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Moreira NFF, Ribeirinho-Soares S, Viana AT, Graça CAL, Ribeiro ARL, Castelhano N, Egas C, Pereira MFR, Silva AMT, Nunes OC. Rethinking water treatment targets: Bacteria regrowth under unprovable conditions. WATER RESEARCH 2021; 201:117374. [PMID: 34214892 DOI: 10.1016/j.watres.2021.117374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Ozonation is among the currently used technologies to remove chemical and biological contaminants from secondary treated urban wastewater (UWW). Despite its effectiveness on the abatement of organic micropollutants (OMPs) and disinfection, previous studies have shown that regrow of bacteria may occur upon storage of the ozonated UWW. This reactivation has been attributed to the high content of assimilable organic carbon after treatment. In order to investigate if ozonation by-products are the main biological regrowth drivers in stored ozonated UWW, the ozonation surviving cells were resuspended in sterile bottled mineral water (MW), simulating a pristine oligotrophic environment. After 7 days storage, organisms such as Acinetobacter, Methylobacterium, Cupriavidus, Massilia, Acidovorax and Pseudomonas were dominant in both ozonated UWW and pristine MW, demonstrating that bacterial regrowth is not strictly related to the eventual presence of ozonation by-products, but instead with the ability of the surviving cells to cope with nutrient-poor environments. The resistome of UWW before and after ozonation was analysed by metagenomic techniques. Draft metagenome assembled genomes (dMAGs), recovered from both ozonated UWW and after cell resuspension in MW, harboured genes conferring resistance to diverse antibiotics classes. Some of these antibiotic resistance genes (ARGs) were located in the vicinity of mobile genetic elements, suggesting their potential to be mobilized. Among these, dMAGs affiliated to taxa with high relative abundance in stored water, such as P. aeruginosa and Acinetobacter spp., harboured ARGs conferring resistance to 12 and 4 families of antibiotics, respectively, including those encoding carbapenem hydrolysing oxacillinases. The results herein obtained point out that the design and development of new wastewater treatment technologies should include measures to attenuate the imbalance of the bacterial communities promoted by storage of the final treated wastewater, even when applying processes with high mineralization rates.
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Affiliation(s)
- Nuno F F Moreira
- LSRE-LCM - Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Sara Ribeirinho-Soares
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana Teresa Viana
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Cátia A L Graça
- LSRE-LCM - Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana Rita L Ribeiro
- LSRE-LCM - Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nadine Castelhano
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - M Fernando R Pereira
- LSRE-LCM - Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Adrián M T Silva
- LSRE-LCM - Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Olga C Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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Ojha A, Zhang W. A comparative study of microbial community and dynamics of Asaia in the brown planthopper from susceptible and resistant rice varieties. BMC Microbiol 2019; 19:139. [PMID: 31234788 PMCID: PMC6591912 DOI: 10.1186/s12866-019-1512-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/10/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The brown planthopper (BPH) is likely the most destructive, piercing and sucking monophagous insect pest of rice that causes substantial economic losses to farmers. Although yeast-like symbionts (YLS) and virus transmission have been observed in the BPH, the bacterial population inhabiting the BPH has received minimal research attention. Labelling BPH-associated bacterial species may shed light on BPH biology and the interaction between the BPH and rice to provide novel approaches for the efficient control of this insect pest. RESULTS We examined RNA-seq results to identify bacterial populations present in different generations of BPHs maintained on susceptible or resistant rice varieties. Overall, 87 operational taxonomic units (OTUs) were determined from the BPH-F0, F6 and F16 generations. These OTUs had Shannon and Simpson index values of 0.37-0.6 and 0.56-1.19, respectively. The evenness values of 0.7-1.00 showed the vastness of the bacterial diversity recovered from the BPH samples. The results showed high species diversity in the BPHs collected from susceptible rice and a high number of members of unclassified bacteria in the BPHs isolated from resistant rice. We noticed that Proteobacteria OTUs were predominant across all samples. Furthermore, PCR data of Asaia species showed variable DNA amplification across the BPH samples collected from susceptible or resistant varieties. The identification of Asaia in BPH eggs and BPH-egg-infected rice revealed its influence on the interaction between the BPH egg and rice. CONCLUSIONS The BPHs had clear differences in their microbiomes and in their ability to feed on different rice hosts. These variations could have an essential impact on host adaptation and interaction. These results provide a better understanding of the bacterial diversity and interaction of the microbiome of different generations of BPHs. Furthermore, PCR data of Asaia sp. variation across the BPH samples (isolated from different host genotypes selected from the field and laboratory, including BPH eggs and egg-infected rice tissues), suggest that Asaia could be an important member of the insect microbiome involved in adaptation, its interaction with rice and, most importantly, as a paratransgenic tool for insect control.
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Affiliation(s)
- Abhishek Ojha
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
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3
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Minard G, Tran FH, Raharimalala FN, Hellard E, Ravelonandro P, Mavingui P, Valiente Moro C. Prevalence, genomic and metabolic profiles of Acinetobacter and Asaia associated with field-caught Aedes albopictus from Madagascar. FEMS Microbiol Ecol 2012; 83:63-73. [PMID: 22808994 DOI: 10.1111/j.1574-6941.2012.01455.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 06/26/2012] [Accepted: 07/06/2012] [Indexed: 11/29/2022] Open
Abstract
The presence of cultivable bacteria Acinetobacter and Asaia was recently demonstrated in the mosquito vector Aedes albopictus. However, it is not known how prevalent these bacteria are in field populations. Here, the presence of these bacteria in Ae. albopictus populations from Madagascar was diagnosed by amplification of 16S rRNA gene fragments. Both genera were detected at relatively high frequencies, 46% for Asaia and 74% for Acinetobacter. The prevalence of Acinetobacter correlated significantly with mosquito gender, and the prevalence of Asaia with the interaction between mosquito gender and the sampling site. For each bacterial genus, more male than female mosquitoes were infected. Using pulse field gel electrophoresis, no significant difference in genome size was found between Acinetobacter isolates from mosquitoes compared with free-living Acinetobacter. However, a great diversity was observed in plasmid numbers (from 1 to 12) and sizes (from < 8 to 690 kb). Mosquito isolates utilized fewer substrates than free-living isolates, but some substrates known as blood or plant components were specifically utilized by mosquito isolates. Therefore it is likely that a specific subpopulation of Acinetobacter is selected by Ae. albopictus. Overall, this study emphasizes the need to gain a global view on the bacterial partners in mosquito vectors.
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Affiliation(s)
- Guillaume Minard
- Université de Lyon, UMR5557 Ecologie Microbienne, CNRS, USC1190 INRA, VetAgro Sup, Université Lyon 1, Villeurbanne, France
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Suriyamongkol P, Weselake R, Narine S, Moloney M, Shah S. Biotechnological approaches for the production of polyhydroxyalkanoates in microorganisms and plants - a review. Biotechnol Adv 2006; 25:148-75. [PMID: 17222526 DOI: 10.1016/j.biotechadv.2006.11.007] [Citation(s) in RCA: 192] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Revised: 11/23/2006] [Accepted: 11/23/2006] [Indexed: 11/18/2022]
Abstract
The increasing effect of non-degradable plastic wastes is a growing concern. Polyhydroxyalkanoates (PHAs), macromolecule-polyesters naturally produced by many species of microorganisms, are being considered as a replacement for conventional plastics. Unlike petroleum-derived plastics that take several decades to degrade, PHAs can be completely bio-degraded within a year by a variety of microorganisms. This biodegradation results in carbon dioxide and water, which return to the environment. Attempts based on various methods have been undertaken for mass production of PHAs. Promising strategies involve genetic engineering of microorganisms and plants to introduce production pathways. This challenge requires the expression of several genes along with optimization of PHA synthesis in the host. Although excellent progress has been made in recombinant hosts, the barriers to obtaining high quantities of PHA at low cost still remain to be solved. The commercially viable production of PHA in crops, however, appears to be a realistic goal for the future.
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Affiliation(s)
- Pornpa Suriyamongkol
- Plant Biotechnology Unit, Alberta Research Council, Vegreville, Alberta, Canada T9C 1T4
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5
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López NI, Pettinari M, Méndez BS. Detection of reserve polymer synthesis genes in natural bacterial populations. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00364.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Dionisi D, Majone M, Vallini G, Di Gregorio S, Beccari M. Effect of the applied organic load rate on biodegradable polymer production by mixed microbial cultures in a sequencing batch reactor. Biotechnol Bioeng 2005; 93:76-88. [PMID: 16224790 DOI: 10.1002/bit.20683] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article studies the operation of a new process for the production of biopolymers (polyhydroxyalkanoates, PHAs) at different applied organic load rates (OLRs). The process is based on the aerobic enrichment of activated sludge to obtain mixed cultures able to store PHAs at high rates and yields. A mixture of acetic, lactic, and propionic acids at different concentrations (in the range 8.5-31.25 gCOD/L) was fed every 2 h in a sequencing batch reactor (SBR). The resulting applied OLR was in the range 8.5-31.25 gCOD/L/day. Even though, as expected, the increase in the OLR caused an increase in biomass concentration (up to about 8.7 g COD/L), it also caused a relevant decrease of maximal polymer production rate. This decrease in polymer production rate was related to the different extent of "feast and famine" conditions, as function of the applied OLR and of the start-up conditions. As a consequence the best performance of the process was obtained at an intermediate OLR (20 gCOD/L/day) where both biomass productivity and PHA storage were high enough. However, at this high OLR the process was unstable and sudden decrease of performance was also observed. The sludge characterized by the highest PHA storage response was investigated by 16S rDNA clone library. The clone library contained sequences mostly from PHA producers (e.g., Alcaligenes and Comamonas genera); however many genera and among them, one of the dominant (Thauera), were never described before in relation to PHA storage response.
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Affiliation(s)
- Davide Dionisi
- Department of Chemistry, University of Rome La Sapienza, P.le Aldo Moro 5, Italy.
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Seviour RJ, Mino T, Onuki M. The microbiology of biological phosphorus removal in activated sludge systems. FEMS Microbiol Rev 2003; 27:99-127. [PMID: 12697344 DOI: 10.1016/s0168-6445(03)00021-4] [Citation(s) in RCA: 448] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Activated sludge systems are designed and operated globally to remove phosphorus microbiologically, a process called enhanced biological phosphorus removal (EBPR). Yet little is still known about the ecology of EBPR processes, the microbes involved, their functions there and the possible reasons why they often perform unreliably. The application of rRNA-based methods to analyze EBPR community structure has changed dramatically our understanding of the microbial populations responsible for EBPR, but many substantial gaps in our knowledge of the population dynamics of EBPR and its underlying mechanisms remain. This review critically examines what we once thought we knew about the microbial ecology of EBPR, what we think we now know, and what still needs to be elucidated before these processes can be operated and controlled more reliably than is currently possible. It looks at the history of EBPR, the currently available biochemical models, the structure of the microbial communities found in EBPR systems, possible identities of the bacteria responsible, and the evidence why these systems might operate suboptimally. The review stresses the need to extend what have been predominantly laboratory-based studies to full-scale operating plants. It aims to encourage microbiologists and process engineers to collaborate more closely and to bring an interdisciplinary approach to bear on this complex ecosystem.
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Affiliation(s)
- Robert J Seviour
- Institute of Environmental Studies, Graduate School of Frontier Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan.
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Steinbüchel A, Hein S. Biochemical and molecular basis of microbial synthesis of polyhydroxyalkanoates in microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2001; 71:81-123. [PMID: 11217418 DOI: 10.1007/3-540-40021-4_3] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Intensive research on the physiology, biochemistry, and molecular genetics of the metabolism of polyhydroxyalkanoates (PHA) during the last 15 years has revealed a dramatic increase of our knowledge on the biosynthesis of these polyesters in bacteria. This mainly very basic research has revealed several new, hitherto not described enzymes and pathways. In addition, many genes encoding the enzymes of these pathways and in particular the key enzyme of PHA biosynthesis, PHA synthase, were cloned and characterized at a molecular level. This knowledge was utilized to establish PHA biosynthesis in many prokaryotic and eukaryotic organisms, which were unable to synthesize PHAs, and to apply the methodology of metabolic engineering, thus opening new perspectives for the production of various PHAs by fermentation biotechnology or agriculture in economically feasible processes. This contribution summarizes the properties of PHA synthases and gives an overview on the genes for these enzymes and other enzymes of PHA biosynthesis that have been cloned and are available. It also summarizes our current knowledge on the regulation at the enzyme and gene level of PHA biosynthesis in bacteria.
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Affiliation(s)
- A Steinbüchel
- Institut für Mikrobiologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149 Münster, Germany.
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Taroncher-Oldenburg G, Nishina K, Stephanopoulos G. Identification and analysis of the polyhydroxyalkanoate-specific beta-ketothiolase and acetoacetyl coenzyme A reductase genes in the cyanobacterium Synechocystis sp. strain PCC6803. Appl Environ Microbiol 2000; 66:4440-8. [PMID: 11010896 PMCID: PMC92322 DOI: 10.1128/aem.66.10.4440-4448.2000] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synechocystis sp. strain PCC6803 possesses a polyhydroxyalkanoate (PHA)-specific beta-ketothiolase encoded by phaA(Syn) and an acetoacetyl-coenzyme A (CoA) reductase encoded by phaB(Syn). A similarity search of the entire Synechocystis genome sequence identified a cluster of two putative open reading frames (ORFs) for these genes, slr1993 and slr1994. Sequence analysis showed that the ORFs encode proteins having 409 and 240 amino acids, respectively. The two ORFs are colinear and most probably coexpressed, as revealed by sequence analysis of the promoter regions. Heterologous transformation of Escherichia coli with the two genes and the PHA synthase of Synechocystis resulted in accumulation of PHAs that accounted for up to 12.3% of the cell dry weight under high-glucose growth conditions. Targeted disruption of the above gene cluster in Synechocystis eliminated the accumulation of PHAs. ORFs slr1993 and slr1994 thus encode the PHA-specific beta-ketothiolase and acetoacetyl-CoA reductase of Synechocystis and, together with the recently characterized PHA synthase genes in this organism (S. Hein, H. Tran, and A. Steinbüchel, Arch. Microbiol. 170:162-170, 1998), form the first complete PHA biosynthesis pathway known in cyanobacteria. Sequence alignment of all known short-chain-length PHA-specific acetoacetyl-CoA reductases also suggests an extended signature sequence, VTGXXXGIG, for this group of proteins. Phylogenetic analysis further places the origin of phaA(Syn) and phaB(Syn) in the gamma subdivision of the division Proteobacteria.
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Affiliation(s)
- G Taroncher-Oldenburg
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Sheu DS, Wang YT, Lee CY. Rapid detection of polyhydroxyalkanoate-accumulating bacteria isolated from the environment by colony PCR. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 8):2019-2025. [PMID: 10931906 DOI: 10.1099/00221287-146-8-2019] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Colony PCR and semi-nested PCR techniques were employed for screening polyhydroxyalkanoate (PHA) producers isolated from the environment. Three degenerate primers were designed based on multiple sequence alignment results and were used as PCR primers to detect PHA synthase genes. Optimized colony PCR conditions were achieved by adding 3% DMSO combined with 1 M betaine to the reaction mixture. The sensitivity limit of the colony PCR was 1x 10(5) viable cells for Ralstonia eutropha. Nineteen PHA-positive bacteria were used to evaluate this PCR protocol; fifteen of the nineteen could be detected by colony PCR, and the other four could be detected by applying semi-nested PCR detection following colony PCR. In a preliminary screening project, 38 PHA-positive strains were isolated from environmental samples by applying the PCR protocol, and their phenotype was further confirmed by Nile blue A staining assay. By combining the colony PCR and semi-nested PCR techniques, a rapid, reliable and highly accurate detection method has been developed for detecting PHA producers. This protocol is suitable for screening large numbers of environmental isolates. The PHA accumulation ability of well-separated colonies isolated from environmental samples can be directly validated by PCR with no further culturing or chromosomal DNA extraction procedures. In addition to its application to the screening of wild-type isolates, the individual PCR-amplified product is also suitable as a specific probe for PHA operon cloning. The results suggest that the application of this PCR protocol for rapid detection of PHA producers from the environment is plausible.
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Affiliation(s)
- Der-Shyan Sheu
- Graduate Institute of Agricultural Chemistry, National Taiwan University, 1, Sec. 4, Roosevelt Rd, Taipei 106, Taiwan1
| | - Yun-Ting Wang
- Graduate Institute of Agricultural Chemistry, National Taiwan University, 1, Sec. 4, Roosevelt Rd, Taipei 106, Taiwan1
| | - Chia-Yin Lee
- Graduate Institute of Agricultural Chemistry, National Taiwan University, 1, Sec. 4, Roosevelt Rd, Taipei 106, Taiwan1
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11
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Hoppert M, Mayer F. Principles of macromolecular organization and cell function in bacteria and archaea. Cell Biochem Biophys 2000; 31:247-84. [PMID: 10736750 DOI: 10.1007/bf02738242] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Structural organization of the cytoplasm by compartmentation is a well established fact for the eukaryotic cell. In prokaryotes, compartmentation is less obvious. Most prokaryotes do not need intracytoplasmic membranes to maintain their vital functions. This review, especially dealing with prokaryotes, will point out that compartmentation in prokaryotes is present, but not only achieved by membranes. Besides membranes, the nucleoid, multienzyme complexes and metabolons, storage granules, and cytoskeletal elements are involved in compartmentation. In this respect, the organization of the cytoplasm of prokaryotes is similar to that in the eukaryotic cell. Compartmentation influences properties of water in cells.
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Affiliation(s)
- M Hoppert
- Abteilung Strukfurelle Mikrobiologie, Georg-August-Universitat, Göttingen, Germany.
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12
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Donald HM, Scaife W, Amyes SG, Young HK. Sequence analysis of ARI-1, a novel OXA beta-lactamase, responsible for imipenem resistance in Acinetobacter baumannii 6B92. Antimicrob Agents Chemother 2000; 44:196-9. [PMID: 10602749 PMCID: PMC89654 DOI: 10.1128/aac.44.1.196-199.2000] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sequence of the bla(ARI-1) gene from imipenem-resistant Acinetobacter baumannii 6B92 has been determined. The structural gene encodes a 273-amino-acid protein which is most related to the OXA class D beta-lactamases. The conserved S-T-F-K and K-T-G motifs were identified in the ARI-1 protein sequence, also named OXA-23, but significantly, a point mutation (Y-->F) was identified in the Y-G-N conserved motif, also known to function in the active site.
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Affiliation(s)
- H M Donald
- Department of Biological Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
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Rehm BH, Steinbüchel A. Biochemical and genetic analysis of PHA synthases and other proteins required for PHA synthesis. Int J Biol Macromol 1999; 25:3-19. [PMID: 10416645 DOI: 10.1016/s0141-8130(99)00010-0] [Citation(s) in RCA: 244] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyhydroxyalkanoic acids (PHA) represent a complex class of storage polyesters that are synthesized by a wide range of different gram-positive and gram-negative bacteria as well as by some Archaea and that are deposited as insoluble cytoplasmic inclusions. PHA synthases, which are the key enzymes for PHA biosynthesis, have been characterized in much detail. At present 42 PHA synthase structural genes from 38 different bacteria have been cloned, and from 30 genes the nucleotide sequences were obtained. The strategies successfully employed to clone these genes and the current knowledge on the organization of the PHA synthase genes and other genes encoding proteins related to PHA metabolism will be compiled. In addition, the primary structures of the 30 PHA synthases were aligned and analyzed with respect to highly conserved amino acids and biochemical features. The direction, in which research should proceed, in order to increase our knowledge on biosynthesis of PHAs and to utilize this knowledge for the development of technically and economically feasible processes for the production of these polyesters will be outlined.
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Affiliation(s)
- B H Rehm
- Institut für Mikrobiologie, Westfälische Wilhelms-Universität Münster, Germany
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Madison LL, Huisman GW. Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic. Microbiol Mol Biol Rev 1999; 63:21-53. [PMID: 10066830 PMCID: PMC98956 DOI: 10.1128/mmbr.63.1.21-53.1999] [Citation(s) in RCA: 881] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological diversity in PHA formation exists, with at least 100 different PHA constituents and at least five different dedicated PHA biosynthetic pathways. This diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic engineering to develop optimal PHA-producing organisms. Commercial processes for PHA production were initially developed by W. R. Grace in the 1960s and later developed by Imperial Chemical Industries, Ltd., in the United Kingdom in the 1970s and 1980s. Since the early 1990s, Metabolix Inc. and Monsanto have been the driving forces behind the commercial exploitation of PHA polymers in the United States. The gram-negative bacterium Ralstonia eutropha, formerly known as Alcaligenes eutrophus, has generally been used as the production organism of choice, and intracellular accumulation of PHA of over 90% of the cell dry weight have been reported. The advent of molecular biological techniques and a developing environmental awareness initiated a renewed scientific interest in PHAs, and the biosynthetic machinery for PHA metabolism has been studied in great detail over the last two decades. Because the structure and monomeric composition of PHAs determine the applications for each type of polymer, a variety of polymers have been synthesized by cofeeding of various substrates or by metabolic engineering of the production organism. Classical microbiology and modern molecular bacterial physiology have been brought together to decipher the intricacies of PHA metabolism both for production purposes and for the unraveling of the natural role of PHAs. This review provides an overview of the different PHA biosynthetic systems and their genetic background, followed by a detailed summation of how this natural diversity is being used to develop commercially attractive, recombinant processes for the large-scale production of PHAs.
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Affiliation(s)
- L L Madison
- Metabolix, Inc., Cambridge, Massachusetts 02142, USA
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Choi JI, Lee SY, Han K. Cloning of the Alcaligenes latus polyhydroxyalkanoate biosynthesis genes and use of these genes for enhanced production of Poly(3-hydroxybutyrate) in Escherichia coli. Appl Environ Microbiol 1998; 64:4897-903. [PMID: 9835580 PMCID: PMC90940 DOI: 10.1128/aem.64.12.4897-4903.1998] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are microbial polyesters that can be used as completely biodegradable polymers, but the high production cost prevents their use in a wide range of applications. Recombinant Escherichia coli strains harboring the Ralstonia eutropha PHA biosynthesis genes have been reported to have several advantages as PHA producers compared with wild-type PHA-producing bacteria. However, the PHA productivity (amount of PHA produced per unit volume per unit time) obtained with these recombinant E. coli strains has been lower than that obtained with the wild-type bacterium Alcaligenes latus. To endow the potentially superior PHA biosynthetic machinery to E. coli, we cloned the PHA biosynthesis genes from A. latus. The three PHA biosynthesis genes formed an operon with the order PHA synthase, beta-ketothiolase, and reductase genes and were constitutively expressed from the natural promoter in E. coli. Recombinant E. coli strains harboring the A. latus PHA biosynthesis genes accumulated poly(3-hydroxybutyrate) (PHB), a model PHA product, more efficiently than those harboring the R. eutropha genes. With a pH-stat fed-batch culture of recombinant E. coli harboring a stable plasmid containing the A. latus PHA biosynthesis genes, final cell and PHB concentrations of 194.1 and 141.6 g/liter, respectively, were obtained, resulting in a high productivity of 4.63 g of PHB/liter/h. This improvement should allow recombinant E. coli to be used for the production of PHB with a high level of economic competitiveness.
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Affiliation(s)
- J I Choi
- Department of Chemical Engineering, Korea Advanced Institute of Science and Technology, 373-1 Kusong-dong, Yusong-gu, Taejon 305-701, Korea
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Fukui T, Doi Y. Cloning and analysis of the poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) biosynthesis genes of Aeromonas caviae. J Bacteriol 1997; 179:4821-30. [PMID: 9244271 PMCID: PMC179330 DOI: 10.1128/jb.179.15.4821-4830.1997] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A 5.0-kbp EcoRV-EcoRI restriction fragment was cloned and analyzed from genomic DNA of Aeromonas caviae, a bacterium producing a copolyester of (R)-3-hydroxybutyrate (3HB) and (R)-3-hydroxyhexanoate (3HHx) [P(3HB-co-3HHx)] from alkanoic acids or oils. The nucleotide sequence of this region showed a 1,782-bp poly (3-hydroxyalkanoate) (PHA) synthase gene (phaC(Ac) [i.e., the phaC gene from A. caviae]) together with four open reading frames (ORF1, -3, -4, and -5) and one putative promoter region. The cloned fragments could not only complement PHA-negative mutants of Alcaligenes eutrophus and Pseudomonas putida, but also confer the ability to synthesize P(3HB-co-3HHx) from octanoate or hexanoate on the mutants' hosts. Furthermore, coexpression of ORF1 and ORF3 genes with phaC(Ac) in the A. eutrophus mutant resulted in a decrease in the polyester content of the cells. Escherichia coli expressing ORF3 showed (R)-enoyl-coenzyme A (CoA) hydratase activity, suggesting that (R)-3-hydroxyacyl-CoA monomer units are supplied via the (R)-specific hydration of enoyl-CoA in A. caviae. The transconjugant of the A. eutrophus mutant expressing only phaC(Ac) effectively accumulated P(3HB-co-3HHx) up to 96 wt% of the cellular dry weight from octanoate in one-step cultivation.
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Affiliation(s)
- T Fukui
- Polymer Chemistry Laboratory, Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama, Japan
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Ueda S, Yabutani T, Maehara A, Yamane T. Molecular analysis of the poly(3-hydroxyalkanoate) synthase gene from a methylotrophic bacterium, Paracoccus denitrificans. J Bacteriol 1996; 178:774-9. [PMID: 8550512 PMCID: PMC177724 DOI: 10.1128/jb.178.3.774-779.1996] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A 3.6-kb EcoRI-SalI fragment of Paracoccus denitrificans DNA hybridized with a DNA probe carrying the poly(3-hydroxyalkanoate) (PHA) synthase gene (phaC) of Alcaligenes eutrophus. Nucleotide sequence analysis of this region showed the presence of a 1,872-bp open reading frame (ORF), which corresponded to a polypeptide with a molecular weight of 69,537. Upstream of the ORF, a promoter-like sequence was found. Escherichia coli carrying the fusion gene between lacZ and the ORF accumulated a level of poly(3-hydroxybutyrate) that was as much as 20 wt% of the cell dry weight in the presence of beta-ketothiolase and acetoacetylcoenzyme A reductase genes of A. eutrophus. The ORF was designated phaCPd. A plasmid vector carrying the phaCPd'-'lacZ fusion gene downstream of the promoter-like sequence expressed beta-galactosidase activity in P. denitrificans. When a multicopy and broad-host-range vector carrying the ORF along with the promoter-like sequence was introduced into P. denitrificans, the PHA content in the cells increased by twofold compared with cells carrying only a vector sequence.
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Affiliation(s)
- S Ueda
- Department of Bioproductive Sciences, Faculty of Agriculture, Utsunomiya University, Japan
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18
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Steinbuchel A, Aerts K, Babel W, Follner C, Liebergesell M, Madkour MH, Mayer F, Pieper-Furst U, Pries A, Valentin HE. Considerations on the structure and biochemistry of bacterial polyhydroxyalkanoic acid inclusions. Can J Microbiol 1995; 41 Suppl 1:94-105. [PMID: 7606669 DOI: 10.1139/m95-175] [Citation(s) in RCA: 218] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Some mathematical calculations were done that provided information about the structure and biochemistry of polyhydroxyalkanoic acid (PHA) granules and about the amounts of the different constituents that contribute to the PHA granules. The data obtained from these calculations are compared with data from the literature, which show that PHA granules consist not only of the polyester but also of phospholipids and proteins. The latter are referred to as granule-associated proteins, and they are always located at the surface of the PHA granules. A concept is proposed that distinguishes four classes of structurally and functionally different granule-associated proteins: (i) class I comprises the PHA synthases, which catalyze the formation of ester linkages between the constituents; (ii) class II comprises the PHA depolymerases, which are responsible for the intracellular degradation of PHA, (iii) class III comprises a new type of protein, which is referred to as phasins and which has most probably a function analogous to that of oleosins in oilseed plants, and (iv) class IV comprises all other proteins, which have been found to be associated with the granules but do not belong to classes I-III. Particular emphasis is placed on the phasins, which constitute a significant fraction of the total cellular protein. Phasins are assumed to form a close protein layer at the surface of the granules, providing the interface between the hydrophilic cytoplasm and the much more hydrophobic core of the PHA inclusion.
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Affiliation(s)
- A Steinbuchel
- Institut fur Mikrobiologie der Westfalischen Wilhelms-Universitat Munster, Germany
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Schembri MA, Woods AA, Bayly RC, Davies JK. Identification of a 13-kDa protein associated with the polyhydroxyalkanoic acid granules from Acinetobacter spp. FEMS Microbiol Lett 1995; 133:277-83. [PMID: 8522143 DOI: 10.1111/j.1574-6968.1995.tb07897.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Proteins associated with poly-beta-hydroxybutyrate (PHB) granules were purified from four Acinetobacter strains isolated from modified activated sludge treatment plants. Four predominant proteins of 64 kDa, 41 kDa, 38 kDa and 13 kDa were identified. N-terminal amino acid sequencing of the 64-kDa and 13-kDa proteins from Acinetobacter RA3849 identified these proteins as the products of the phaCAc and phaPAc (formerly designated ORF1) genes, respectively. The expression of the 13-kDa protein (referred to as GA13) is shown to be required for the accumulation of large amounts of PHB in a recombinant Escherichia coli strain.
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Affiliation(s)
- M A Schembri
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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Schembri MA, Bayly RC, Davies JK. Phosphate concentration regulates transcription of the Acinetobacter polyhydroxyalkanoic acid biosynthetic genes. J Bacteriol 1995; 177:4501-7. [PMID: 7635832 PMCID: PMC177202 DOI: 10.1128/jb.177.15.4501-4507.1995] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The polyhydroxyalkanoic acid (PHA) biosynthetic gene locus was cloned and characterized from an Acinetobacter sp. isolated from activated sludge. Nucleotide sequence analysis identified three clustered genes, phaAAc (encoding a beta-ketothiolase), phaBAc (encoding an acetoacetyl coenzyme A reductase), and phaCAc (encoding a PHA synthase). In addition, an open reading frame (ORF1) with potential to encode a 13-kDa protein was identified within this locus. The sequence of the putative translational product of ORF1 does not show significant similarity to any sequences in the database. A plasmid containing the Acinetobacter pha locus conferred the ability to accumulate poly-beta-hydroxybutyrate on its Escherichia coli host. These genes appear to lie in an operon transcribed by two promoters upstream of phaBAc, an apparent constitutive promoter, and a second promoter induced by phosphate starvation and under pho regulon control. These as well as a number of additional potential transcription start points were identified by a combination of primer extension and promoter-chloramphenicol acetyltransferase gene fusion studies carried out in Acinetobacter or E. coli transformants.
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Affiliation(s)
- M A Schembri
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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