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Xiong X, Wang X, Chen S. Engineering of an L-arabinose metabolic pathway in Rhodococcus jostii RHA1 for biofuel production. J Ind Microbiol Biotechnol 2016; 43:1017-25. [PMID: 27143134 DOI: 10.1007/s10295-016-1778-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/11/2016] [Indexed: 01/17/2023]
Abstract
The oleaginous bacterium, Rhodococcus jostii RHA1 has attracted considerable attention due to its capability to accumulate significant levels of triacylglycerol as renewable hydrocarbon. To enable the strain to utilize arabinose derived from lignocellulosic biomass, the metabolic pathway of L-arabinose utilization was introduced into R. jostii RHA1 by heterogenous expression of the operon, araBAD from Escherichia coli. The results showed that recombinant bearing araBAD could grow on L-arabinose as the sole carbon source, and additional expression of araFGH encoding the arabinose transporter from E. coli could improve the cell biomass yield from high contents of arabinose. We further increased the content of lipid produced from arabinose in the recombinants from 47.9 to 56.8 % of the cell dry weight (CDW) by overexpression of a gene, atf1 encoding a diglyceride acyltransferase from R. opacus PD630. This work demonstrated the feasibility of producing lipid from arabinose by genetic modification of the rhodococci strain.
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Affiliation(s)
- Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, L.J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA
| | - Xi Wang
- Department of Biological Systems Engineering, Washington State University, L.J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, L.J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA.
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Amara S, Seghezzi N, Otani H, Diaz-Salazar C, Liu J, Eltis LD. Characterization of key triacylglycerol biosynthesis processes in rhodococci. Sci Rep 2016; 6:24985. [PMID: 27126051 PMCID: PMC4850399 DOI: 10.1038/srep24985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
Oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. Genes whose transcripts were more abundant under N-limitation included those involved in ammonium assimilation, benzoate catabolism, fatty acid biosynthesis and the methylmalonyl-CoA pathway. Of the 16 atf genes potentially encoding diacylglycerol O-acyltransferases, atf8 transcripts were the most abundant during N-limitation (~50-fold more abundant than during N-excess). Consistent with Atf8 being a physiological determinant of TAG accumulation, a Δatf8 mutant accumulated 70% less TAG than wild-type RHA1 while atf8 overexpression increased TAG accumulation 20%. Genes encoding type-2 phosphatidic acid phosphatases were not significantly expressed. By contrast, three genes potentially encoding phosphatases of the haloacid dehalogenase superfamily and that cluster with, or are fused with other Kennedy pathway genes were dysregulated. Overall, these findings advance our understanding of TAG metabolism in mycolic acid-containing bacteria and provide a framework to engineer strains for increased TAG production.
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Affiliation(s)
- Sawsan Amara
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nicolas Seghezzi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Hiroshi Otani
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Carlos Diaz-Salazar
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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Röttig A, Hauschild P, Madkour MH, Al-Ansari AM, Almakishah NH, Steinbüchel A. Analysis and optimization of triacylglycerol synthesis in novel oleaginous Rhodococcus and Streptomyces strains isolated from desert soil. J Biotechnol 2016; 225:48-56. [PMID: 27034020 DOI: 10.1016/j.jbiotec.2016.03.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 01/30/2023]
Abstract
As oleaginous microorganisms represent an upcoming novel feedstock for the biotechnological production of lipids or lipid-derived biofuels, we searched for novel, lipid-producing strains in desert soil. This was encouraged by the hypothesis that neutral lipids represent an ideal storage compound, especially under arid conditions, as several animals are known to outlast long periods in absence of drinking water by metabolizing their body fat. Ten lipid-accumulating bacterial strains, affiliated to the genera Bacillus, Cupriavidus, Nocardia, Rhodococcus and Streptomyces, were isolated from arid desert soil due to their ability to synthesize poly(β-hydroxybutyrate), triacylglycerols or wax esters. Particularly two Streptomyces sp. strains and one Rhodococcus sp. strain accumulate significant amounts of TAG under storage conditions under optimized cultivation conditions. Rhodococcus sp. A27 and Streptomyces sp. G49 synthesized approx. 30% (w/w) fatty acids from fructose or cellobiose, respectively, while Streptomyces isolate G25 reached a cellular fatty acid content of nearly 50% (w/w) when cultivated with cellobiose. The stored triacylglycerols were composed of 30-40% branched fatty acids, such as anteiso-pentadecanoic or iso-hexadecanoic acid. To date, this represents by far the highest lipid content described for streptomycetes. A biotechnological production of such lipids using (hemi)cellulose-derived raw material could be used to obtain sustainable biodiesel with a high proportion of branched-chain fatty acids to improve its cold-flow properties and oxidative stability.
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Affiliation(s)
- Annika Röttig
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Philippa Hauschild
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Mohamed H Madkour
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Ahmed M Al-Ansari
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Naief H Almakishah
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany; Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia.
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Yano T, Funamizu Y, Yoshida N. Intracellular accumulation of trehalose and glycogen in an extreme oligotroph, Rhodococcus erythropolis N9T-4. Biosci Biotechnol Biochem 2016; 80:610-3. [DOI: 10.1080/09168451.2015.1107467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
An extreme oligotroph, Rhodococcus erythropolis N9T-4, showed intracellular accumulation of trehalose and glycogen under oligotrophic conditions. No trehalose accumulation was observed in cells grown on the rich medium. Deletion of the polyphosphate kinase genes enhanced the trehalose accumulation and decreases the intracellular glycogen contents, suggesting an oligotrophic relationship between among the metabolic pathways of trehalose, glycogen, and inorganic polyphosphate biosyntheses.
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Affiliation(s)
- Takanori Yano
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Yuhei Funamizu
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Nobuyuki Yoshida
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
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Indest KJ, Eberly JO, Hancock DE, Jung CM, Carr MR, Blakeney GA. Rhodococcus jostii RHA1 TadA-homolog deletion mutants accumulate less polyhydroxyalkanoates (PHAs) than the parental strain. J GEN APPL MICROBIOL 2016; 62:213-6. [DOI: 10.2323/jgam.2016.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Karl J. Indest
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Jed O. Eberly
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Dawn E. Hancock
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Carina M. Jung
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Matthew R. Carr
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Gary A. Blakeney
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
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Alvarez HM. Triacylglycerol and wax ester-accumulating machinery in prokaryotes. Biochimie 2015; 120:28-39. [PMID: 26343555 DOI: 10.1016/j.biochi.2015.08.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/31/2015] [Indexed: 12/13/2022]
Abstract
Gram negative bacteria as well as Gram positive actinobacteria possess the ability to accumulate variable amounts of wax esters (WE) and/or triacylglycerols (TAG) under nitrogen limiting conditions. In recent years many advances have been made to obtain insight into neutral lipid biosynthesis and accumulation in prokaryotes. The clinical and industrial relevance of bacterial WE/TAG significantly promoted basic and applied research in this field. The recent integrated omic studies as well as the functional characterization of diverse genes are contributing to unravel the composition of the WE/TAG-accumulating machinery in bacteria. This will be a valuable data for designing new drugs against bacteria with clinical importance, such as Mycobacterium tuberculosis, or for transferring and optimizing lipid accumulation in bacterial hosts naturally unable to produce such lipids, such as Escherichia coli. In this article, recent investigations addressing WE/TAG biosynthesis and storage in prokaryotes are presented. A comprehensive view of the current knowledge on the different genes/proteins involved in WE/TAG biosynthesis is included.
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Affiliation(s)
- Héctor M Alvarez
- Centro Regional de Investigación y Desarrollo Científico Tecnológico (CRIDECIT), Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, CIT-CHUBUT, CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
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Tajparast M, Frigon D. Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition. BMC SYSTEMS BIOLOGY 2015; 9:43. [PMID: 26248853 PMCID: PMC4528721 DOI: 10.1186/s12918-015-0190-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 07/28/2015] [Indexed: 11/20/2022]
Abstract
Background Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and triacylglycerols (TAG). Under nitrogen-limited (N-limited) condition, the level of storage increases as is commonly observed for other bacteria. The proportion of each storage compound changes with substrate, but it remains unclear what modelling approach should be adopted to predict the relative composition of the mixture of the storage compounds. We analyzed the growth of R. jostii RHA1 under N-limited conditions using a genome-scale metabolic modelling approach to determine which global metabolic objective function could be used for the prediction. Results The R. jostii RHA1 model (iMT1174) produced during this study contains 1,243 balanced metabolites, 1,935 unique reactions, and 1,174 open reading frames (ORFs). Seven objective functions used with flux balance analysis (FBA) were compared for their capacity to predict the mixture of storage compounds accumulated after the sudden onset of N-limitation. Predictive abilities were determined using a Bayesian approach. Experimental data on storage accumulation mixture (glycogen, polyhydroxyalkanoates, and triacylglycerols) were obtained for batch cultures grown on glucose or acetate. The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA). The FBA solutions for the non-limited growth conditions were simply constrained by the objective function of growth rate maximization. Measurement of central metabolic fluxes by 13C-labelling experiments of amino acids further supported the application of the environmental MOMA principle in the context of changing environment. Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected. Conclusions The genome-scale metabolic model analysis of R. jostii RHA1 cultures suggested that the intracellular reaction flux profile immediately after the onset of N-limited condition are impacted by the values of the same fluxes during the period of non-limited growth. PHA turned out to be the main storage pool of the mixture in R. jostii RHA1. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0190-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohammad Tajparast
- Microbial Community Engineering Laboratory, Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke Street West, Montreal, QC, H3A 0C3, Canada.
| | - Dominic Frigon
- Microbial Community Engineering Laboratory, Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke Street West, Montreal, QC, H3A 0C3, Canada.
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Herrero OM, Alvarez HM. Whey as a renewable source for lipid production byRhodococcusstrains: Physiology and genomics of lactose and galactose utilization. EUR J LIPID SCI TECH 2015. [DOI: 10.1002/ejlt.201500080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- O. Marisa Herrero
- Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia; San Juan Bosco, Comodoro Rivadavia Chubut Argentina
- Oil m&s; Comodoro Rivadavia Chubut Argentina
| | - Héctor M. Alvarez
- Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia; San Juan Bosco, Comodoro Rivadavia Chubut Argentina
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59
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Dávila Costa JS, Leichert L, Alvarez HM, Herrero OM. Label-free and redox proteomic analyses of the triacylglycerol-accumulating Rhodococcus jostii RHA1. Microbiology (Reading) 2015; 161:593-610. [DOI: 10.1099/mic.0.000028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Hernández MA, Comba S, Arabolaza A, Gramajo H, Alvarez HM. Overexpression of a phosphatidic acid phosphatase type 2 leads to an increase in triacylglycerol production in oleaginous Rhodococcus strains. Appl Microbiol Biotechnol 2014; 99:2191-207. [PMID: 25213912 DOI: 10.1007/s00253-014-6002-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/28/2023]
Abstract
Oleaginous Rhodococcus strains are able to accumulate large amounts of triacylglycerol (TAG). Phosphatidic acid phosphatase (PAP) enzyme catalyzes the dephosphorylation of phosphatidic acid (PA) to yield diacylglycerol (DAG), a key precursor for TAG biosynthesis. Studies to establish its role in lipid metabolism have been mainly focused in eukaryotes but not in bacteria. In this work, we identified and characterized a putative PAP type 2 (PAP2) encoded by the ro00075 gene in Rhodococcus jostii RHA1. Heterologous expression of ro00075 in Escherichia coli resulted in a fourfold increase in PAP activity and twofold in DAG content. The conditional deletion of ro00075 in RHA1 led to a decrease in the content of DAG and TAG, whereas its overexpression in both RHA1 and Rhodococcus opacus PD630 promoted an increase up to 10 to 15 % by cellular dry weight in TAG content. On the other hand, expression of ro00075 in the non-oleaginous strain Rhodococcus fascians F7 promoted an increase in total fatty acid content up to 7 % at the expense of free fatty acid (FFA), DAG, and TAG fractions. Moreover, co-expression of ro00075/atf2 genes resulted in a fourfold increase in total fatty acid content by a further increase of the FFA and TAG fractions. The results of this study suggest that ro00075 encodes for a PAP2 enzyme actively involved in TAG biosynthesis. Overexpression of this gene, as single one or with an atf gene, provides an alternative approach to increase the biosynthesis and accumulation of bacterial oils as a potential source of raw material for biofuel production.
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Affiliation(s)
- Martín A Hernández
- Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria, 9000, Comodoro Rivadavia, Chubut, Argentina
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Liu Y, Huang S, Zhang Y, Xu F. Isolation and characterization of a thermophilic Bacillus shackletonii K5 from a biotrickling filter for the production of polyhydroxybutyrate. J Environ Sci (China) 2014; 26:1453-1462. [PMID: 25079994 DOI: 10.1016/j.jes.2014.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/09/2013] [Accepted: 12/08/2013] [Indexed: 06/03/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are aliphatic polyesters accumulated intracellularly by both Gram-negative and Gram-positive bacteria. However, compared to the PHAs of Gram-negative bacteria, few endotoxins (lipopolysaccharides, LPS), which would be co-purified with PHAs and cause immunogenic reactions, are found in the PHAs produced by Gram-positive bacteria. A thermophilic Gram-positive bacterium K5, which exhibited good growth and polyhydroxybutyrate (PHB)-accumulating ability, has been isolated and characterized from a biotrickling filter designed for the removal of NOx from flue gas in a coal-fired power plant in China. Based on the biochemical characterization and 16S rRNA gene sequence (Genbank accession no. JX437933), the strain K5 has been identified as Bacillus shackletonii, which has rarely been reported in the literature, and this report is the first time that B. shackletonii has been found to accumulate PHB. The strain K5 was able to utilize glucose as carbon source to synthesize PHB at a broad range of temperatures (from 35 to 50°C), and the ideal temperature was 45°C. The strain K5 could effectively yield PHB of up to 69.9% of its cell dry weight (CDW) (2.28 g/L) in flask experiments employing glucose as carbon source at 45°C, followed by 56.8% and 52.3% of its CDW when using sodium succinate and glycerol as carbon source, respectively. For batch cultivation, the strain K5 was able to produce PHB of up to 72.6% of its cell dry weight (9.76 g/L) employing glucose as carbon source at 45°C and pH7.0.
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Affiliation(s)
- Yong Liu
- Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, College of Environment and Energy, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Shaobin Huang
- Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, College of Environment and Energy, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education China, Guangzhou 510006, China; The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institutions, Guangzhou 510006, China.
| | - Yongqing Zhang
- Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, College of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education China, Guangzhou 510006, China
| | - Fuqian Xu
- Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, College of Environment and Energy, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
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Induction and carbon catabolite repression of phenol degradation genes in Rhodococcus erythropolis and Rhodococcus jostii. Appl Microbiol Biotechnol 2014; 98:8267-79. [DOI: 10.1007/s00253-014-5881-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/04/2014] [Indexed: 10/25/2022]
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Urbano SB, Di Capua C, Cortez N, Farías ME, Alvarez HM. Triacylglycerol accumulation and oxidative stress in Rhodococcus species: differential effects of pro-oxidants on lipid metabolism. Extremophiles 2014; 18:375-84. [DOI: 10.1007/s00792-013-0623-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 12/29/2013] [Indexed: 11/28/2022]
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64
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Rhodococcus UKMP-5M, an endogenous lipase producing actinomycete from Peninsular Malaysia. Biologia (Bratisl) 2013. [DOI: 10.2478/s11756-013-0308-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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65
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An oleaginous bacterium that intrinsically accumulates long-chain free Fatty acids in its cytoplasm. Appl Environ Microbiol 2013; 80:1126-31. [PMID: 24296497 DOI: 10.1128/aem.03056-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Medium- and long-chain fatty acids are present in organisms in esterified forms that serve as cell membrane constituents and storage compounds. A large number of organisms are known to accumulate lipophilic materials as a source of energy and carbon. We found a bacterium, designated GK12, that intrinsically accumulates free fatty acids (FFAs) as intracellular droplets without exhibiting cytotoxicity. GK12 is an obligatory anaerobic, mesophilic lactic acid bacterium that was isolated from a methanogenic reactor. Phylogenetic analysis based on 16S rRNA gene sequences showed that GK12 is affiliated with the family Erysipelotrichaceae in the phylum Firmicutes but is distantly related to type species in this family (less than 92% similarity in 16S rRNA gene sequence). Saturated fatty acids with carbon chain lengths of 14, 16, 18, and 20 were produced from glucose under stress conditions, including higher-than-optimum temperatures and the presence of organic solvents that affect cell membrane integrity. FFAs were produced at levels corresponding to up to 25% (wt/wt) of the dry cell mass. Our data suggest that FFA accumulation is a result of an imbalance between excess membrane fatty acid biosynthesis due to homeoviscous adaptation and limited β-oxidation activity due to anaerobic growth involving lactic acid fermentation. FFA droplets were not further utilized as an energy and carbon source, even under conditions of starvation. A naturally occurring bacterium that accumulates significant amounts of long-chain FFAs with noncytotoxicity would provide useful strategies for microbial biodiesel production.
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Chen Y, Yang L, Ding Y, Zhang S, He T, Mao F, Zhang C, Zhang H, Huo C, Liu P. Tracing evolutionary footprints to identify novel gene functional linkages. PLoS One 2013; 8:e66817. [PMID: 23825567 PMCID: PMC3692504 DOI: 10.1371/journal.pone.0066817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events.
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Affiliation(s)
- Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (PL); (YC)
| | - Li Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tong He
- School of Applied Mathematics, Central University of Finance and Economics, Beijing, China
| | - Fenglou Mao
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Congyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huina Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chaoxing Huo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (PL); (YC)
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Eberly JO, Ringelberg DB, Indest KJ. Physiological characterization of lipid accumulation and in vivo ester formation in Gordonia sp. KTR9. J Ind Microbiol Biotechnol 2012. [PMID: 23207981 DOI: 10.1007/s10295-012-1218-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Previous work has demonstrated the feasibility of in vivo biodiesel synthesis in Escherichia coli, however, ethyl ester formation was dependent on an external fatty acid feedstock. In contrast to E. coli, actinomycetes may be ideal organisms for direct biodiesel synthesis because of their capacity to synthesize high levels of triacylglcerides (TAGs). In this study, we investigated the physiology and associated TAG accumulation along with the in vivo ability to catalyze ester formation from exogenous short chain alcohol sources in Gordonia sp. KTR9, a strain that possesses a large number of genes dedicated to fatty acid and lipid biosynthesis. Total lipid fatty acids content increased by 75 % and TAG content increased by 50 % under nitrogen starvation conditions in strain KTR9. Strain KTR9 tolerated the exogenous addition of up to 4 % methanol, 4 % ethanol and 2 % propanol in the media. Increasing alcohol concentrations resulted in a decrease in the degree of saturation of recovered fatty acid alcohol esters and a slight increase in the fatty acid chain length. A linear dose dependency in fatty alcohol ester synthesis was observed in the presence of 0.5-2 % methanol and ethanol compared to control KTR9 strains grown in the absence of alcohols. An inspection of the KTR9 genome revealed the presence of several putative wax ester synthase/acyl-coenzyme A : diacylglycerol acyltransferase (WS/DGAT) enzymes, encoded by atf gene homologs, that may catalyze the in vivo synthesis of fatty acid esters from short chain alcohols. Collectively, these results indicate that Gordonia sp. KTR9 may be a suitable actinomycete host strain for in vivo biodiesel synthesis.
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Affiliation(s)
- Jed O Eberly
- Environmental Laboratory, CEERD EP-P, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS 39180, USA
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68
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Procópio L, Macrae A, van Elsas JD, Seldin L. The putative α/β-hydrolases of Dietzia cinnamea P4 strain as potential enzymes for biocatalytic applications. Antonie van Leeuwenhoek 2012; 103:635-46. [PMID: 23142860 DOI: 10.1007/s10482-012-9847-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
Abstract
The draft genome of the soil actinomycete Dietzia cinnamea P4 reveals a versatile group of α/β-hydrolase fold enzymes. Phylogenetic and comparative sequence analyses were used to classify the α/β-hydrolases of strain P4 into six different groups: (i) lipases, (ii) esterases, (iii) epoxide hydrolases, (iv) haloacid dehalogenases, (v) C-C breaking enzymes and (vi) serine peptidases. The high number of lipases/esterases (41) and epoxide hydrolase enzymes (14) present in the relatively small (3.6 Mb) P4 genome is unusual; it is likely to be linked to the survival of strain P4 in its natural environment. Strain P4 is thus equipped with a large number of genes which would appear to confer survivability in harsh hot tropical soil. As such, this highly resilient soil bacterial strain provides an interesting genome for enzyme mining for applications in the field of biotransformations of polymeric compounds.
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Affiliation(s)
- Luciano Procópio
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Prof. Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941.590, Brazil
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69
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Hernández MA, Arabolaza A, Rodríguez E, Gramajo H, Alvarez HM. The atf2 gene is involved in triacylglycerol biosynthesis and accumulation in the oleaginous Rhodococcus opacus PD630. Appl Microbiol Biotechnol 2012; 97:2119-30. [DOI: 10.1007/s00253-012-4360-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 08/07/2012] [Accepted: 08/09/2012] [Indexed: 10/28/2022]
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70
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Proteomic analysis of survival of Rhodococcus jostii RHA1 during carbon starvation. Appl Environ Microbiol 2012; 78:6714-25. [PMID: 22798368 DOI: 10.1128/aem.01293-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus jostii RHA1, a catabolically diverse soil actinomycete, is highly resistant to long-term nutrient starvation. After 2 years of carbon starvation, 10% of the bacterial culture remained viable. To study the molecular basis of such resistance, we monitored the abundance of about 1,600 cytosolic proteins during a 2-week period of carbon source (benzoate) starvation. Hierarchical cluster analysis elucidated 17 major protein clusters and showed that most changes occurred during transition to stationary phase. We identified 196 proteins. A decrease in benzoate catabolic enzymes correlated with benzoate depletion, as did induction of catabolism of alternative substrates, both endogenous (lipids, carbohydrates, and proteins) and exogenous. Thus, we detected a transient 5-fold abundance increase for phthalate, phthalate ester, biphenyl, and ethyl benzene catabolic enzymes, which coincided with at least 4-fold increases in phthalate and biphenyl catabolic activities. Stationary-phase cells demonstrated an ∼250-fold increase in carbon monoxide dehydrogenase (CODH) concurrent with a 130-fold increase in CODH activity, suggesting a switch to CO or CO(2) utilization. We observed two phases of stress response: an initial response occurred during the transition to stationary phase, and a second response occurred after the cells had attained stationary phase. Although SigG synthesis was induced during starvation, a ΔsigG deletion mutant showed only minor changes in cell survival. Stationary-phase cells underwent reductive cell division. The extreme capacity of RHA1 to survive starvation does not appear to involve novel mechanisms; rather, it seems to be due to the coordinated combination of earlier-described mechanisms.
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71
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Differences in substrate specificities of five bacterial wax ester synthases. Appl Environ Microbiol 2012; 78:5734-45. [PMID: 22685145 DOI: 10.1128/aem.00534-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wax esters are produced in certain bacteria as a potential carbon and energy storage compound. The final enzyme in the biosynthetic pathway responsible for wax ester production is the bifunctional wax ester synthase/acyl-coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT), which utilizes a range of fatty alcohols and fatty acyl-CoAs to synthesize the corresponding wax ester. We report here the isolation and substrate range characterization for five WS/DGAT enzymes from four different bacteria: Marinobacter aquaeolei VT8, Acinetobacter baylyi, Rhodococcus jostii RHA1, and Psychrobacter cryohalolentis K5. The results from kinetic studies of isolated enzymes reveal a differential activity based on the order of substrate addition and reveal subtle differences between the substrate selectivity of the different enzymes. These in vitro results are compared to the wax ester and triacylglyceride product profiles obtained from each organism grown under neutral lipid accumulating conditions, providing potential insights into the role that the WS/DGAT enzyme plays in determining the final wax ester products that are produced under conditions of nutrient stress in each of these bacteria. Further, the analysis revealed that one enzyme in particular from M. aquaeolei VT8 showed the greatest potential for future study based on rapid purification and significantly higher activity than was found for the other isolated WS/DGAT enzymes. The results provide a framework to test prospective differences between these enzymes for potential biotechnological applications such as high-value petrochemicals and biofuel production.
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72
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Abstract
The two metabolically versatile actinobacteria Rhodococcus opacus PD630 and R. jostii RHA1 can efficiently convert diverse organic substrates into neutral lipids mainly consisting of triacylglycerol (TAG), the precursor of energy-rich hydrocarbon. Neither, however, is able to utilize xylose, the important component present in lignocellulosic biomass, as the carbon source for growth and lipid accumulation. In order to broaden their substrate utilization range, the metabolic pathway of d-xylose utilization was introduced into these two strains. This was accomplished by heterogenous expression of two well-selected genes, xylA, encoding xylose isomerase, and xylB, encoding xylulokinase from Streptomyces lividans TK23, under the control of the tac promoter with an Escherichia coli-Rhodococcus shuttle vector. The recombinant R. jostii RHA1 bearing xylA could grow on xylose as the sole carbon source, and additional expression of xylB further improved the biomass yield. The recombinant could consume both glucose and xylose in the sugar mixture, although xylose metabolism was still affected by the presence of glucose. The xylose metabolic pathway was also introduced into the high-lipid-producing strain R. opacus PD630 by expression of xylA and xylB. Under nitrogen-limited conditions, the fatty acid composition was determined, and lipid produced from xylose by recombinants of R. jostii RHA1 and R. opacus PD630 carrying xylA and xylB represented up to 52.5% and 68.3% of the cell dry weight (CDW), respectively. This work demonstrates that it is feasible to produce lipid from the sugars, including xylose, derived from renewable feedstock by genetic modification of rhodococcus strains.
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73
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Beg QK, Zampieri M, Klitgord N, Collins SB, Altafini C, Serres MH, Segrè D. Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Res 2012; 40:7132-49. [PMID: 22638572 PMCID: PMC3424579 DOI: 10.1093/nar/gks467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
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Affiliation(s)
- Qasim K Beg
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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74
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Ding Y, Yang L, Zhang S, Wang Y, Du Y, Pu J, Peng G, Chen Y, Zhang H, Yu J, Hang H, Wu P, Yang F, Yang H, Steinbüchel A, Liu P. Identification of the major functional proteins of prokaryotic lipid droplets. J Lipid Res 2012; 53:399-411. [PMID: 22180631 PMCID: PMC3276463 DOI: 10.1194/jlr.m021899] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 12/15/2011] [Indexed: 11/20/2022] Open
Abstract
Storage of cellular triacylglycerols (TAGs) in lipid droplets (LDs) has been linked to the progression of many metabolic diseases in humans, and to the development of biofuels from plants and microorganisms. However, the biogenesis and dynamics of LDs are poorly understood. Compared with other organisms, bacteria seem to be a better model system for studying LD biology, because they are relatively simple and are highly efficient in converting biomass to TAG. We obtained highly purified LDs from Rhodococcus sp. RHA1, a bacterium that can produce TAG from many carbon sources, and then comprehensively characterized the LD proteome. Of the 228 LD-associated proteins identified, two major proteins, ro02104 and PspA, constituted about 15% of the total LD protein. The structure predicted for ro02104 resembles that of apolipoproteins, the structural proteins of plasma lipoproteins in mammals. Deletion of ro02104 resulted in the formation of supersized LDs, indicating that ro02104 plays a critical role in cellular LD dynamics. The putative α helix of the ro02104 LD-targeting domain (amino acids 83-146) is also similar to that of apolipoproteins. We report the identification of 228 proteins in the proteome of prokaryotic LDs, identify a putative structural protein of this organelle, and suggest that apolipoproteins may have an evolutionarily conserved role in the storage and trafficking of neutral lipids.
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Affiliation(s)
- Yunfeng Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China; National Laboratory of Biomacromolecules, Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Li Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China; National Laboratory of Biomacromolecules, Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China
| | - Yang Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China; National Laboratory of Biomacromolecules, Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Yalan Du
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China; National Laboratory of Biomacromolecules, Department of Histology and Embryology, University of South China, Hengyang, Hunan Province, China
| | - Jing Pu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China; National Laboratory of Biomacromolecules, Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Gong Peng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China; National Laboratory of Biomacromolecules, Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China
| | - Huina Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China
| | - Jinhai Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China; National Laboratory of Biomacromolecules, Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Haiying Hang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China
| | - Peng Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China
| | - Fuquan Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China
| | - Hongyuan Yang
- National Laboratory of Biomacromolecules, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Alexander Steinbüchel
- National Laboratory of Biomacromolecules, Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, D-48149 Münster, Germany, and King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China.
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75
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Revellame ED, Hernandez R, French W, Holmes WE, Benson TJ, Pham PJ, Forks A, Callahan II R. Lipid storage compounds in raw activated sludge microorganisms for biofuels and oleochemicals production. RSC Adv 2012. [DOI: 10.1039/c2ra01078j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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76
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Willis RM, Wahlen BD, Seefeldt LC, Barney BM. Characterization of a fatty acyl-CoA reductase from Marinobacter aquaeolei VT8: a bacterial enzyme catalyzing the reduction of fatty acyl-CoA to fatty alcohol. Biochemistry 2011; 50:10550-8. [PMID: 22035211 DOI: 10.1021/bi2008646] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fatty alcohols are of interest as a renewable feedstock to replace petroleum compounds used as fuels, in cosmetics, and in pharmaceuticals. One biological approach to the production of fatty alcohols involves the sequential action of two bacterial enzymes: (i) reduction of a fatty acyl-CoA to the corresponding fatty aldehyde catalyzed by a fatty acyl-CoA reductase, followed by (ii) reduction of the fatty aldehyde to the corresponding fatty alcohol catalyzed by a fatty aldehyde reductase. Here, we identify, purify, and characterize a novel bacterial enzyme from Marinobacter aquaeolei VT8 that catalyzes the reduction of fatty acyl-CoA by four electrons to the corresponding fatty alcohol, eliminating the need for a separate fatty aldehyde reductase. The enzyme is shown to reduce fatty acyl-CoAs ranging from C8:0 to C20:4 to the corresponding fatty alcohols, with the highest rate found for palmitoyl-CoA (C16:0). The dependence of the rate of reduction of palmitoyl-CoA on substrate concentration was cooperative, with an apparent K(m) ~ 4 μM, V(max) ~ 200 nmol NADP(+) min(-1) (mg protein)(-1), and n ~ 3. The enzyme also reduced a range of fatty aldehydes with decanal having the highest activity. The substrate cis-11-hexadecenal was reduced in a cooperative manner with an apparent K(m) of ~50 μM, V(max) of ~8 μmol NADP(+) min(-1) (mg protein)(-1), and n ~ 2.
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Affiliation(s)
- Robert M Willis
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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77
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Holder JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J, Zeng Q, Leach ALB, Ghiviriga I, Dancel C, Abeel T, Gevers D, Kodira CD, Desany B, Affourtit JP, Birren BW, Sinskey AJ. Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genet 2011; 7:e1002219. [PMID: 21931557 PMCID: PMC3169528 DOI: 10.1371/journal.pgen.1002219] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 06/17/2011] [Indexed: 11/18/2022] Open
Abstract
The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.
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Affiliation(s)
- Jason W. Holder
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Jil C. Ulrich
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anthony C. DeBono
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul A. Godfrey
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Jeremy Zucker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Alex L. B. Leach
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ion Ghiviriga
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Christine Dancel
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Thomas Abeel
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Dirk Gevers
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Brian Desany
- 454 Life Sciences, Branford, Connecticut, United States of America
| | | | - Bruce W. Birren
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Anthony J. Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Engineering Systems Division, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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78
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Fanget NVJ, Foley S. Starvation/stationary-phase survival of Rhodococcus erythropolis SQ1: a physiological and genetic analysis. Arch Microbiol 2010; 193:1-13. [DOI: 10.1007/s00203-010-0638-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Revised: 09/12/2010] [Accepted: 09/30/2010] [Indexed: 11/24/2022]
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79
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Hernández MA, Alvarez HM. Glycogen formation by Rhodococcus species and the effect of inhibition of lipid biosynthesis on glycogen accumulation in Rhodococcus opacus PD630. FEMS Microbiol Lett 2010; 312:93-9. [DOI: 10.1111/j.1574-6968.2010.02108.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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80
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Isolation of polyhydroxyalkanoate-producing bacteria from a polluted soil and characterization of the isolated strain Bacillus cereus YB-4. Polym Degrad Stab 2010. [DOI: 10.1016/j.polymdegradstab.2010.01.033] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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81
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Schreiberová O, Krulikovská T, Sigler K, Čejková A, Řezanka T. RP-HPLC/MS-APCI Analysis of Branched Chain TAG Prepared by Precursor-Directed Biosynthesis with Rhodococcus erythropolis. Lipids 2010; 45:743-56. [DOI: 10.1007/s11745-010-3447-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 06/29/2010] [Indexed: 10/19/2022]
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82
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Characterization of indigenous Rhodococcus sp. 602, a strain able to accumulate triacylglycerides from naphthyl compounds under nitrogen-starved conditions. Res Microbiol 2010; 161:198-207. [PMID: 20144706 DOI: 10.1016/j.resmic.2010.01.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 01/04/2010] [Accepted: 01/20/2010] [Indexed: 11/19/2022]
Abstract
An indigenous bacterium (strain 602) isolated in this study from a polluted soil sample collected in Patagonia (Argentina) was investigated in relation to its metabolic responses under unbalanced growth conditions. This strain was identified as Rhodococcus sp. by molecular analyses. Strain 602 showed the ability to degrade a wide range of compounds and to synthesize triacylglycerols under nitrogen-limiting conditions. Cells were also able to accumulate triacylglycerols during cultivation on naphthalene and naphthyl-1-dodecanoate. Triacylglycerols produced by resting cells in the presence of naphthyl-1-dodecanoate contained only short-chain length fatty acids (from C(8) to C(12)), suggesting an initial attack of the substrate by an esterase releasing 1-naphthol and dodecanoic acid, which was subsequently degraded by beta-oxidation. On the other hand, naphthalene seemed to be degraded by a mono-oxygenase yielding 1-naphthol, which was then transformed to 4-hydroxy-1-tetralone and to other possible metabolic intermediates. On the basis of the results obtained, a pathway involved in the metabolism of both aromatic compounds under nitrogen starvation by strain 602 is proposed. The results also demonstrated that Rhodococcus sp. 602 maintains its metabolic activity even in the absence of a nitrogen source. Intracellular triacylglycerols may help cells to maintain their catabolic activities under these growth-restricting conditions.
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83
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Seibold GM, Hagmann CT, Schietzel M, Emer D, Auchter M, Schreiner J, Eikmanns BJ. The transcriptional regulators RamA and RamB are involved in the regulation of glycogen synthesis in Corynebacterium glutamicum. MICROBIOLOGY-SGM 2010; 156:1256-1263. [PMID: 20056699 DOI: 10.1099/mic.0.036756-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
When grown in glucose-, fructose- or sucrose-containing medium, the amino acid producer Corynebacterium glutamicum transiently accumulates large amounts of glycogen (up to 10% of its dry weight), whereas only a marginal amount of glycogen is formed during growth with acetate. This carbon-source-dependent regulation is at least partially due to transcriptional control of glgC, encoding ADP-glucose pyrophosphorylase, the first enzyme of glycogen synthesis from glucose-1-phosphate. Here, we have analysed a possible regulatory role for the transcriptional regulators RamA and RamB on glycogen content of the cells and on control of expression of glgC and of glgA, which encodes the second enzyme of glycogen synthesis, glycogen synthase. Determination of the glycogen content of RamA- and RamB-deficient C. glutamicum indicated that RamA and RamB influence glycogen synthesis positively and negatively, respectively. In accordance with the identification of putative RamA and RamB binding sites upstream of glgC and glgA, both regulators were found to bind specifically to the glgC-glgA intergenic promoter region. Promoter activity assays in wild-type and RamA- and RamB-deficient strains of C. glutamicum revealed that (i) RamA is a positive regulator of glgC and glgA, (ii) RamB is a negative regulator of glgA and (iii) neither RamA nor RamB alone is responsible for the carbon-source-dependent regulation of glycogen synthesis in C. glutamicum.
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Affiliation(s)
- Gerd M Seibold
- Institute of Biochemistry, University of Cologne, D-50674 Cologne, Germany.,Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Christian T Hagmann
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Melanie Schietzel
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Denise Emer
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Marc Auchter
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Joy Schreiner
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Bernhard J Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
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84
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Alvarez HM, Steinbüchel A. Physiology, Biochemistry, and Molecular Biology of Triacylglycerol Accumulation by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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