About

Kate Adamala, PhD, is an Associate Professor affiliated with the Department of Genetics, Cell Biology & Development at the University of Minnesota. Her research focuses on synthetic minimal cells, which are programmable bioreactors with some, but not all, functions of live natural cells. These designable biological systems enable the study of natural life processes, investigation of genetic pathways at the single-cell level, and modeling of species and population interactions. Her work also involves engineering novel pathways and artificial biological systems for applications in biotechnology, basic science, space exploration, biosafety, and biomedical fields.

Research topics

• Computer Science
• Biology
• Computational biology
• Genetics
• Engineering
• Biochemical engineering
• Ecology
• Cell biology
• Mechanical engineering
• Telecommunications
• Neuroscience
• Biophysics
• Materials science
• Biological system
• Waste management
• Biotechnology
• Environmental science
• Process engineering
• Pulp and paper industry
• Physics
• Nanotechnology

Selected publications

• CyanoConstruct: simple platform for cyanobacterial expression construct assembly and translational tuning

  BMC Biotechnology · 2026-02-16 · 2 citations

  articleOpen access

  Despite the advances in synthetic biology, the construction of efficient and balanced artificial pathways remains challenging and a general bottleneck in bacterial strain development. Although translational tuning can be applied for balancing consecutive catalytic steps at protein expression level, the potential remains underexplored in cyanobacterial engineering. To complement existing modular cloning systems for this purpose the objective here was to simplify the construct assembly procedure to make translational tuning more accessible for expression optimization in cyanobacteria. This study describes the design and use of a one-pot DNA construct assembly system (CyanoConstruct) for the generation transformation-ready multi-gene expression plasmids in a single Golden Gate reaction. This approach allows the user to select the ribosome binding site element (RBS) for each target gene, thus serving as a tool for independently modulating the translation efficiency of the individual overexpressed enzymes. For easy adaptation, a custom online tool (www.cyanoconstruct.com) guides the sequence design of new compatible parts and the assembly of constructs from user-specified parts in silico. We demonstrate the use of the system by assembling different two-gene and three-gene expression constructs from parts selected specifically for optimal performance in Synechocystis sp PCC 6803; the constructs functioned as intended in vivo and showed different pathway fluxes construed by alternative RBS combinations. The efficiency and specificity of the assembly were shown to be high, enabling the generation of the final expression plasmids from the library parts in one assembly cycle. CyanoConstruct offers a simple strategy for building bacterial operon-based expression constructs, specifically facilitating the use of modular cloning systems for RBS optimization in routine cyanobacterial engineering. With the help of the web-based design tool that also serves as a sequence repository, the part library described in this work (https://www.addgene.org/browse/article/28263931/) can be easily expanded with user-specified sequences. By increasing the throughput for generating pathway variants with different translational patterns, the system is expected to advance the design of more efficient strains with higher flux to the desired end-product, thereby contributing to the development of next-generation biotechnologies.

  PublisherDOI

• Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems

  Nucleic Acids Research · 2026-02-24 · 1 citations

  articleOpen accessSenior author

  Transfer RNAs (tRNAs) are utilized by the ribosome to decode the nucleic acid alphabet. tRNA structure, stability, aminoacylation efficiency, and decoding efficacy are governed by their extensive post-transcriptional modifications. In most studies, individual tRNAs are generated using in vitro transcription, which produces tRNAs devoid of these critical site-specific modifications, negatively affecting translation yields and fidelity. To address this challenge, we have developed a purification method that couples tRNA overexpression to DNA hybridization-based purification. Using this approach, we produced native tRNAs from Escherichia coli in high yield and purity while retaining their complement of native post-transcriptional modifications and translational activity. We extend this technique to the purification of Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}$, tRNAs of critical importance for genetic code expansion. We confirmed that both Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}$ contain native E. coli post-transcriptional modifications and provide the first complete modification profiles of each. Moreover, we found that in vivo-generated Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}\ $significantly outperform their in vitro-generated counterparts in amber codon suppression in cell-free translation reactions. Finally, we purified an engineered variant of E. coli$tRNA_{CCA}^{Trp}$, extending our studies to synthetic tRNAs. We present a flexible method that generates modified tRNAs in high yield and purity, addressing a critical and persistent challenge in RNA biochemistry.

  PublisherDOI

• Engineering biology and the positive regulatory pathway in Brazil

  Annals of Applied Biology · 2025-02-18 · 1 citations

  article

  Abstract Engineering Biology in Brazil's transition from oil reliance to bioproduction emphasizes the importance of precision biology in enhancing biodiversity through sustainable agricultural practices. Gene editing can improve food and chemical production, nutritional value, and disease resistance in crops, thus reducing the need for chemical pesticides and unsustainable farming practices. We outline the pivotal role of precision biology in Brazil's transition, highlighting the potential of gene editing to enhance agricultural sustainability. This approach aligns with the United Nations Sustainable Development Goals and benefits from a stable, positive regulatory framework established by the Brazilian Biosafety Committee. Jointly, these advances contribute to global food security while addressing public concerns about safety and ethics.

  PublisherDOI

• A roadmap toward the synthesis of life

  Chem · 2025-02-06 · 30 citations

  articleOpen access

  <h2>Summary</h2> The synthesis of life from non-living matter has captivated and divided scientists for centuries. This bold goal aims at unraveling the fundamental principles of life and leveraging its unique features, such as its resilience, sustainability, and ability to evolve. Synthetic life represents more than an academic milestone—it has the potential to revolutionize biotechnology, medicine, and materials science. Although the fields of synthetic biology, systems chemistry, and biophysics have made great strides toward synthetic life, progress has been hindered by social, philosophical, and technical challenges, such as vague goals, misaligned interdisciplinary efforts, and incompletely addressing public and ethical concerns. Our perspective offers a roadmap toward the synthesis of life based on discussions during a 2-week workshop with scientists from around the globe.

  PublisherDOI

• An Expanded Repertoire of tRNA Sources for Cell-Free Protein Synthesis

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-21 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Cell-free expression systems (CFE) are flexible protein translation platforms that simplify the central dogma into an accessible reaction space. Within these systems, bulk transfer RNAs (tRNAs) are critical substrates which deliver amino acids to the elongating ribosome. For years, CFE systems were completed with commercially available tRNA isolated from E. coli MRE600. All commercial sources of tRNA have since been discontinued, jeopardizing future work in all applications of cell-free translation. Here, we address this need by repurposing previously described tRNA isolation methods to produce tRNAs suitable for CFE applications. We isolated the tRNA pools of E. coli strains A19, BL21(DE3), and Rosetta2 BL21(DE3), finding A19 tRNAs but not BL21(DE3) or Rosetta2 BL21(DE3) capable of robust in vitro translation. We determined the abundances of individual tRNAs using tRNA-seq, finding BL21(DE3) and Rosetta2 BL21(DE3) contained outsized abundances of several tRNAs, compromising translation activity. Using codon optimization strategies which align codon usage to tRNA abundance, we were able to mitigate the impact of misaligned tRNA abundances. We extended these studies to V. natriegens , a promising platform for synthetic biology and CFE. We find that neither exogenous V. natriegens tRNAs nor codon optimization are viable options to improve translation yields. Our work here highlights the importance of tRNA abundance within the context of CFE, and simultaneously addresses a critical challenge within cell-free translation.

  PublisherOA PDFDOI

• Building a Synthetic Cell Together

  Nature Communications · 2025-08-12 · 11 citations

  reviewOpen access

  Synthetic cells (SynCells) are artificial constructs designed to mimic cellular functions, offering insights into fundamental biology, as well as promising impact in the fields of medicine, biotechnology, and bioengineering. Achieving a functional SynCell from the bottom up, i.e. by assembling it from molecular components, requires a global collaboration to overcome the many challenges of engineering and assembling life-like modules while addressing biosafety, equity, and ethical concerns in order to guide responsible innovation. Here, we highlight major scientific hurdles, such as the integration of functional modules by ensuring compatibility across diverse synthetic subsystems, and we propose strategies to advance the field. Synthetic cells are artificial constructs designed to mimic cellular functions, offering insights into fundamental biology, as well as promising impact in the fields of medicine, biotechnology, and bioengineering. In this perspective, the authors highlight major scientific hurdles, such as the integration of functional modules by ensuring compatibility across diverse synthetic subsystems, and propose strategies to advance the field.

  PublisherOA PDFDOI

• Quencher-Free Fluorescence Monitoring of G-Quadruplex Folding

  ACS Omega · 2025-01-15 · 3 citations

  articleOpen access

  Guanine-rich sequences exhibit a high degree of polymorphism and can form single-stranded, Watson-Crick duplex, and four-stranded G-quadruplex structures. These sequences have found a wide range of uses in synthetic biology applications, arising in part from their structural plasticity. High-throughput, low-cost tools for monitoring the folding and unfolding transitions of G-rich sequences would provide an enabling technology for accelerating the prototyping of synthetic biological systems and for accelerating design-build-test cycles. Here, we show that unfolding transitions of a range of G-quadruplex-forming DNA sequences can be monitored in a FRET-like format using DNA sequences that possess only a single dye label, with no quencher. These quencher-free assays can be performed at low cost, with both cost and lead times ca. 1 order of magnitude lower than FRET-labeled strands. Thus, quencher-free secondary structure monitoring promises to be a valuable tool for the testing and development of synthetic biology systems employing G-quadruplexes.

  PublisherDOI

• High Yield, Low Magnesium Flexizyme Reactions in a Water-Ice Eutectic Phase

  Biochemistry · 2025-08-20 · 1 citations

  articleSenior authorCorresponding

  Flexizymes enable the stoichiometric acylation of tRNAs with a variety of compounds, enabling the in vitro translation of peptides with both non-natural backbones and side chains. However, flexizyme reactions have several drawbacks, including single-turnover kinetics, high Mg(II) carryover, inhibiting in vitro translation, and rapid product hydrolysis. Here we present flexizyme reactions utilizing an ice-eutectic phase, with high yields, 30 times lower Mg(II), and long-term product stability. The eutectic flexizyme reactions increase the ease of use, yield and flexibility of aminoacylation and significantly increase the in vitro protein production.

  PublisherDOI

• Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-10 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Transfer RNAs (tRNAs) are utilized by the ribosome to decode the nucleic acid alphabet. tRNA structure, stability, aminoacylation efficiency, and decoding efficacy are governed by their extensive post-transcriptional modifications. In most studies, individual tRNAs are generated using in vitro transcription, which produces tRNAs devoid of these critical site-specific modifications, negatively affecting translation yields and fidelity. To address this, we have developed a purification method which couples tRNA overexpression to DNA hybridization-based purification. Using this approach, we produced native tRNAs from E. coli in high yield and purity while retaining their complement of native post-transcriptional modifications and translational activity. We extend this technique to the purification of and , tRNAs of critical importance for genetic code expansion. We confirmed that both and contain native E. coli post-transcriptional modifications and provide the first complete modification profiles of each. Moreover, we found that in vivo- generated significantly outperforms its in vitro- generated counterpart in amber codon suppression in cell-free translation reactions. Finally, we purified an engineered variant of E. coli , extending our studies to synthetic tRNAs. We present a flexible method which generates modified tRNAs in high yield and purity, addressing a critical and persistent challenge in RNA biochemistry. This toolkit enables future structural and cell-free studies through scalable access to native and engineered tRNAs, advancing the broader field of translation and synthetic biology.

  PublisherDOI

• One-pot cloning and protein expression platform for genetic engineering

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-29 · 1 citations

  preprintOpen accessSenior authorCorresponding

  In this work, we present a streamlined one-pot cloning and protein expression platform that integrates mutagenesis, plasmid assembly, and functional protein testing in a single reaction. By combining Golden Gate cloning with cell-free transcription-translation, we demonstrate efficient generation and screening of genetic variants without the need for intermediate purification or bacterial amplification. Using fluorescent proteins, luciferase enzymes, antibiotic-converting enzymes, and the violacein biosynthetic pathway, we validate the versatility of this approach for single- and multi-site mutagenesis, combinatorial variant libraries, metabolic pathway programming, and whole-plasmid assembly. By demonstrating compatibility with multiplexed reactions and multi-cistronic constructs, we establish this approach as a generalizable and automatable method for high-throughput cloning and protein engineering in synthetic biology.

  PublisherOA PDFDOI

Recent grants

• SemiSynBio: Collaborative Research: Very Large-Scale Genetic Circuit Design Automation

  NSF · $276k · 2018–2022

Frequent coauthors

• Aaron E. Engelhart

  University of Minnesota

  70 shared

• Jack W. Szostak

  69 shared

• Nathaniel J. Gaut

  University of Minnesota

  24 shared

• Albert C. Fahrenbach

  UNSW Sydney

  17 shared

• Christopher Deich

  University of Minnesota

  16 shared

• Wakana Sato

  University of Tokyo Hospital

  13 shared

• Tony Z. Jia

  Blue Marble Space

  13 shared

• Lin Jin

  Wuhan Institute of Bioengineering

  12 shared