1
|
Morey K, Khakhar A. Exploring the frontier of rapid prototyping technologies for plant synthetic biology and what could lie beyond. New Phytol 2024; 242:903-908. [PMID: 38426415 DOI: 10.1111/nph.19650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Realizing the full potential of plant synthetic biology both to elucidate the relationship between genotype and phenotype and to apply these insights to engineer traits requires rapidly iterating through design-build-test cycles. However, the months-long process of transgenesis, the long generation times, and the size-based limitations on experimentation have stymied progress by limiting the speed and scale of these cycles. Herein, we review a representative sample of recent studies that demonstrate a variety of rapid prototyping technologies that overcome some of these bottlenecks and accelerate progress. However, each of them has caveats that limit their broad utility. Their complementary strengths and weaknesses point to the intriguing possibility that these strategies could be combined in the future to enable rapid and scalable deployment of synthetic biology in plants.
Collapse
Affiliation(s)
- Kevin Morey
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80525, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80525, USA
| |
Collapse
|
2
|
Bull T, Khakhar A. Design principles for synthetic control systems to engineer plants. Plant Cell Rep 2023; 42:1875-1889. [PMID: 37789180 DOI: 10.1007/s00299-023-03072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
KEY MESSAGE Synthetic control systems have led to significant advancement in the study and engineering of unicellular organisms, but it has been challenging to apply these tools to multicellular organisms like plants. The ability to predictably engineer plants will enable the development of novel traits capable of alleviating global problems, such as climate change and food insecurity. Engineering predictable multicellular phenotypes will require the development of synthetic control systems that can precisely regulate how the information encoded in genomes is translated into phenotypes. Many efficient control systems have been developed for unicellular organisms. However, it remains challenging to use such tools to study or engineer multicellular organisms. Plants are a good chassis within which to develop strategies to overcome these challenges, thanks to their capacity to withstand large-scale reprogramming without lethality. Additionally, engineered plants have great potential for solving major societal problems. Here we briefly review the progress of control system development in unicellular organisms, and how that information can be leveraged to characterize control systems in plants. Further, we discuss strategies for developing control systems designed to regulate the expression of transgenes or endogenous loci and generate dosage-dependent or discrete traits. Finally, we discuss the utility that mathematical models of biological processes have for control system deployment.
Collapse
Affiliation(s)
- Tawni Bull
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
3
|
Khakhar A. A roadmap for the creation of synthetic lichen. Biochem Biophys Res Commun 2023; 654:87-93. [PMID: 36898228 DOI: 10.1016/j.bbrc.2023.02.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Lichens represent a charismatic corner of biology that has a rich history of scientific exploration, but to which modern biological techniques have been sparsely applied. This has limited our understanding of phenomena unique to lichen, such as the emergent development of physically coupled microbial consortia or distributed metabolisms. The experimental intractability of natural lichens has prevented studies of the mechanistic underpinnings of their biology. Creating synthetic lichen from experimentally tractable, free-living microbes has the potential to overcome these challenges. They could also serve as powerful new chassis for sustainable biotechnology. In this review we will first briefly introduce what lichen are, what remains mysterious about their biology, and why. We will then articulate the scientific insights that creating a synthetic lichen will generate and lay out a roadmap for how this could be achieved using synthetic biology. Finally, we will explore the translational applications of synthetic lichen and detail what is needed to advance the pursuit of their creation.
Collapse
Affiliation(s)
- Arjun Khakhar
- Biology Department, Colorado State University, 251 West Pitkin Drive, Fort Collins, CO, 80525, USA.
| |
Collapse
|
4
|
Liu Y, Yuan G, Hassan MM, Abraham PE, Mitchell JC, Jacobson D, Tuskan GA, Khakhar A, Medford J, Zhao C, Liu CJ, Eckert CA, Doktycz MJ, Tschaplinski TJ, Yang X. Biological and Molecular Components for Genetically Engineering Biosensors in Plants. Biodes Res 2022; 2022:9863496. [PMID: 37850147 PMCID: PMC10521658 DOI: 10.34133/2022/9863496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/08/2022] [Indexed: 10/19/2023] Open
Abstract
Plants adapt to their changing environments by sensing and responding to physical, biological, and chemical stimuli. Due to their sessile lifestyles, plants experience a vast array of external stimuli and selectively perceive and respond to specific signals. By repurposing the logic circuitry and biological and molecular components used by plants in nature, genetically encoded plant-based biosensors (GEPBs) have been developed by directing signal recognition mechanisms into carefully assembled outcomes that are easily detected. GEPBs allow for in vivo monitoring of biological processes in plants to facilitate basic studies of plant growth and development. GEPBs are also useful for environmental monitoring, plant abiotic and biotic stress management, and accelerating design-build-test-learn cycles of plant bioengineering. With the advent of synthetic biology, biological and molecular components derived from alternate natural organisms (e.g., microbes) and/or de novo parts have been used to build GEPBs. In this review, we summarize the framework for engineering different types of GEPBs. We then highlight representative validated biological components for building plant-based biosensors, along with various applications of plant-based biosensors in basic and applied plant science research. Finally, we discuss challenges and strategies for the identification and design of biological components for plant-based biosensors.
Collapse
Affiliation(s)
- Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - June Medford
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Cheng Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Carrie A. Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| |
Collapse
|
5
|
Khakhar A, Wang C, Swanson R, Stokke S, Rizvi F, Sarup S, Hobbs J, Voytas DF. VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype. Plant Physiol 2021; 186:2222-2238. [PMID: 34009393 PMCID: PMC8331131 DOI: 10.1093/plphys/kiab197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/01/2021] [Indexed: 05/05/2023]
Abstract
Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work, we developed a technology called VipariNama (ViN) in which vectors based on the tobacco rattle virus are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, ViN accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.
Collapse
Affiliation(s)
- Arjun Khakhar
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Cecily Wang
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Ryan Swanson
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Sydney Stokke
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Furva Rizvi
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Surbhi Sarup
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - John Hobbs
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Daniel F Voytas
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| |
Collapse
|
6
|
Khakhar A, Voytas DF. RNA Viral Vectors for Accelerating Plant Synthetic Biology. Front Plant Sci 2021; 12:668580. [PMID: 34249040 PMCID: PMC8261061 DOI: 10.3389/fpls.2021.668580] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/19/2021] [Indexed: 05/03/2023]
Abstract
The tools of synthetic biology have enormous potential to help us uncover the fundamental mechanisms controlling development and metabolism in plants. However, their effective utilization typically requires transgenesis, which is plagued by long timescales and high costs. In this review we explore how transgenesis can be minimized by delivering foreign genetic material to plants with systemically mobile and persistent vectors based on RNA viruses. We examine the progress that has been made thus far and highlight the hurdles that need to be overcome and some potential strategies to do so. We conclude with a discussion of biocontainment mechanisms to ensure these vectors can be used safely as well as how these vectors might expand the accessibility of plant synthetic biology techniques. RNA vectors stand poised to revolutionize plant synthetic biology by making genetic manipulation of plants cheaper and easier to deploy, as well as by accelerating experimental timescales from years to weeks.
Collapse
Affiliation(s)
- Arjun Khakhar
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, United States
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, United States
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
| |
Collapse
|
7
|
Khakhar A, Starker CG, Chamness JC, Lee N, Stokke S, Wang C, Swanson R, Rizvi F, Imaizumi T, Voytas DF. Correction: Building customizable auto-luminescent luciferase-based reporters in plants. eLife 2020; 9:60938. [PMID: 32662767 PMCID: PMC7360363 DOI: 10.7554/elife.60938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
8
|
Khakhar A, Starker CG, Chamness JC, Lee N, Stokke S, Wang C, Swanson R, Rizvi F, Imaizumi T, Voytas DF. Building customizable auto-luminescent luciferase-based reporters in plants. eLife 2020; 9:52786. [PMID: 32209230 PMCID: PMC7164954 DOI: 10.7554/elife.52786] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/24/2020] [Indexed: 01/09/2023] Open
Abstract
Bioluminescence is a powerful biological signal that scientists have repurposed as a reporter for gene expression in plants and animals. However, there are downsides associated with the need to provide a substrate to these reporters, including its high cost and non-uniform tissue penetration. In this work we reconstitute a fungal bioluminescence pathway (FBP) in planta using a composable toolbox of parts. We demonstrate that the FBP can create luminescence across various tissues in a broad range of plants without external substrate addition. We also show how our toolbox can be used to deploy the FBP in planta to build auto-luminescent reporters for the study of gene-expression and hormone fluxes. A low-cost imaging platform for gene expression profiling is also described. These experiments lay the groundwork for future construction of programmable auto-luminescent plant traits, such as light driven plant-pollinator interactions or light emitting plant-based sensors.
Collapse
Affiliation(s)
- Arjun Khakhar
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Colby G Starker
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - James C Chamness
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Nayoung Lee
- Department of Biology, University of Washington, Seattle, United States
| | - Sydney Stokke
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Cecily Wang
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Ryan Swanson
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Furva Rizvi
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, United States
| | - Daniel F Voytas
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| |
Collapse
|
9
|
Galli M, Khakhar A, Lu Z, Chen Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A. The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Nat Commun 2018; 9:4526. [PMID: 30375394 PMCID: PMC6207667 DOI: 10.1038/s41467-018-06977-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/23/2018] [Indexed: 01/19/2023] Open
Abstract
AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes. We use DAP-seq to generate genome-wide in vitro TF:DNA interaction maps for fourteen maize ARFs from the evolutionarily conserved A and B clades. Comparative analysis reveal a high degree of binding site overlap for ARFs of the same clade, but largely distinct clade A and B binding. Many sites are however co-occupied by ARFs from both clades, suggesting transcriptional coordination for many genes. Among these, we investigate known QTLs and use machine learning to predict the impact of cis-regulatory variation. Overall, large-scale comparative analysis of ARF binding suggests that auxin response specificity may be determined by factors other than individual ARF binding site selection.
Collapse
Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Arjun Khakhar
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Zefu Lu
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Sidharth Sen
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Trupti Joshi
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.,Department of Health Management and Informatics and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | | | - Robert J Schmitz
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA. .,Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
| |
Collapse
|
10
|
Lovesley D, John S, Khakhar A, Ramamurthy A. Nutritional prehab to rehab of liver transplant patients: An indian perspective. Clin Nutr 2018. [DOI: 10.1016/j.clnu.2018.06.1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Khakhar A, Leydon AR, Lemmex AC, Klavins E, Nemhauser JL. Synthetic hormone-responsive transcription factors can monitor and re-program plant development. eLife 2018; 7:34702. [PMID: 29714687 PMCID: PMC5976440 DOI: 10.7554/elife.34702] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/30/2018] [Indexed: 01/06/2023] Open
Abstract
Developmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity (Doebley et al., 1997; Khush, 2001). Hormones coordinate these programs, creating chemical circuitry (Vanstraelen and Benková, 2012) that has been represented in mathematical models (Refahi et al., 2016; Prusinkiewicz et al., 2009); however, model-guided engineering of plant morphology has been limited by a lack of tools (Parry et al., 2009; Voytas and Gao, 2014). Here, we introduce a novel set of synthetic and modular hormone activated Cas9-based repressors (HACRs) in Arabidopsis thaliana that respond to three hormones: auxin, gibberellins and jasmonates. We demonstrate that HACRs are sensitive to both exogenous hormone treatments and local differences in endogenous hormone levels associated with development. We further show that this capability can be leveraged to reprogram development in an agriculturally relevant manner by changing how the hormonal circuitry regulates target genes. By deploying a HACR to re-parameterize the auxin-induced expression of the auxin transporter PIN-FORMED1 (PIN1), we decreased shoot branching and phyllotactic noise, as predicted by existing models (Refahi et al., 2016; Prusinkiewicz et al., 2009). The genetic information of plants contains sets of instructions that shape a growing seedling. These ‘developmental programs’ are under the control of a range of hormones, such as auxin. Typically, the information from the hormones is relayed to the genetic material through proteins called transcription factors, which can act on DNA to turn specific genes on or off. Scientists have a good understanding of the roles of hormones, and they have created mathematical models that predict how changes in hormone levels affect the shape of a plant. However, it is still difficult to manipulate hormones inside a plant and test these models. Here, Khakhar et al. created artificial transcription factors, referred to as HACRs, and put them into a plant called Arabidopsis thaliana. An HACR is made of different molecular modules stitched together. Each module has a precise role; for example, one turns off a specific gene, while another targets the HACR for destruction if a given hormone is present. First, Khakhar et al. showed that HACRs could help track the levels of auxin in a developing plant. Arabidopsis plants were genetically engineered so that they would always produce a fluorescent protein. Then, an HACR was created that would switch off the gene for that fluorescent protein, so that no fluorescence would be present in the cell. If auxin was present, the HACR would get degraded, meaning fluorescence would appear. This helped to finely assess the amount of the hormone in various parts of the plant. By changing the modules in the HACRs, this approach could be applied to at least three other types of hormones. Second, HACRs were used to reprogram Arabidopsis and change its appearance. For example, it is well known that auxin controls the number and location of branches on a plant. This complex process depends on how strongly auxin promotes the expression of a gene called PIN1. Khakhar et al. engineered an HACR that represses PIN1, and created a mathematical model that described the impact of this intervention. As predicted by the simulation, the HACR changed the strength of the relationship between PIN1 and auxin, which resulted in plants with fewer branches – a trait that is of interest in farming. HACRs are a new type of technology that is likely to work in a wide range of species. Ultimately, these artificial transcription factors could help to engineer plants that can face the disruptions brought by climate change, which would ensure better food security for people around the world.
Collapse
Affiliation(s)
- Arjun Khakhar
- Department of Electrical Engineering, University of Washington, Seattle, United States
| | | | - Andrew C Lemmex
- Department of Biology, University of Washington, Seattle, United States
| | - Eric Klavins
- Department of Electrical Engineering, University of Washington, Seattle, United States
| | | |
Collapse
|
12
|
Groves B, Khakhar A, Nadel CM, Gardner RG, Seelig G. Rewiring MAP kinases in Saccharomyces cerevisiae to regulate novel targets through ubiquitination. eLife 2016; 5. [PMID: 27525484 PMCID: PMC5019841 DOI: 10.7554/elife.15200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/14/2016] [Indexed: 12/18/2022] Open
Abstract
Evolution has often copied and repurposed the mitogen-activated protein kinase (MAPK) signaling module. Understanding how connections form during evolution, in disease and across individuals requires knowledge of the basic tenets that govern kinase-substrate interactions. We identify criteria sufficient for establishing regulatory links between a MAPK and a non-native substrate. The yeast MAPK Fus3 and human MAPK ERK2 can be functionally redirected if only two conditions are met: the kinase and substrate contain matching interaction domains and the substrate includes a phospho-motif that can be phosphorylated by the kinase and recruit a downstream effector. We used a panel of interaction domains and phosphorylation-activated degradation motifs to demonstrate modular and scalable retargeting. We applied our approach to reshape the signaling behavior of an existing kinase pathway. Together, our results demonstrate that a MAPK can be largely defined by its interaction domains and compatible phospho-motifs and provide insight into how MAPK-substrate connections form. DOI:http://dx.doi.org/10.7554/eLife.15200.001 Nature has evolved a number of ways to link signals from a cell’s environment, like the concentration of a hormone, to the behavior of that cell. These new connections often form by reusing certain common signaling components, such as mitogen-activated protein kinases. These enzymes – referred to as MAPKs for short – are activated by specific signals and alter the activity of target proteins in the cell by adding a phosphate group to them: a process called phosphorylation. These connections thus dictate how cells respond to their environments – and consequently, disruptions to the connections are a common source of disease. Groves, Khakhar et al. set out to understand how connections can be made between a MAPK and a new target protein to gain insights into how these links emerge through evolution and how they might break in disease. Their approach focused on one of the ways that phosphorylation can alter the activity of a target protein: marking it for degradation. Experiments with budding yeast showed that a MAPK could only achieve this if two conditions are met. First, the target protein and kinase need to bind to each other. Second, the target needs to contain a site that when phosphorylated is subsequently recognized by the cell’s protein degradation machinery. By engineering proteins so that they fulfilled these two criteria, Groves, Khakhar et al. created new connections between a yeast MAPK called Fus3 or a human MAPK called ERK2 and a variety of targets. The results showed that the parts of the proteins involved in the interaction step could be completely separate from the parts that are involved in the phosphorylation step. This suggests that connections between kinases and their targets can be rewired simple by mixing together parts of other existing proteins. Finally, Groves, Khakhar et al. confirmed that engineered connections between kinases and targets could predictably change how yeast cells responded to a hormone that normally controls the yeast’s reproductive cycle. Together these results bring us one step closer to understanding how cells assemble the signaling pathways that they use to process information. However further work is needed to see if these findings can be generalized to other signaling components, and if so, to explore if new connections can be built to yield more complicated cellular behaviors. DOI:http://dx.doi.org/10.7554/eLife.15200.002
Collapse
Affiliation(s)
- Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, United States
| | - Arjun Khakhar
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Cory M Nadel
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, United States.,Department of Computer Science and Engineering, University of Washington, Seattle, United States
| |
Collapse
|
13
|
Pochekailov S, Black RR, Chavali VP, Khakhar A, Seelig G. A Fluorescent Readout for the Oxidation State of Electron Transporting Proteins in Cell Free Settings. ACS Synth Biol 2016; 5:662-71. [PMID: 27049848 DOI: 10.1021/acssynbio.5b00274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Pathways involving sequential electron transfer between multiple proteins are ubiquitous in nature. Here, we demonstrate a new class of fluorescent protein-based reporters for monitoring electron transport through such multistage cascades, specifically those involving ferredoxin-like electron transporters. We created protein fusions between mammalian Adrenodoxin (Adx) and plant Ferredoxin (Fdx) with fluorescent proteins of different colors and found that the fluorescence of such fusions is highly sensitive to the redox state of the electron transporter. The increase in fluorescence from the oxidized to the reduced state was inversely proportional to the linker length between the fusion partners. We first used our approach to quantitatively characterize electron transfer from NADPH through Adrenodoxin Reductase (AdR) to Adrenodoxin (Adx). Our data allowed us to build a detailed mathematical model of this mitochondrial electron transfer chain and validate previously proposed mechanisms. Then, we showed that an Adx-GFP fusion could serve as a sensor for the activity of bacterial Type I Cytochrome P450s (CYPs), a very large class of enzymes with important roles in biotechnology. We further showed that fluorescence of a direct fusion between CYP and GFP was sensitive to CYP activity, suggesting that our approach is applicable to an even broader class of proteins, which undergo a redox state change during their work cycle.
Collapse
Affiliation(s)
- Sergii Pochekailov
- Department
of Electrical Engineering, University of Washington, Seattle, 98195 Washington, United States
| | - Rebecca R. Black
- Department
of Electrical Engineering, University of Washington, Seattle, 98195 Washington, United States
| | - Venkata Pramod Chavali
- Department
of Electrical Engineering, University of Washington, Seattle, 98195 Washington, United States
| | - Arjun Khakhar
- Department
of Electrical Engineering, University of Washington, Seattle, 98195 Washington, United States
| | - Georg Seelig
- Department
of Electrical Engineering, University of Washington, Seattle, 98195 Washington, United States
- Department
of Computer Science and Engineering, University of Washington, Seattle, 98195 Washington, United States
| |
Collapse
|
14
|
Khakhar A, Bolten NJ, Nemhauser J, Klavins E. Cell-Cell Communication in Yeast Using Auxin Biosynthesis and Auxin Responsive CRISPR Transcription Factors. ACS Synth Biol 2016; 5:279-86. [PMID: 26102245 DOI: 10.1021/acssynbio.5b00064] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An engineering framework for synthetic multicellular systems requires a programmable means of cell-cell communication. Such a communication system would enable complex behaviors, such as pattern formation, division of labor in synthetic microbial communities, and improved modularity in synthetic circuits. However, it remains challenging to build synthetic cellular communication systems in eukaryotes due to a lack of molecular modules that are orthogonal to the host machinery, easy to reconfigure, and scalable. Here, we present a novel cell-to-cell communication system in Saccharomyces cerevisiae (yeast) based on CRISPR transcription factors and the plant hormone auxin that exhibits several of these features. Specifically, we engineered a sender strain of yeast that converts indole-3-acetamide (IAM) into auxin via the enzyme iaaH from Agrobacterium tumefaciens. To sense auxin and regulate transcription in a receiver strain, we engineered a reconfigurable library of auxin-degradable CRISPR transcription factors (ADCTFs). Auxin-induced degradation is achieved through fusion of an auxin-sensitive degron (from IAA corepressors) to the CRISPR TF and coexpression with an auxin F-box protein. Mirroring the tunability of auxin perception in plants, our family of ADCTFs exhibits a broad range of auxin sensitivities. We characterized the kinetics and steady-state behavior of the sender and receiver independently as well as in cocultures where both cell types were exposed to IAM. In the presence of IAM, auxin is produced by the sender cell and triggers deactivation of reporter expression in the receiver cell. The result is an orthogonal, rewireable, tunable, and, arguably, scalable cell-cell communication system for yeast and other eukaryotic cells.
Collapse
Affiliation(s)
- Arjun Khakhar
- Department of Bioengineering, ‡Department of Electrical Engineering, §Department of Biology, University of Washington , Seattle, Washington 98195, United States
| | - Nicholas J Bolten
- Department of Bioengineering, ‡Department of Electrical Engineering, §Department of Biology, University of Washington , Seattle, Washington 98195, United States
| | - Jennifer Nemhauser
- Department of Bioengineering, ‡Department of Electrical Engineering, §Department of Biology, University of Washington , Seattle, Washington 98195, United States
| | - Eric Klavins
- Department of Bioengineering, ‡Department of Electrical Engineering, §Department of Biology, University of Washington , Seattle, Washington 98195, United States
| |
Collapse
|
15
|
Wright RC, Khakhar A, Eshleman JR, Ostermeier M. Advancements in the development of HIF-1α-activated protein switches for use in enzyme prodrug therapy. PLoS One 2014; 9:e114032. [PMID: 25426963 PMCID: PMC4245239 DOI: 10.1371/journal.pone.0114032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/03/2014] [Indexed: 12/25/2022] Open
Abstract
While gene-directed enzyme prodrug therapy has shown potential as a cancer therapeutic in animal and clinical trials, concerns over the efficacy, selectivity, and safety of gene delivery vehicles have restricted its advance. In an attempt to relieve some of the demands on targeted gene delivery vehicles and achieve the full potential of enzyme prodrug therapy, cancer-targeted activity can be engineered into the enzyme itself. We previously engineered a switchable prodrug-activating enzyme that selectively kills human cancer cells accumulating the cancer marker hypoxia-inducible factor-1α (HIF-1α). This HIF-1α-activated protein switch (Haps59) is designed to increase its ability to convert the prodrug 5-fluorocytosine into the chemotherapeutic 5-fluorouracil in a HIF-1α-dependent manner. However, in cancer cell lines expressing Haps59 the 5FC sensitivity difference between the presence and absence of HIF-1α was not as large as desired. In this work, we aimed to improve the cancer specificity of this switch via a directed evolution approach utilizing random mutagenesis, linker mutagenesis, and random insertion and circular permutation. We identified improved HIF-1α-activated protein switches that confer E. coli with modest increases in HIF-1α-dependent 5FC toxicity. Additionally, the current bottleneck in the development of improved HIF-1α-activated protein switches is screening switch candidates in mammalian cells. To accommodate higher throughput and reduce experimental variability, we explored the use of Flp recombinase-mediated isogenic integration in 293 cells. These experiments raised the possibility that Haps59 can be activated by other interactors of the CH1 domain, and experiments in E. coli indicated that CITED2 can also activate Haps59. Although many CH1 binding partners are also oncogenes, CH1's promiscuous binding and subsequent off-target activation of Haps59 needs to be examined under normal physiological conditions to identify off-target activators. With aberrant activating molecules identified, further directed evolution can be performed to improve the cancer specificity of HIF-1α-activated protein switches.
Collapse
Affiliation(s)
- R. Clay Wright
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Arjun Khakhar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James R. Eshleman
- Departments of Pathology and Oncology, Sol Goldman Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
16
|
Jayaraman S, Khakhar A, Yang H, Bainbridge D, Quan D. The association between central venous pressure, pneumoperitoneum, and venous carbon dioxide embolism in laparoscopic hepatectomy. Surg Endosc 2009; 23:2369-73. [PMID: 19266234 DOI: 10.1007/s00464-009-0359-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Revised: 11/18/2008] [Accepted: 01/12/2009] [Indexed: 02/06/2023]
Abstract
BACKGROUND Laparoscopic hepatectomy (LH) is increasingly used. However, the safety and outcomes of LH have yet to be elucidated. The risk of venous gas embolism is increased during liver parenchymal transection. This risk may be increased with positive pressure carbon dioxide (CO(2)) pneumoperitoneum (PP). This may be exacerbated further when low central venous pressure (CVP) anesthesia is used to minimize hemorrhage during liver resection. METHODS To determine the risk of CO(2) venous embolism, hand-assisted laparoscopic left hepatic lobectomy was performed for 26 domestic pigs. They were divided into three groups involving, respectively, positive gradient (normal-pressure PP of 12-14 mmHg and low CVP of 5-7 mmHg), negative gradient (low-pressure PP of 7-8 mmHg and normal CVP of 10-12 mmHg), and neutral gradient (normal-pressure PP and normal CVP or low-pressure PP and low CVP). Transesophageal echocardiography (TEE) was used intraoperatively to assess the presence of emboli in the suprahepatic vena cava and the right side of the heart. The TEE was recorded and analyzed by blinded observers. Carbon dioxide embolism also was monitored using end-tidal CO(2) and compared with TEE. RESULTS Carbon dioxide embolism was demonstrated in 19 of the 26 cases. The majority of gas emboli were small gas bubbles associated with dissection of the major hepatic veins. No statistically significant difference in the occurrence of gas emboli was observed between the groups. Of the 19 animals, 18 experienced no significant hemodynamic changes. One pig in the positive gradient group experienced hypotension in relation to gas embolism. The effects were only transient and did not preclude safe completion of the operation. CONCLUSIONS Carbon dioxide embolism during LH occurs frequently. Clinically, this finding appears to be nominal, but care must be taken when dissection around large veins is performed, and awareness by the surgical and anesthesiology teams of potential venous air embolism is essential. Further evaluation of this phenomenon is required.
Collapse
Affiliation(s)
- S Jayaraman
- Division of General Surgery, Schulich School of Medicine and Dentistry, University of Western Ontario, 339 Windermere Road, London, ON, N6A-5A5, Canada
| | | | | | | | | |
Collapse
|
17
|
McAlister VC, Quan D, Solano E, Khakhar A, Yang H, Mahy JN, Wall WJ. IMPACT OF VENOUS DRAINAGE AND REPERFUSION TECHNIQUE ON REPERFUSION INJURY AFTER ORTHOTOPIC LIVER TRANSPLANTATION. Transplantation 2004. [DOI: 10.1097/00007890-200407271-00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
18
|
Khakhar A, Solano E, Stell D, Bloch M, Dale C, Burns P, Ghent C, Quan D, McAlister V, Marotta P, Wall WJ. Survival after liver transplantation for hepatocellular carcinoma. Transplant Proc 2003; 35:2438-41. [PMID: 14611981 DOI: 10.1016/j.transproceed.2003.08.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Selection criteria for patients with hepatocellular carcinoma (HCC) suitable for liver transplantation (LT) include tumor size and number and vascular invasion. There has been a recent trend to expand the transplant criteria for HCC. We reviewed our experience to determine survival following LT based on tumor characteristics. METHODS A retrospective analysis was performed on 72 patients with HCC who underwent LT between 1985 and July 2002. The Milan criteria were applied for LT candidacy for HCCs that were deemed unresectable from anatomical considerations and/or the severity of underlying cirrhosis. Patients were divided into four groups: group 1: patients with known HCC who satisfied the selection criteria (n = 22); group 2: patients with known HCC that exceeded the criteria (n = 17); group 3: patients with incidental HCC found at pathological examination of the explant (n = 33); group 4: contemporary LT recipients without HCC (n = 935). RESULTS In the known HCC group, the interval between listing as status 2 and transplantation was 72.2 +/- 133.6 days (median 23 days). Three-year patient survival was 80.2% in group 1, 35.8% in group 2, 63.2% in group 3, and 81.5% in group 4. In group 2 patients, the tumors were significantly larger, had more nodules, and were more often bilobar. In group 3, five (15%) exceeded the criteria mainly because of tumor size and four patients died within 3 years post-LT (three from tumor recurrence). CONCLUSION Liver transplantation for HCC yields acceptable survival in early-stage tumors, particularly if transplanted soon after listing. Long-term survival was inferior in patients with multiple tumors and tumors that were greater than 5 cm in diameter.
Collapse
Affiliation(s)
- A Khakhar
- Multiorgan Transplant Program, London Health Sciences Centre, University of Western Ontario, London, Ontario, Canada.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
UNLABELLED Primary sclerosing cholangitis (PSC) is a chronic cholestatic disease that progresses to end-stage liver disease. This report is a retrospective analysis of a Canadian centre experience with liver transplantation (LT) for PSC. Of 1107 LTs performed between 1984 and 2002, 132 were performed on 111 patients with PSC. Patient survival at 1, 3, 5, and 10 years was 84.5%, 84.5%, 83.4%, and 68.9%, respectively. Graft survival at 1, 3, 5, and 10 years was 80.8%, 79.8%, 72.7%, and 55.3%. These were not significantly different from overall patient survival (P =.91) or graft survival (P =.28) in non-PSC patients transplanted over the same time period. Early mortality was predominantly related to primary nonfunction and multi-organ failure; late mortality was predominantly related to malignancy. No patient with known cholangiocarcinoma (CCA) underwent LT, but three patients had an incidental CCA noted on explant pathology. All three died of widespread metastatic disease (10.8, 38.0, and 39.8 months after LT). Nineteen patients lost their primary grafts requiring retransplantation, and two of these patients required a third transplant. Recurrent PSC was detected in six patients and suspected in another six. Four patients have been retransplanted for recurrent PSC. Chronic rejection was detected in nine patients. Eight have required retransplantation. The incidence of biliary complications was 16.2%. CONCLUSIONS LT is effective therapy for PSC. Patient and graft survival is comparable to that seen in patients transplanted for indications other than PSC, but long-term graft survival may be lower. Recurrent PSC and chronic rejection are the major determinants of graft loss.
Collapse
Affiliation(s)
- E Solano
- Multi-Organ Transplant Program, London Health Sciences Centre, London, Ontario, Canada.
| | | | | | | | | | | | | | | |
Collapse
|