bacteria, respectively. We have recently reported the evolutionary and functional equivalence of these enzymes, suggesting that thiolase II could be the rate limiting enzyme in these pathways and presented evidence indicating that this enzyme modulates the availability of reducing equivalents during abiotic stress adaptation in bacteria and plants. However, these results are not sufficient to clarify why thiolase II was evolutionary selected as a critical enzyme in the production of antioxidant compounds. Regarding this intriguing topic, we propose that thiolase II could sense changes in the acetyl-CoA/CoA ratio induced by the inhibition of the tricarboxylic acid cycle under abiotic stress. Thus, the high level of evolutionary and functional constraint of thiolase II may be due to the connection of this enzyme with an ancient and conserved metabolic route.
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Affiliation(s)
- Ana Romina Fox
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917, C1033AAJ Cuidad Autónoma de Buenos Aires, Argentina
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Cuyeu R, Rosso B, Pagano E, Soto G, Fox R, Ayub ND. Genetic diversity in a world germplasm collection of tall fescue. Genet Mol Biol 2013. [PMID: 23885206 DOI: 10.1590/s1415‐47572013005000021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.
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Affiliation(s)
- Romina Cuyeu
- Instituto de Genética Ewald A. Favret, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Provincia de Buenos Aires, Argentina
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Cuyeu R, Rosso B, Pagano E, Soto G, Fox R, Ayub ND. Genetic diversity in a world germplasm collection of tall fescue. Genet Mol Biol 2013; 36:237-42. [PMID: 23885206 PMCID: PMC3715290 DOI: 10.1590/s1415-47572013005000021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 03/20/2013] [Indexed: 12/02/2022] Open
Abstract
Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.
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Affiliation(s)
- Romina Cuyeu
- Instituto de Genética Ewald A. Favret, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Provincia de Buenos Aires, Argentina
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