Mining Microbial Genomes


Sweedler, J. V. (2016). The Midwest Universities Analytical Chemistry Conference: Still the Midwest's Secret Weapon? Analytical Chemistry, 88(21), 10337. DOI: 10.1021/acs.analchem.6b04076
Chen, X., Love, J. C., Navin, N. E., Pachter, L., Stubbington, M. J. T., Svensson, V., ... Teichmann, S. A. (2016). Single-cell analysis at the threshold. Nature Biotechnology, 34(11), 1111-1118. DOI: 10.1038/nbt.3721
Li, B., Comi, T. J., Si, T., Dunham, S. J. B., & Sweedler, J. V. (2016). A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms. Journal of Mass Spectrometry, 51(11), 1030-1035. DOI: 10.1002/jms.3827
Peck, S. C., & van der Donk, W. A. (2016). Go it alone: four-electron oxidations by mononuclear non-heme iron enzymes. Journal of Biological Inorganic Chemistry, 1-14. DOI: 10.1007/s00775-016-1399-y
Huang, Z., Wang, K. K. A., & Van Der Donk, W. A. (2016). New insights into the biosynthesis of fosfazinomycin. Chemical Science, 7(8), 5219-5223. DOI: 10.1039/c6sc01389a
Walker, M. C., & van der Donk, W. A. (2016). The many roles of glutamate in metabolism. Journal of Industrial Microbiology and Biotechnology, 43(2-3), 419-430. DOI: 10.1007/s10295-015-1665-y
Thibodeaux, C. J., Wagoner, J., Yu, Y., & Van Der Donk, W. A. (2016). Leader Peptide Establishes Dehydration Order, Promotes Efficiency, and Ensures Fidelity during Lacticin 481 Biosynthesis. Journal of the American Chemical Society, 138(20), 6436-6444. DOI: 10.1021/jacs.6b00163
Ding, W., Liu, W. Q., Jia, Y., Li, Y., Van Der Donk, W. A., & Zhang, Q. (2016). Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in Ascomycetes. Proceedings of the National Academy of Sciences of the United States of America, 113(13), 3521-3526. DOI: 10.1073/pnas.1522907113
Ulrich, E. C., & van der Donk, W. A. (2016). Cameo appearances of aminoacyl-tRNA in natural product biosynthesis. Current Opinion in Chemical Biology, 35, 29-36. DOI: 10.1016/j.cbpa.2016.08.018
Tang, W., Thibodeaux, G. N., & Van Der Donk, W. A. (2016). The Enterococcal Cytolysin Synthetase Coevolves with Substrate for Stereoselective Lanthionine Synthesis. ACS Chemical Biology, 11(9), 2438-2446. DOI: 10.1021/acschembio.6b00397
Sun, H., Yeo, W. L., Lim, Y. H., Chew, X., Smith, D. J., Xue, B., ... Ang, E. L. (2016). Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-native Substrate. Angewandte Chemie - International Edition. DOI: 10.1002/anie.201606722
Tawfik, D. S., & van der Donk, W. A. (2016). Editorial overview: Biocatalysis and Biotransformation: Esoteric, Niche Enzymology. Current Opinion in Chemical Biology. DOI: 10.1016/j.cbpa.2016.03.002
Huo, L., & Van Der Donk, W. A. (2016). Discovery and Characterization of Bicereucin, an Unusual d -Amino Acid-Containing Mixed Two-Component Lantibiotic. Journal of the American Chemical Society, 138(16), 5254-5257. DOI: 10.1021/jacs.6b02513
Zhao, X., & Van Der Donk, W. A. (2016). Structural Characterization and Bioactivity Analysis of the Two-Component Lantibiotic Flv System from a Ruminant Bacterium. Cell Chemical Biology, 23(2), 246-256. DOI: 10.1016/j.chembiol.2015.11.014
Ortega, M. A., & Van Der Donk, W. A. (2016). New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products. Cell Chemical Biology, 23(1), 31-44. DOI: 10.1016/j.chembiol.2015.11.012
Sweedler, J. V. (2016). Choosing an Important Project: Take Two. Analytical Chemistry, 88(19), 9327. DOI: 10.1021/acs.analchem.6b03694
Metcalf, W. W. (2016). Classic spotlight: What's on (in) your plate today? Journal of Bacteriology, 198(21), 2897-2898. DOI: 10.1128/JB.00609-16
Cuculis, L., Abil, Z., Zhao, H., & Schroeder, C. M. (2016). TALE proteins search DNA using a rotationally decoupled mechanism. Nature Chemical Biology, 12(10), 831-837. DOI: 10.1038/nchembio.2152
Lian, J., Jin, R., & Zhao, H. (2016). Construction of plasmids with tunable copy numbers in Saccharomyces cerevisiae and their applications in pathway optimization and multiplex genome integration. Biotechnology and Bioengineering, 113(11), 2462-2473. DOI: 10.1002/bit.26004
Jansson, E. T., Comi, T. J., Rubakhin, S. S., & Sweedler, J. V. (2016). Single Cell Peptide Heterogeneity of Rat Islets of Langerhans. ACS Chemical Biology, 11(9), 2588-2595. DOI: 10.1021/acschembio.6b00602
Thiaville, J. J., Flood, J., Yurgel, S., Prunetti, L., Elbadawi-Sidhu, M., Hutinet, G., ... De Crécy-Lagard, V. (2016). Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite. ACS Chemical Biology, 11(8), 2304-2311. DOI: 10.1021/acschembio.6b00279
Price, N. P. J., Labeda, D. P., Naumann, T. A., Vermillion, K. E., Bowman, M. J., Berhow, M. A., ... Bischoff, K. M. (2016). Quinovosamycins: New tunicamycin-type antibiotics in which the α, β-1',11'-linked N-acetylglucosamine residue is replaced by N-acetylquinovosamine. Journal of Antibiotics, 69(8), 637-646. DOI: 10.1038/ja.2016.49
Henke, S. K., & Cronan, J. E. (2016). The Staphylococcus aureus group II biotin protein ligase BirA is an effective regulator of biotin operon transcription and requires the DNA binding domain for full enzymatic activity. Molecular Microbiology. DOI: 10.1111/mmi.13470
Deane, C. D., Burkhart, B. J., Blair, P. M., Tietz, J. I., Lin, A., & Mitchell, D. A. (2016). In Vitro Biosynthesis and Substrate Tolerance of the Plantazolicin Family of Natural Products. ACS Chemical Biology, 11(8), 2232-2243. DOI: 10.1021/acschembio.6b00369
Clemons, N. C., Luo, S., Ho, M., & Wilson, B. A. (2016). Selective membrane redistribution and depletion of Gαq-protein by Pasteurella multocida toxin. Toxins, 8(8), [233]. DOI: 10.3390/toxins8080233
Hu, C. K., Southey, B. R., Romanova, E. V., Maruska, K. P., Sweedler, J. V., & Fernald, R. D. (2016). Identification of prohormones and pituitary neuropeptides in the African cichlid, Astatotilapia burtoni. BMC Genomics, 17(1), [660]. DOI: 10.1186/s12864-016-2914-9
Zhao, H., & Medema, M. H. (2016). Standardization for natural product synthetic biology. Natural Product Reports, 33(8), 920-924. DOI: 10.1039/c6np00030d
Zhang, M. M., Wang, Y., Ang, E. L., & Zhao, H. (2016). Engineering microbial hosts for production of bacterial natural products. Natural Product Reports, 33(8), 963-987. DOI: 10.1039/c6np00017g
Medema, M. H., & Zhao, H. (2016). Editorial: Synthetic biology and bioinformatics. Natural Product Reports, 33(8), 913-914. DOI: 10.1039/c6np90031c
Labeda, D. P., Rong, X., Huang, Y., Doroghazi, J. R., Ju, K. S., & Metcalf, W. W. (2016). Taxonomic evaluation of species in the streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade. International Journal of Systematic and Evolutionary Microbiology, 66(6), 2444-2450. DOI: 10.1099/ijsem.0.001017
Lian, J., & Zhao, H. (2016). Functional Reconstitution of a Pyruvate Dehydrogenase in the Cytosol of Saccharomyces cerevisiae through Lipoylation Machinery Engineering. ACS Synthetic Biology, 5(7), 689-697. DOI: 10.1021/acssynbio.6b00019
Zhang, X., Carter, M. S., Vetting, M. W., Francisco, B. S., Zhao, S., Al-Obaidi, N. F., ... Gerlt, J. A. (2016). Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proceedings of the National Academy of Sciences of the United States of America, 113(29), E4161-E4169. DOI: 10.1073/pnas.1605546113
Wendt, K. E., Ungerer, J., Cobb, R. E., Zhao, H., & Pakrasi, H. B. (2016). CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973. Microbial Cell Factories, 15(1), [115]. DOI: 10.1186/s12934-016-0514-7
Zhang, H., Li, X., Su, X., Ang, E. L., Zhang, Y., & Zhao, H. (2016). Production of Adipic Acid from Sugar Beet Residue by Combined Biological and Chemical Catalysis. ChemCatChem, 8(8), 1500-1506. DOI: 10.1002/cctc.201600069
Chang, S., Fornasiero, P., Gunnoe, T. B., Jones, C. W., Linic, S., Ooi, T., ... Zhao, H. (2016). ACS Catalysis and the Scope of Papers Sought in Three Catalysis Subdisciplines: Biocatalysis and Enzymology, Molecular Catalysis for Organic Synthesis, and Heterogeneous Photocatalysis. ACS Catalysis, 6(7), 4782-4785. DOI: 10.1021/acscatal.6b01749
Wang, M., Yu, C., & Zhao, H. (2016). Identification of an important motif that controls the activity and specificity of sugar transporters. Biotechnology and Bioengineering. DOI: 10.1002/bit.25926
Liang, Y., Ang, E. L., & Zhao, H. (2016). A step through the looking glass. Science China Life Sciences, 59(9), 979-980. DOI: 10.1007/s11427-016-0170-6
Lee, C. Y., Fan, Y., Rubakhin, S. S., Yoon, S., & Sweedler, J. V. (2016). A neuron-in-capillary platform for facile collection and mass spectrometric characterization of a secreted neuropeptide. Scientific Reports, 6, [26940]. DOI: 10.1038/srep26940
Tasan, I., Jain, S., & Zhao, H. (2016). Use of genome-editing tools to treat sickle cell disease. Human Genetics, 135(9), 1011-1028. DOI: 10.1007/s00439-016-1688-0
Si, T., Li, B., Zhang, K., Xu, Y., Zhao, H., & Sweedler, J. V. (2016). Characterization of bacillus subtilis colony biofilms via mass spectrometry and fluorescence imaging. Journal of Proteome Research, 15(6), 1955-1962. DOI: 10.1021/acs.jproteome.6b00127
Cronan, J. E. (2016). Assembly of lipoic acid on its cognate enzymes: An extraordinary and essential biosynthetic pathway. Microbiology and Molecular Biology Reviews, 80(2), 429-450. DOI: 10.1128/MMBR.00073-15
Wu, Q., Comi, T. J., Li, B., Rubakhin, S. S., & Sweedler, J. V. (2016). On-Tissue Derivatization via Electrospray Deposition for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Endogenous Fatty Acids in Rat Brain Tissues. Analytical Chemistry, 88(11), 5988-5995. DOI: 10.1021/acs.analchem.6b01021
Yadava, U., Vetting, M. W., Al Obaidi, N., Carter, M. S., Gerlt, J. A., & Almo, S. C. (2016). Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine. Acta Crystallographica Section:F Structural Biology Communications, 72, 467-472. DOI: 10.1107/S2053230X16007500
Molloy, E. M., Tietz, J. I., Blair, P. M., & Mitchell, D. A. (2016). Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. Bioorganic and Medicinal Chemistry. DOI: 10.1016/j.bmc.2016.05.021
Molohon, K. J., Blair, P. M., Park, S., Doroghazi, J. R., Maxson, T., Hershfield, J. R., ... Mitchell, D. A. (2016). Plantazolicin Is an Ultranarrow-Spectrum Antibiotic That Targets the Bacillus anthracis Membrane. ACS Infectious Diseases, 2(3), 207-220. DOI: 10.1021/acsinfecdis.5b00115
Stumpf, R. M., Gomez, A., Amato, K. R., Yeoman, C. J., Polk, J. D., Wilson, B. A., ... Leigh, S. R. (2016). Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biological Conservation, 199, 56-66. DOI: 10.1016/j.biocon.2016.03.035
Shi, S., Si, T., Liu, Z., Zhang, H., Ang, E. L., & Zhao, H. (2016). Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae. Scientific Reports, 6, [25675]. DOI: 10.1038/srep25675
Freestone, T. S., & Zhao, H. (2016). Combinatorial pathway engineering for optimized production of the anti-malarial FR900098. Biotechnology and Bioengineering, 113(2), 384-392. DOI: 10.1002/bit.25719
Ong, T. H., Romanova, E. V., Roberts-Galbraith, R. H., Yang, N., Zimmerman, T. A., Collins, J. J., ... Sweedler, J. V. (2016). Mass spectrometry imaging and identification of peptides associated with cephalic ganglia regeneration in Schmidtea mediterranea. Journal of Biological Chemistry, 291(15), 8109-8120. DOI: 10.1074/jbc.M115.709196
Quarterman, J., Skerker, J. M., Feng, X., Liu, I. Y., Zhao, H., Arkin, A. P., & Jin, Y. S. (2016). Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae. Journal of Biotechnology, 229, 13-21. DOI: 10.1016/j.jbiotec.2016.04.041
Ortega, M. A., Hao, Y., Walker, M. C., Donadio, S., Sosio, M., Nair, S. K., & van der Donk, W. (2016). Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis. Cell Chemical Biology, 23(3), 370-380. DOI: 10.1016/j.chembiol.2015.11.017
Metcalf, W. W. (2016). Classic spotlight: Electron bifurcation, a unifying concept for energy conservation in anaerobes. Journal of Bacteriology, 198(9), 1358. DOI: 10.1128/JB.00185-16
Tietz, J. I., & Mitchell, D. A. (2016). Using genomics for natural product structure elucidation. Current Topics in Medicinal Chemistry, 16(15), 1645-1694.
Huang, H., Carter, M. S., Vetting, M. W., Al-Obaidi, N., Patskovsky, Y., Almo, S. C., & Gerlt, J. A. (2016). Correction to "a General Strategy for the Discovery of Metabolic Pathways: D -Threitol, l -Threitol, and Erythritol Utilization in Mycobacterium smegmatis" (J. Am. Chem. Soc. (2015) 137 (14570-14573) 10.1021/jacs.5b08968). Journal of the American Chemical Society, 138(12), 4267. DOI: 10.1021/jacs.6b01906
Wang, Y., Cobb, R. E., & Zhao, H. (2016). High-Efficiency Genome Editing of Streptomyces Species by an Engineered CRISPR/Cas System. Methods in Enzymology. DOI: 10.1016/bs.mie.2016.03.014
Vlčková, K., Gomez, A., Petrželková, K. J., Whittier, C. A., Todd, A. F., Yeoman, C. J., ... Leigh, S. R. (2016). Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla). Microbial Ecology, 72(4), 943-954. DOI: 10.1007/s00248-016-0745-5
Gomez, A., Petrzelkova, K. J., Burns, M. B., Yeoman, C. J., Amato, K. R., Vlckova, K., ... Blekhman, R. (2016). Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Reports, 14(9), 2142-2153. DOI: 10.1016/j.celrep.2016.02.013
Dunham, S. J. B., Comi, T. J., Ko, K., Li, B., Baig, N. F., Morales-Soto, N., ... Sweedler, J. V. (2016). Metal-assisted polyatomic SIMS and laser desorption/ionization for enhanced small molecule imaging of bacterial biofilms. Biointerphases, 11(2), [02A325]. DOI: 10.1116/1.4942884
Guo, W., Sheng, J., Zhao, H., & Feng, X. (2016). Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose. Microbial Cell Factories, 15(1), [24]. DOI: 10.1186/s12934-016-0423-9
Cronan, J. E. (2016). PBR322 vectors having tetracycline-dependent replication. Plasmid, 84-85, 20-26. DOI: 10.1016/j.plasmid.2016.02.004
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Yang, C. Y., Yu, K., Wang, Y., Chen, S. A., Liu, D. D., Wang, Z. Y., ... Jing, J. (2016). Aplysia locomotion: Network and behavioral actions of GdFFD, a D-amino acid-containing neuropeptide. PLoS One, 11(1), [e0147335]. DOI: 10.1371/journal.pone.0147335
Luo, Y., Enghiad, B., & Zhao, H. (2016). New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters. Natural Product Reports, 33(2), 174-182. DOI: 10.1039/c5np00085h
Li, B., Dunham, S. J. B., Dong, Y., Yoon, S., Zeng, M., & Sweedler, J. V. (2016). Analytical capabilities of mass spectrometry imaging and its potential applications in food science. Trends in Food Science and Technology, 47, 50-63. DOI: 10.1016/j.tifs.2015.10.018
Bao, Z., Cobb, R. E., & Zhao, H. (2016). Accelerated genome engineering through multiplexing. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 8(1), 5-21. DOI: 10.1002/wsbm.1319
Blodgett, J. A., Zhang, J. K., Yu, X., & Metcalf, W. W. (2016). Conserved biosynthetic pathways for phosalacine, bialaphos and newly discovered phosphonic acid natural products. Journal of Antibiotics, 69(1), 15-25. DOI: 10.1038/ja.2015.77
Wang, M., Yu, C., & Zhao, H. (2016). Directed evolution of xylose specific transporters to facilitate glucose-xylose co-utilization. Biotechnology and Bioengineering, 113(3), 484-491. DOI: 10.1002/bit.25724
Chekan, J. R., Cogan, D. P., & Nair, S. K. (2016). Molecular basis for resistance against phosphonate antibiotics and herbicides. MedChemComm, 7(1), 28-36. DOI: 10.1039/c5md00351b
Gomez, A., Rothman, J. M., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Umaña, J. D., ... Leigh, S. R. (2016). Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME Journal, 10(2), 514-526. DOI: 10.1038/ismej.2015.146
Yuan, Y., Andersen, E., & Zhao, H. (2016). Flexible and Versatile Strategy for the Construction of Large Biochemical Pathways. ACS Synthetic Biology, 5(1), 46-52. DOI: 10.1021/acssynbio.5b00117
Vetting, M. W., Bouvier, J. T., Gerlt, J. A., & Almo, S. C. (2016). Purification, crystallization and structural elucidation of d-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation. Acta Crystallographica Section:F Structural Biology Communications, 72, 36-41. DOI: 10.1107/S2053230X15023286
Maxson, T., & Mitchell, D. A. (2016). Targeted treatment for bacterial infections: prospects for pathogen-specific antibiotics coupled with rapid diagnostics. Tetrahedron, 72(25), 3609-3624. DOI: 10.1016/j.tet.2015.09.069
Wang, M., Li, S., & Zhao, H. (2016). Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 113(1), 206-215. DOI: 10.1002/bit.25676
Shi, S., Liang, Y., Zhang, M. M., Ang, E. L., & Zhao, H. (2016). A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metabolic Engineering, 33, 19-27. DOI: 10.1016/j.ymben.2015.10.011