Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering

Synthetic and Systems Biotechnology - Tập 3 - Trang 20-33 - 2018
Kevin B. Reed1, Hal S. Alper1,2
1McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
2Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA

Tài liệu tham khảo

Curran, 2012, Expanding the chemical palate of cells by combining systems biology and metabolic engineering, Metab Eng, 14, 289, 10.1016/j.ymben.2012.04.006 Sun, 2015, Metabolic engineering of strains: from industrial-scale to lab-scale chemical production, J Ind Microbiol Biotechnol, 42, 423, 10.1007/s10295-014-1539-8 Markham, 2015, Synthetic biology for specialty chemicals, Annu Rev Chem Biomol Eng, 6, 35, 10.1146/annurev-chembioeng-061114-123303 Ro, 2006, Production of the antimalarial drug precursor artemisinic acid in engineered yeast, Nature, 440, 940, 10.1038/nature04640 Alper, 2005, Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets, Nat Biotechnol, 23, 612, 10.1038/nbt1083 Ehrenworth, 2017, Accelerating the semisynthesis of alkaloid-based drugs through metabolic engineering, Nat Chem Biol, 13, 249, 10.1038/nchembio.2308 Blazeck, 2014, Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production, Nat Commun, 5, 10.1038/ncomms4131 King, 2016, Accessing Nature's diversity through metabolic engineering and synthetic biology, F1000Research, 5 Zhang, 2008, Expanding metabolism for biosynthesis of nonnatural alcohols, Proc Natl Acad Sci, 105, 20653, 10.1073/pnas.0807157106 Zhang, 2010, Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine, Proc Natl Acad Sci, 107, 6234, 10.1073/pnas.0912903107 Waldman, 2017, Heteroatom–heteroatom bond formation in natural product biosynthesis, Chem Rev, 117, 5784, 10.1021/acs.chemrev.6b00621 Yim, 2011, Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol, Nat Chem Biol, 7, 445, 10.1038/nchembio.580 Latham, 2017, Development of halogenase enzymes for use in synthesis, Chem Rev Breydo, 2013, Boron, biologically active compounds, 295 Pereira, 2015, Metallic nanoparticles: microbial synthesis and unique properties for biotechnological applications, bioavailability and biotransformation, Crit Rev Biotechnol, 35, 114, 10.3109/07388551.2013.819484 Ladner, 2016, Harnessing natural product assembly lines: structure, promiscuity, and engineering, J Ind Microbiol Biotechnol, 43, 371, 10.1007/s10295-015-1704-8 Ravikumar, 2015, Unnatural amino acid mutagenesis-based enzyme engineering, Trends Biotechnol, 33, 462, 10.1016/j.tibtech.2015.05.002 Rovner, 2015, Recoded organisms engineered to depend on synthetic amino acids, Nature, 518, 89, 10.1038/nature14095 Sardar, 2016, Chapter one - directing biosynthesis: practical supply of natural and unnatural cyanobactins, vol. 575, 1 Baumann, 2017, Prospects of in vivo incorporation of non-canonical amino acids for the chemical diversification of antimicrobial peptides, Front Microbiol, 8, 10.3389/fmicb.2017.00124 Wagner, 2009, Biohalogenation: nature's way to synthesize halogenated metabolites, J Nat Prod, 72, 540, 10.1021/np800651m Brown, 2015, Halogenase engineering for the generation of new natural product analogues, ChemBioChem, 16, 2129, 10.1002/cbic.201500338 Jedinák, 2017, The suzuki–Miyaura cross-coupling reaction of halogenated aminopyrazoles: method development, scope, and mechanism of dehalogenation side reaction, J Org Chem, 82, 157, 10.1021/acs.joc.6b02306 Frampton, 2017, Biocatalysis in silicon chemistry, Chem Asian J, 12, 1153, 10.1002/asia.201700214 Adkins, 2012, Engineering microbial chemical factories to produce renewable “biomonomers.”, Front Microbiol, 3, 10.3389/fmicb.2012.00313 Schippers, 2013, Biomining: metal recovery from ores with microorganisms, 1 Mishra, 2017, Integrated approach of agri-nanotechnology: challenges and future trends, Front Plant Sci, 8, 10.3389/fpls.2017.00471 Dicks, 2014 Agarwal, 2017, Enzymatic halogenation and dehalogenation reactions: pervasive and mechanistically diverse, Chem Rev, 117, 5619, 10.1021/acs.chemrev.6b00571 Gribble, 2015, Biological activity of recently discovered halogenated marine natural products, Mar Drugs, 13, 4044, 10.3390/md13074044 Gribble, 2009 Littlechild, 1999, Haloperoxidases and their role in biotransformation reactions, Curr Opin Chem Biol, 3, 28, 10.1016/S1367-5931(99)80006-4 Borozan, 2013, Stojanović SĐ. Halogen bonding in complexes of proteins and non-natural amino acids, Comput Biol Chem, 47, 231, 10.1016/j.compbiolchem.2013.10.002 Ohtake, 2015, Protein stabilization utilizing a redefined codon, Sci Rep, 5 Deb Roy, 2010, Gene expression enabling synthetic diversification of natural products: chemogenetic generation of pacidamycin analogs, J Am Chem Soc, 132, 12243, 10.1021/ja1060406 Salah Ayoup, 2015, Fluorine containing amino acids: synthesis and peptide coupling of amino acids containing the all- cis tetrafluorocyclohexyl motif, Org Biomol Chem, 13, 5621, 10.1039/C5OB00650C O'Hagan, 2015, Enzymatic fluorination and biotechnological developments of the fluorinase, Chem Rev, 115, 634, 10.1021/cr500209t Deng, 2004, Fluorometabolite biosynthesis and the fluorinase from Streptomyces cattleya, Nat Prod Rep, 21, 773, 10.1039/b415087m Ma, 2015, Identification of a fluorometabolite from Streptomyces sp. MA37: (2R3S4S)-5-fluoro-2,3,4-trihydroxypentanoic acid, Chem Sci, 6, 1414, 10.1039/C4SC03540B Ma, 2016, Biological fluorination from the sea: discovery of a SAM-dependent nucleophilic fluorinating enzyme from the marine-derived bacterium Streptomyces xinghaiensis NRRL B24674, RSC Adv, 6, 27047, 10.1039/C6RA00100A Carvalho, 2017, Natural production of fluorinated compounds and biotechnological prospects of the fluorinase enzyme, Crit Rev Biotechnol, 0, 1 Zhu, 2015, Biosynthesis of the fluorinated natural product nucleocidin in Streptomyces calvus is dependent on the blda-specified Leu-tRNAUUA molecule, ChemBioChem, 16, 2498, 10.1002/cbic.201500402 Grüschow, 2009, New pacidamycin antibiotics through precursor-directed biosynthesis, Chembiochem Eur J Chem Biol, 10, 355, 10.1002/cbic.200800575 Goss, 2010, An expeditious route to fluorinated rapamycin analogues by utilising mutasynthesis, ChemBioChem, 11, 698, 10.1002/cbic.200900723 Walker, 2013, Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways, Science, 341, 1089, 10.1126/science.1242345 Ad, 2017, Elucidating the mechanism of fluorinated extender unit loading for improved production of fluorine-containing polyketides, Proc Natl Acad Sci, 114, E660, 10.1073/pnas.1614196114 Odar, 2015, Fluoro amino acids: a rarity in nature, yet a prospect for protein engineering, Biotechnol J, 10, 427, 10.1002/biot.201400587 Yu, 2014, Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code, Genome Biol Evol, 6, 629, 10.1093/gbe/evu044 Arntson, 2016, Protein-observed fluorine NMR: a bioorthogonal approach for small molecule discovery, J Med Chem, 59, 5158, 10.1021/acs.jmedchem.5b01447 Montclare, 2009, Biosynthesis and stability of coiled-coil peptides containing (2S,4R)-5,5,5-trifluoroleucine and (2S,4S)-5,5,5-trifluoroleucine, ChemBioChem, 10, 84, 10.1002/cbic.200800164 Baker, 2011, Enhanced refoldability and thermoactivity of fluorinated phosphotriesterase, ChemBioChem, 12, 1845, 10.1002/cbic.201100221 Merkel, 2012, Organic fluorine as a polypeptide building element: in vivo expression of fluorinated peptides, proteins and proteomes, Org Biomol Chem, 10, 7241, 10.1039/c2ob06922a Rivera-Chávez, 2017, Biosynthesis of fluorinated peptaibols using a site-directed building block incorporation approach, J Nat Prod, 80, 1883, 10.1021/acs.jnatprod.7b00189 Sánchez, 2005, Combinatorial biosynthesis of antitumor indolocarbazole compounds, Proc Natl Acad Sci U S A, 102, 461, 10.1073/pnas.0407809102 Okada, 2017, Combinatorial biosynthesis of (+)-Daurichromenic acid and its halogenated analogue, Org Lett, 19, 3183, 10.1021/acs.orglett.7b01288 Glenn, 2011, Reengineering a tryptophan halogenase to preferentially chlorinate a direct alkaloid precursor, J Am Chem Soc, 133, 19346, 10.1021/ja2089348 Payne, 2015, Directed evolution of RebH for site-selective halogenation of large biologically active molecules, Angew Chem Int Ed, 54, 4226, 10.1002/anie.201411901 Andorfer, 2016, Directed evolution of RebH for catalyst-controlled halogenation of indole C–H bonds, Chem Sci, 7, 3720, 10.1039/C5SC04680G Shepherd, 2016, A structure-guided switch in the regioselectivity of a tryptophan halogenase, Chembiochem, 17, 821, 10.1002/cbic.201600051 Zhou, 2010, Insights into radicicol biosynthesis via heterologous synthesis of intermediates and analogs, J Biol Chem, 285, 41412, 10.1074/jbc.M110.183574 Wang, 2015, Metabolic engineering of Escherichia coli for the biosynthesis of various phenylpropanoid derivatives, Metab Eng, 29, 153, 10.1016/j.ymben.2015.03.011 Xu, 2016, Selective biochlorination of hydroxyquinolines by a flavin-dependent halogenase, Tetrahedron Lett, 57, 5262, 10.1016/j.tetlet.2016.10.044 Zeng, 2013, Specific chlorination of isoquinolines by a fungal flavin-dependent halogenase, Bioorg Med Chem Lett, 23, 1001, 10.1016/j.bmcl.2012.12.038 Menon B, Brandenburger E, Sharif H, Klemstein U, Shepherd S, Greaney M, et al. RadH a versatile halogenase for integration into synthetic pathways. Angew Chem Int Ed n.d.:n/a-n/a. doi:10.1002/anie.201706342. Mitchell, 2016, Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5, Nat Chem Biol, 12, 636, 10.1038/nchembio.2112 Hillwig, 2016, Discovery of a promiscuous non-heme iron halogenase in ambiguine alkaloid biogenesis: implication for an evolvable enzyme family for Late-stage halogenation of aliphatic carbons in small molecules, Angew Chem Int Ed, 55, 5780, 10.1002/anie.201601447 Chankhamjon, 2016, Regioselective dichlorination of a non-activated aliphatic carbon atom and phenolic bismethylation by a multifunctional fungal flavoenzyme, Angew Chem Int Ed, 55, 11955, 10.1002/anie.201604516 Nakamura, 2017, A new strategy for aromatic ring alkylation in cylindrocyclophane biosynthesis, Nat Chem Biol, 10.1038/nchembio.2421 Zhu, 2013, Deciphering and engineering of the final step halogenase for improved chlortetracycline biosynthesis in industrial Streptomyces aureofaciens, Metab Eng, 19, 69, 10.1016/j.ymben.2013.06.003 Komatsu, 2013, Engineered Streptomyces avermitilis host for heterologous expression of biosynthetic gene cluster for secondary metabolites, ACS Synth Biol, 2, 384, 10.1021/sb3001003 Teufel, 2016, Unusual flavoenzyme catalysis in marine bacteria, Curr Opin Chem Biol, 31, 31, 10.1016/j.cbpa.2016.01.001 Ross, 2015, Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform, ACS Synth Biol, 4, 414, 10.1021/sb500280q Agarwal, 2014, Enzymatic synthesis of polybrominated dioxins from the marine environment, ACS Chem Biol, 9, 1980, 10.1021/cb5004338 Sharma, 2017, Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo, Nat Commun, 8, 229, 10.1038/s41467-017-00194-3 Wang, 2013, Halogenated organic molecules of rhodomelaceae origin: chemistry and biology, Chem Rev, 113, 3632, 10.1021/cr9002215 Wang, 2014, Naturally occurring organoiodines, RSC Adv, 4, 57350, 10.1039/C4RA09833A Pasternak, 2012, Clinical pharmacology, uses, and adverse reactions of iodinated contrast agents: a primer for the non-radiologist, Mayo Clin Proc, 87, 390, 10.1016/j.mayocp.2012.01.012 Aiello, 2010, Iodocionin, a cytotoxic iodinated metabolite from the mediterranean ascidian ciona edwardsii, Mar Drugs, 8, 285, 10.3390/md8020285 Gonzali, 2017, Iodine biofortification of crops: agronomic biofortification, metabolic engineering and iodine bioavailability, Curr Opin Biotechnol, 44, 16, 10.1016/j.copbio.2016.10.004 Bayer, 2009, Synthesis of methyl halides from biomass using engineered microbes, J Am Chem Soc, 131, 6508, 10.1021/ja809461u Agarwal, 2015, Complexity of naturally produced polybrominated diphenyl ethers revealed via mass spectrometry, Environ Sci Technol, 49, 1339, 10.1021/es505440j Andorfer, 2017, Understanding flavin-dependent halogenase reactivity via substrate activity profiling, ACS Catal, 7, 1897, 10.1021/acscatal.6b02707 Lin, 2012, Tailoring enzymes acting on carrier protein-tethered substrates in natural product biosynthesis, Meth Enzymol, 516, 321, 10.1016/B978-0-12-394291-3.00008-3 Schnepel, 2016, A high-throughput fluorescence assay to determine the activity of tryptophan halogenases, Angew Chem Int Ed, 55, 14159, 10.1002/anie.201605635 Hosford, 2014, A high-throughput assay for arylamine halogenation based on a peroxidase-mediated quinone–amine coupling with applications in the screening of enzymatic halogenations, Chem Weinh Bergstr Ger, 20, 16759 Lin, 2017, Enabling tools for high-throughput detection of metabolites: metabolic engineering and directed evolution applications, Biotechnol Adv, 10.1016/j.biotechadv.2017.07.005 Abatemarco, 2013, Expanding the metabolic engineering toolbox with directed evolution, Biotechnol J, 8, 1397, 10.1002/biot.201300021 Böck, 1991, Selenocysteine: the 21st amino acid, Mol Microbiol, 5, 515, 10.1111/j.1365-2958.1991.tb00722.x Kieliszek, 2015, Accumulation and metabolism of selenium by yeast cells, Appl Microbiol Biotechnol, 99, 5373, 10.1007/s00253-015-6650-x 2017 Azad, 2014, Ebselen, a promising antioxidant drug: mechanisms of action and targets of biological pathways, Mol Biol Rep, 41, 4865, 10.1007/s11033-014-3417-x Geng, 2017, Selenium: roles in cancer prevention and therapies, 39 Herrero, 2015, Yeast as a model system to study metabolic impact of selenium compounds, Microb Cell, 2, 139, 10.15698/mic2015.05.200 Rao, 2010, Mapping of selenium metabolic pathway in yeast by Liquid Chromatography−Orbitrap mass spectrometry, Anal Chem, 82, 8121, 10.1021/ac1011798 Řezanka, 2008, Biologically active compounds of semi-metals, Stud Nat Prod Chem, 35, 835, 10.1016/S1572-5995(08)80018-X Zhou, 2009, Involvement of a broccoli COQ5 methyltransferase in the production of volatile selenium compounds, Plant Physiol, 151, 528, 10.1104/pp.109.142521 Ranjard, 2002, Methylation of inorganic and organic selenium by the bacterial thiopurine methyltransferase, J Bacteriol, 184, 3146, 10.1128/JB.184.11.3146-3149.2002 Pusztahelyi, 2015, Selenite-stress selected mutant strains of probiotic bacteria for Se source production, J Trace Elem Med Biol, 30, 96, 10.1016/j.jtemb.2014.11.003 Mapelli, 2012, The interplay between sulphur and selenium metabolism in yeast influences the intracellular redox balance, FEMS Yeast Res, 12, 20, 10.1111/j.1567-1364.2011.00757.x Burow, 2008, Sulfur-containing secondary metabolites and their role in plant defense, 201 Sun, 2013, 2-Selenouridine triphosphate synthesis and Se-RNA transcription, RNA N Y N, 19, 1309, 10.1261/rna.038075.112 Chaudhary, 2016, Selenium nanomaterials: an overview of recent developments in synthesis, properties and potential applications, Prog Mater Sci, 83, 270, 10.1016/j.pmatsci.2016.07.001 Dobias, 2011, Role of proteins in controlling selenium nanoparticle size, Nanotechnology, 22, 195605, 10.1088/0957-4484/22/19/195605 Tugarova, 2017, Proteins in microbial synthesis of selenium nanoparticles, Talanta, 174, 539, 10.1016/j.talanta.2017.06.013 Lenz, 2011, Shedding light on selenium biomineralization: proteins associated with bionanominerals, Appl Environ Microbiol, 10.1128/AEM.01713-10 Elahian, 2017, High-throughput bioaccumulation, biotransformation, and production of silver and selenium nanoparticles using genetically engineered Pichia pastoris, Nanomed Nanotechnol Biol Med, 13, 853, 10.1016/j.nano.2016.10.009 Fellowes, 2011, Use of biogenic and abiotic elemental selenium nanospheres to sequester elemental mercury released from mercury contaminated museum specimens, J Hazard Mater, 189, 660, 10.1016/j.jhazmat.2011.01.079 Dembitsky, 2002, Natural occurrence of boron-containing compounds in plants, algae and microorganisms, Plant Sci, 163, 931, 10.1016/S0168-9452(02)00174-7 Wolkenstein, 2015, Structure and absolute configuration of jurassic polyketide-derived spiroborate pigments obtained from microgram quantities, J Am Chem Soc, 137, 13460, 10.1021/jacs.5b08191 Chen, 1981, Biosynthesis of the boron-containing macrolide antibiotic aplasmomycin by Streptomyces griseus, J Am Chem Soc, 103, 4565, 10.1021/ja00405a044 Galloway, 2011, Quorum sensing in gram-negative bacteria: small-molecule modulation of AHL and AI-2 quorum sensing pathways, Chem Rev, 111, 28, 10.1021/cr100109t Diaz, 2017, The versatility of boron in biological target engagement, Nat Chem, 9, 731, 10.1038/nchem.2814 Frampton, 2009, Organosilicon biotechnology, Siliconindia, 1, 147, 10.1007/s12633-009-9021-3 Fernandes, 2014, Self-assembly in biosilicification and biotemplated silica materials, Nanomaterials, 4, 792, 10.3390/nano4030792 Jain, 2017, 11 Tacke, 1983, Microbiological Transformation of Silicon Compounds: enantioselective Reduction of Trimethylsilylalkyl Acetoacetates and their Carba-Analogues, Zeitschrift für Naturforschung B, 10.1515/znb-1983-0516 Zani, 2001, Biotransformations of organosilicon compounds: enantioselective reduction of acyl silanes by means of baker's yeast, J Mol Catal B Enzym, 11, 279, 10.1016/S1381-1177(00)00052-7 Smith, 2008, Enzymatic dihydroxylation of aryl silanes, vol. 999, 434 Kan, 2016, Directed evolution of cytochrome c for carbon–silicon bond formation: bringing silicon to life, Science, 354, 1048, 10.1126/science.aah6219 Kaur, 2013, Biochemistry of nucleic acids functionalized with sulfur, selenium, and tellurium: roles of the single-atom substitution, vol. 1152, 89 Swearingen, 2004, Identification of biogenic organotellurides in Escherichia coli K-12 headspace gases using solid-phase microextraction and gas chromatography, Anal Biochem, 331, 106, 10.1016/S0003-2697(04)00407-5 Turner, 2012, Microbial processing of tellurium as a tool in biotechnology, Biotechnol Adv, 30, 954, 10.1016/j.biotechadv.2011.08.018 Silberman, 2016, The anticancer activity of organotelluranes: potential role in integrin inactivation, ChemBioChem, 17, 918, 10.1002/cbic.201500614 Zare, 2012, Biosynthesis and recovery of rod-shaped tellurium nanoparticles and their bactericidal activities, Mater Res Bull, 47, 3719, 10.1016/j.materresbull.2012.06.034 Borghese, 2016, Extracellular production of tellurium nanoparticles by the photosynthetic bacterium Rhodobacter capsulatus, J Hazard Mater, 309, 202, 10.1016/j.jhazmat.2016.02.011 Espinosa-Ortiz, 2017, Biomineralization of tellurium and selenium-tellurium nanoparticles by the white-rot fungus Phanerochaete chrysosporium, Int Biodeterior Biodegrad, 10.1016/j.ibiod.2017.05.009 Zonaro, 2015, Biogenic selenium and tellurium nanoparticles synthesized by environmental microbial isolates efficaciously inhibit bacterial planktonic cultures and biofilms, Front Microbiol, 6, 10.3389/fmicb.2015.00584 Barton, 2007, The bacterial metallome: composition and stability with specific reference to the anaerobic bacterium Desulfovibrio desulfuricans, BioMetals, 20, 291, 10.1007/s10534-006-9059-2 Nancharaiah, 2016, Biological and bioelectrochemical recovery of critical and scarce metals, Trends Biotechnol, 34, 137, 10.1016/j.tibtech.2015.11.003 Hulkoti, 2014, Biosynthesis of nanoparticles using microbes—a review, Colloids Surf B Biointerfaces, 121, 474, 10.1016/j.colsurfb.2014.05.027 de Lorenzo, 2016, Bioremediation at a global scale: from the test tube to planet Earth, Microb Biotechnol, 9, 618, 10.1111/1751-7915.12399 Giebner, 2015, Three adapted methods to quantify biomass and activity of microbial leaching cultures, Miner Eng, 79, 169, 10.1016/j.mineng.2015.05.016 Key, 2016, Abiological catalysis by artificial haem proteins containing noble metals in place of iron, Nature, 534, 534, 10.1038/nature17968 Jeschek, 2016, Directed evolution of artificial metalloenzymes for in vivo metathesis, Nature, 537, 661, 10.1038/nature19114 Lewis, 2013, Artificial metalloenzymes and metallopeptide catalysts for organic synthesis, ACS Catal, 3, 2954, 10.1021/cs400806a Swain, 2017, Recovery and recycling of lithium: a review, Sep Purif Technol, 172, 388, 10.1016/j.seppur.2016.08.031 Rezza, 1997, Extraction of lithium from spodumene by bioleaching, Lett Appl Microbiol, 25, 172, 10.1046/j.1472-765X.1997.00199.x Marcincakova, 2015, Lithium bioleaching from lepidolite using the yeast Rhodotorula Rubra, Inż Miner, 16 Marcincakova, 2014, The influence of spore age of Aspergillus Niger on lithium dissolution from lepidolite, Inż Miner, 15 Hefnawy, 2002, Fungal leaching of uranium from its geological ores in alloga area, west central sinai, Egypt. J Biol Sci, 2, 346, 10.3923/jbs.2002.346.350 Rashidi, 2012, Modeling of uranium bioleaching by Acidithiobacillus ferrooxidans, Ann Nucl Energy, 43, 13, 10.1016/j.anucene.2011.12.020 Kulkarni, 2016, Interaction of uranium with bacterial cell surfaces: inferences from phosphatase-mediated uranium precipitation, Appl Environ Microbiol, 82, 4965, 10.1128/AEM.00728-16 Bhattacharyya, 2017, Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits, Nat Commun, 8, 10.1038/ncomms15538 Bendale, 2012, Green synthesis, characterization and anticancer potential of platinum nanoparticles Bioplatin, J Chin Integr Med, 10, 681, 10.3736/jcim20120613 Syed, 2012, Extracellular biosynthesis of platinum nanoparticles using the fungus Fusarium oxysporum, Colloids Surf B Biointerfaces, 97, 27, 10.1016/j.colsurfb.2012.03.026 Riddin, 2009, Two different hydrogenase enzymes from sulphate-reducing bacteria are responsible for the bioreductive mechanism of platinum into nanoparticles, Enzym Microb Technol, 45, 267, 10.1016/j.enzmictec.2009.06.006 Gaidhani, 2014, Bio-reduction of hexachloroplatinic acid to platinum nanoparticles employing Acinetobacter calcoaceticus, Process Biochem, 49, 2313, 10.1016/j.procbio.2014.10.002 Deplanche, 2010, Involvement of hydrogenases in the formation of highly catalytic Pd(0) nanoparticles by bioreduction of Pd(II) using Escherichia coli mutant strains, Microbiology, 156, 2630, 10.1099/mic.0.036681-0 Zhu, 2016, Selective hydrogenation using palladium bioinorganic catalyst, Appl Catal B Environ, 199, 108, 10.1016/j.apcatb.2016.05.060 Omajali, 2015, Characterization of intracellular palladium nanoparticles synthesized by Desulfovibrio desulfuricans and Bacillus benzeovorans, J Nanoparticle Res, 17, 264, 10.1007/s11051-015-3067-5 Deplanche, 2008, Biorecovery of gold by Escherichia coli and Desulfovibrio desulfuricans, Biotechnol Bioeng, 99, 1055, 10.1002/bit.21688 Mishra, 2011, Microbial synthesis of gold nanoparticles using the fungus Penicillium brevicompactum and their cytotoxic effects against mouse mayo blast cancer C2C12 cells, Appl Microbiol Biotechnol, 92, 617, 10.1007/s00253-011-3556-0 Zhu, 2016, Biorecovery of gold as nanoparticles and its catalytic activities for p-nitrophenol degradation, Environ Sci Pollut Res, 23, 7627, 10.1007/s11356-015-6033-y Gericke, 2006, Microbial production of gold nanoparticles, Gold Bull, 39, 22, 10.1007/BF03215529 Husseiny, 2015, Biosynthesis of size controlled silver nanoparticles by Fusarium oxysporum, their antibacterial and antitumor activities, Beni-Suef Univ J Basic Appl Sci, 4, 225, 10.1016/j.bjbas.2015.07.004 Apte, 2013, Psychrotrophic yeast Yarrowia lipolytica NCYC 789 mediates the synthesis of antimicrobial silver nanoparticles via cell-associated melanin, AMB Express, 3, 32, 10.1186/2191-0855-3-32 Bhainsa, 2006, Extracellular biosynthesis of silver nanoparticles using the fungus Aspergillus fumigatus, Colloids Surf B Biointerfaces, 47, 160, 10.1016/j.colsurfb.2005.11.026 U P, 2017, Biologically synthesized PbS nanoparticles for the detection of arsenic in water, Int Biodeterior Biodegrad, 119, 78, 10.1016/j.ibiod.2016.10.009 Bao, 2010, Extracellular microbial synthesis of biocompatible CdTe quantum dots, Acta Biomater, 6, 3534, 10.1016/j.actbio.2010.03.030 Jacob, 2016, Microbial synthesis of chalcogenide semiconductor nanoparticles: a review, Microb Biotechnol, 9, 11, 10.1111/1751-7915.12297 Bansal, 2006, Room-Temperature biosynthesis of ferroelectric barium titanate nanoparticles, J Am Chem Soc, 128, 11958, 10.1021/ja063011m Zheng, 2010, Preparation and application of a novel vanillin sensor based on biosynthesis of Au–Ag alloy nanoparticles, Sens Actuators B Chem, 148, 247, 10.1016/j.snb.2010.04.031 Park, 2010, In vivo synthesis of diverse metal nanoparticles by recombinant Escherichia coli, Angew Chem Int Ed, 49, 7019, 10.1002/anie.201001524 Park, 2016, Advances in microbial biosynthesis of metal nanoparticles, Appl Microbiol Biotechnol, 100, 521, 10.1007/s00253-015-6904-7 Singla, 2017, Role of bacteria in nanocompound formation and their application in medical, vol. 2, 3 Butu, 2016, Potential of microbial functional communities for high-tech critical metals recovery, Stud Univ Vasile Goldis Ser Stiintele Vietii Life Sci Ser, 26, 287 Eustáquio, 2008, Mutasynthesis of fluorosalinosporamide, a potent and reversible inhibitor of the proteasome, Angew Chem Int Ed, 47, 3936, 10.1002/anie.200800177 Swearingen, 2006, Expression of the ubiE gene of Geobacillus stearothermophilus V in Escherichia coli K-12 mediates the evolution of selenium compounds into the headspace of selenite- and selenate-amended cultures, Appl Environ Microbiol, 72, 963, 10.1128/AEM.72.1.963-967.2006 Tse Sum Bui, 2006, Escherichia coli biotin synthase produces selenobiotin. Further evidence of the involvement of the [2Fe-2S]2+ cluster in the sulfur insertion step, Biochemistry (Mosc), 45, 3824, 10.1021/bi052388m Dembitsky, 2011, Natural and synthetic small boron-containing molecules as potential inhibitors of bacterial and fungal quorum sensing, Chem Rev, 111, 209, 10.1021/cr100093b Elshahawi, 2013, Boronated tartrolon antibiotic produced by symbiotic cellulose-degrading bacteria in shipworm gills, Proc Natl Acad Sci, 110, E295, 10.1073/pnas.1213892110 Marrero, 2015, Recovery of nickel and cobalt from laterite tailings by reductive dissolution under aerobic conditions using acidithiobacillus species, Environ Sci Technol, 49, 6674, 10.1021/acs.est.5b00944 Srivastava, 2012, Room temperature biogenic synthesis of multiple nanoparticles (Ag, Pd, Fe, Rh, Ni, Ru, Pt, Co, and Li) by Pseudomonas aeruginosa SM1, J Nanoparticle Res, 14, 831, 10.1007/s11051-012-0831-7 Acevedo, 2013, Application of bioleaching to copper mining in Chile, Electron J Biotechnol, 16 Cuevas, 2015, Extracellular biosynthesis of copper and copper oxide nanoparticles by Stereum hirsutum, a native white-rot fungus from chilean forests, J Nanomater, 10.1155/2015/789089 Horiike, 2015, A new fungal isolate, Penidiella sp. Strain T9, accumulates the rare earth element dysprosium, Appl Environ Microbiol, 81, 3062, 10.1128/AEM.00300-15 Ozaki, 2004, Sorption behavior of europium(III) and curium(III) on the cell surfaces of microorganisms, Radiochim Acta, 92, 741, 10.1524/ract.92.9.741.55006 Marrero, 2017, Anaerobic and aerobic reductive dissolutions of iron-rich nickel laterite overburden by Acidithiobacillus, Hydrometallurgy, 168, 49, 10.1016/j.hydromet.2016.08.012 Ahmad, 2015, Anticancer activity of biostabilized selenium nanorods synthesized by Streptomyces bikiniensis strain Ess_amA-1, Int J Nanomedicine, 10, 3389 Balaji, 2009, Extracellular biosynthesis of functionalized silver nanoparticles by strains of Cladosporium cladosporioides fungus, Colloids Surf B Biointerfaces, 68, 88, 10.1016/j.colsurfb.2008.09.022 Cecchi, 2017, Native fungi as metal remediators: silver myco-accumulation from metal contaminated waste-rock dumps (Libiola Mine, Italy), J Environ Sci Health Part B, 52, 191, 10.1080/03601234.2017.1261549 Chernyh, 2007, Characterization of technetium(vII) reduction by cell suspensions of thermophilic bacteria and archaea, Appl Microbiol Biotechnol, 76, 467, 10.1007/s00253-007-1034-5 Jiang, 2012, Post-adsorption process of Yb phosphate nano-particle formation by Saccharomyces cerevisiae, Geochem Cosmochim Acta, 93, 30, 10.1016/j.gca.2012.06.016 Sethurajan, 2017, Bioleaching and selective biorecovery of zinc from zinc metallurgical leach residues from the Três Marias zinc plant (Minas Gerais, Brazil), J Chem Technol Biotechnol, 92, 512, 10.1002/jctb.5026 Deplanche, 2012, Microbial synthesis of core/shell gold/palladium nanoparticles for applications in green chemistry, J R Soc Interface, 9, 1705, 10.1098/rsif.2012.0003 Yan, 2014, Green biosynthesis of biocompatible CdSe quantum dots in living Escherichia coli cells, Mater Res Express, 1, 10.1088/2053-1591/1/1/015401 Bao, 2010, Biosynthesis of biocompatible cadmium telluride quantum dots using yeast cells, Nano Rev, 3, 481 Khan, 2013, Fungus mediated synthesis of biomedically important cerium oxide nanoparticles, Mater Res Bull, 48, 4134, 10.1016/j.materresbull.2013.06.038 Jha, 2012, Biological synthesis of cobalt ferrite nanoparticles, Nanotechnol Dev, 2, 9, 10.4081/nd.2012.e9 Ajay, 2010, Biological synthesis of copper oxide nano particles using Escherichia coli, Curr Nanosci, 6, 365, 10.2174/157341310791659062 Vaidyanathan, 2016, Bacteria-templated NiO nanoparticles/microstructure for an enzymeless glucose sensor, Int J Mol Sci, 17, 1104, 10.3390/ijms17071104 Seshadri, 2011, Green synthesis of lead sulfide nanoparticles by the lead resistant marine yeast, Rhodosporidium diobovatum, Biotechnol Prog, 27, 1464, 10.1002/btpr.651 Show, 2015, Bacterial (BKH1) assisted silica nanoparticles from silica rich substrates: a facile and green approach for biotechnological applications, Colloids Surf B Biointerfaces, 126, 245, 10.1016/j.colsurfb.2014.12.039 Kirthi, 2011, Biosynthesis of titanium dioxide nanoparticles using bacterium Bacillus subtilis, Mater Lett, 65, 2745, 10.1016/j.matlet.2011.05.077 Bansal, 2007, Zirconia enrichment in zircon sand by selective fungus-mediated bioleaching of silica, Langmuir, 23, 4993, 10.1021/la062535x Bansal, 2004, Biosynthesis of zirconia nanoparticles using the fungus Fusarium oxysporum, J Mater Chem, 14, 3303, 10.1039/b407904c