Shao, Zengyi

Zengyi Shao image

Zengyi Shao

Email:

Title(s):

Associate Professor

Office

4140 Biorenewables Research Laboratory
617 Bissell Rd.
Ames, IA 50011-1098

Information

Education

  • Ph.D. Chemical Engineering, University of Illinois Urbana-Champaign, 2009
  • M.S. Chemical Engineering, University of Illinois Urbana-Champaign, 2005
  • B.S. Biochemistry and Molecular Biology, Nankai University, China, 2002

Interest Areas

  • Synthetic Biology
  • Genome Engineering
  • Metabolic Engineering
  • Biochemical Engineering and Biorenewables
  • Biomedical Engineering

The advent of synthetic biology has revolutionized our ability to understand molecular mechanisms in complex biological processes, re-program genetic coding, and create novel functions. The long-term goal of the Shao Lab is to elucidate the ‘functional genomics’ of high-performing microbial species that have unique biochemical, metabolic, and physiological features. We strive for developing platform technologies to provide generalizable strain-engineering solutions, enabling rapid, functional modifications of high-performance microbes, and expanding the current collection of microbial factories.

  • Building Novel Microbial Manufacturing Platforms and Integrating Biocatalysis and Catalysis: Our group designs various microbial factories for producing high-value compounds with applications in polymer precursors, nutraceuticals, and pharmaceuticals. Distinct from the mainstream research that is centered on exploiting the model microbial species, Our group emphasizes on “tailoring host selection according to the specific need.” For example, Scheffersomyces stipitis is explored to produce plant-sourced flavonoids and alkaloids (nutraceuticals and pharmaceuticals) because this microorganism renders higher precursor availability for the upstream shikimate pathway; Issatchenkia orientalis is being exploited to produce dicarboxylic acids (polymer precursors) owing to its superior acid tolerance; and Yarrowia lipolytica is selected as the producer to synthesize wax esters (premier lubricant and skin care additives) based on its exceptional oleaginous nature, which yields sufficient starting molecules. In addition, aligning with the mission of the CBiRC to nurture a sustainable biorenewable chemical industry, our group has been collaborating with the chemists in CBiRC and polymer scientists to streamline the integration of biocatalysis and catalysis. 
  • Elucidating Core Design Principles to Streamline Nonconventional Microbial Host Development: In the course of selecting microbial production hosts, we recognized that the limited model microbial species are not the only hosts of potential scientific and economic importance. Numerous other nonconventional microorganisms exhibit highly unusual metabolic, biosynthetic, physiological, and fermentative capacities. As outcomes of long-term natural evolution in particular environments, these high-performance characteristics are conferred by a network of genes via a hierarchy of regulations that are intrinsically complex, rendering the horizontal transfer of these functions into model hosts highly challenging. However, significant technology hurdles lie in front of exploiting high potential nonconventional microorganisms. This research theme is aimed at providing the main avenues for enabling rapid functional modifications of challenging nonconventional species and genome-scale genotype–phenotype profiling. At present, our group is establishing in silico principles to predict the genetic elements vital to the creation of stable expression platforms for convenient gene and pathway manipulations. We are also developing a high throughput pipeline for transcriptome engineering and reprogramming the genome-scale regulatory network to enhance the desired cellular function. This research is geared toward elucidating systematic rules and enabling generalizable platform technologies that can be effectively applied across species.
  • Creating Microbial Consortia to Perform Complex Tasks: Microbial consortia, composed of multiple interacting microbial populations, can carry out complicated tasks that are more challenging for individual populations to perform. Cooperation and division of labor is common in nature, wherein organisms have established a wide variety of relationships. The co-culture technology has also been utilized in industrial processes such as food processing and waste degradation. Our group is developing a yeast consortium to produce shikimate pathway derivatives with nutraceutical and pharmaceutical values. In a collaborative project with ISU faculty Laura Jarboe, we are also engineering an isogenic self-tuning bacterial consortium for converting mixed substrates and producing mixed products. In another collaborative project with ISU faculty Emily Smith and Ames Lab scientist Tanya Prozorov, our group is building microbial consortia and collaborating with the microscopy specialists to study the deconstruction of plant materials as an inexpensive feedstock for producing biofuels and chemicals.
  • Exploring Nucleosome-depleted Sequences for Novel Applications in Synthetic Biology: Functional genomics has been primarily focused on elucidating the roles of coding elements. Accumulating evidence demonstrates that the large amount of noncoding regions of a genome is not garbage. Their spatial arrangement and interaction with the coding elements play an important role in guiding cellular behaviors. In synthetic biology, the canonical Design–Build–Test–Learn cycle dissects complex natural biological subjects into distinct functional parts through a “subtraction” hierarchy. Numerous efforts are then focused on characterizing individual parts and modules at one layer of complexity at a time. However, the interplay among multiple layers in the new combinations interferes with the simplistic mix-and-match workflow and causes undesirable design imprecision. Our group aims at addressing the challenge of the frequently encountered “low orthogonality” between well-characterized biological components and their genetic contexts using nucleosome-depleted sequences. We are seeking novel bioengineering solutions using these previously overlooked sequences to streamline the development of advanced microbial factories.

Publications

(* denotes equal contribution; † denotes corresponding authors)

[1] M. Suastegui*, J. E. Matthiesen*, J. M. Carraher, N. Hernandez, N. R. Quiroz, A. Okerlund, E. W. Cochran, Z. Shao†, and J.-P. Tessonnier†. “Combining Metabolic Engineering and Electrocatalysis: Application to the Production of Polyamides from Sugar”, Angewandte Chemie International Edition, 55, 2368–2373 (2016, highlighted in the front cover). DOI: 10.1002/anie.201509653

[2] Y. Zhao, M. Cao, J. F. McClelland, Z. Shao, and M. Lu†, “A Photoacoustic Immunoassay for Biomarker Detection”, Biosensors and Bioelectronics, 85, 261-266, DOI: 10.1016/j.bios.2016.05.028 (2016). 

[3] M. Suastegui, W. Guo, X. Feng†, and Z. Shao†. “Investigating Strain Dependency in the Production of Aromatic Compounds in Saccharomyces cerevisiae”, Biotechnology and Bioengineering, 113, 2676-2685 (2016). DOI: 10.1002/bit.26037.

[4] M. Suastegui and Z. Shao†, “Yeast Factories for Production of Aromatic Compounds: from Building Blocks to Plant Secondary Metabolites”, Journal of Industrial Microbiology and Biotechnology, 43(11), 611-1624, DOI: 10.1007/s10295-016-1824-9 (2016, the front cover). 

[5] M. Gao, M. Cao, M. Suastegui, J. Walker, N. R. Quiroz, Y. Wu, D. Tribby, A. Okerlund, L. Stanley, J. V. Shanks, and Z. Shao†, “Innovating a Nonconventional Yeast Platform for Producing Shikimic Acid as the Building Block of High-value Aromatics”, ACS Synthetic Biology, 6, 29–38 (2017). DOI: 10.1021/acssynbio.6b00132.

[6] J. Matthiesen, M. Suastegui, Y. Wu, M. Viswanathan, Y. Qu, M. Cao, N. Rodriguez-Quiroz, A. Okerlund, G. Kraus, R. Raman, Z. Shao, and J.-P.Tessonnier†, “Electrochemical Conversion of Biologically-Produced Muconic Acid: Key Considerations for Scale-up and Corresponding Technoeconomic Analysis”, ACS Sustainable Chemistry & Engineering, 4 (12), 7098–7109, DOI: 10.1021/acssuschemeng.6b01981 (2016). 

[7] M. Suastegui, M. Gao, and Z. Shao†, “Pathway Assembly and Optimization”, Biotechnologies for Biofuel Production and Optimization, 1st Edition, Elsevier, 139-164 DOI:10.1016/B978-0-444-63475-7.00006-6 (2016).

[8] M. Cao, M. Gao, C. Lopez, Y. Wu, A. Seetharam, A. Severin, and Z. Shao†, “Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering”, ACS Synthetic Biology, 6, 1545–1553 (2017). DOI: 10.1021/acssynbio.7b00046.

[9] M. Suastegui, C. Y. Ng, A. Chowdhury, W. Sun, E. House, C. D. Maranas, and Z. Shao†, “Multilevel Engineering of the Upstream Module of Aromatic Amino Acid Biosynthesis in Saccharomyces cerevisiae for High Production of Polymer and Drug Precursors”, Metabolic Engineering, 42, 134–144 (2017). DOI: 10.1016/j.ymben.2017.06.008.

[10] M. Cao, A. Seetharam, A. Severin, and Z. Shao†, “Rapid Isolation of Centromeres from Scheffersomyces stipitis”, ACS Synthetic Biology, 6, 2028-2034, DOI: 10.1021/acssynbio.7b00166 (2017). 

[11] L. Zhao, Z. Shao, and J. V. Shanks†, “Chapter 8 Anti-cancer Drugs”, Industrial Biotechnology: Products and Processes, Wiley-VCH, Volume 4, 239-269 DOI: 10.1002/9783527807833.ch8 (2017).

[12] J. Sun*, L. Zhao*, Z. Shao, J. V. Shanks, and C. Peebles†, “Expression of Tabersonine 16-Hydroxylase and 16-Hydroxytabersonine-O-methyltransferase in Catharanthus roseus Hairy Roots”, Biotechnology and Bioengineering, 115, 673-683, DOI: 10.1002/bit.26487 (2018). 

[13] M. Cao, M. Gao, D. Ploessl, C. Song, and Z. Shao†, “CRISPR–Mediated Genome Editing and Gene Repression in Scheffersomyces stipitis”, Biotechnology Journal, 13(9):e1700598 (2018). DOI:10.1002/biot.201700598.

[14] M. Gao, D. Ploessl, and Z. Shao†, “Enhancing the Co-utilization of Biomass-derived Mixed Sugars by Yeasts”, Frontiers in Microbiology, 9:3264 (2018). DOI: 10.3389/fmicb.2018.03264.

[15] M. Cao, M. Gao, M. Suastegui, Y. Mei, and Z. Shao†, “Building Microbial Factories for the Production of Aromatic Amino Acid Pathway Derivatives: From Commodity Chemicals to Plant-Sourced Natural Products”, Metabolic Engineering, 58, 94–132 (2020). DOI: 10.1016/j.ymben.2019.08.008.

[16] A. Londono-Calderon, W. Sun, Z. Shao, D.H. Alsem, T. Prozorov, “Correlative Microbially-Assisted Imaging of Cellulose Deconstruction with Electron Microscopy”, Microscopy and Microanalysis, 24 (S1), 382-383, DOI: doi.org/10.1017/S1431927618002404 (2018). 

[17] Y. Zhao, Z. Yao, D. Ploessl, S. Ghosh, M. Monti, D. Schindler, M. Gao, Y. Cai, M. Qiao, C. Yang, M. Cao, and Z. Shao†, “Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories”, ACS Synthetic Biology, 9, 7, 1736-1752, DOI: 10.1021/acssynbio.0c00123 (2020).

[18] C. Lopez, Y. Zhao, and Z. Shao†, “Modulating Pathway Performance by Perturbing Local Genetic Context”, ACS Synthetic Biology, 9, 4, 706-717, DOI: 10.1021/acssynbio.9b00445 (2020).

[19] W. Sun, A. Vila-Santa, N. Liu, T. Prozorov, D. Xie, N. T. Faria, F. C. Ferreira, N. P. Mira, and Z. Shao, “Metabolic Engineering of an Acid-tolerant Yeast Strain Pichia kudriavzevii for Itaconic Acid Production”, Metabolic Engineering Communications, DOI: 10.1016/j.mec.2020.e00124 (2020)

[20] Y. Chen, E. Boggess, E. Ocasio, A. Warner, L. Kerns, V. Drapal, C. Gossling, W. Ross, Z. Shao, J. A. Dickerson, T. J. Mansell, and L. R. Jarboe, “Reverse Engineering of Fatty Acid-tolerant Escherichia coli Identifies Design Strategies for Robust Microbial Cell Factories”, Metabolic Engineering, DOI: 10.1016/j.ymben.2020.05.001 (2020)

[21] M. Cao, Z. Fatma, X. Song, P.-H. Hsieh, V. G. Tran, W. L. Lyon, M. Sayadi, Z. Shao, Y. Yoshikuni, and H. Zhao, “A Genetic Toolbox for Metabolic Engineering of Issatchenkia orientalis”, Metabolic Engineering, DOI: 10.1016/j.ymben.2020.01.005 (2020)

Departments

Affiliations

Interests

Quick Search

Advanced Search