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Hernández MA, Ledesma AE, Moncalián G, Alvarez HM. MLDSR, the transcriptional regulator of the major lipid droplets protein MLDS, is controlled by long-chain fatty acids and contributes to the lipid-accumulating phenotype in oleaginous Rhodococcus strains. FEBS J 2024; 291:1457-1482. [PMID: 38135896 DOI: 10.1111/febs.17043] [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: 08/31/2023] [Revised: 11/08/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023]
Abstract
Microorganism lipid droplet small regulator (MLDSR) is a transcriptional regulator of the major lipid droplet (LD)-associated protein MLDS in Rhodococcus jostii RHA1 and Rhodococcus opacus PD630. In this study, we investigated the role of MLDSR on lipid metabolism and triacylglycerol (TAG) accumulation in R. jostii RHA1 at physiological and molecular levels. MLDSR gene deletion promoted a significant decrease of TAG accumulation, whereas inhibition of de novo fatty acid biosynthesis by the addition of cerulenin significantly repressed the expression of the mldsr-mlds cluster under nitrogen-limiting conditions. In vitro and in vivo approaches revealed that MLDSR-DNA binding is inhibited by fatty acids and acyl-CoA residues through changes in the oligomeric or conformational state of the protein. RNAseq analysis indicated that MLDSR not only controls the expression of its own gene cluster but also of several genes involved in central, lipid, and redox metabolism, among others. We also identified putative MLDSR-binding sites on the upstream regions of genes coding for lipid catabolic enzymes and validated them by EMSA assays. Overexpression of mldsr gene under nitrogen-rich conditions promoted an increase of TAG accumulation, and further cell lysis with TAG release to the culture medium. Our results suggested that MLDSR is a fatty acid-responsive regulator that plays a dual role in cells by repression or activation of several metabolic genes in R. jostii RHA1. MLDSR seems to play an important role in the fine-tuning regulation of TAG accumulation, LD formation, and cellular lipid homeostasis, contributing to the oleaginous phenotype of R. jostii RHA1 and R. opacus PD630.
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Affiliation(s)
- Martín A Hernández
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Comodoro Rivadavia, Argentina
| | - Ana E Ledesma
- CIBAAL (Centro de Investigación en Biofísica Aplicada y Alimentos), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, Argentina
| | - Gabriel Moncalián
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
| | - Héctor M Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Comodoro Rivadavia, Argentina
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2
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Herrero OM, Alvarez HM. Fruit residues as substrates for single-cell oil production by Rhodococcus species: physiology and genomics of carbohydrate catabolism. World J Microbiol Biotechnol 2024; 40:61. [PMID: 38177966 DOI: 10.1007/s11274-023-03866-z] [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: 08/09/2023] [Accepted: 12/03/2023] [Indexed: 01/06/2024]
Abstract
Strains belonging to R. opacus, R. jostii, R. fascians, R. erythropolis and R. equi exhibited differential ability to grow and produce lipids from fruit residues (grape marc and apple pomace), as well as single carbohydrates, such as glucose, gluconate, fructose and sucrose. The oleaginous species, R. opacus (strains PD630 and MR22) and R. jostii RHA1, produced higher yields of biomass (5.1-5.6 g L-1) and lipids (38-44% of CDW) from apple juice wastes, in comparison to R. erythropolis DSM43060, R. fascians F7 and R. equi ATCC6939 (4.1-4.3 g L-1 and less than 10% CDW of lipids). The production of cellular biomass and lipids were also higher in R. opacus and R. jostii (6.8-7.2 g L-1 and 33.9-36.5% of CDW of lipids) compared to R. erythropolis, R. fascians, and R. equi (3.0-3.6 g L-1 and less than 10% CDW of lipids), during cultivation of cells on wine grape waste. A genome-wide bioinformatic analysis of rhodococci indicated that oleaginous species possess a complete set of genes/proteins necessary for the efficient utilization of carbohydrates, whereas genomes from non-oleaginous rhodococcal strains lack relevant genes coding for transporters and/or enzymes for the uptake, catabolism and assimilation of carbohydrates, such as gntP, glcP, edd, eda, among others. Results of this study highlight the potential use of the oleaginous rhodococcal species to convert sugar-rich agro-industrial wastes, such as apple pomace and grape marc, into single-cell oils.
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Affiliation(s)
- O Marisa Herrero
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria, 9000, Comodoro Rivadavia, Chubut, Argentina
| | - Héctor M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria, 9000, Comodoro Rivadavia, Chubut, Argentina.
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3
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Zhao ZM, Liu ZH, Zhang T, Meng R, Gong Z, Li Y, Hu J, Ragauskas AJ, Li BZ, Yuan YJ. Unleashing the capacity of Rhodococcus for converting lignin into lipids. Biotechnol Adv 2024; 70:108274. [PMID: 37913947 DOI: 10.1016/j.biotechadv.2023.108274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/11/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
Bioconversion of bioresources/wastes (e.g., lignin, chemical pulping byproducts) represents a promising approach for developing a bioeconomy to help address growing energy and materials demands. Rhodococcus, a promising microbial strain, utilizes numerous carbon sources to produce lipids, which are precursors for synthesizing biodiesel and aviation fuels. However, compared to chemical conversion, bioconversion involves living cells, which is a more complex system that needs further understanding and upgrading. Various wastes amenable to bioconversion are reviewed herein to highlight the potential of Rhodococci for producing lipid-derived bioproducts. In light of the abundant availability of these substrates, Rhodococcus' metabolic pathways converting them to lipids are analyzed from a "beginning-to-end" view. Based on an in-depth understanding of microbial metabolic routes, genetic modifications of Rhodococcus by employing emerging tools (e.g., multiplex genome editing, biosensors, and genome-scale metabolic models) are presented for promoting the bioconversion. Co-solvent enhanced lignocellulose fractionation (CELF) strategy facilitates the generation of a lignin-derived aromatic stream suitable for the Rhodococcus' utilization. Novel alkali sterilization (AS) and elimination of thermal sterilization (ETS) approaches can significantly enhance the bioaccessibility of lignin and its derived aromatics in aqueous fermentation media, which promotes lipid titer significantly. In order to achieve value-added utilization of lignin, biodiesel and aviation fuel synthesis from lignin and lipids are further discussed. The possible directions for unleashing the capacity of Rhodococcus through synergistically modifying microbial strains, substrates, and fermentation processes are proposed toward a sustainable biological lignin valorization.
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Affiliation(s)
- Zhi-Min Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States; Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tongtong Zhang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Rongqian Meng
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Zhiqun Gong
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yibing Li
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Jing Hu
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Arthur J Ragauskas
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States; Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, United States; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, United States.
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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4
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Tyumina E, Bazhutin G, Kostrikina N, Sorokin V, Mulyukin A, Ivshina I. Phenotypic and metabolic adaptations of Rhodococcus cerastii strain IEGM 1243 to separate and combined effects of diclofenac and ibuprofen. Front Microbiol 2023; 14:1275553. [PMID: 38125575 PMCID: PMC10730942 DOI: 10.3389/fmicb.2023.1275553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The increasing use of non-steroidal anti-inflammatory drugs (NSAIDs) has raised concerns regarding their environmental impact. To address this, understanding the effects of NSAIDs on bacteria is crucial for bioremediation efforts in pharmaceutical-contaminated environments. The primary challenge in breaking down persistent compounds lies not in the biochemical pathways but in capacity of bacteria to surmount stressors. Methods In this study, we examined the biodegradative activity, morphological and physiological changes, and ultrastructural adaptations of Rhodococcus cerastii strain IEGM 1243 when exposed to ibuprofen, diclofenac, and their mixture. Results and Discussion Our findings revealed that R. cerastii IEGM 1243 exhibited moderate biodegradative activity towards the tested NSAIDs. Cellular respiration assay showed higher metabolic activity in the presence of NSAIDs, indicating their influence on bacterial metabolism. Furthermore, catalase activity in R. cerastii IEGM 1243 exposed to NSAIDs showed an initial decrease followed by fluctuations, with the most significant changes observed in the presence of DCF and the NSAID mixture, likely influenced by bacterial growth phases, active NSAID degradation, and the formation of multicellular aggregates, suggesting potential intercellular synergy and task distribution within the bacterial community. Morphometric analysis demonstrated alterations in size, shape, and surface roughness of cells exposed to NSAIDs, with a decrease in surface area and volume, and an increase in surface area-to-volume ratio (SA/V). Moreover, for the first time, transmission electron microscopy confirmed the presence of lipid inclusions, polyphosphates, and intracellular membrane-like structures in the ibuprofen-treated cells. Conclusion These results provide valuable insights into the adaptive responses of R. cerastii IEGM 1243 to NSAIDs, shedding light on the possible interaction between bacteria and pharmaceutical compounds in the environment.
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Affiliation(s)
- Elena Tyumina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Grigory Bazhutin
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Nadezhda Kostrikina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Irina Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
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5
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Pandey SP, Upadhyay R, Prakash R, Kumar S. Performance and emission analysis of blends of bio-oil obtained by catalytic pyrolysis of Argemone mexicana seeds with diesel in a CI engine. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:125034-125047. [PMID: 36502482 PMCID: PMC9741757 DOI: 10.1007/s11356-022-24648-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Because of their adaptability and user-friendliness, internal combustion engines are widely used for a variety of purposes, including the generation of consistent power as well as transportation. As a result, the question of whether or not these engines can make use of bio-oils is an important one today. Bio-oils derived from biomass pyrolysis differ significantly from those derived from petroleum-based fuels and biodiesel. They could, however, be valuable alternatives to fossil fuels in order to attain a carbon-neutral future. Bio-oil obtained from catalytic pyrolysis of Argemone Mexicana seed using titanium oxide (TiO2) nanoparticles was employed in IC engine to check its suitability as an alternative fuel. Engine performance analysis was conducted at B5, B10, B15, B20, B25, and B30 blend for different parameters such as brake thermal efficiency, exhaust gas temperature, and brake-specific fuel consumption with change in engine load. Emission analysis was also carried out for carbon monoxide, hydrocarbon, nitrogen oxides, and carbon dioxide emissions. It was found that B30 blend resembled best performance and the bio-oil produced from catalytic pyrolysis of Argemone mexicana seed can be utilised as a substitute of fossil fuels in IC engine.
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Affiliation(s)
- Satya Prakash Pandey
- Department of Energy Engineering, Central University of Jharkhand, Ranchi, India
| | - Rakesh Upadhyay
- Department of Energy Engineering, Central University of Jharkhand, Ranchi, India
| | - Ramakrishnan Prakash
- Department of Thermal and Energy Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | - Sachin Kumar
- Department of Energy Engineering, Central University of Jharkhand, Ranchi, India
- Centre of Excellence – Green and Efficient Energy Technology (CoE-GEET), CUJ, Ranchi, India
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6
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Dargham T, Mallick I, Kremer L, Santucci P, Canaan S. Intrabacterial lipid inclusion-associated proteins: a core machinery conserved from saprophyte Actinobacteria to the human pathogen Mycobacterium tuberculosis. FEBS Open Bio 2023; 13:2306-2323. [PMID: 37872001 PMCID: PMC10699116 DOI: 10.1002/2211-5463.13721] [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: 09/05/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the aetiologic agent of tuberculosis (TB), stores triacylglycerol (TAG) in the form of intrabacterial lipid inclusions (ILI) to survive and chronically persist within its host. These highly energetic molecules represent a major source of carbon to support bacterial persistence and reactivation, thus playing a leading role in TB pathogenesis. However, despite its physiological and clinical relevance, ILI metabolism in Mtb remains poorly understood. Recent discoveries have suggested that several ILI-associated proteins might be widely conserved across TAG-producing prokaryotes, but still very little is known regarding the nature and the biological functions of these proteins. Herein, we performed an in silico analysis of three independent ILI-associated proteomes previously reported to computationally define a potential core ILI-associated proteome, referred to as ILIome. Our investigation revealed the presence of 70 orthologous proteins that were strictly conserved, thereby defining a minimal ILIome core. We further narrowed our analysis to proteins involved in lipid metabolism and discuss here their putative biological functions, along with their molecular interactions and dynamics at the surface of these bacterial organelles. We also highlight the experimental limitations of the original proteomic investigations and of the present bioinformatic analysis, while describing new technological approaches and presenting biological perspectives in the field. The in silico investigation presented here aims at providing useful datasets that could constitute a scientific resource of broad interest for the mycobacterial community, with the ultimate goal of enlightening ILI metabolism in prokaryotes with a special emphasis on Mtb pathogenesis.
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Affiliation(s)
- Tonia Dargham
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
- IHU Méditerranée InfectionAix‐Marseille Univ.France
| | - Ivy Mallick
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM)Université de MontpellierFrance
- INSERM, Institut de Recherche en Infectiologie de MontpellierFrance
| | - Pierre Santucci
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
| | - Stéphane Canaan
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
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7
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Kumar M, Paul T, Kumar PVA, Pugazhenthi G, Pakshirajan K. Both biogenic and chemically synthesized metal sulfide nanoparticles induce oxidative stress and enhance lipid accumulation in Rhodococcus opacus. Biometals 2023; 36:1047-1058. [PMID: 37165109 DOI: 10.1007/s10534-023-00504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Metallic nanoparticles (NPs) find applications in many different industrial sectors. However, the fate of these NPs in the environment and their potential impact on organisms living in different ecosystems are not fully known. In this work, the individual effect of biogenic and chemically synthesized lead sulfide nanoparticles (PbSNPs) and cadmium sulfide nanoparticles (CdSNPs) on the activity of the oleaginous bacterium Rhodococcus opacus PD630 which belongs to an ecologically important genus Rhodococcus was investigated. A dose-dependent increase in PbSNPs and CdSNPs uptake by the bacterium was observed upto a maximum of 16.4 and 15.6 mg/g cell, corresponding to 98% and 95% uptake. In the case of chemically synthesized NPs, the specific PbSNPs and CdSNPs uptake were slightly less [15.5 and 14.8 mg/g cell], corresponding to 93.2% and 88.4% uptake. Both biogenic and chemically synthesized PbSNPs and CdSNPs did not affect the bacterial growth. On the other hand, the triacylglycerol (biodiesel) content in the bacterium increased from 30% to a maximum of 75% and 73% CDW due to oxidative stress induced by biogenic PbSNPs and CdSNPs. The results of induced oxidative stress by biogenic metal nanoparticle were similar to that induced by the chemically synthesized NPs.
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Affiliation(s)
- Manoj Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Tanushree Paul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - P V Ajay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - G Pugazhenthi
- Department of Chemical Engineering, Indian Institute Technology Guwahati, Guwahati, Assam, 781039, India
| | - Kannan Pakshirajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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8
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Roell G, Schenk C, Anthony WE, Carr RR, Ponukumati A, Kim J, Akhmatskaya E, Foston M, Dantas G, Moon TS, Tang YJ, García Martín H. A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism. ACS Synth Biol 2023; 12:1632-1644. [PMID: 37186551 PMCID: PMC10278598 DOI: 10.1021/acssynbio.2c00618] [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: 11/16/2022] [Indexed: 05/17/2023]
Abstract
Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism based on its genomic sequence and associated data. The model includes 1773 genes, 3025 reactions, and 1956 metabolites, was developed in a reproducible manner using CarveMe, and was evaluated through Metabolic Model tests (MEMOTE). We combine the model with two Constraint-Based Reconstruction and Analysis (COBRA) methods that use transcriptomics data to predict growth rates and fluxes: E-Flux2 and SPOT (Simplified Pearson Correlation with Transcriptomic data). Growth rates are best predicted by E-Flux2. Flux profiles are more accurately predicted by E-Flux2 than flux balance analysis (FBA) and parsimonious FBA (pFBA), when compared to 44 central carbon fluxes measured by 13C-Metabolic Flux Analysis (13C-MFA). Under glucose-fed conditions, E-Flux2 presents an R2 value of 0.54, while predictions based on pFBA had an inferior R2 of 0.28. We attribute this improved performance to the extra activity information provided by the transcriptomics data. For phenol-fed metabolism, in which the substrate first enters the TCA cycle, E-Flux2's flux predictions display a high R2 of 0.96 while pFBA showed an R2 of 0.93. We also show that glucose metabolism and phenol metabolism function with similar relative ATP maintenance costs. These findings demonstrate that iGR1773 can help the metabolic engineering community predict aromatic substrate utilization patterns and perform computational strain design.
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Affiliation(s)
- Garrett
W. Roell
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Christina Schenk
- BCAM
- Basque Center for Applied Mathematics, Bilbao 48009, Spain
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Lab, Berkeley, California 94720, United States
| | - Winston E. Anthony
- The Edison
Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Pathology and Immunology, Washington
University in St. Louis School of Medicine, St. Louis, Missouri 63108, United States
| | - Rhiannon R. Carr
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Aditya Ponukumati
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joonhoon Kim
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
- DOE
Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Elena Akhmatskaya
- BCAM
- Basque Center for Applied Mathematics, Bilbao 48009, Spain
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Lab, Berkeley, California 94720, United States
- IKERBASQUE,
Basque Foundation for Science, Bilbao 48009, Spain
| | - Marcus Foston
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Gautam Dantas
- The Edison
Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Pathology and Immunology, Washington
University in St. Louis School of Medicine, St. Louis, Missouri 63108, United States
- Department
of Biomedical Engineering, Washington University
in St. Louis, St Louis, Missouri 63130, United States
- Department
of Molecular Microbiology, Washington University
in St. Louis School of Medicine, St. Louis, Missouri 63108, United States
- Department
of Pediatrics, Washington University School
of Medicine in St Louis, St Louis, Missouri 63110, United States
| | - Tae Seok Moon
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Yinjie J. Tang
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Hector García Martín
- BCAM
- Basque Center for Applied Mathematics, Bilbao 48009, Spain
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Lab, Berkeley, California 94720, United States
- DOE
Joint BioEnergy Institute, Emeryville, California 94608, United States
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9
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Mason-Jones K, Breidenbach A, Dyckmans J, Banfield CC, Dippold MA. Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth. Nat Commun 2023; 14:2240. [PMID: 37076457 PMCID: PMC10115882 DOI: 10.1038/s41467-023-37713-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 03/28/2023] [Indexed: 04/21/2023] Open
Abstract
The concept of biomass growth is central to microbial carbon (C) cycling and ecosystem nutrient turnover. Microbial biomass is usually assumed to grow by cellular replication, despite microorganisms' capacity to increase biomass by synthesizing storage compounds. Resource investment in storage allows microbes to decouple their metabolic activity from immediate resource supply, supporting more diverse microbial responses to environmental changes. Here we show that microbial C storage in the form of triacylglycerides (TAGs) and polyhydroxybutyrate (PHB) contributes significantly to the formation of new biomass, i.e. growth, under contrasting conditions of C availability and complementary nutrient supply in soil. Together these compounds can comprise a C pool 0.19 ± 0.03 to 0.46 ± 0.08 times as large as extractable soil microbial biomass and reveal up to 279 ± 72% more biomass growth than observed by a DNA-based method alone. Even under C limitation, storage represented an additional 16-96% incorporation of added C into microbial biomass. These findings encourage greater recognition of storage synthesis as a key pathway of biomass growth and an underlying mechanism for resistance and resilience of microbial communities facing environmental change.
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Affiliation(s)
- Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany.
| | - Andreas Breidenbach
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany
- Geo-Biosphere Interactions, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Jens Dyckmans
- Centre for Stable Isotope Research and Analysis, Georg-August University of Göttingen, Göttingen, Germany
| | - Callum C Banfield
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany
- Geo-Biosphere Interactions, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Michaela A Dippold
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany.
- Geo-Biosphere Interactions, Department of Geosciences, University of Tübingen, Tübingen, Germany.
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10
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Coyle H, Wawrousek K. Rhodococcus opacus PD630 Bioconversion of Molasses Desugarized Solubles for Fatty Acid Production. Ind Biotechnol (New Rochelle N Y) 2022. [DOI: 10.1089/ind.2022.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Hanley Coyle
- Chemical Engineering, University of Wyoming, Laramie, WY 82071
| | - Karen Wawrousek
- Chemical Engineering, University of Wyoming, Laramie, WY 82071
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11
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Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630. Commun Biol 2022; 5:1109. [PMID: 36261484 DOI: 10.1038/s42003-022-04069-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Rhodococcus opacus PD630 has considerable potential as a platform for valorizing lignin due to its innate "biological funneling" pathways. However, the transcriptional regulation of the aromatic catabolic pathways and the mechanisms controlling aromatic catabolic operons in response to different aromatic mixtures are still underexplored. Here, we identified and studied the transcription factors for aromatic degradation using GFP-based sensors and comprehensive deletion analyses. Our results demonstrate that the funneling pathways for phenol, guaiacol, 4-hydroxybenzoate, and vanillate are controlled by transcriptional activators. The two different branches of the β-ketoadipate pathway, however, are controlled by transcriptional repressors. Additionally, promoter activity assays revealed that the substrate hierarchy in R. opacus may be ascribed to the transcriptional cross-regulation of the individual aromatic funneling pathways. These results provide clues to clarify the molecule-level mechanisms underlying the complex regulation of aromatic catabolism, which facilitates the development of R. opacus as a promising chassis for valorizing lignin.
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12
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Sah D, Rai JPN, Ghosh A, Chakraborty M. A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils. 3 Biotech 2022; 12:218. [PMID: 35965658 PMCID: PMC9365905 DOI: 10.1007/s13205-022-03277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/01/2022] Open
Abstract
The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.
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Affiliation(s)
- Diksha Sah
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - J. P. N. Rai
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Ankita Ghosh
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Moumita Chakraborty
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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13
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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14
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Microbial storage and its implications for soil ecology. THE ISME JOURNAL 2022; 16:617-629. [PMID: 34593996 PMCID: PMC8857262 DOI: 10.1038/s41396-021-01110-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]
Abstract
Organisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.
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15
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Firrincieli A, Grigoriev B, Dostálová H, Cappelletti M. The Complete Genome Sequence and Structure of the Oleaginous Rhodococcus opacus Strain PD630 Through Nanopore Technology. Front Bioeng Biotechnol 2022; 9:810571. [PMID: 35252163 PMCID: PMC8892189 DOI: 10.3389/fbioe.2021.810571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/27/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Beatrice Grigoriev
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- *Correspondence: Martina Cappelletti,
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16
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Bhutada G, Menard G, Bhunia RK, Hapeta PP, Ledesma-Amaro R, Eastmond PJ. Production of human milk fat substitute by engineered strains of Yarrowia lipolytica. Metab Eng Commun 2022; 14:e00192. [PMID: 35036316 PMCID: PMC8752951 DOI: 10.1016/j.mec.2022.e00192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/09/2021] [Accepted: 01/03/2022] [Indexed: 01/05/2023] Open
Abstract
Human milk fat has a distinctive stereoisomeric structure where palmitic acid is esterified to the middle (sn-2) position on the glycerol backbone of the triacylglycerol and unsaturated fatty acids to the outer (sn-1/3) positions. This configuration allows for more efficient nutrient absorption in the infant gut. However, the fat used in most infant formulas originates from plants, which exclude palmitic acid from the sn-2 position. Oleaginous yeasts provide an alternative source of lipids for human nutrition. However, these yeasts also exclude palmitic acid from the sn-2 position of their triacylglycerol. Here we show that Yarrowia lipolytica can be engineered to produce triacylglycerol with more than 60% of the palmitic acid in the sn-2 position, by expression of lysophosphatidic acid acyltransferases with palmitoyl-Coenzyme A specificity. The engineered Y. lipolytica strains can be cultured on glycerol, glucose, palm oil or a mixture of substrates, under nitrogen limited condition, to produce triacylglycerol with a fatty acid composition that resembles human milk fat, in terms of the major molecular species (palmitic, oleic and linoleic acids). Culture on palm oil or a mixture of glucose and palm oil produced the highest lipid titre and a triacylglycerol composition that is most similar with human milk fat. Our data show that an oleaginous yeast can be engineered to produce a human milk fat substitute (β-palmitate), that could be used as an ingredient in infant formulas. Yarrowia lipolytica was engineered to make a human milk fat substitute. Palmitate was directed to the sn-2 position of triacylglycerol by expressing Chlamydomonas reinhardtii LPAAT2. Culture with palm oil produced a fatty acyl composition more similar with human milk fat.
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Affiliation(s)
- Govindprasad Bhutada
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Guillaume Menard
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Rupam Kumar Bhunia
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.,Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140306, India
| | - Piotr P Hapeta
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Peter J Eastmond
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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17
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Parada C, Neri-Badillo IC, Vallecillo AJ, Segura E, Silva-Miranda M, Guzmán-Gutiérrez SL, Ortega PA, Coronado-Aceves EW, Cancino-Villeda L, Torres-Larios A, Aceves Sánchez MDJ, Flores Valdez MA, Espitia C. New Insights into the Methylation of Mycobacterium tuberculosis Heparin Binding Hemagglutinin Adhesin Expressed in Rhodococcus erythropolis. Pathogens 2021; 10:pathogens10091139. [PMID: 34578171 PMCID: PMC8467707 DOI: 10.3390/pathogens10091139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
In recent years, knowledge of the role that protein methylation is playing on the physiopathogenesis of bacteria has grown. In Mycobacterium tuberculosis, methylation of the heparin binding hemagglutinin adhesin modulates the immune response, making this protein a subunit vaccine candidate. Through its C-terminal lysine-rich domain, this surface antigen interacts with heparan sulfate proteoglycans present in non-phagocytic cells, leading to extrapulmonary dissemination of the pathogen. In this study, the adhesin was expressed as a recombinant methylated protein in Rhodococcus erythropolis L88 and it was found associated to lipid droplets when bacteria were grown under nitrogen limitation. In order to delve into the role methylation could have in host–pathogen interactions, a comparative analysis was carried out between methylated and unmethylated protein produced in Escherichia coli. We found that methylation had an impact on lowering protein isoelectric point, but no differences between the proteins were found in their capacity to interact with heparin and A549 epithelial cells. An important finding was that HbhA is a Fatty Acid Binding Protein and differences in the conformational stability of the protein in complex with the fatty acid were observed between methylated and unmethylated protein. Together, these results suggest that the described role for this mycobacteria protein in lipid bodies formation could be related to its capacity to transport fatty acids. Obtained results also provide new clues about the role HbhA methylation could have in tuberculosis and point out the importance of having heterologous expression systems to obtain modified proteins.
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Affiliation(s)
- Cristina Parada
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Isabel Cecilia Neri-Badillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Antonio J. Vallecillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Facultad de Ciencias Agropecuarias, Universidad de Cuenca, Cuenca 010220, Ecuador
| | - Erika Segura
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Mayra Silva-Miranda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Silvia Laura Guzmán-Gutiérrez
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Paola A. Ortega
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Enrique Wenceslao Coronado-Aceves
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Laura Cancino-Villeda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Alfredo Torres-Larios
- Department of Biochemistry and Structural Biology, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Michel de Jesús Aceves Sánchez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Mario Alberto Flores Valdez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Correspondence:
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18
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Characterization of Two Hydrogen Peroxide Resistant Peroxidases from Rhodococcus opacus 1CP. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11177941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dye-decolorizing peroxidases (DyP) are a family of heme-dependent enzymes present on a broad spectrum of microorganisms. While the natural function of these enzymes is not fully understood, their capacity to degrade highly contaminant pigments such as azo dyes or anthraquinones make them excellent candidates for applications in bioremediation and organic synthesis. In this work, two novel DyP peroxidases from the organism Rhodococcus opacus 1CP (DypA and DypB) were cloned and expressed in Escherichia coli. The enzymes were purified and biochemically characterized. The activities of the two DyPs via 2,2′-azino-bis [3-ethylbenzthiazoline-6-sulphonic acid] (ABTS) assay and against Reactive Blue 5 were assessed and optimized. Results showed varying trends for DypA and DypB. Remarkably, these enzymes presented a particularly high tolerance towards H2O2, retaining its activities at about 10 mM H2O2 for DypA and about 4.9 mM H2O2 for DypB.
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19
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Alvarez HM, Hernández MA, Lanfranconi MP, Silva RA, Villalba MS. Rhodococcus as Biofactories for Microbial Oil Production. Molecules 2021; 26:molecules26164871. [PMID: 34443455 PMCID: PMC8401914 DOI: 10.3390/molecules26164871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/20/2023] Open
Abstract
Bacteria belonging to the Rhodococcus genus are frequent components of microbial communities in diverse natural environments. Some rhodococcal species exhibit the outstanding ability to produce significant amounts of triacylglycerols (TAG) (>20% of cellular dry weight) in the presence of an excess of the carbon source and limitation of the nitrogen source. For this reason, they can be considered as oleaginous microorganisms. As occurs as well in eukaryotic single-cell oil (SCO) producers, these bacteria possess specific physiological properties and molecular mechanisms that differentiate them from other microorganisms unable to synthesize TAG. In this review, we summarized several of the well-characterized molecular mechanisms that enable oleaginous rhodococci to produce significant amounts of SCO. Furthermore, we highlighted the ability of these microorganisms to degrade a wide range of carbon sources coupled to lipogenesis. The qualitative and quantitative oil production by rhodococci from diverse industrial wastes has also been included. Finally, we summarized the genetic and metabolic approaches applied to oleaginous rhodococci to improve SCO production. This review provides a comprehensive and integrating vision on the potential of oleaginous rhodococci to be considered as microbial biofactories for microbial oil production.
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20
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Review of advances in the development of laccases for the valorization of lignin to enable the production of lignocellulosic biofuels and bioproducts. Biotechnol Adv 2021; 54:107809. [PMID: 34333091 DOI: 10.1016/j.biotechadv.2021.107809] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/30/2022]
Abstract
Development and deployment of commercial biorefineries based on conversion of lignocellulosic biomass into biofuels and bioproducts faces many challenges that must be addressed before they are commercially viable. One of the biggest challenges faced is the efficient and scalable valorization of lignin, one of the three major components of the plant cell wall. Lignin is the most abundant aromatic biopolymer on earth, and its presence hinders the extraction of cellulose and hemicellulose that is essential to biochemical conversion of lignocellulose to fuels and chemicals. There has been a significant amount of work over the past 20 years that has sought to develop innovative processes designed to extract and recycle lignin into valuable compounds and help reduce the overall costs of the biorefinery process. Due to the complex matrix of lignin, which is essential for plant survival, the development of a reliable and efficient lignin conversion technology has been difficult to achieve. One approach that has received significant interest relies on the use of enzymes, notably laccases, a class of multi‑copper green oxidative enzymes that catalyze bond breaking in lignin to produce smaller oligomers. In this review, we first assess the different innovations of lignin valorization using laccases within the context of a biorefinery process, and then assess the latest economical advances that these innovations offered. Finally, we review laccase characterization and optimization, as well as the prospects and bottlenecks of this class of enzymes within the industrial and biorefining sectors.
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21
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Mallick I, Santucci P, Poncin I, Point V, Kremer L, Cavalier JF, Canaan S. Intrabacterial lipid inclusions in mycobacteria: unexpected key players in survival and pathogenesis? FEMS Microbiol Rev 2021; 45:6283747. [PMID: 34036305 DOI: 10.1093/femsre/fuab029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterial species, including Mycobacterium tuberculosis, rely on lipids to survive and chronically persist within their hosts. Upon infection, opportunistic and strict pathogenic mycobacteria exploit metabolic pathways to import and process host-derived free fatty acids, subsequently stored as triacylglycerols under the form of intrabacterial lipid inclusions (ILI). Under nutrient-limiting conditions, ILI constitute a critical source of energy that fuels the carbon requirements and maintain redox homeostasis, promoting bacterial survival for extensive periods of time. In addition to their basic metabolic functions, these organelles display multiple other biological properties, emphasizing their central role in the mycobacterial lifecycle. However, despite of their importance, the dynamics of ILI metabolism and their contribution to mycobacterial adaptation/survival in the context of infection has not been thoroughly documented. Herein, we provide an overview of the historical ILI discoveries, their characterization, and current knowledge regarding the micro-environmental stimuli conveying ILI formation, storage and degradation. We also review new biological systems to monitor the dynamics of ILI metabolism in extra- and intracellular mycobacteria and describe major molecular actors in triacylglycerol biosynthesis, maintenance and breakdown. Finally, emerging concepts regarding to the role of ILI in mycobacterial survival, persistence, reactivation, antibiotic susceptibility and inter-individual transmission are also discuss.
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Affiliation(s)
- Ivy Mallick
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille Univ., Marseille, France
| | - Pierre Santucci
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Isabelle Poncin
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Vanessa Point
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, Montpellier, France.,IRIM, INSERM, Montpellier, France
| | | | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
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22
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DeLorenzo DM, Diao J, Carr R, Hu Y, Moon TS. An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus. ACS Synth Biol 2021; 10:786-798. [PMID: 33787248 DOI: 10.1021/acssynbio.0c00591] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rhodococcus opacus is a nonmodel bacterium that is well suited for valorizing lignin. Despite recent advances in our systems-level understanding of its versatile metabolism, studies of its gene functions at a single gene level are still lagging. Elucidating gene functions in nonmodel organisms is challenging due to limited genetic engineering tools that are convenient to use. To address this issue, we developed a simple gene repression system based on CRISPR interference (CRISPRi). This gene repression system uses a T7 RNA polymerase system to express a small guide RNA, demonstrating improved repression compared to the previously demonstrated CRISPRi system (i.e., the maximum repression efficiency improved from 58% to 85%). Additionally, our cloning strategy allows for building multiple CRISPRi plasmids in parallel without any PCR step, facilitating the engineering of this GC-rich organism. Using the improved CRISPRi system, we confirmed the annotated roles of four metabolic pathway genes, which had been identified by our previous transcriptomic analysis to be related to the consumption of benzoate, vanillate, catechol, and acetate. Furthermore, we showed our tool's utility by demonstrating the inducible accumulation of muconate that is a precursor of adipic acid, an important monomer for nylon production. While the maximum muconate yield obtained using our tool was 30% of the yield obtained using gene knockout, our tool showed its inducibility and partial repressibility. Our CRISPRi tool will be useful to facilitate functional studies of this nonmodel organism and engineer this promising microbial chassis for lignin valorization.
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Affiliation(s)
- Drew M. DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jinjin Diao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Rhiannon Carr
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Yifeng Hu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Liang Y, Yu H. Genetic toolkits for engineering Rhodococcus species with versatile applications. Biotechnol Adv 2021; 49:107748. [PMID: 33823269 DOI: 10.1016/j.biotechadv.2021.107748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 02/09/2023]
Abstract
Rhodococcus spp. are a group of non-model gram-positive bacteria with diverse catabolic activities and strong adaptive capabilities, which enable their wide application in whole-cell biocatalysis, environmental bioremediation, and lignocellulosic biomass conversion. Compared with model microorganisms, the engineering of Rhodococcus is challenging because of the lack of universal molecular tools, high genome GC content (61% ~ 71%), and low transformation and recombination efficiencies. Nevertheless, because of the high interest in Rhodococcus species for bioproduction, various genetic elements and engineering tools have been recently developed for Rhodococcus spp., including R. opacus, R. jostii, R. ruber, and R. erythropolis, leading to the expansion of the genetic toolkits for Rhodococcus engineering. In this article, we provide a comprehensive review of the important developed genetic elements for Rhodococcus, including shuttle vectors, promoters, antibiotic markers, ribosome binding sites, and reporter genes. In addition, we also summarize gene transfer techniques and strategies to improve transformation efficiency, as well as random and precise genome editing tools available for Rhodococcus, including transposition, homologous recombination, recombineering, and CRISPR/Cas9. We conclude by discussing future trends in Rhodococcus engineering. We expect that more synthetic and systems biology tools (such as multiplex genome editing, dynamic regulation, and genome-scale metabolic models) will be adapted and optimized for Rhodococcus.
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Affiliation(s)
- Youxiang Liang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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Hwangbo M, Gill JJ, Young R, Chu KH. Dual-function oleaginous biocatalysts for non-sterile cultivation and solvent-free biolipid bioextraction to reduce biolipid-based biofuel production costs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143969. [PMID: 33333303 PMCID: PMC8061307 DOI: 10.1016/j.scitotenv.2020.143969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/31/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
Triacylglycerols (TAGs) are starting materials for the production of biolipid-based fuels such as biodiesel and biojet fuel. While various microorganisms can produce TAGs from renewable resources, the cultivation of TAG-producing microorganisms under sterilization conditions to avoid microbial contamination and application of solvent to extract TAGs from the TAG-filled microorganisms are costly. To overcome these challenges, this study reports the feasibility of a non-sterile cultivation of an oleaginous bacterium Rhodococcus opacus PD631SpAHB under saline conditions, followed by the use of a solvent-free, phage-lysis-protein-based bioextraction approach for TAGs release. The engineered strain PD631SpAHB was developed by introducing a recombinant plasmid carrying a phage lytic gene cassette (pAHB) into Rhodococcus opacus PD631 via transformation, followed by adaptive evolution under saline conditions. This newly developed strain is a salt-tolerant strain with the inducible plasmid pAHB to enable TAGs release into the supernatant upon induction. Cell lysis of PD631SpAHB was confirmed by the decrease of the optical density of cell suspension, by the loss of cell membrane integrity, and by the detection of TAGs in the culture medium. Up to 38% of the total TAGs accumulated in PD631SpAHB was released into supernatant after the expression of the lytic genes. PD631SpAHB strain is a promising candidate to produce TAGs from non-sterile growth medium and release of its TAGs without solvent extraction - a new approach to reduce the overall cost of biolipid-based biofuel production.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Jason J Gill
- Department of Animal Science, Texas A&M University, College Station, TX 77843, United States; Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States
| | - Ry Young
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States.
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25
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Pátek M, Grulich M, Nešvera J. Stress response in Rhodococcus strains. Biotechnol Adv 2021; 53:107698. [PMID: 33515672 DOI: 10.1016/j.biotechadv.2021.107698] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Rhodococci are bacteria which can survive under various extreme conditions, in the presence of toxic compounds, and in other hostile habitats. Their tolerance of unfavorable conditions is associated with the structure of their cell wall and their large array of enzymes, which degrade or detoxify harmful compounds. Their physiological and biotechnological properties, together with tools for their genetic manipulation, enable us to apply them in biotransformations, biodegradation and bioremediation. Many such biotechnological applications cause stresses that positively or negatively affect their efficiency. Whereas numerous reviews on rhodococci described their enzyme activities, the optimization of degradation or production processes, and corresponding technological solutions, only a few reviews discussed some specific effects of stresses on the physiology of rhodococci and biotechnological processes. This review aims to comprehensively describe individual stress responses in Rhodococcus strains, the interconnection of different types of stresses and their consequences for cell physiology. We examine here the responses to (1) environmental stresses (desiccation, heat, cold, osmotic and pH stress), (2) the presence of stress-inducing compounds (metals, organic compounds and antibiotics) in the environment (3) starvation and (4) stresses encountered during biotechnological applications. Adaptations of the cell envelope, the formation of multicellular structures and stresses induced by the interactions of hosts with pathogenic rhodococci are also included. The roles of sigma factors of RNA polymerase in the global regulation of stress responses in rhodococci are described as well. Although the review covers a large number of stressful conditions, our intention was to provide an overview of the selected stress responses and their possible connection to biotechnological processes, not an exhaustive survey of the scientific literature. The findings on stress responses summarized in this review and the demonstration of gaps in current knowledge may motivate researchers working to fill these gaps.
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Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Michal Grulich
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Jan Nešvera
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
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26
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Cappelletti M, Presentato A, Piacenza E, Firrincieli A, Turner RJ, Zannoni D. Biotechnology of Rhodococcus for the production of valuable compounds. Appl Microbiol Biotechnol 2020; 104:8567-8594. [PMID: 32918579 PMCID: PMC7502451 DOI: 10.1007/s00253-020-10861-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 12/31/2022]
Abstract
Bacteria belonging to Rhodococcus genus represent ideal candidates for microbial biotechnology applications because of their metabolic versatility, ability to degrade a wide range of organic compounds, and resistance to various stress conditions, such as metal toxicity, desiccation, and high concentration of organic solvents. Rhodococcus spp. strains have also peculiar biosynthetic activities that contribute to their strong persistence in harsh and contaminated environments and provide them a competitive advantage over other microorganisms. This review is focused on the metabolic features of Rhodococcus genus and their potential use in biotechnology strategies for the production of compounds with environmental, industrial, and medical relevance such as biosurfactants, bioflocculants, carotenoids, triacylglycerols, polyhydroxyalkanoate, siderophores, antimicrobials, and metal-based nanostructures. These biosynthetic capacities can also be exploited to obtain high value-added products from low-cost substrates (industrial wastes and contaminants), offering the possibility to efficiently recover valuable resources and providing possible waste disposal solutions. Rhodococcus spp. strains have also recently been pointed out as a source of novel bioactive molecules highlighting the need to extend the knowledge on biosynthetic capacities of members of this genus and their potential utilization in the framework of bioeconomy. KEY POINTS: • Rhodococcus possesses promising biosynthetic and bioconversion capacities. • Rhodococcus bioconversion capacities can provide waste disposal solutions. • Rhodococcus bioproducts have environmental, industrial, and medical relevance. Graphical abstract.
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Affiliation(s)
- Martina Cappelletti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy.
| | - Alessandro Presentato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Elena Piacenza
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), Florence, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Raymond J Turner
- Department of Biological Sciences, Calgary University, Calgary, AB, Canada
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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27
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Zhang LS, Chu MY, Zong MH, Yang JG, Lou WY. Facile and Green Production of Human Milk Fat Substitute through Rhodococcus opacus Fermentation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9368-9376. [PMID: 32700528 DOI: 10.1021/acs.jafc.0c03185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Human milk fat substitute (HMFS) is a class of structured lipids widely used in infant formulas. Herein, HMFS was prepared by Rhodococcus opacus fermentation. The substrate oils suitable for HMFS production were coconut oil (66.1-57.5%), soybean oil (17.5-26.5%), high oleic acid sunflower oil (5.4-4.5%), Antarctic krill oil (9-9.5%), and fungal oil (2%). Six HMFSs were prepared, among which HMFS V and VI were similar to human milk fat from Chinese in terms of fatty acid composition and triacylglycerol species. The sn-2 position of HMFS was occupied by palmitic acid (49.31 and 43.48% in HMFS V and VI, respectively). The major triacylglycerols were OPL, OPO, and LPL, accounting for 15.90, 9.49, and 6.84 and 17.52, 8.44, and 8.55% in HMFS V and VI, respectively. This study is the first to prepare structured lipids intended for infant formula through fermentation, providing a novel strategy for the edible oil industry.
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Affiliation(s)
- Lin-Shang Zhang
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China
| | - Mei-Yun Chu
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China
| | - Min-Hua Zong
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China
| | - Ji-Guo Yang
- South China Institute of Collaborative Innovation, Xincheng Road, Dongguan 523808, China
| | - Wen-Yong Lou
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China
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28
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Chatterjee A, DeLorenzo DM, Carr R, Moon TS. Bioconversion of renewable feedstocks by Rhodococcus opacus. Curr Opin Biotechnol 2020; 64:10-16. [DOI: 10.1016/j.copbio.2019.08.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/19/2019] [Accepted: 08/25/2019] [Indexed: 12/18/2022]
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29
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Sundararaghavan A, Mukherjee A, Suraishkumar GK. Investigating the potential use of an oleaginous bacterium, Rhodococcus opacus PD630, for nano-TiO 2 remediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:27394-27406. [PMID: 31493086 DOI: 10.1007/s11356-019-06388-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
The occurrence of titanium dioxide nanoparticles (nTiO2), in the effluents released from wastewater treatment plants, has raised concerns. The fate of nTiO2 and their potential impact on organisms from different ecosystems are widely investigated. For the first time, in this work, we report the responses of an oleaginous bacteria Rhodococcus opacus PD630, belonging to an ecologically important genus Rhodococcus to environmentally relevant concentrations of nTiO2, under dark and UV light conditions. We observed a dose-dependent increase in nTiO2 uptake by the bacteria that reached a maximum of 1.4 mg nTiO2 (g cell)-1 under mid-log UV exposure, corresponding to 97% uptake. The nTiO2 induced oxidative stress in bacteria that increased from 25.1 to a maximum of 100.3, 44.1, and 51.7 μmol .OH (g cell)-1 under dark, continuous, and mid-log UV, respectively. However, nTiO2 did not affect bacterial viability. Further, due to oxidative stress, the triacylglycerol (biodiesel) content from bacteria increased from 30% to a maximum of 54% CDW. Based on our findings, we propose an application of R. opacus PD 630 in nTiO2 remediation due to their high nTiO2 uptake and resistance.
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Affiliation(s)
- Archanaa Sundararaghavan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences building, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Amitava Mukherjee
- Centre for Nanobiotechnology, VIT University, Vellore, 632014, India
| | - Gadi K Suraishkumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences building, Indian Institute of Technology Madras, Chennai, 600036, India.
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30
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Greening C, Lithgow T. Formation and function of bacterial organelles. Nat Rev Microbiol 2020; 18:677-689. [PMID: 32710089 DOI: 10.1038/s41579-020-0413-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 01/28/2023]
Abstract
Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by a lipid bilayer (such as thylakoids, magnetosomes and anammoxosomes), whereas others are defined by a lipid monolayer (such as lipid bodies), a proteinaceous coat (such as carboxysomes) or have a phase-defined boundary (such as nucleolus-like compartments). These diverse organelles have various metabolic and physiological functions, facilitating adaptation to different environments and driving the evolution of cellular complexity. This Review highlights that, despite the diversity of reported organelles, some unifying concepts underlie their formation, structure and function. Bacteria have fundamental mechanisms of organelle formation, through which conserved processes can form distinct organelles in different species depending on the proteins recruited to the luminal space and the boundary of the organelle. These complex subcellular compartments provide evolutionary advantages as well as enabling metabolic specialization, biogeochemical processes and biotechnological advances. Growing evidence suggests that the presence of organelles is the rule, rather than the exception, in bacterial cells.
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Affiliation(s)
- Chris Greening
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
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31
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Gibson L, Larke-Mejía NL, Murrell JC. Complete Genome of Isoprene Degrading Nocardioides sp. WS12. Microorganisms 2020; 8:microorganisms8060889. [PMID: 32545487 PMCID: PMC7355492 DOI: 10.3390/microorganisms8060889] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 01/20/2023] Open
Abstract
Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene.
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32
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Murrell JC, McGenity TJ, Crombie AT. Microbial metabolism of isoprene: a much-neglected climate-active gas. MICROBIOLOGY-SGM 2020; 166:600-613. [PMID: 32441612 PMCID: PMC7657509 DOI: 10.1099/mic.0.000931] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.
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Affiliation(s)
- J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Terry J McGenity
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Lundquist PK, Shivaiah KK, Espinoza-Corral R. Lipid droplets throughout the evolutionary tree. Prog Lipid Res 2020; 78:101029. [PMID: 32348789 DOI: 10.1016/j.plipres.2020.101029] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/11/2020] [Accepted: 04/18/2020] [Indexed: 12/11/2022]
Abstract
Intracellular lipid droplets are utilized for lipid storage and metabolism in organisms as evolutionarily diverse as animals, fungi, plants, bacteria, and archaea. These lipid droplets demonstrate great diversity in biological functions and protein and lipid compositions, yet fundamentally share common molecular and ultrastructural characteristics. Lipid droplet research has been largely fragmented across the diversity of lipid droplet classes and sub-classes. However, we suggest that there is great potential benefit to the lipid community in better integrating the lipid droplet research fields. To facilitate such integration, we survey the protein and lipid compositions, functional roles, and mechanisms of biogenesis across the breadth of lipid droplets studied throughout the natural world. We depict the big picture of lipid droplet biology, emphasizing shared characteristics and unique differences seen between different classes. In presenting the known diversity of lipid droplets side-by-side it becomes necessary to offer for the first time a consistent system of categorization and nomenclature. We propose a division into three primary classes that reflect their sub-cellular location: i) cytoplasmic lipid droplets (CYTO-LDs), that are present in the eukaryotic cytoplasm, ii) prokaryotic lipid droplets (PRO-LDs), that exist in the prokaryotic cytoplasm, and iii) plastid lipid droplets (PL-LDs), that are found in plant plastids, organelles of photosynthetic eukaryotes. Within each class there is a remarkable array of sub-classes displaying various sizes, shapes and compositions. A more integrated lipid droplet research field will provide opportunities to better build on discoveries and accelerate the pace of research in ways that have not been possible.
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Affiliation(s)
- Peter K Lundquist
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Kiran-Kumar Shivaiah
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Roberto Espinoza-Corral
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
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34
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Sundararaghavan A, Mukherjee A, Sahoo S, Suraishkumar GK. Mechanism of the oxidative stress‐mediated increase in lipid accumulation by the bacterium,R. opacusPD630: Experimental analysis and genome‐scale metabolic modeling. Biotechnol Bioeng 2020; 117:1779-1788. [DOI: 10.1002/bit.27330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/22/2020] [Accepted: 03/09/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Archanaa Sundararaghavan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences buildingIndian Institute of Technology Madras Chennai India
| | | | - Swagatika Sahoo
- Department of Chemical Engineering and Initiative for Biological Systems EngineeringIndian Institute of Technology Madras Chennai India
| | - G. K. Suraishkumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences buildingIndian Institute of Technology Madras Chennai India
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35
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Garrido-Sanz D, Sansegundo-Lobato P, Redondo-Nieto M, Suman J, Cajthaml T, Blanco-Romero E, Martin M, Uhlik O, Rivilla R. Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence. Microb Genom 2020; 6. [PMID: 32238227 PMCID: PMC7276702 DOI: 10.1099/mgen.0.000363] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.
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Affiliation(s)
- Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Paula Sansegundo-Lobato
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Laboratory of Environmental Biotechnology, Institute of Microbiology, Czech Academy of Sciences v.v.i., Vídeňská 1083, 14200 Prague, Czech Republic
| | - Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Marta Martin
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
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Dornau A, Robson JF, Thomas GH, McQueen-Mason SJ. Robust microorganisms for biofuel and chemical production from municipal solid waste. Microb Cell Fact 2020; 19:68. [PMID: 32178677 PMCID: PMC7077162 DOI: 10.1186/s12934-020-01325-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/06/2020] [Indexed: 01/30/2023] Open
Abstract
Background Worldwide 3.4 billion tonnes of municipal solid waste (MSW) will be produced annually by 2050, however, current approaches to MSW management predominantly involve unsustainable practices like landfilling and incineration. The organic fraction of MSW (OMSW) typically comprises ~ 50% lignocellulose-rich material but is underexplored as a biomanufacturing feedstock due to its highly inconsistent and heterogeneous composition. This study sought to overcome the limitations associated with studying MSW-derived feedstocks by using OMSW produced from a realistic and reproducible MSW mixture on a commercial autoclave system. The resulting OMSW fibre was enzymatically hydrolysed and used to screen diverse microorganisms of biotechnological interest to identify robust species capable of fermenting this complex feedstock. Results The autoclave pre-treated OMSW fibre contained a polysaccharide fraction comprising 38% cellulose and 4% hemicellulose. Enzymatic hydrolysate of OMSW fibre was high in d-glucose (5.5% w/v) and d-xylose (1.8%w/v) but deficient in nitrogen and phosphate. Although relatively low levels of levulinic acid (30 mM) and vanillin (2 mM) were detected and furfural and 5-hydroxymethylfurfural were absent, the hydrolysate contained an abundance of potentially toxic metals (0.6% w/v). Hydrolysate supplemented with 1% yeast extract to alleviate nutrient limitation was used in a substrate-oriented shake-flask screen with eight biotechnologically useful microorganisms (Clostridium saccharoperbutylacetonicum, Escherichia coli, Geobacillus thermoglucosidasius, Pseudomonas putida, Rhodococcus opacus, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Zymomonas mobilis). Each species’ growth and productivity were characterised and three species were identified that robustly and efficiently fermented OMSW fibre hydrolysate without significant substrate inhibition: Z. mobilis, S. cerevisiae and R. opacus, respectively produced product to 69%, 70% and 72% of the maximum theoretical fermentation yield and could theoretically produce 136 kg and 139 kg of ethanol and 91 kg of triacylglycerol (TAG) per tonne of OMSW. Conclusions Developing an integrated biorefinery around MSW has the potential to significantly alleviate the environmental burden of current waste management practices. Substrate-oriented screening of a representative and reproducible OMSW-derived fibre identified microorganisms intrinsically suited to growth on OMSW hydrolysates. These species are promising candidates for developing an MSW biorefining platform and provide a foundation for future studies aiming to valorise this underexplored feedstock.
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Affiliation(s)
- Aritha Dornau
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, YO10 5DD, York, UK
| | - James F Robson
- Department of Biology, University of York, Heslington, YO10 5DD, York, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Heslington, YO10 5DD, York, UK
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, YO10 5DD, York, UK.
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Nahar A, Baker AL, Nichols DS, Bowman JP, Britz ML. Application of Thin-Layer Chromatography-Flame Ionization Detection (TLC-FID) to Total Lipid Quantitation in Mycolic-Acid Synthesizing Rhodococcus and Williamsia Species. Int J Mol Sci 2020; 21:ijms21051670. [PMID: 32121355 PMCID: PMC7084869 DOI: 10.3390/ijms21051670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/15/2020] [Accepted: 02/25/2020] [Indexed: 12/25/2022] Open
Abstract
In addition to cell membrane phospholipids, Actinobacteria in the order Corynebacteriales possess a waxy cell envelope containing mycolic acids (MA). In optimized culture condition, some species can also accumulate high concentrations of intracellular triacylglycerols (TAG), which are a potential source of biodiesel. Bacterial lipid classes and composition alter in response to environmental stresses, including nutrient availability, thus understanding carbon flow into different lipid classes is important when optimizing TAG synthesis. Quantitative and qualitative analysis of lipid classes normally requires combinations of different extraction, derivatization, chromatographic and detection methods. In this study, a single-step thin-layer chromatography-flame ionization detection (TLC-FID) technique was applied to quantify lipid classes in six sub-Antarctic Corynebacteriales strains identified as Rhodococcus and Williamsia species. A hexane:diethyl-ether:acetic acid solvent system separated the total cellular lipids extracted from cells lysed by bead beating, which released more bound and unbound MA than sonication. Typical profiles included a major broad non-polar lipid peak, TAG and phospholipids, although trehalose dimycolates, when present, co-eluted with phospholipids. Ultra-performance liquid chromatography-tandem mass-spectrometry and nuclear magnetic resonance spectroscopy detected MA signatures in the non-polar lipid peak and indicated that these lipids were likely bound, at least in part, to sugars from cell wall arabinogalactan. Waxy esters were not detected. The single-solvent TLC-FID procedure provides a useful platform for the quantitation and preliminary screening of cellular lipid classes when testing the impacts of growth conditions on TAG synthesis.
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Affiliation(s)
- Akhikun Nahar
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
| | - Anthony L. Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
| | - David S. Nichols
- Central Science Laboratory, Division of Research, University of Tasmania, Hobart, TAS 7005, Australia;
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
| | - Margaret L. Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
- Correspondence:
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Steryl Ester Formation and Accumulation in Steroid-Degrading Bacteria. Appl Environ Microbiol 2020; 86:AEM.02353-19. [PMID: 31704679 DOI: 10.1128/aem.02353-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/01/2019] [Indexed: 11/20/2022] Open
Abstract
Steryl esters (SEs) are important storage compounds in many eukaryotes and are often prominent components of intracellular lipid droplets. Here, we demonstrate that selected Actino- and Proteobacteria growing on sterols are also able to synthesize SEs and to sequester them in cytoplasmic lipid droplets. We found cholesteryl ester (CE) formation in members of the actinobacterial genera Rhodococcus, Mycobacterium, and Amycolatopsis, as well as several members of the proteobacterial Cellvibrionales order. CEs maximally accumulated under nitrogen-limiting conditions, suggesting that steryl ester formation plays a crucial role for storing excess energy and carbon under adverse conditions. Rhodococcus jostii RHA1 was able to synthesize phytosteryl and cholesteryl esters, the latter reaching up to 7% of its cellular dry weight and 69% of its lipid droplets. Purified lipid droplets from RHA1 contained CEs, free cholesterol, and triacylglycerols. In addition, we found formation of CEs in Mycobacterium tuberculosis when it was grown with cholesterol plus an additional fatty acid substrate. This study provides a basis for the application of bacterial whole-cell systems in the biotechnological production of SEs for use in functional foods and cosmetics.IMPORTANCE Oleaginous bacteria exhibit great potential for the production of high-value neutral lipids, such as triacylglycerols and wax esters. This study describes the formation of steryl esters (SEs) as neutral lipid storage compounds in sterol-degrading oleaginous bacteria, providing a basis for biotechnological production of SEs using bacterial systems with potential applications in the functional food, nutraceutical, and cosmetic industries. We found cholesteryl ester (CE) formation in several sterol-degrading Actino- and Proteobacteria under nitrogen-limiting conditions, suggesting an important role of this process in storing energy and carbon under adverse conditions. In addition, Mycobacterium tuberculosis grown on cholesterol accumulated CEs in the presence of an additional fatty acid substrate.
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Dong Q, Xing X, Han Y, Wei X, Zhang S. De Novo Organelle Biogenesis in the Cyanobacterium TDX16 Released from the Green Alga <i>Haematococcus pluvialis</i>. Cell 2020. [DOI: 10.4236/cellbio.2020.91003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chu M, Zhang L, Lou W, Zong M, Tang Y, Yang J. Preparation and Characterization of Oil Rich in Odd Chain Fatty Acids from Rhodococcus opacusPD630. J AM OIL CHEM SOC 2020. [DOI: 10.1002/aocs.12304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mei‐Yun Chu
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Lin‐Shang Zhang
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Wen‐Yong Lou
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Min‐Hua Zong
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Yu‐Qian Tang
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
- South China Institute of Collaborative Innovation, Xincheng Road Dongguan 523808 China
| | - Ji‐Guo Yang
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
- South China Institute of Collaborative Innovation, Xincheng Road Dongguan 523808 China
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Tao W, Kasuga T, Li S, Huang H, Fan Z. Homoethanol production from cellobionate and glycerol using recombinant Klebsiella oxytoca strains. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Roell GW, Carr RR, Campbell T, Shang Z, Henson WR, Czajka JJ, Martín HG, Zhang F, Foston M, Dantas G, Moon TS, Tang YJ. A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630. Metab Eng 2019; 55:120-130. [DOI: 10.1016/j.ymben.2019.06.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/19/2019] [Accepted: 06/30/2019] [Indexed: 01/28/2023]
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Mandal B, Prabhu A, Pakshirajan K, Veeranki Dasu V. Construction and parameters modulation of a novel variant Rhodococcus opacus BM985 to achieve enhanced triacylglycerol-a biodiesel precursor, using synthetic dairy wastewater. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Levy-Booth DJ, Fetherolf MM, Stewart GR, Liu J, Eltis LD, Mohn WW. Catabolism of Alkylphenols in Rhodococcus via a Meta-Cleavage Pathway Associated With Genomic Islands. Front Microbiol 2019; 10:1862. [PMID: 31481940 PMCID: PMC6710988 DOI: 10.3389/fmicb.2019.01862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/29/2019] [Indexed: 01/01/2023] Open
Abstract
The bacterial catabolism of aromatic compounds has considerable promise to convert lignin depolymerization products to commercial chemicals. Alkylphenols are a key class of depolymerization products whose catabolism is not well-elucidated. We isolated Rhodococcus rhodochrous EP4 on 4-ethylphenol and applied genomic and transcriptomic approaches to elucidate alkylphenol catabolism in EP4 and Rhodococcus jostii RHA1. RNA-Seq and RT-qPCR revealed a pathway encoded by the aphABCDEFGHIQRS genes that degrades 4-ethylphenol via the meta-cleavage of 4-ethylcatechol. This process was initiated by a two-component alkylphenol hydroxylase, encoded by the aphAB genes, which were upregulated ~3,000-fold. Purified AphAB from EP4 had highest specific activity for 4-ethylphenol and 4-propylphenol (~2,000 U/mg) but did not detectably transform phenol. Nevertheless, a ΔaphA mutant in RHA1 grew on 4-ethylphenol by compensatory upregulation of phenol hydroxylase genes (pheA1-3). Deletion of aphC, encoding an extradiol dioxygenase, prevented growth on 4-alkylphenols but not phenol. Disruption of pcaL in the β-ketoadipate pathway prevented growth on phenol but not 4-alkylphenols. Thus, 4-alkylphenols are catabolized exclusively via meta-cleavage in rhodococci while phenol is subject to ortho-cleavage. A putative genomic island encoding aph genes was identified in EP4 and several other rhodococci. Overall, this study identifies a 4-alkylphenol pathway in rhodococci, demonstrates key enzymes involved, and presents evidence that the pathway is encoded in a genomic island. These advances are of particular importance for wide-ranging industrial applications of rhodococci, including upgrading of lignocellulose biomass.
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Affiliation(s)
- David J Levy-Booth
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Morgan M Fetherolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Gordon R Stewart
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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DeLorenzo DM, Moon TS. Construction of Genetic Logic Gates Based on the T7 RNA Polymerase Expression System in Rhodococcus opacus PD630. ACS Synth Biol 2019; 8:1921-1930. [PMID: 31362487 DOI: 10.1021/acssynbio.9b00213] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rhodococcus opacus PD630 (R. opacus) is a nonmodel, Gram-positive bacterium that holds promise as a biological catalyst for the conversion of lignocellulosic biomass to value-added products. In particular, it demonstrates both a high tolerance for and an ability to consume inhibitory lignin-derived aromatics, generates large quantities of lipids, exhibits a relatively rapid growth rate, and has a growing genetic toolbox for engineering. However, the availability of genetic parts for tunable, high-activity gene expression is still limited in R. opacus. Furthermore, genetic logic circuits for sophisticated gene regulation have never been demonstrated in Rhodococcus spp. To address these shortcomings, two inducible T7 RNA polymerase-based expression systems were implemented for the first time in R. opacus and applied to the construction of AND and NAND genetic logic gates. Additionally, three isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible promoters were created by inserting LacI binding sites into newly characterized constitutive promoters. Furthermore, four novel aromatic sensors for 4-hydroxybenzoic acid, vanillic acid, sodium benzoate, and guaiacol were developed, expanding the gene expression toolbox. Finally, the T7 RNA polymerase platform was combined with a synthetic IPTG-inducible promoter to create an IMPLY logic gate. Overall, this work represents the first demonstration of a heterologous RNA polymerase system and synthetic genetic logic in R. opacus, enabling complex and tunable gene regulation in this promising nonmodel host for bioproduction.
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Affiliation(s)
- Drew M. DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Santucci P, Johansen MD, Point V, Poncin I, Viljoen A, Cavalier JF, Kremer L, Canaan S. Nitrogen deprivation induces triacylglycerol accumulation, drug tolerance and hypervirulence in mycobacteria. Sci Rep 2019; 9:8667. [PMID: 31209261 PMCID: PMC6572852 DOI: 10.1038/s41598-019-45164-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/29/2019] [Indexed: 11/09/2022] Open
Abstract
Mycobacteria share with other actinomycetes the ability to produce large quantities of triacylglycerol (TAG), which accumulate as intracytoplasmic lipid inclusions (ILI) also known as lipid droplets (LD). Mycobacterium tuberculosis (M. tb), the etiologic agent of tuberculosis, acquires fatty acids from the human host which are utilized to synthesize TAG, subsequently stored in the form of ILI to meet the carbon and nutrient requirements of the bacterium during long periods of persistence. However, environmental factors governing mycobacterial ILI formation and degradation remain poorly understood. Herein, we demonstrated that in the absence of host cells, carbon excess and nitrogen starvation promote TAG accumulation in the form of ILI in M. smegmatis and M. abscessus, used as surrogate species of M. tb. Based on these findings, we developed a simple and reversible in vitro model to regulate ILI biosynthesis and hydrolysis in mycobacteria. We also showed that TAG formation is tgs1 dependent and that lipolytic enzymes mediate TAG breakdown. Moreover, we confirmed that the nitrogen-deprived and ILI-rich phenotype was associated with an increased tolerance towards several drugs used for treating mycobacterial infections. Importantly, we showed that the presence of ILI substantially enhanced the bacterial burden and granuloma abundance in zebrafish embryos infected with lipid-rich M. abscessus as compared to embryos infected with lipid-poor M. abscessus, suggesting that ILI are actively contributing to mycobacterial virulence and pathogenesis.
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Affiliation(s)
- Pierre Santucci
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Matt D Johansen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293, Montpellier, France
| | - Vanessa Point
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Isabelle Poncin
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293, Montpellier, France
| | | | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293, Montpellier, France.,INSERM, IRIM, 34293, Montpellier, France
| | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France.
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Biomass and lipid production by Rhodococcus opacus PD630 in molasses-based media with and without osmotic-stress. J Biotechnol 2019; 297:1-8. [DOI: 10.1016/j.jbiotec.2019.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/03/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022]
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Homoethanol Production from Glycerol and Gluconate Using Recombinant Klebsiella oxytoca Strains. Appl Environ Microbiol 2019; 85:AEM.02122-18. [PMID: 30578264 DOI: 10.1128/aem.02122-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
Gluconic acid, an oxidized cellulose degradation product, could be produced from cellulosic biomass. Glycerol is an inexpensive and renewable resource for fuels and chemicals production and is available as a byproduct of biodiesel production. Gluconate is a more oxidized substrate than glucose, whereas glycerol is a more reduced substrate than glucose. Although the production of homoethanol from glucose can be achieved, the conversion of gluconate to ethanol is accompanied by the production of oxidized byproduct such as acetate, and reduced byproducts such as 1,3-propanediol are produced, along with ethanol, when glycerol is used as the carbon source. When gluconate and glycerol are used as the sole carbon source by Klebsiella oxytoca BW21, the ethanol yield is about 62 to 64%. Coutilization of both gluconate and glycerol in batch fermentation increased the yield of ethanol to about 78.7% and decreased by-product accumulation (such as acetate and 1,3-propanediol) substantially. Decreasing by-product formation by deleting the pta, frd, ldh, pflA, and pduC genes in strain BW21 increased the ethanol yield to 89.3% in the batch fermentation of a glycerol-gluconate mixture. These deletions produced the strain K. oxytoca WT26. However, the utilization rate of glycerol was significantly slower than that of gluconate in batch fermentation. In addition, substantial amounts of glycerol remain unutilized after gluconate was depleted in batch fermentation. Continuous fed-batch fermentation was used to solve the utilization rate mismatch problem for gluconate and glycerol. An ethanol yield of 97.2% was achieved in continuous fed-batch fermentation of these two substrates, and glycerol was completely used at the end of the fermentation.IMPORTANCE Gluconate is a biomass-derived degradation product, and glycerol can be obtained as a biodiesel byproduct. Compared to glucose, using them as the sole substrate is accompanied by the production of by-products. Our study shows that through pathway engineering and adoption of a fed-batch culture system, high-yield homoethanol production that usually can be achieved by using glucose as the substrate is achievable using gluconate and glycerol as cosubstrates. The same strategy is expected to be able to achieve homofermentative production of other products, such as lactate and 2,3-butanediol, which can be typically achieved using glucose as the substrate and inexpensive biodiesel-derived glycerol and biomass-derived gluconate as the cosubstrates.
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Anthony WE, Carr RR, DeLorenzo DM, Campbell TP, Shang Z, Foston M, Moon TS, Dantas G. Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:192. [PMID: 31404385 PMCID: PMC6683499 DOI: 10.1186/s13068-019-1535-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/24/2019] [Indexed: 05/09/2023]
Abstract
The current extraction and use of fossil fuels has been linked to extensive negative health and environmental outcomes. Lignocellulosic biomass-derived biofuels and bioproducts are being actively considered as renewable alternatives to the fuels, chemicals, and materials produced from fossil fuels. A major challenge limiting large-scale, economic deployment of second-generation biorefineries is the insufficient product yield, diversity, and value that current conversion technologies can extract from lignocellulose, in particular from the underutilized lignin fraction. Rhodococcus opacus PD630 is an oleaginous gram-positive bacterium with innate catabolic pathways and tolerance mechanisms for the inhibitory aromatic compounds found in depolymerized lignin, as well as native or engineered pathways for hexose and pentose sugars found in the carbohydrate fractions of biomass. As a result, R. opacus holds potential as a biological chassis for the conversion of lignocellulosic biomass into biodiesel precursors and other value-added products. This review begins by examining the important role that lignin utilization will play in the future of biorefineries and by providing a concise survey of the current lignin conversion technologies. The genetic machinery and capabilities of R. opacus that allow the bacterium to tolerate and metabolize aromatic compounds and depolymerized lignin are also discussed, along with a synopsis of the genetic toolbox and synthetic biology methods now available for engineering this organism. Finally, we summarize the different feedstocks that R. opacus has been demonstrated to consume, and the high-value products that it has been shown to produce. Engineered R. opacus will enable lignin valorization over the coming years, leading to cost-effective conversion of lignocellulose into fuels, chemicals, and materials.
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Affiliation(s)
- Winston E. Anthony
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Rhiannon R. Carr
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Drew M. DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tayte P. Campbell
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Zeyu Shang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Marcus Foston
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
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