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Yo Suzuki is an associate professor working in the Synthetic Biology group. Dr. Suzuki’s research is focused on systematic investigation of gene functions in various organisms. This includes studies of phenotypes involving inactivation or hyperactivation of multiple genes that can reveal novel gene functions. In some cases, these functions can be incorporated into microbial organisms through genome engineering to serve specific purposes in industrial or biomedical applications.
Prior to his appointment at JCVI, Dr. Suzuki was a postdoctoral fellow at Harvard Medical School. He began is career as a research associate with the Howard Hughes Medical Institute in Boulder, Colorado.
He received his PhD from University of Colorado at Boulder in molecular biology. His undergraduate degree is from Nagoya University in Japan.
Research Priorities
Understanding cellular life
- Systematic analysis of gene functions for all genes in the genome using conditional gene inactivation via CRISPRi in a minimal bacterial cell.
Engineering deep-skin microbiotas toward a treatment for type 1 diabetes
- Construction of bacteria that can respond to rising blood glucose levels and produce a variant of insulin in a suitable layer of the skin to serve as a surrogate for the insulin-producing cell in the body.
- Eventual development of a safe, non-invasive, non-immunoreactive, and fully automated system for glucose sensing and insulin administration.
Developing organisms for producing fuels and valuable compounds from biomass
- Establishment of synthetic biology pipelines for designing, building, and testing organisms and other biological systems.
- Application of advanced genome engineering technologies to the engineering of bacteria with the capacity to utilize aromatic compounds derived from lignin.
- Identification of synergistic interactions among cellulases and incorporation of these interactions into designer cellulosomes for efficient release of sugar from biomass.
Using drug-sensitive yeast strains to rapidly identify mechanisms of action for drugs
- Identification of candidate targets for antimalarials and anti-cancer compounds using whole genome sequencing in yeast strains that acquired mutations to resist these compounds.
- Validation of causal mutations for the resistance phenotypes using genetic engineering.
- Acceleration of the identification of compound targets in native organisms with information from facile yeast experiments.
Publications
Frontiers in microbiology. 2024-05-31; 15.1411609.
Cloning and sequencing analysis of whole Spiroplasma genome in yeast
Mizutani M, Omori S, Yamane N, Suzuki Y, Glass JI, Chuang RY, Fukatsu T, Kakizawa S
PMID: 38881660
ACS synthetic biology. 2023-09-15; 12.9: 2778-2782.
Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs
Hernandez Hernandez D, Ding L, Murao A, Dahlin LR, Li G, Arnolds KL, Amezola M, Klein A, Mitra A, Mecacci S, Linger JG, Guarnieri MT, Suzuki Y
PMID: 37582217
Communications biology. 2022-02-11; 5.1: 128.
Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance
Ottilie S, Luth MR, Hellemann E, Goldgof GM, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, Abraham M, Tarsio M, LeBlanc E, Whitesell L, Schenken J, Gunawan F, Patel R, Smith J, Love MS, Williams RM, McNamara CW, Gerwick WH, Ideker T, Suzuki Y, Wirth DF, Lukens AK, Kane PM, Cowen LE, Durrant JD, Winzeler EA
PMID: 35149760
Cellular microbiology. 2021-12-01; 23.12: e13392.
Blockade of endoplasmic reticulum stress-induced cell death by Ureaplasma parvum vacuolating factor
Nishiumi F, Kawai Y, Nakura Y, Yoshimura M, Wu HN, Hamaguchi M, Kakizawa S, Suzuki Y, Glass JI, Yanagihara I
PMID: 34490709
Current opinion in biotechnology. 2021-10-01; 71.25-31.
Biotechnology for secure biocontainment designs in an emerging bioeconomy
Arnolds KL, Dahlin LR, Ding L, Wu C, Yu J, Xiong W, Zuniga C, Suzuki Y, Zengler K, Linger JG, Guarnieri MT
PMID: 34091124
Cell systems. 2020-01-22; 10.1: 25-38.e10.
Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network
Celaj A, Gebbia M, Musa L, Cote AG, Snider J, Wong V, Ko M, Fong T, Bansal P, Mellor JC, Seesankar G, Nguyen M, Zhou S, Wang L, Kishore N, Stagljar I, Suzuki Y, Yachie N, Roth FP
PMID: 31668799
ACS synthetic biology. 2018-06-15; 7.6: 1538-1552.
Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells
Mariscal AM, Kakizawa S, Hsu JY, Tanaka K, González-González L, Broto A, Querol E, Lluch-Senar M, Piñero-Lambea C, Sun L, Weyman PD, Wise KS, Merryman C, Tse G, Moore AJ, Hutchison CA, Smith HO, Tomita M, Venter JC, Glass JI, Piñol J, Suzuki Y
PMID: 29786424
Cancer prevention research (Philadelphia, Pa.). 2017-04-01; 10.4: 226-234.
The Human Microbiome and Cancer
Rajagopala SV, Vashee S, Oldfield LM, Suzuki Y, Venter JC, Telenti A, Nelson KE
PMID: 28096237
PLoS pathogens. 2016-07-28; 12.7: e1005763.
Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond
Van Voorhis WC, Adams JH, Adelfio R, Ahyong V, Akabas MH, Alano P, Alday A, Alemán Resto Y, Alsibaee A, Alzualde A, Andrews KT, Avery SV, Avery VM, Ayong L, Baker M, Baker S, Ben Mamoun C, Bhatia S, Bickle Q, Bounaadja L, Bowling T, Bosch J, Boucher LE, Boyom FF, Brea J, Brennan M, Burton A, Caffrey CR, Camarda G, Carrasquilla M, Carter D, Belen Cassera M, Chih-Chien Cheng K, Chindaudomsate W, Chubb A, Colon BL, Colón-López DD, Corbett Y, Crowther GJ, Cowan N, D'Alessandro S, Le Dang N, Delves M, DeRisi JL, Du AY, Duffy S, Abd El-Salam El-Sayed S, Ferdig MT, Fernández Robledo JA, Fidock DA, Florent I, Fokou PV, Galstian A, Gamo FJ, Gokool S, Gold B, Golub T, Goldgof GM, Guha R, Guiguemde WA, Gural N, Guy RK, Hansen MA, Hanson KK, Hemphill A, Hooft van Huijsduijnen R, Horii T, Horrocks P, Hughes TB, Huston C, Igarashi I, Ingram-Sieber K, Itoe MA, Jadhav A, Naranuntarat Jensen A, Jensen LT, Jiang RH, Kaiser A, Keiser J, Ketas T, Kicka S, Kim S, Kirk K, Kumar VP, Kyle DE, Lafuente MJ, Landfear S, Lee N, Lee S, Lehane AM, Li F, Little D, Liu L, Llinás M, Loza MI, Lubar A, Lucantoni L, Lucet I, Maes L, Mancama D, Mansour NR, March S, McGowan S, Medina Vera I, Meister S, Mercer L, Mestres J, Mfopa AN, Misra RN, Moon S, Moore JP, Morais Rodrigues da Costa F, Müller J, Muriana A, Nakazawa Hewitt S, Nare B, Nathan C, Narraidoo N, Nawaratna S, Ojo KK, Ortiz D, Panic G, Papadatos G, Parapini S, Patra K, Pham N, Prats S, Plouffe DM, Poulsen SA, Pradhan A, Quevedo C, Quinn RJ, Rice CA, Abdo Rizk M, Ruecker A, St Onge R, Salgado Ferreira R, Samra J, Robinett NG, Schlecht U, Schmitt M, Silva Villela F, Silvestrini F, Sinden R, Smith DA, Soldati T, Spitzmüller A, Stamm SM, Sullivan DJ, Sullivan W, Suresh S, Suzuki BM, Suzuki Y, Swamidass SJ, Taramelli D, Tchokouaha LR, Theron A, Thomas D, Tonissen KF, Townson S, Tripathi AK, Trofimov V, Udenze KO, Ullah I, Vallieres C, Vigil E, Vinetz JM, Voong Vinh P, Vu H, Watanabe NA, Weatherby K, White PM, Wilks AF, Winzeler EA, Wojcik E, Wree M, Wu W, Yokoyama N, Zollo PH, Abla N, Blasco B, Burrows J, Laleu B, Leroy D, Spangenberg T, Wells T, Willis PA
PMID: 27467575
Scientific reports. 2016-06-13; 6.27806.
Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor
Goldgof GM, Durrant JD, Ottilie S, Vigil E, Allen KE, Gunawan F, Kostylev M, Henderson KA, Yang J, Schenken J, LaMonte GM, Manary MJ, Murao A, Nachon M, Stanhope R, Murray R, Prescott M, McNamara CW, Slayman CW, Amaro RE, Suzuki Y, Winzeler EA
PMID: 27291296
Science (New York, N.Y.). 2016-03-25; 351.6280: aad6253.
Design and synthesis of a minimal bacterial genome
Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC
PMID: 27013737
Journal of virology. 2015-04-01; 89.8: 4706.
Correction for Joseph et al., Adaptation of pandemic H2N2 influenza A viruses in humans
Joseph U, Linster M, Suzuki Y, Krauss S, Halpin RA, Vijaykrishna D, Fabrizio TP, Bestebroer TM, Maurer-Stroh S, Webby RJ, Wentworth DE, Fouchier RA, Bahl J, Smith GJ
PMID: 25792756
Genome research. 2015-03-01; 25.3: 435-44.
Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling
Suzuki Y, Assad-Garcia N, Kostylev M, Noskov VN, Wise KS, Karas BJ, Stam J, Montague MG, Hanly TJ, Enriquez NJ, Ramon A, Goldgof GM, Richter RA, Vashee S, Chuang RY, Winzeler EA, Hutchison CA, Gibson DG, Smith HO, Glass JI, Venter JC
PMID: 25654978
Journal of virology. 2015-02-01; 89.4: 2442-7.
Adaptation of pandemic H2N2 influenza A viruses in humans
Joseph U, Linster M, Suzuki Y, Krauss S, Halpin RA, Vijaykrishna D, Fabrizio TP, Bestebroer TM, Maurer-Stroh S, Webby RJ, Wentworth DE, Fouchier RA, Bahl J, Smith GJ, CEIRS H2N2 Working Group
PMID: 25505070
PloS one. 2015-01-01; 10.9: e0137466.
Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies
Kostylev M, Otwell AE, Richardson RE, Suzuki Y
PMID: 26348330
Antimicrobial agents and chemotherapy. 2015-01-01; 59.1: 536-43.
Genomic and transcriptomic analyses of colistin-resistant clinical isolates of Klebsiella pneumoniae reveal multiple pathways of resistance
Wright MS, Suzuki Y, Jones MB, Marshall SH, Rudin SD, van Duin D, Kaye K, Jacobs MR, Bonomo RA, Adams MD
PMID: 25385117
Nature protocols. 2014-04-01; 9.4: 743-50.
Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing
Karas BJ, Jablanovic J, Irvine E, Sun L, Ma L, Weyman PD, Gibson DG, Glass JI, Venter JC, Hutchison CA, Smith HO, Suzuki Y
PMID: 24603933
Frontiers in microbiology. 2014-01-01; 5.369.
Rescue of mutant fitness defects using in vitro reconstituted designer transposons in Mycoplasma mycoides
Karas BJ, Wise KS, Sun L, Venter JC, Glass JI, Hutchison CA, Smith HO, Suzuki Y
PMID: 25101070
Nature methods. 2013-05-01; 10.5: 410-2.
Direct transfer of whole genomes from bacteria to yeast
Karas BJ, Jablanovic J, Sun L, Ma L, Goldgof GM, Stam J, Ramon A, Manary MJ, Winzeler EA, Venter JC, Weyman PD, Gibson DG, Glass JI, Hutchison CA, Smith HO, Suzuki Y
PMID: 23542886
ACS synthetic biology. 2012-07-20; 1.7: 267-73.
Assembly of large, high G+C bacterial DNA fragments in yeast
Noskov VN, Karas BJ, Young L, Chuang RY, Gibson DG, Lin YC, Stam J, Yonemoto IT, Suzuki Y, Andrews-Pfannkoch C, Glass JI, Smith HO, Hutchison CA, Venter JC, Weyman PD
PMID: 23651249
Molecular systems biology. 2011-11-08; 7.544.
Systematic exploration of synergistic drug pairs
Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP
PMID: 22068327
Nature methods. 2011-02-01; 8.2: 159-64.
Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection
Suzuki Y, St Onge RP, Mani R, King OD, Heilbut A, Labunskyy VM, Chen W, Pham L, Zhang LV, Tong AH, Nislow C, Giaever G, Gladyshev VN, Vidal M, Schow P, Lehár J, Roth FP
PMID: 21217751
12-Mar-2024
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