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Chaisupa P, Wright RC. State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering. SLAS Technol 2024; 29:100113. [PMID: 37918525 PMCID: PMC11314541 DOI: 10.1016/j.slast.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States; Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, United States.
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2
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Park H, Joachimiak MP, Jungbluth SP, Yang Z, Riehl WJ, Canon RS, Arkin AP, Dehal PS. A bacterial sensor taxonomy across earth ecosystems for machine learning applications. mSystems 2024; 9:e0002623. [PMID: 38078749 PMCID: PMC10804942 DOI: 10.1128/msystems.00026-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/23/2023] [Indexed: 01/24/2024] Open
Abstract
Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.
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Affiliation(s)
- Helen Park
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcin P. Joachimiak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sean P. Jungbluth
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ziming Yang
- Computational Science Initiative, Brookhaven National Laboratory, Upton, New York, USA
| | - William J. Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - R. Shane Canon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Paramvir S. Dehal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Highly multiplexed selection of RNA aptamers against a small molecule library. PLoS One 2022; 17:e0273381. [PMID: 36107884 PMCID: PMC9477273 DOI: 10.1371/journal.pone.0273381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/08/2022] [Indexed: 02/03/2023] Open
Abstract
Applications of synthetic biology spanning human health, industrial bioproduction, and ecosystem monitoring often require small molecule sensing capabilities, typically in the form of genetically encoded small molecule biosensors. Critical to the deployment of greater numbers of these systems are methods that support the rapid development of such biosensors against a broad range of small molecule targets. Here, we use a previously developed method for selection of RNA biosensors against unmodified small molecules (DRIVER) to perform a selection against a densely multiplexed mixture of small molecules, representative of those employed in high-throughput drug screening. Using a mixture of 5,120 target compounds randomly sampled from a large diversity drug screening library, we performed a 95-round selection and then analyzed the enriched RNA biosensor library using next generation sequencing (NGS). From our analysis, we identified RNA biosensors with at least 2-fold change in signal in the presence of at least 217 distinct target compounds with sensitivities down to 25 nM. Although many of these biosensors respond to multiple targets, clustering analysis indicated at least 150 different small-molecule sensing patterns. We also built a classifier that was able to predict whether the biosensors would respond to a new compound with an average precision of 0.82. Since the target compound library was designed to be representative of larger diversity compound libraries, we expect that the described approach can be used with similar compound libraries to identify aptamers against other small molecules with a similar success rate. The new RNA biosensors (or their component aptamers) described in this work can be further optimized and used in applications such as biosensing, gene control, or enzyme evolution. In addition, the data presented here provide an expanded compendium of new RNA aptamers compared to the 82 small molecule RNA aptamers published in the literature, allowing further bioinformatic analyses of the general classes of small molecules for which RNA aptamers can be found.
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Zhao Y, Shen Y, Wen Y, Campbell RE. High-Performance Intensiometric Direct- and Inverse-Response Genetically Encoded Biosensors for Citrate. ACS CENTRAL SCIENCE 2020; 6:1441-1450. [PMID: 32875085 PMCID: PMC7453566 DOI: 10.1021/acscentsci.0c00518] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Indexed: 05/02/2023]
Abstract
Motivated by the growing recognition of citrate as a central metabolite in a variety of biological processes associated with healthy and diseased cellular states, we have developed a series of high-performance genetically encoded citrate biosensors suitable for imaging of citrate concentrations in mammalian cells. The design of these biosensors was guided by structural studies of the citrate-responsive sensor histidine kinase and took advantage of the same conformational changes proposed to propagate from the binding domain to the catalytic domain. Following extensive engineering based on a combination of structure guided mutagenesis and directed evolution, we produced an inverse-response biosensor (ΔF/F min ≈ 18) designated Citroff1 and a direct-response biosensor (ΔF/F min ≈ 9) designated Citron1. We report the X-ray crystal structure of Citron1 and demonstrate the utility of both biosensors for qualitative and quantitative imaging of steady-state and pharmacologically perturbed citrate concentrations in live cells.
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Affiliation(s)
- Yufeng Zhao
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yi Shen
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yurong Wen
- Department
of Talent Highland, The First Affiliated
Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi 710061, China
- . (Y.W.; regarding x-ray crystallography)
| | - Robert E. Campbell
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- . (R.E.C.)
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Abstract
Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.
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Affiliation(s)
- Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), SFR ICAT 4208, UNIV Angers, UNIV Brest, Angers, France
| | - Ann M Stock
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
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