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Abstract
This review summarises the characterised bacterial terpene cyclases and their products and discusses the enzyme mechanisms.
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Affiliation(s)
- Jeroen S. Dickschat
- University of Bonn
- Kekulé-Institute of Organic Chemistry and Biochemistry
- 53121 Bonn
- Germany
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52
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Wang Z, Xiao P, Song G, Li Y, Li R. Isolation and characterization of a new reported cyanobacterium Leptolyngbya bijugata coproducing odorous geosmin and 2-methylisoborneol. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:12133-12140. [PMID: 25893620 DOI: 10.1007/s11356-015-4470-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
The earthy-musty compounds geosmin and 2-methylisoborneol (MIB) produced by cyanobacteria are considered as the main biological causes of off-flavor events, especially in aquatic ecosystems. More than 50 filamentous cyanobacteria species have been documented as geosmin or MIB producers; however, little is known about the species coproducing these two metabolites. In this study, an epiphytic sample was collected from a river in Hubei, China. Three isolated strains (A2, B2, and B4) producing earthy odors were successfully isolated and identified as the cyanobacterium Leptolyngbya bijugata Anagnostidis et Komárek 1988 based on morphology and 16S rDNA sequences. Gas chromatography analysis confirmed that the isolated L. bijugata strains were geosmin and MIB coproducers, with accumulation ranging from 13.6 to 22.4 and 12.3 to 57.5 μg L(-1), respectively. The partial fragments of geosmin and MIB synthesis genes in the L. bijugata strains were cloned and sequenced. Further sequences and phylogenetic analysis indicated the high conservation and a common origin of these genes in cyanobacteria. This study is the first to report and characterize the coproduction of geosmin and MIB by L. bijugata, representing a new source for potential risk of off-flavor events.
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Affiliation(s)
- Zhongjie Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
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53
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Bacha N, Echarki Z, Mathieu F, Lebrihi A. Development of a novel quantitative PCR assay as a measurement for the presence of geosmin-producing fungi. J Appl Microbiol 2015; 118:1144-51. [PMID: 25580564 DOI: 10.1111/jam.12747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 01/04/2015] [Accepted: 01/04/2015] [Indexed: 11/30/2022]
Abstract
AIMS To provide an efficient technique for monitoring the off-flavoured fungal compound geosmin. METHODS AND RESULTS Geosmin-associated gpe1 gene of Penicillium expansum displayed ≥99% similarity to cytochrome P450 gene of geosmin-producing P. restrictum, but ≤40% similarities to geosmin biosynthesis, non-cytochromic gene of Streptomyces avermitilis and cytochrome P450 genes of non-geosmin-producing Neotyphodium lolii, Phoma betae and P. paxilli. Serial 10-fold dilutions of P. expansum's DNA was subjected to a previously reported qPCR assay (Atoui et al. 2007), utilizing gpe1 specific primer pair 'SNgpe1F/SNgpe1R'. A linear relationship between DNA quantity and Cycle Threshold (Ct ), with strong correlative coefficient, was observed. Using the available physico-chemical method, geosmin was quantified in 188 grape samples. Penicillium spp's DNA was quantified in these samples, utilizing the developed qPCR assay. A strong positive correlation (R(2) = 0·97) between Penicillium's DNA and geosmin concentration was observed. Furthermore, <50 ng μl(-1) Penicillium's DNA corresponds to geosmin level below the permitted intensity limit i.e. 4, for 'Flavour Profile Analysis'. CONCLUSIONS Penicillium spp., genomic DNA level can provide an efficient way to quantify geosmin. SIGNIFICANCE AND IMPACT OF THE STUDY This particular qPCR technique can be utilized in numerous food industries, for the timely detection and monitoring of geosmin contamination.
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Affiliation(s)
- N Bacha
- Center of Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan; Laboratoire de Génie Chimique, INPT-UPS, Université de Toulouse, Castanet-Tolosan Cedex, France
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54
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Effects of light and temperature on the odor production of 2-methylisoborneol-producing Pseudanabaena sp. and geosmin-producing Anabaena ucrainica (cyanobacteria). BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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55
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Pattanaik B, Lindberg P. Terpenoids and their biosynthesis in cyanobacteria. Life (Basel) 2015; 5:269-93. [PMID: 25615610 PMCID: PMC4390852 DOI: 10.3390/life5010269] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/14/2015] [Indexed: 12/21/2022] Open
Abstract
Terpenoids, or isoprenoids, are a family of compounds with great structural diversity which are essential for all living organisms. In cyanobacteria, they are synthesized from the methylerythritol-phosphate (MEP) pathway, using glyceraldehyde 3-phosphate and pyruvate produced by photosynthesis as substrates. The products of the MEP pathway are the isomeric five-carbon compounds isopentenyl diphosphate and dimethylallyl diphosphate, which in turn form the basic building blocks for formation of all terpenoids. Many terpenoid compounds have useful properties and are of interest in the fields of pharmaceuticals and nutrition, and even potentially as future biofuels. The MEP pathway, its function and regulation, and the subsequent formation of terpenoids have not been fully elucidated in cyanobacteria, despite its relevance for biotechnological applications. In this review, we summarize the present knowledge about cyanobacterial terpenoid biosynthesis, both regarding the native metabolism and regarding metabolic engineering of cyanobacteria for heterologous production of non-native terpenoids.
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Affiliation(s)
- Bagmi Pattanaik
- Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden.
| | - Pia Lindberg
- Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden.
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56
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Yamada Y, Kuzuyama T, Komatsu M, Shin-Ya K, Omura S, Cane DE, Ikeda H. Terpene synthases are widely distributed in bacteria. Proc Natl Acad Sci U S A 2015; 112:857-62. [PMID: 25535391 PMCID: PMC4311827 DOI: 10.1073/pnas.1422108112] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Odoriferous terpene metabolites of bacterial origin have been known for many years. In genome-sequenced Streptomycetaceae microorganisms, the vast majority produces the degraded sesquiterpene alcohol geosmin. Two minor groups of bacteria do not produce geosmin, with one of these groups instead producing other sesquiterpene alcohols, whereas members of the remaining group do not produce any detectable terpenoid metabolites. Because bacterial terpene synthases typically show no significant overall sequence similarity to any other known fungal or plant terpene synthases and usually exhibit relatively low levels of mutual sequence similarity with other bacterial synthases, simple correlation of protein sequence data with the structure of the cyclized terpene product has been precluded. We have previously described a powerful search method based on the use of hidden Markov models (HMMs) and protein families database (Pfam) search that has allowed the discovery of monoterpene synthases of bacterial origin. Using an enhanced set of HMM parameters generated using a training set of 140 previously identified bacterial terpene synthase sequences, a Pfam search of 8,759,463 predicted bacterial proteins from public databases and in-house draft genome data has now revealed 262 presumptive terpene synthases. The biochemical function of a considerable number of these presumptive terpene synthase genes could be determined by expression in a specially engineered heterologous Streptomyces host and spectroscopic identification of the resulting terpene products. In addition to a wide variety of terpenes that had been previously reported from fungal or plant sources, we have isolated and determined the complete structures of 13 previously unidentified cyclic sesquiterpenes and diterpenes.
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Affiliation(s)
- Yuuki Yamada
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, University of Tokyo, Tokyo 113-8657, Japan
| | - Mamoru Komatsu
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Satoshi Omura
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108-8461, Japan; and
| | - David E Cane
- Department of Chemistry, Brown University, Providence, RI 02912-9108
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan;
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Suurnäkki S, Gomez-Saez GV, Rantala-Ylinen A, Jokela J, Fewer DP, Sivonen K. Identification of geosmin and 2-methylisoborneol in cyanobacteria and molecular detection methods for the producers of these compounds. WATER RESEARCH 2015; 68:56-66. [PMID: 25462716 DOI: 10.1016/j.watres.2014.09.037] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 09/10/2014] [Accepted: 09/13/2014] [Indexed: 06/04/2023]
Abstract
Geosmin and 2-methylisoborneol (MIB) are muddy/earthy off-flavor metabolites produced by a range of bacteria. Cyanobacteria are the major producers of the volatile metabolites geosmin and MIB which produce taste and odor problems in drinking water and fish worldwide. Here we detected geosmin and MIB by studying 100 cyanobacteria strains using solid phase microextraction gas chromatography mass spectrometry (SPME GC-MS). A total of 21 geosmin producers were identified from six cyanobacteria genera. Two of the geosmin producers also produced MIB. A PCR protocol for the detection of geoA and MIB synthase genes involved in the biosynthesis of geosmin and MIB was developed. The geoA and MIB synthase genes were detected in all strains shown to produce geosmin and MIB, respectively. Cyanobacterial geoA and MIB synthase sequences showed homology to terpene synthases genes of actinobacteria and proteobacteria. Additional off-flavor compounds, nor-carotenoids β-ionone and β-cyclocitral, were found from 55 strains among the 100 cyanobacterial strains studied; β-ionone was present in 45 and β-cyclocitral in 10 strains. Six of the cyanobacteria which contain off-flavor compounds also produced toxins, anatoxin-a or microcystins. The molecular method developed is a useful tool in monitoring potential cyanobacterial producers of geosmin and MIB.
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Affiliation(s)
- Suvi Suurnäkki
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, PO Box 56, FI-00014 University of Helsinki, Finland
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58
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Genetic Basis for Geosmin Production by the Water Bloom-Forming Cyanobacterium, Anabaena ucrainica. WATER 2014. [DOI: 10.3390/w7010175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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59
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Grishko VV, Nogovitsina YM, Ivshina IB. Bacterial transformation of terpenoids. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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60
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Dickschat JS, Pahirulzaman KAK, Rabe P, Klapschinski TA. An improved technique for the rapid chemical characterisation of bacterial terpene cyclases. Chembiochem 2014; 15:810-4. [PMID: 24573945 DOI: 10.1002/cbic.201300763] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Indexed: 11/06/2022]
Abstract
A derivative of the pET28c(+) expression vector was constructed. It contains a yeast replication system (2μ origin of replication) and a yeast selectable marker (URA3), and can be used for gene cloning in yeast by efficient homologous recombination, and for heterologous expression in E. coli. The vector was used for the expression and chemical characterisation of three bacterial terpene cyclases.
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Affiliation(s)
- Jeroen S Dickschat
- Institut für Organische Chemie, TU Braunschweig, Hagenring 30, 38106 Braunschweig (Germany).
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61
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Kakimoto M, Ishikawa T, Miyagi A, Saito K, Miyazaki M, Asaeda T, Yamaguchi M, Uchimiya H, Kawai-Yamada M. Culture temperature affects gene expression and metabolic pathways in the 2-methylisoborneol-producing cyanobacterium Pseudanabaena galeata. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:292-300. [PMID: 24140001 DOI: 10.1016/j.jplph.2013.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/21/2013] [Accepted: 09/04/2013] [Indexed: 06/02/2023]
Abstract
A volatile metabolite, 2-methylisoborneol (2-MIB), causes an unpleasant taste and odor in tap water. Some filamentous cyanobacteria produce 2-MIB via a two-step biosynthetic pathway: methylation of geranyl diphosphate (GPP) by methyl transferase (GPPMT), followed by the cyclization of methyl-GPP by monoterpene cyclase (MIBS). We isolated the genes encoding GPPMT and MIBS from Pseudanabaena galeata, a filamentous cyanobacterium known to be a major causal organism of 2-MIB production in Japanese lakes. The predicted amino acid sequence showed high similarity with that of Pseudanabaena limnetica (96% identity in GPPMT and 97% identity in MIBS). P. galeata was cultured at different temperatures to examine the effect of growth conditions on the production of 2-MIB and major metabolites. Gas chromatograph-mass spectrometry (GC-MS) measurements showed higher accumulation of 2-MIB at 30 °C than at 4 °C or 20 °C after 24 h of culture. Real-time-RT PCR analysis showed that the expression levels of the genes encoding GPPMT and MIBS decreased at 4 °C and increased at 30 °C, compared with at 20 °C. Furthermore, metabolite analysis showed dramatic changes in primary metabolite concentrations in cyanobacteria grown at different temperatures. The data indicate that changes in carbon flow in the TCA cycle affect 2-MIB biosynthesis at higher temperatures.
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Affiliation(s)
- Masayuki Kakimoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Saitama City Institute of Health Science and Research, 7-5-12 Suzuya, Chuo-ku, Saitama City, Saitama 338-0013, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Atsuko Miyagi
- Institute for Environmental Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kazuaki Saito
- Saitama City Institute of Health Science and Research, 7-5-12 Suzuya, Chuo-ku, Saitama City, Saitama 338-0013, Japan
| | - Motonobu Miyazaki
- Saitama City Institute of Health Science and Research, 7-5-12 Suzuya, Chuo-ku, Saitama City, Saitama 338-0013, Japan
| | - Takashi Asaeda
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Masatoshi Yamaguchi
- Institute for Environmental Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hirofumi Uchimiya
- Institute for Environmental Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Institute for Environmental Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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63
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Rabe P, Citron CA, Dickschat JS. Volatile Terpenes from Actinomycetes: A Biosynthetic Study Correlating Chemical Analyses to Genome Data. Chembiochem 2013; 14:2345-54. [DOI: 10.1002/cbic.201300329] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Indexed: 11/10/2022]
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64
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Köksal M, Chou WKW, Cane DE, Christianson DW. Unexpected reactivity of 2-fluorolinalyl diphosphate in the active site of crystalline 2-methylisoborneol synthase. Biochemistry 2013; 52:5247-55. [PMID: 23844678 DOI: 10.1021/bi400797c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of 2-methylisoborneol synthase (MIBS) from Streptomyces coelicolor A3(2) has been determined in its unliganded state and in complex with two Mg(2+) ions and 2-fluoroneryl diphosphate at 1.85 and 2.00 Å resolution, respectively. Under normal circumstances, MIBS catalyzes the cyclization of the naturally occurring, noncanonical 11-carbon isoprenoid substrate, 2-methylgeranyl diphosphate, which first undergoes an ionization-isomerization-ionization sequence through the tertiary diphosphate intermediate 2-methyllinalyl diphosphate to enable subsequent cyclization chemistry. MIBS does not exhibit catalytic activity with 2-fluorogeranyl diphosphate, and we recently reported the crystal structure of MIBS complexed with this unreactive substrate analogue [ Köksal, M., Chou, W. K. W., Cane, D. E., Christianson, D. W. (2012) Biochemistry 51 , 3011-3020 ]. However, cocrystallization of MIBS with the fluorinated analogue of the tertiary allylic diphosphate intermediate, 2-fluorolinalyl diphosphate, reveals unexpected reactivity for the intermediate analogue and yields the crystal structure of the complex with the primary allylic diphosphate, 2-fluoroneryl diphosphate. Comparison with the structure of the unliganded enzyme reveals that the crystalline enzyme active site remains partially open, presumably due to the binding of only two Mg(2+) ions. Assays in solution indicate that MIBS catalyzes the generation of (1R)-(+)-camphor from the substrate 2-fluorolinalyl diphosphate, suggesting that both 2-fluorolinalyl diphosphate and 2-methyllinalyl diphosphate follow the identical cyclization mechanism leading to 2-substituted isoborneol products; however, the initially generated 2-fluoroisoborneol cyclization product is unstable and undergoes elimination of hydrogen fluoride to yield (1R)-(+)-camphor.
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Affiliation(s)
- Mustafa Köksal
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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65
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Ariyawutthiphan O, Ose T, Minami A, Sinde S, Tsuda M, Gao YG, Yao M, Oikawa H, Tanaka I. Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependentC-methylation. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1558-69. [DOI: 10.1107/s0907444912038486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/07/2012] [Indexed: 11/10/2022]
Abstract
In the typical isoprenoid-biosynthesis pathway, condensation of the universal C5-unit precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) occursviathe common intermediates prenyl pyrophosphates (C10–C20). The diversity of isoprenoids reflects differences in chain length, cyclization and further additional modification after cyclization. In contrast, the biosynthesis of 2-methylisonorneol (2-MIB), which is responsible for taste and odour problems in drinking water, is unique in that it primes the enzymatic methylation of geranyl pyrophosphate (GPP) before cyclization, which is catalyzed by anS-adenosyl-L-methionine-dependent methyltransferase (GPPMT). The substrate of GPPMT contains a nonconjugated olefin and the reaction mechanism is expected to be similar to that of the steroid methyltransferase (SMT) family. Here, structural analysis of GPPMT in complex with its cofactor and substrate revealed the mechanisms of substrate recognition and possible enzymatic reaction. Using the structures of these complexes, methyl-group transfer and the subsequent proton-abstraction mechanism are discussed. GPPMT and SMTs contain a conserved glutamate residue that is likely to play a role as a general base. Comparison with the reaction mechanism of the mycolic acid cyclopropane synthase (MACS) family also supports this result. This enzyme represented here is the first model of the enzymaticC-methylation of a nonconjugated olefin in the isoprenoid-biosynthesis pathway. In addition, an elaborate system to avoid methylation of incorrect substrates is proposed.
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Li Z, Hobson P, An W, Burch MD, House J, Yang M. Earthy odor compounds production and loss in three cyanobacterial cultures. WATER RESEARCH 2012; 46:5165-5173. [PMID: 22818951 DOI: 10.1016/j.watres.2012.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/05/2012] [Accepted: 06/06/2012] [Indexed: 06/01/2023]
Abstract
Geosmin and 2-methylisoborneol (MIB) related odor events caused by cyanobacteria have been a very common problem to water supply. This paper investigated the effects of temperature (18 and 25 °C) and light intensity (10 and 100 μmol photons m(-2) s(-1)) on the production behaviors of earthy odor compounds by three odorous cyanobacteria, i.e., the geosmin-producing planktonic Anabaena circinalis (Ana 318), geosmin-producing benthic Phormidium amoenum (Pho 012) and MIB-producing benthic Phormidium sp. (Pho 689). At the same time, the effects of biodegradation and volatilization on the fates of the released odor compounds in water were also evaluated. The combination of high temperature (25 °C) and light intensity (100 μmol photons m(-2) s(-1)) favored the growth of the three cyanobacteria and the production of chl-a and odor compounds. However, higher chl-a and odor yields (average odor compounds per cell) were achieved for the two benthic cyanobacteria at the temperature of 18 °C. Most of geosmin was included within the cells for Ana 318 (95-99%) and Pho 012 (85-60%), while only 20-40% MIB was bound to the cells for Pho 689. The half-life times of MIB and geosmin due to volatilization varied between 18.8 and 35.4 days, while 8 out of 10 samples exhibited a half-life time (t(1/2)) for geosmin biodegradation shorter than 1 day (0.38-15.0 h), showing that biodegradation could affect the fate of geosmin significantly in aquatic environments. In comparison, biodegradation of MIB was much slower (t(1/2): 122-2166 h). Denaturing gradient gel electrophoresis (DGGE) analysis showed that Pseudomonas- and Sphingomonas-like bacteria coexisted with cyanobacteria in the cultures, and may have played an important role in geosmin/MIB biodegradation. The result of this study will be helpful for better understanding and managing the earthy odor problems caused by cyanobacteria in water supply.
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Affiliation(s)
- Zonglai Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Chuang LY, Chang HW, Tsai JH, Yang CH. Features for computational operon prediction in prokaryotes. Brief Funct Genomics 2012; 11:291-9. [PMID: 22753776 DOI: 10.1093/bfgp/els024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accurate prediction of operons can improve the functional annotation and application of genes within operons in prokaryotes. Here, we review several features: (i) intergenic distance, (ii) metabolic pathways, (iii) homologous genes, (iv) promoters and terminators, (v) gene order conservation, (vi) microarray, (vii) clusters of orthologous groups, (viii) gene length ratio, (ix) phylogenetic profiles, (x) operon length/size and (xi) STRING database scores, as well as some other features, which have been applied in recent operon prediction methods in prokaryotes in the literature. Based on a comparison of the prediction performances of these features, we conclude that other, as yet undiscovered features, or feature selection with a receiver operating characteristic analysis before algorithm processing can improve operon prediction in prokaryotes.
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Affiliation(s)
- Li-Yeh Chuang
- Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Taiwan
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Köksal M, Chou WKW, Cane DE, Christianson DW. Structure of 2-methylisoborneol synthase from Streptomyces coelicolor and implications for the cyclization of a noncanonical C-methylated monoterpenoid substrate. Biochemistry 2012; 51:3011-20. [PMID: 22455514 DOI: 10.1021/bi201827a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The crystal structure of 2-methylisoborneol synthase (MIBS) from Streptomyces coelicolor A3(2) has been determined in complex with substrate analogues geranyl-S-thiolodiphosphate and 2-fluorogeranyl diphosphate at 1.80 and 1.95 Å resolution, respectively. This terpenoid cyclase catalyzes the cyclization of the naturally occurring, noncanonical C-methylated isoprenoid substrate, 2-methylgeranyl diphosphate, to form the bicyclic product 2-methylisoborneol, a volatile C(11) homoterpene alcohol with an earthy, musty odor. While MIBS adopts the tertiary structure of a class I terpenoid cyclase, its dimeric quaternary structure differs from that previously observed in dimeric terpenoid cyclases from plants and fungi. The quaternary structure of MIBS is nonetheless similar in some respects to that of dimeric farnesyl diphosphate synthase, which is not a cyclase. The structures of MIBS complexed with substrate analogues provide insights regarding differences in the catalytic mechanism of MIBS and the mechanisms of (+)-bornyl diphosphate synthase and endo-fenchol synthase, plant cyclases that convert geranyl diphosphate into products with closely related bicyclic bornyl skeletons, but distinct structures and stereochemistries.
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Affiliation(s)
- Mustafa Köksal
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
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Abstract
Tens of thousands of terpenoids are present in both terrestrial and marine plants, as well as fungi. In the last 5-10 years, however, it has become evident that terpenes are also produced by numerous bacteria, especially soil-dwelling Gram-positive organisms such as Streptomyces and other Actinomycetes. Although some microbial terpenes, such as geosmin, the degraded sesquiterpene responsible for the smell of moist soil, the characteristic odor of the earth itself, have been known for over 100 years, few terpenoids have been identified by classical structure- or activity-guided screening of bacterial culture extracts. In fact, the majority of cyclic terpenes from bacterial species have only recently been uncovered by the newly developed techniques of "genome mining". In this new paradigm for biochemical discovery, bacterial genome sequences are first analyzed with powerful bioinformatic tools, such as the BLASTP program or Profile Hidden Markov models, to screen for and identify conserved protein sequences harboring a characteristic set of universally conserved functional domains typical of all terpene synthases. Of particular importance is the presence of variants of two universally conserved domains, the aspartate-rich DDXX(D/E) motif and the NSE/DTE triad, (N/D)DXX(S/T)XX(K/R)(D/E). Both domains have been implicated in the binding of the essential divalent cation, typically Mg(2+), that is required for cyclization of the universal acyclic terpene precursors, such as farnesyl and geranyl diphosphate. The low level of overall sequence similarity among terpene synthases, however, has so far precluded any simple correlation of protein sequence with the structure of the cyclized terpene product. The actual biochemical function of a cryptic bacterial (or indeed any) terpene synthase must therefore be determined by direct experiment. Two common approaches are (i) incubation of the expressed recombinant protein with acyclic allylic diphosphate substrates and identification of the resultant terpene hydrocarbon or alcohol and (ii) in vivo expression in engineered bacterial hosts that can support the production of terpene metabolites. One of the most attractive features of the coordinated application of genome mining and biochemical characterization is that the discovery of natural products is directly coupled to the simultaneous discovery and exploitation of the responsible biosynthetic genes and enzymes. Bacterial genome mining has proved highly rewarding scientifically, already uncovering more than a dozen newly identified cyclic terpenes (many of them unique to bacteria), as well as several novel cyclization mechanisms. Moreover, bioinformatic analysis has identified more than 120 presumptive genes for bacterial terpene synthases that are now ripe for exploration. In this Account, we review a particularly rich vein we have mined in the genomes of two model Actinomycetes, Streptomyces coelicolor and Streptomyces avermitilis, from which the entire set of terpenoid biosynthetic genes and pathways have now been elucidated. In addition, studies of terpenoid biosynthetic gene clusters have revealed a wealth of previously unknown oxidative enzymes, including cytochromes P450, non-heme iron-dependent dioxygenases, and flavin monooxygenases. We have shown that these enzymes catalyze a variety of unusual biochemical reactions, including two-step ketonization of methylene groups, desaturation-epoxidation of secondary methyl groups, and pathway-specific Baeyer-Villiger oxidations of cyclic ketones.
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Affiliation(s)
- David E. Cane
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, United States
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Minami-ku, Kanagawa 252-0373, Japan
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70
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Abstract
Terpenoid compounds are generally considered to be plant or fungal metabolites, although a small number of odorous terpenoid metabolites of bacterial origin have been known for many years. Recently, extensive bacterial genome sequencing and bioinformatic analysis of deduced bacterial proteins using a profile hidden Markov model have revealed more than a hundred distinct predicted terpene synthase genes. Although some of these synthase genes might be silent in the parent microorganisms under normal laboratory culture conditions, the controlled overexpression of these genes in a versatile heterologous host has made it possible to identify the biochemical function of cryptic genes and isolate new terpenoid metabolites.
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71
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Citron CA, Gleitzmann J, Laurenzano G, Pukall R, Dickschat JS. Terpenoids are widespread in actinomycetes: a correlation of secondary metabolism and genome data. Chembiochem 2011; 13:202-14. [PMID: 22213220 DOI: 10.1002/cbic.201100641] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Indexed: 11/06/2022]
Abstract
The genomes of all bacteria with publicly available sequenced genomes have been screened for the presence of sesquiterpene cyclase homologues, resulting in the identification of 55 putative geosmin synthases, 23 homologues of 2-methylisoborneol synthases, and 98 other sesquiterpene cyclase homologues. Most of these enzymes by far were found in actinomycetes. The terpenoid volatiles from 35 strains, including 31 actinomycetes and four strains from other taxa, were collected by using a closed-loop stripping apparatus and identified by GC-MS. All of these bacteria apart from one strain encode sesquiterpene cyclase homologues in their genomes. The identified volatile terpenoids were grouped according to structural similarities and their biosynthetic relationship, and the results of these analyses were correlated to the available genome information, resulting in valuable new insights into bacterial terpene biosynthesis.
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Affiliation(s)
- Christian A Citron
- Institut für Organische Chemie, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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72
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Auffret M, Pilote A, Proulx E, Proulx D, Vandenberg G, Villemur R. Establishment of a real-time PCR method for quantification of geosmin-producing Streptomyces spp. in recirculating aquaculture systems. WATER RESEARCH 2011; 45:6753-6762. [PMID: 22060964 DOI: 10.1016/j.watres.2011.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 09/26/2011] [Accepted: 10/16/2011] [Indexed: 05/31/2023]
Abstract
Geosmin and 2-methylisoborneol (MIB) have been associated with off-flavour problems in fish and seafood products, generating a strong negative impact for aquaculture industries. Although most of the producers of geosmin and MIB have been identified as Streptomyces species or cyanobacteria, Streptomyces spp. are thought to be responsible for the synthesis of these compounds in indoor recirculating aquaculture systems (RAS). The detection of genes involved in the synthesis of geosmin and MIB can be a relevant indicator of the beginning of off-flavour events in RAS. Here, we report a real-time polymerase chain reaction (qPCR) protocol targeting geoA sequences that encode a germacradienol synthase involved in geosmin synthesis. New geoA-related sequences were retrieved from eleven geosmin-producing Actinomycete strains, among them two Streptomyces strains isolated from two RAS. Combined with geoA-related sequences available in gene databases, we designed primers and standards suitable for qPCR assays targeting mainly Streptomyces geoA. Using our qPCR protocol, we succeeded in measuring the level of geoA copies in sand filter and biofilters in two RAS. This study is the first to apply qPCR assays to detect and quantify the geosmin synthesis gene (geoA) in RAS. Quantification of geoA in RAS could permit the monitoring of the level of geosmin producers prior to the occurrence of geosmin production. This information will be most valuable for fish producers to manage further development of off-flavour events.
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Affiliation(s)
- Marc Auffret
- INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada.
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73
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Nakano C, Kim HK, Ohnishi Y. Identification and Characterization of the Linalool/Nerolidol Synthase from Streptomyces clavuligerus. Chembiochem 2011; 12:2403-7. [DOI: 10.1002/cbic.201100501] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Indexed: 12/30/2022]
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74
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Chou WKW, Ikeda H, Cane DE. Cloning and characterization of Pfl_1841, a 2-methylenebornane synthase in Pseudomonas fluorescens PfO-1. Tetrahedron 2011; 67:6627-6632. [PMID: 21804650 DOI: 10.1016/j.tet.2011.05.084] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The pfl_1841 gene from Pseudomonas fluorescens PfO-1 is the only gene in any of the three sequenced genomes of the Gram-negative bacterium Pseudomonas fluorescens that is annotated as a putative terpene synthase. The predicted Pfl_1841 protein, which harbors the two strictly conserved divalent metal binding domains found in all terpene cyclases, is closely related to several known or presumed 2-methylisoborneol synthases, with the closest match being to the MOL protein of Micromonaspora olivasterospora KY11048 that has been implicated as a 2-methylenebornane synthase. A synthetic gene encoding P. fluorescens Pfl_1841 and optimized for expression in Escherichia coli was expressed and purified as an N-terminal His(6)-tagged protein. Incubation of recombinant Pfl_1841 with 2-methylgeranyl diphosphate produced 2-methylenebornane as the major product accompanied by 1-methyl camphene as well as other minor, monomethyl-homomonoterpene hydrocarbons and alcohols. The steady-state kinetic parameters for the Pfl_1841-catalyzed reaction were K(M) = 110 ± 13 nM and k(cat) = 2.4 ± 0.1 × 10(-2) s(-1). Attempts to identify the P. fluorescens SAM-dependent 2-methylgeranyl diphosphate synthase have so far been unsuccessful.
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Affiliation(s)
- Wayne K W Chou
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108 USA
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75
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Nakano C, Kim HK, Ohnishi Y. Identification of the First Bacterial Monoterpene Cyclase, a 1,8-Cineole Synthase, that Catalyzes the Direct Conversion of Geranyl Diphosphate. Chembiochem 2011; 12:1988-91. [DOI: 10.1002/cbic.201100330] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Indexed: 01/09/2023]
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76
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Wang Z, Xu Y, Shao J, Wang J, Li R. Genes associated with 2-methylisoborneol biosynthesis in cyanobacteria: isolation, characterization, and expression in response to light. PLoS One 2011; 6:e18665. [PMID: 21490938 PMCID: PMC3072421 DOI: 10.1371/journal.pone.0018665] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Accepted: 03/08/2011] [Indexed: 11/18/2022] Open
Abstract
The volatile microbial metabolite 2-methylisoborneol (2-MIB) is a root cause of taste and odor issues in freshwater. Although current evidence suggests that 2-MIB is not toxic, this compound degrades water quality and presents problems for water treatment. To address these issues, cyanobacteria and actinomycetes, the major producers of 2-MIB, have been investigated extensively. In this study, two 2-MIB producing strains, coded as Pseudanabaena sp. and Planktothricoids raciborskii, were used in order to elucidate the genetic background, light regulation, and biochemical mechanisms of 2-MIB biosynthesis in cyanobacteria. Genome walking and PCR methods revealed that two adjacent genes, SAM-dependent methyltransferanse gene and monoterpene cyclase gene, are responsible for GPP methylation and subsequent cyclization to 2-MIB in cyanobacteria. These two genes are located in between two homologous cyclic nucleotide-binding protein genes that may be members of the Crp-Fnr regulator family. Together, this sequence of genes forms a putative operon. The synthesis of 2-MIB is similar in cyanobacteria and actinomycetes. Comparison of the gene arrangement and functional sites between cyanobacteria and other organisms revealed that gene recombination and gene transfer probably occurred during the evolution of 2-MIB-associated genes. All the microorganisms examined have a common origin of 2-MIB biosynthesis capacity, but cyanobacteria represent a unique evolutionary lineage. Gene expression analysis suggested that light is a crucial, but not the only, active regulatory factor for the transcription of 2-MIB synthesis genes. This light-regulated process is immediate and transient. This study is the first to identify the genetic background and evolution of 2-MIB biosynthesis in cyanobacteria, thus enhancing current knowledge on 2-MIB contamination of freshwater.
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Affiliation(s)
- Zhongjie Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yao Xu
- College of Geography Science, Nanjing Normal University, Nanjing, People's Republic of China
| | - Jihai Shao
- Resources and Environment College, Hunan Agricultural University, Changsha, People's Republic of China
| | - Jie Wang
- College of Life Science, Shanxi University, Taiyuan, People's Republic of China
| | - Renhui Li
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- * E-mail:
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77
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Dickschat JS. Isoprenoids in three-dimensional space: the stereochemistry of terpene biosynthesis. Nat Prod Rep 2011; 28:1917-36. [DOI: 10.1039/c1np00063b] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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