About

Michael Smanski, PhD, is a McKnight Land Grant Professor at the University of Minnesota. He holds a PhD in Microbiology from the University of Wisconsin. His research leverages the latest tools in DNA synthesis, assembly, and genome modification to engineer biotechnologies that address global problems in health, agriculture, and the environment. His lab focuses on developing innovative genetic engineering techniques to create solutions for complex biological challenges.

Research topics

• Biology
• Genetics
• Computational biology
• Evolutionary biology

Selected publications

• Identifying Target Genes for Engineered Genetic Incompatibility in Fish

  Marine Biotechnology · 2026-04-25

  articleOpen accessSenior authorCorresponding

  Genetic biocontrol approaches promise to complement existing physical and chemical methods as part of integrated pest management (IPM) strategies for the control of aquatic invasive species (AIS). Engineered Genetic Incompatibility (EGI) is a strategy for producing organisms that are reproductively isolated from wild conspecifics and could be used as non-persistent genetic biocontrol agents. Previously successfully demonstrated in yeast and insects, here we report early-stage research and development results towards translating this approach from insects into fish. Using Danio rerio (zebrafish) as a model system, we report the identification of target genes and sequence-programmable transcriptional activators (PTAs) that are suitable for EGI development in fish and evaluate their performance in vivo, in a model organism. We also describe several challenges faced when integrating the component parts into a complete system capable of displaying complete genetic incompatibility with wild-type conspecifics. Lastly, we discuss the steps needed to translate EGI from a model fish species to a target invasive species such as common carp (Cyprinus carpio).

  PublisherOA PDFDOI

• Improving Perennial Ryegrass Transformation Protocols with Developmental Regulators

  Plant and Cell Physiology · 2025-10-15

  preprintOpen accessCorresponding

  Abstract The development of genetically modified (GM) or gene edited (GE) turfgrass requires transformation systems that are both efficient and broadly applicable across genotypes. However, traditional Agrobacterium -mediated callus culture methods remain limited by low transformation efficiency, extended culture durations, and strong genotype dependence. In this study, we compare a modified classical callus culture protocol with an approach that incorporates the developmental regulator genes WUSCHEL2 ( wus2 ) and BABY BOOM ( bbm ), along with an inducible Cre recombinase and a dual luciferase assay to test variable promoter strengths in perennial ryegrass ( Lolium perenne L.). We show that traditional protocols failed to regenerate plants, despite successful callus formation and transgene expression. In contrast, the developmental regulator system enabled efficient callus induction and plant regeneration independent of genotype. This optimized protocol significantly reduces the time and genotype constraints of perennial ryegrass transformation, offering a practical platform for advanced genetic engineering applications of an important turf and forage grass.

  PublisherOA PDFDOI

• Heterologous expression of microbial nitroreductases for TNT degradation in transgenic animals

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-11

  preprintOpen access

  Abstract TNT (2,4,6-trinitrotoluene) from unexploded ordinances is a common environmental pollutant near munitions factories, military training sites, and areas of armed conflict. As physical and chemical approaches for TNT remediation are costly and difficult to scale, in situ bioremediation is an attractive alternative. TNT is a phytoaccumulative pollutant. Herbivores engineered to detoxify TNT are a potentially cost-effective platform to bioremediate large areas of contaminated sites while grazing or browsing. As a first step towards engineering herbivores with metabolic capabilities for TNT degradation, we engineered the animal genetic model, Drosophila melanogaster , to screen a library of microbial nitroreductases that can catalyse the initial degradation steps required for TNT degradation. We find strong, cofactor-dependent activity in fly lysates engineered to express NsfA from Escherichia coli , and NsfI from Enterobacter cloacae .

  PublisherOA PDFDOI

• Coproducing a Technology Readiness Level framework for non-persistent genetic biocontrol of aquatic invasive species

  Journal of Environmental Management · 2025-07-15 · 2 citations

  reviewSenior author
  PublisherDOI

• Towards engineering hybrid incompatibility in plants

  Plant Biotechnology Journal · 2025-04-22 · 2 citations

  articleOpen accessSenior authorCorresponding

  The potential for gene flow between genetically modified organisms (GMOs) and non-GMO relatives poses a significant challenge to the development and regulatory approval of GMO crops (Wedger et al., 2024), for example, the spread of herbicide resistance transgenes from crops such as rice or sorghum to cross-pollinating weedy species. Addressing this concern, we developed Engineered Genetic Incompatibility (EGI) (Maselko et al., 2017), a system that establishes species-like barriers to gene flow between otherwise sexually compatible populations. EGI employs Programmable Transcriptional Activators (PTAs) to drive lethal over- and/or ectopic expression of tightly regulated genes following undesired hybridization events (Figure 1a,b). A benign mutation of the target promoter in the EGI organism protects it from ill effects of the PTA, which acts as a sentinel for the wild-type (WT) promoter sequence. Given numerous potential PTA targets, multiple mutually incompatible subpopulations are feasible (Maselko et al., 2020). EGI has been demonstrated in yeast as a proof-of-concept (Maselko et al., 2017) and in insects as a strategy for genetic biocontrol of pests (Maselko et al., 2020; Upadhyay et al., 2022). EGI in plants would provide a strategy to halt gene flow between engineered crops and their domestic and wild relatives without altering normal cultivation or propagation practices. Here, we present promising results towards the demonstration of EGI in plants and highlight technical challenges that still need to be overcome. In the model plant, Arabidopsis thaliana, we targeted the WUSCHEL (AtWUS) gene for the development of EGI. AtWUS is crucial for early embryo formation and development. Ectopic, postembryonic AtWUS expression induces aberrant somatic embryogenesis, resulting in callus formation or post-germination growth arrest and death (Zuo et al., 2002). Prior work has shown that single guide RNAs (sgRNAs) targeting PTAs to regions upstream of the transcriptional start sites (TSS) trigger strong transcriptional activation (Casas-Mollano et al., 2023). Thus, we targeted four sites within 500 bp of the TSS in AtWUS (Figure 1c) for activation with the SunTag PTA (Papikian et al., 2019). SunTag utilizes activation domain (AD) scaffolding, where a VP64 AD is fused to a scFv antibody while a multimeric GCN4 epitope tail is fused to dCas9. Each scFv antibody recognizes a GCN4 epitope, recruiting multiple ADs to a single dCas9 molecule (Papikian et al., 2019). We crossed a PTA expressing line with a line expressing 4 sgRNAs targeting the AtWUS promoter. The expected ectopic embryo formation in the F1 progeny was observed (Figure S1), giving us confidence to pursue EGI using WUS overexpression. Individual sgRNAs were expressed in Arabidopsis protoplasts with sgRNA1 showing the strongest AtWUS activation (Figure 1c), guiding subsequent EGI construction. We then mutated the AtWUS promoter to block PTA binding in the EGI plant. A vector (Figure S2) expressing a catalytically active Cas9, sgRNA1 and the RFP-based FAST marker gene (Shimada et al., 2010) for Cas9 selection was used to transform Arabidopsis plants. Screening RFP-positive T1 plants confirmed multiple unique fixed biallelic AtWUS promoter indels across 30 T1 lines. After segregating out Cas9 in the T2 generation (RFP-negative plants), we advanced two lines for EGI prototyping that have homozygous AtWUS promoter indels (Figures 1d and S3) and no apparent phenotype. We transformed these lines with a T-DNA containing the PTA, sgRNA1 targeting the WT AtWUS promoter and FAST marker (Figure S4). Evidence of successful transformation included accumulation of RFP in seeds (Figure S5). This EGI system uses MoonTag PTAs, which we have found to outperform SunTag PTAs in transgenic plants (Casas-Mollano et al., 2023; Zinselmeier et al., 2024). After floral dip transformation, RFP+ T1 seeds were germinated in soil, showing no obvious phenotype, suggesting that the promoter mutations successfully prevent PTA binding and subsequent AtWUS over- or ectopic expression. We next wanted to test if the molecular components of EGI are functional in these T1 lines even though they do not contain a complete EGI genotype. They are homozygous for the protective promoter mutation, but presumably hemizygous for the PTA construct. Homozygosing the PTA construct would generate a complete EGI genotype. However, the T1 plants provide a convenient screening strain to test for hybrid lethality via outcrosses to WT plants. Such crosses yield approximately equal numbers of RFP+ seeds (that inherit the PTA construct) and RFP- seeds (that do not inherit the PTA construct) to serve as age- and treatment-matched negative controls. We expect poor fitness in the RFP+, but not in the RFP- seedlings. We crossed the T1 lines with WT plants to generate hybrid lines, named T1-Hyb (Figures 1e and S5). RFP+ T1-Hyb seedlings were smaller than parental EGI lines, exhibiting cotyledon browning or ectopic embryos from roots, whereas RFP- seedlings appeared normal. Seedlings with cotyledon browning died upon longer incubation. Upon transfer of non-necrotic seedlings to soil, some died, while survivors were smaller, with abnormal flowers and siliques (Figure 1f). Because we tested independent T1 EGI lines, the number of seedlings with phenotypes varied for each cross (Table S1). Many RFP+ seedlings that appeared normal after germination showed delayed or abnormal development when transferred to soil. Phenotypic observations suggest AtWUS over- or ectopic expression in T1-Hyb seedlings. Endogenous AtWUS expression is restricted to meristematic regions (Mayer et al., 1998) and is absent from most differentiated tissues. AtWUS showed minimal expression in WT, EGI and RFP- T1-Hyb seedlings. RFP+ T1-Hyb exhibited AtWUS overexpression, albeit to differing degrees (Figure S6a). The variation is partially explained by variations in expression of the MoonTag components (Figure S6b). AtWUS expression in T1-Hyb lines was used to select which T1 lines to homozygose at the PTA allele to make complete EGI genotypes. Several seedlings from crosses between T2 homozygous EGI lines and WT plants (named T2-hyb) displayed a yellowing phenotype, delayed germination and slower growth compared to WT plants (Figure 1g–i). Once again, the yellowing seedlings died on the plates before they could be transferred to soil. However, no ectopic embryogenesis was observed, unlike in T1-Hyb. T2-Hyb plants showed ~100-500-fold AtWUS activation compared to Col-0 and EGI lines, which correlates with the yellowing phenotype (Figure 1j). T2-hyb seeds were planted directly to soil, and they were severely delayed in germination and growth (Figure S7). EGI T2 lines also exhibited delayed germination, albeit to a lesser extent (Figure S7). EGI has been demonstrated to provide complete hybrid lethality in model insects. Substantial differences in the developmental biology of plants and insects may require modifications to the system before gene flow can be controlled via this approach in plants. We were able to drive up to 500-fold overexpression of our target gene, AtWUS, only in hybrid plants (Figure 1j). Unfortunately, this was not sufficient for complete hybrid lethality. New target genes whose over- or ectopic expression is more potently lethal may need to be identified. Alternatively, driving higher expression of AtWUS by targeting the promoter with multiple sgRNAs, or driving MoonTag expression using more effective promoters, is expected to increase hybrid lethality. Interestingly, there is a striking growth phenotype in the T2 EGI lines compared to WT that is only apparent when seeds are germinated directly in soil (e.g. Figure 1i vs. Figure S7). Similar fitness defects were not observed in other systems (Maselko et al., 2017, 2020). This cannot be explained by activation of the target gene, as AtWUS is expressed at WT levels in the EGI lines. Potentially, off-target effects of expressing the MoonTag PTA are the cause. Controlling gene flow in plants is a challenging but impactful goal that will have myriad applications in agriculture and biomanufacturing. These promising results not only confirm that the underlying components needed to engineer a genetic incompatibility function as required in plants, but also show that the system needs to be optimized prior to use for biocontainment. MHZ and DFV are supported by the Department of Energy Office of Science, Office of Biological and Environmental Research, Grant No. DE-SC0023160. MHZ, JAC-M, JC, SSF and MJS are supported by the Department of Energy Office of Science, Office of Biological and Environmental Research, Grant No. DE-SC0023142, USDA grant 2018-33522-28747 and by the Advanced Plant Technologies program, DARPA Award HR001118C0146. MHZ is supported by an NIH NIGMS Biotechnology Training grant NIHT32GM008347. M.H.Z., D.F.V. and M.J.S. conceived this study. M.H.Z., J.A.C.-M. and J.C. designed and conducted experiments. M.H.Z., J.A.C.-M., S.S.F., D.F.V. and M.J.S. analysed data. S.S.F. and M.J.S. wrote the manuscript and all authors provided revisions. The editors have granted permission for both M.H.Z. and J.A.C.-M. to list their names in the first position when reporting this manuscript on their CVs. All authors read and approved the final manuscript. M.H.Z., J.A.C.-M. and M.J.S. are co-inventors of a provisional patent, No. 63/693796, regarding the work in this publication. The data that supports the findings of this study are available in the supplementary material of this article. Tables S1–S4. Figures S1–S7. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

  PublisherOA PDFDOI

• Corrigendum to “Bacterial diterpene synthases: New opportunities for mechanistic enzymology and engineered biosynthesis” [Curr Opin Chem Biol, 16 (2012) 132–141

  Current Opinion in Chemical Biology · 2025-03-27

  erratumOpen access1st author
  PublisherDOI

• Selection for toxin production in spatially structured environments increases with growth rate

  The ISME Journal · 2025-01-01 · 1 citations

  articleOpen access

  Microbes adopt diverse strategies to successfully compete with coexisting strains for space and resources. One common strategy is the production of toxic compounds to inhibit competitors, but the strength and direction of selection for this strategy vary depending on the environment. Existing theoretical and experimental evidence suggests that growth in spatially structured environments makes toxin production more beneficial because competitive interactions are localized. Because higher growth rates reduce the length scale of interactions in structured environments, theory predicts that toxin production should be especially beneficial under these conditions. We tested this hypothesis by developing a genome-scale metabolic modeling approach and complementing it with comparative genomics to investigate the impact of growth rate on selection for costly toxin production. Our modeling approach expands the current abilities of the dynamic flux balance analysis platform Computation Of Microbial Ecosystems in Time and Space (COMETS) to incorporate signaling and toxin production. Using this capability, we find that our modeling framework predicts that the strength of selection for toxin production increases as growth rate increases. This finding is supported by comparative genomics analyses that include diverse microbial species. Our work emphasizes that toxin production is more likely to be maintained in rapidly growing, spatially structured communities, thus improving our ability to manage microbial communities and informing natural product discovery.

  PublisherOA PDFDOI

• Dynamic timelines required for development of new insect genetic pest control technologies

  Entomologia Generalis · 2025-11-04

  article1st authorCorresponding
  PublisherDOI

• Biosynthesis of tauro-ursodeoxycholic acid (TUDCA) in Saccharomyces cerevisiae

  Microbial Cell Factories · 2025-10-02 · 2 citations

  articleOpen accessSenior author

  Tauroursodeoxycholic acid (TUDCA) is a microbial bile acid known for its diverse yet still largely unexplored biological activities. Traditionally used in Asian medicine, TUDCA and the taurine-free form, ursodeoxycholic acid (UDCA), share similar therapeutic properties. Recent studies suggest that TUDCA is a promising lead compound for developing neuroprotective agents to prevent neurodegenerative diseases such as Parkinson's disease and Huntington's disease. However, sustainable and ethical sources for large-scale TUDCA production remain unavailable. To address this, we are engineering a yeast-based microbial platform capable of producing TUDCA via fermentation. Here we report strains capable of converting the more widely available primary bile acid, chenodeoxycholic acid (CDCA) into TUDCA. This was achieved by introducing heterologous genes enabling taurine conjugation and taurine biosynthesis, providing a sustainable and scalable approach for TUDCA production.

  PublisherOA PDFDOI

• High-throughput investigation of genetic design constraints in domesticated Influenza A Virus for transient gene delivery

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-15

  preprintOpen accessSenior authorCorresponding

  Replication-incompetent single cycle infectious Influenza A Virus (sciIAV) has demonstrated utility as a research and vaccination platform. Protein-based therapeutics are increasingly attractive due to their high selectivity and potent efficacy but still suffer from low bioavailability and high manufacturing cost. Transient RNA-mediated delivery is a safe alternative that allows for expression of protein-based therapeutics within the target cells or tissues but is limited by delivery efficiency. Here, we develop recombinant sciIAV as a platform for transient gene delivery in vivo and in vitro for therapeutic, research, and manufacturing applications ( in vivo antimicrobial production, cell culture contamination clearance, and production of antiviral proteins in vitro ). While adapting the system to deliver new protein cargo we discovered expression differences presumably resulting from genetic context effects. We applied a high-throughput screen to map these within the 3 ′ -untranslated and coding regions of the hemagglutinin-encoding segment 4. This screen revealed permissible mutations in the 3 ′ -UTR and depletion of RNA level motifs in the N-terminal coding region.

  PublisherOA PDFDOI

Frequent coauthors

• Adam Sychla

  Biotechnology Institute

  48 shared

• Maciej Maselko

  Macquarie University

  39 shared

• Stephen C. Heinsch

  Biotechnology Institute

  37 shared

• Siba R. Das

  University of Minnesota

  35 shared

• Nathan R. Feltman

  Biotechnology Institute

  29 shared

• Ambuj Upadhyay

  Biotechnology Institute

  27 shared

• Ben Shen

  University of Florida

  24 shared

• Matthew H. Zinselmeier

  University of Minnesota

  24 shared

Awards & honors

• Dr. James E. Rubin Medical Memorial Award
• Graduating Medical Student Research Award
• Veneziale-Steer Award
• Dr. Marvin and Hadassah Bacaner Research Awards
• Schmidt Steer Award