Publications

Research Publications

	Yew Lab's Publications
2022
1	Structure-guided engineering of prenyltransferase NphB for high-yield and regioselective cannabinoid production Lim K. J. H., Hartono Y. D., Xue B., Go M. K., Fan H. and Yew, W.S. *ACS Catalysis 12: 4628-4639 (2022)* https://doi.org/10.1021/acscatal.2c00786
2	Reconstituting the complete biosynthesis of D-lysergic acid in yeast Wong G., Lim L. R., Tan Y. Q., Go M. K., Bell D. J., Freemont P. S., andYew, W.S. *Nature Communications 13: 712 (2022)* https://doi.org/10.1038/s41467-022-28386-6
3	Recent advances in structure, function, and pharmacology of class A lipid GPCRs: opportunities and challenges for drug discovery Krishna Deepak R. N. V., Verma R. K., Hartono Y. D., Yew, W.S., and Fan H. *Pharmaceuticals 15(1): 12 (2022)* https://doi.org/10.3390/ph15010012
4	Biologically engineered microbes for bioremediation of electronic waste: wayposts, challenges and future directions Han P., Teo W. Z., and Yew, W.S. *Engineering Biology 6(1): 23-24 (2022)* https://doi.org/10.1049/enb2.12020

2021
5	A high-throughput pipeline for scalable kit-free RNA extraction Han P., Go M. K., Chow J. Y., Xue B., Lim Y. P., Crone M. A., Storch M., Freemont P. S., and Yew, W.S. *Scientific Reports 11: 23260 (2021)* https://doi.org/10.1038/s41598-021-02742-w
6	A novel lipase from Lasiodiplodia theobromae efficiently hydrolyses C8-C10 methyl esters for the preparation of medium-chain triglycerides precursors Ng, A.M.J., Yang, R., Zhang, H., Xue, B., Yew, W.S., and Nguyen, G.J.T. *International Journal of Molecular Sciences 22(19): 10339 (2021)* https://doi.org/10.3390/ijms221910339
7	Heterologous expression of cyanobacterial gas vesicle proteins in Saccharomyces cerevisiae Jung, H., Ling, H., Tan, Y.Q., Chua, N.H., Yew, W.S., and Chang, M.W. https://doi.org/10.1002/biot.202100059
8	Scalable workflow for green manufacturing: discovery of bacterial lipases for biodiesel production Chow, J.Y., Choo, K.L.S., Lim, Y.P., Ling, L.H., Nguyen, K.T.G., Xue, B., Chua, N.H., and Yew, W.S. *ACS Sustainable Chemistry and Engineering 9 (40): 13450-13459 (2021)* https://doi.org/10.1021/acssuschemeng.1c03721
9	Structure of a minimal alpha-carboxysome derived shell and its utility in enzyme stabilization Tan, Y.Q., Ali, S., Xue, B., Teo, W.Z., Ling, L.H., Go, M.K., Hong, L., Robinson, R.C., Narita, A., and Yew, W.S. *Biomacromolecules 22 (10): 4095-4109 (2021)* https://doi.org/10.1021/acs.biomac.1c00533
10	Biosynthesis of Nature-Inspired Unnatural Cannabinoids Lim, K.J.H., Lim, Y.P., Hartono, Y.D., Go, M.K., Fan, H., and Yew, W.S. *Molecules 26(10): 2914 (2021)* https://doi.org/10.3390/molecules26102914
11	The Divergent Immunomodulatory Effects of Short Chain Fatty Acids and Medium Chain Fatty Acids Sam, Q.H., Ling, H., Yew, W.S., Tan, Z., Ravikumar, S., Chang, M.W., and Chai, L.Y.A. *International Journal of Molecular Sciences 22: 6453 (2021)* https://doi.org/10.3390/ijms22126453
12	Genetically encodable scaffolds for optimizing enzyme function TTan, Y.Q., Xue, B., and Yew, W.S. *Molecules 26(5): 1389 (2021)* https://doi.org/10.3390/molecules26051389
13	Future trends in synthetic biology in Asia Mao, N., Aggarwal, N., Poh, C.L., Cho, B.K., Kondo, A., Liu, C., Yew, W.S. and Chang, M.W. *Advanced Genetics: e10038 (2021)* https://doi.org/10.1002/ggn2.10038
14	Novel modalities in DNA data storage Lim, C.K., Nirantar, S.,Yew, W.S., and Poh, C.L. *Trends in Biotechnology 39(10): 990-1003 (2021)* https://doi.org/10.1016/j.tibtech.2020.12.008

2020
15	COVID-19 Endocrinopathy with Hindsight from SARS Kothandaraman, N.; Anantharaj, R.; Xue, B.; Yew, W.S.; Velan, S.S.; Karnani, N.; Leow, M. K.-S. *Am J Physiol Endocrinol Metab.* (2020) https://journals.physiology.org/doi/full/10.1152/ajpendo.00480.2020
16	Development of a Proline-Based Selection System for Reliable Genetic Engineering in Chinese Hamster Ovary Cells Sun, T.; Kwok, W. C.; Chua, K. J.; Lo, T. M.; Potter, J.; Yew, W.S.; Chesnut, J. D.; Hwang, I. Y.; Chang, M. W. (2020) *ACS Synth Biol.* 9 (7), 1864-1872. https://pubs.acs.org/doi/10.1021/acssynbio.0c00221
17	Evolving a Thermostable Terminal Deoxynucleotidyl Transferase Chua, J.P.S., Go, M.K., Osothprarop, T., McDonald, S., Karabadzhak, A.G., Yew, W.S., Peisajovich, S., and Nirantar, S. (2020) *ACS Synth Biol.* 9(7), 1725-1735. June 23. doi: 10.1021/acssynbio.0c00078. https://pubs.acs.org/doi/10.1021/acssynbio.0c00078
18	Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily. Go, M.K., Zhao, L.N., Xue, B., Supekar, S., Robinson, R.C., Fan, H., and Yew, W.S. (2020) *Structure* 28, 1-8. June 2. doi: 10.1016/j.str.2020.03.011. https://www.sciencedirect.com/science/article/abs/pii/S0969212620300939
19	Toolkit Development for Cyanogenic and Gold Biorecovery Chassis Chromobacterium violaceum Liow, L.T., Go, M.K., Chang, M.W., and Yew, W.S. (2020) *ACS Synth Biol.* 9(4), 953-961. March 11. doi: 10.1021/acssynbio.0c00064. https://pubs.acs.org/doi/10.1021/acssynbio.0c00064

2019
20	Building a Global Alliance of Biofoundries Hillson, N., et. al. Yew, W.S., Yuan, Y., Zhao, H., and Freemont, P.S. (2019) *Nature Commun.* 10(1):2040. doi: 10.1038/s41467-019-10079-2. https://www.nature.com/articles/s41467-019-10079-2
21	Characterization of Constitutive Promoters from the Anderson library in Chromobacterium violaceum ATCC 12472 Liow, L.T., Go, M.K., and Yew, W.S. (2019) *Engineering Biology* DOI: 10.1049/enb.2018.5007, Online ISSN 2398-6182. https://digital-library.theiet.org/content/journals/10.1049/enb.2018.5007
22	Characterisation of the Bacterial Biosensor GMG in coli BL21 (DE3). Rajasabhai, R., Go, M.K., and Yew, W.S. (2019) *Engineering Biology* DOI: 10.1049/enb.2018.5006, Online ISSN 2398-6182. https://digital-library.theiet.org/content/journals/10.1049/enb.2018.5006

2018
23	Synthetic Enzymology and the Fountain of Youth: Repurposing Biology for Longevity Lim, Y.P., Go, M.K., Raida, M., Inoue, T., Wenk, M.R., Keasling, J.D., Chang, M.W., and Yew, W.S. (2018) *ACS Omega* 3(9): 11050-11061. doi: 10.1021/acsomega.8b01620. https://pubs.acs.org/doi/10.1021/acsomega.8b01620
24	Mutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus Liu, Y., Mo, W.J., Shi, T.F., Wang, M.Z., Zhou, J.G., Yu, Y., Yew, W.S., and Lu, H. (2018) *Microb Cell Fact.* 17(1):144. doi: 10.1186/s12934-018-0993-9. https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-018-0993-9
25	Immunomodulation as Therapy for Fungal Infection: Are We Closer? Sam, Q.H., Yew, W.S., Seneviratne, C.J., Chang, M.W., and Chai, L.Y.A. (2018) *Front. Microbiol.* https://doi.org/10.3389/fmicb.2018.01612. https://www.frontiersin.org/articles/10.3389/fmicb.2018.01612/full
26	Targeted Approaches for In Situ Gut Microbiome Manipulation Lee, H.L., Shen, H., Hwang, I.Y., Ling, H., Yew, W.S., Lee, Y.S., and Chang, M.W. (2018) *Genes* 2;9(7). pii: E351. https://pubmed.ncbi.nlm.nih.gov/30002345/
27	Engineering microbes for targeted strikes against human pathogens Hwang, I.Y., Lee, H.L., Huang, J.G., Lim, Y.Y., Yew, W.S., Lee, Y.S., and Chang, M.W. (2018) *Cell Mol Life Sci.* doi: 10.1007/s00018-018-2827-7. https://link.springer.com/article/10.1007/s00018-018-2827-7
28	Reprogramming Probiotic Lactobacillus reuteri as a Biosensor for Staphylococcus aureus Derived AIP-I Detection Lubkowicz, D., Ho, C.L., Hwang, I.Y., Yew, W.S., Lee, Y.S., and Chang, M.W. (2018) *ACS Synth Biol.* 7(5):1229-1237. https://pubs.acs.org/doi/10.1021/acssynbio.8b00063
29	Directed Evolution of Quorum-Quenching Enzymes: A Method for the Construction of a Directed Evolution Platform and Characterization of a Quorum-Quenching Lactonase from Geobacillus kaustophilus Go, M.K., Chow, J.Y., and, Yew, W.S. (2018) *Methods Mol Biol.* 1673:311-323. https://experiments.springernature.com/articles/10.1007/978-1-4939-7309-5_24
30	Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention Ho, C.L., Tan, H.Q., Chua, K.J., Kang, A., Lim, K.H., Ling, K.L., Yew, W.S., Lee, Y.S., Thiery, J.P., and Chang, M.W. (2018) *Nature Biomedical Engineering.* 2:27-37. https://www.nature.com/articles/s41551-017-0181-y

2017
31	Engineering a Riboswitch-based Genetic Platform for the Self-directed Evolution of Acid-tolerant Phenotypes Pham, H.L., Wong, A., Chua, N., Teo, W.S., Yew, W.S., Chang, M.W. (2017) *Nature Commun.* 8(1):411 https://www.nature.com/articles/s41467-017-00511-w

2016
32	Reprogrammable microbial cell-based therapeutics against antibiotic-resistant bacteria Hwang, I.Y., Koh, E., Kim, H.R., Yew, W.S., and Chang, M.W. (2016) *Drug Resistance Updates* Jul 27:59-71. doi: 10.1016/j.drup.2016.06.002. https://www.sciencedirect.com/science/article/abs/pii/S1368764616300140
33	Exploiting the Biosynthetic Potential of Type III Polyketide Synthases Lim, Y.P., Go, M.K., and Yew, W.S. (2016) *Molecules* Jun 22: 21(6). pii: E806. doi: 10.3390/molecules21060806. https://www.mdpi.com/1420-3049/21/6/806
34	Anti-Virulent Disruption of Pathogenic Biofilms Using Engineered Quorum-Quenching Lactonases Tay, S.B., Chow, J.Y., Go, M.K., and Yew, W.S. (2016) *Journal of Visualized Experiments* Jan1:107. doi: 10.3791/53243. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780937/

2015
35	Synthetic Polyketide Enzymology: Platform for Biosynthesis of Novel Anti-Microbial Polyketides Go, M.K., Wongsantichon, J., Cheung, V.W.N., Chow, J.Y., Robinson, R.C., and Yew, W.S. (2015) *ACS Catalysis* 5(7): 4033–4042. https://pubs.acs.org/doi/abs/10.1021/acscatal.5b00477
36	Engineered strains enhance gold biorecovery from electronic scrap Natarajan, G., Tay, S.B., Yew, W.S., and Ting, Y.P. (2015) *Minerals Engineering* 75, 32-37. https://www.sciencedirect.com/science/article/abs/pii/S0892687515000035

2014
37	Identification of Polyketide Inhibitors Targeting 3-Dehydroquinate Dehydratase in the Shikimate Pathway of Enterococcus faecalis Cheung, V.W.N., Xue, B., Hernandez-Valladares, M., Go, M.K., Tung, A., Aguda, A.H., Robinson, R.C., and Yew, W.S. (2014) *PLoS One* 9(7):e103598. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103598
38	Loss of Quaternary Structure is Associated with Rapid Sequence Divergence in the OSBS Family Odokonyero, D., Sakai, A., Patskovsky, Y., Malashkevich, V.N., Fedorov, A.A., Bonanno, J.B., Fedorov, E.V., Toro, R., Agarwal, R., Wang, C., Ozerova, N.D.S., Yew, W.S., Sauder, J.M., Swaminathan, S., Burley, S.K., Almo, S.C., and Glasner, M.E. (2014) *Proc Natl Acad Sci* 111, 8535-8540. https://www.pnas.org/content/111/23/8535
39	Glycine Decarboxylase is an Unusual Amino Acid Decarboxylase Involved in Tumorigenesis Go, M.K., Zhang, W.C., Lim, B., and Yew, W.S. (2014) *Biochemistry* 53, 947-956. https://pubs.acs.org/doi/10.1021/bi4014227
40	Disruption of Biofilm Formation by the Human Pathogen Acinetobacter baumannii using Engineered Quorum-quenching Lactonases Chow, J.Y., Yang, Y., Tay, S.B., Chua, K.L., and Yew, W.S. (2014) *Antimicrob Agents Chemother.* 58, 1802-1805. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957888/

2013
41	Development of Quorum-Based Anti-Virulence Therapeutics Targeting Gram-Negative Bacterial Pathogens Tay, S.B., and Yew, W.S. (2013) *Int J Mol Sci.*14, 16570-16599. https://www.mdpi.com/1422-0067/14/8/16570
42	Enhancing gold recovery from electronic waste via lixiviant metabolic engineering in Chromobacterium violaceum Tay, S.B., Natarajan, G., Rahim, M.N., Tan, H.T., Chung, M.C., Ting, Y.P., and Yew, W.S. (2013) *Sci Rep.* 3, 2236 https://www.nature.com/articles/srep02236
43	Structural Evidence of a Productive Active Site Architecture for an Evolved Quorum-quenching GKL Lactonase Xue, B., Chow, J.Y., Baldansuren, A., Yap, L.L., Gan, Y.W., Dikanov, S.A., Robinson, R.C., and Yew, W.S. (2013) *Biochemistry* 52, 2359-2370 https://pubs.acs.org/doi/10.1021/bi4000904

2012
44	Establishing a Toolkit for Precursor-directed Polyketide Biosynthesis: Exploring Substrate Promiscuities of Acid-CoA Ligases Go, M.K., Chow, J.Y., Cheung, V.W.N., Lim, Y.P., and Yew, W.S. (2012) *Biochemistry* 51, 4568-4579 https://pubs.acs.org/doi/10.1021/bi300425j

2010
45	Directed evolution of a thermostable quorum-quenching lactonase from the amidohydrolase superfamily Chow, J.Y., Xue, B., Lee, K.H., Tung, A., Wu, L., Robinson, R.C., and Yew, W.S. (2010) *J Biol Chem* 285, 40911-40920 https://doi.org/10.1074/jbc.M110.177139
46	Site-directed mutagenesis on human cystathionine-gamma-lyase reveals insights into the modulation of H₂S production Huang, S., Chua, J.H., Yew, W.S., Sivaraman, J., Moore, P.K., Tan, C.H., and Deng, L.W. (2010) *J Mol Biol.* 396, 708-718 https://doi.org/10.1016/j.jmb.2009.11.058

2009
47	Directed Evolution of a Quorum-Quenching Lactonase from Mycobacterium avium subsp. paratuberculosis K-10 in the Amidohydrolase Superfamily Chow, J.Y., Long, W., and Yew, W.S.(2009) *Biochemistry* 48, 4344-4353 https://doi.org/10.1021/bi9004045

2007
48	Evolution of Enzymatic Activities in the Enolase Superfamily: L-Talarate/Galactarate Dehydratase from Salmonella typhimurium LT2 Yew, W.S., Fedorov, A.A., Fedorov, E.V., Almo, S.C., and Gerlt, J.A. (2007) *Biochemistry* 46, 9564-9577 https://doi.org/10.1021/bi7008882

2006
49	Evolution of Enzymatic Activities in the Enolase Superfamily: D Tartrate Dehydratase from Bradyrhizobium japonicum Yew, W.S., Fedorov, A.A., Fedorov, E.V., Wood, B.M., Almo, S.C., and Gerlt, J.A. (2006) *Biochemistry* 45, 14598-14608 https://doi.org/10.1021/bi061688g
50	Evolution of Enzymatic Activities in the Enolase Superfamily: L-Fuconate Dehydratase from Xanthomonas campestris Yew, W.S., Fedorov, A.A., Fedorov, E.V., Rakus, J.F., Pierce, R.W., Almo, S.C., and Gerlt, J.A. (2006) *Biochemistry* 45, 14582-14597 https://doi.org/10.1021/bi061687o
51	Evolution of Enzymatic Activities in the Enolase Superfamily: N-Succinylamino Acid Racemase and a New Pathway for the Irreversible Conversion of D- to L-Amino Acids Sakai, A., Xiang, D.F., Xu, C., Song, L., Yew, W.S., Raushel, F.M., and Gerlt, J.A. (2006) *Biochemistry* 45, 4455-4462 https://doi.org/10.1021/bi060230b

2005
52	Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Structural Basis for Catalytic Promiscuity in Wild-type and Designed Mutants of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase Wise, E.L., Yew, W.S., Akana, J., Gerlt, J.A., and Rayment, I. (2005) *Biochemistry* 44, 1816-1823 https://doi.org/10.1021/bi0478143
53	Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Enhancing the Promiscuous D-Arabino-Hex-3-ulose 6-Phosphate Synthase Reaction Catalyzed by 3-Keto-L-Gulonate 6-Phosphate Decarboxylase Yew, W.S., Akana, J., Wise, E.L., Rayment, I., and Gerlt, J.A. (2005) *Biochemistry* 44, 1807-1815 https://doi.org/10.1021/bi047815v

2004
54	Evolution of Enzymatic Activities in the Orotidine 5’ Monophosphate Decarboxylase Suprafamily: Crystallographic Evidence for a Proton Relay System in the Active Site of 3-Keto-L-Gulonate 6 Phosphate Decarboxylase Wise, E.L., Yew, W.S., Rayment, I., and Gerlt, J.A. (2004) *Biochemistry* 43, 6438-6446 https://doi.org/10.1021/bi0497392
55	Evolution of Enzymatic Activities in the Orotidine 5’ Monophosphate Decarboxylase Suprafamily: Mechanistic Evidence for a Proton Relay System in the Active Site of 3-Keto-L-Gulonate 6 Phosphate Decarboxylase Yew, W.S., Wise, E.L., Rayment, I., and Gerlt, J.A. (2004) *Biochemistry* 43, 6427-6437 https://doi.org/10.1021/bi049741t

2003
56	Structural Evidence for a 1,2-Enediolate Intermediate in the Reaction Catalyzed by 3-Keto-L-Gulonate 6-Phosphate Decarboxylase, a Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Wise, E.L., Yew, W.S., Gerlt, J.A., and Rayment, I. (2003) *Biochemistry* 42, 12133-12142 https://doi.org/10.1021/bi0348819

2002
57	Homologous (β/α)₈-Barrel Enzymes that Catalyze Unrelated Reactions: Orotidine 5’-Monophosphate Decarboxylase and 3-Keto-L-Gulonate 6-Phosphate Decarboxylase Wise, E.L., Yew, W.S., Babbitt, P.C., Gerlt, J.A., and Rayment, I. (2002) *Biochemistry* 41, 3861-3869 https://doi.org/10.1021/bi012174e * equal authorship. Highlighted in Editor’s Choice, Science* (2002) 295, 1975.*
58	Utilization of L-Ascorbate by Escherichia coli K-12: Assignments of Function to Products of the yjf-sga and yia-sgb Operons Yew, W.S., and Gerlt, J.A. (2002) *J Bacteriol* 184, 302-306 https://doi.org/10.1128/jb.184.1.302-306.2002

2000
59	The Role of Tryptophan Residues in the Hemolytic Activity of Stonustoxin, a Lethal Factor from Stonefish (Synanceja horrida) Venom Yew, W.S., and Khoo, H.E. (2000) *Biochimie* 82, 251-257 https://doi.org/10.1016/S0300-9084(00)00203-0

1999
60	Crystallization and Preliminary Crystallographic Study of Stonustoxin, a Protein Lethal Factor Isolated from the Stonefish (Synanceja horrida) Venom Yew, W.S., Kolatkar, P.R., Kuhn, P., and Khoo, H.E. (1999) *J Struct Biol* 128, 216-218 https://doi.org/10.1006/jsbi.1999.4193

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Publications

Research Publications

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