1
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Qu L, Chi Z, Zou ZP, Zhou Y, Ye BC. Development of ultrasound-visualized tumor-targeting engineered bacteria for precise tumor therapy. Synth Syst Biotechnol 2025; 10:774-782. [PMID: 40270642 PMCID: PMC12018036 DOI: 10.1016/j.synbio.2025.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 03/12/2025] [Accepted: 03/26/2025] [Indexed: 04/25/2025] Open
Abstract
In situ imaging diagnosis and precise treatment of deep tumor tissues are hotspots in life sciences and medical research. In recent years, using focused ultrasound to remotely control engineered bacteria for drug release has become one of the methods for precise in vivo drug delivery. However, non-visualized engineered bacteria pose challenges for precise control within the body. Therefore, there is an urgent need for an engineered bacterial vector capable of deep tissue imaging to precisely locate bacteria in vivo. Acoustic reporter genes (ARGs) are biological elements used for deep tissue imaging, with gene clusters over 8 kb. However, ARGs are often tested on plasmids, which hinders stable expression in vivo and limits the space for inserting components that regulate drug release. Therefore, we used the attenuated Salmonella typhimurium VNP20009, known for its tumor-targeting ability, as the chassis bacteria. By using CRISPR-Cas9 technology, we inserted ARGs into the genome and optimized the promoter strength and copy number for ARG expression, constructing ultrasound-visible engineered bacteria expressing gas vesicles on the genome. Additionally, by knocking out the stress protein gene htrA in VNP20009, we increased the maximum injection dose by tenfold and the tumor specificity by a hundredfold. The constructed ultrasound-visible engineered bacteria can stably synthesize gas vesicles and output ultrasound signals while directly carrying drug plasmids for tumor therapy. Our research provides an effective vector for diagnosis and precise treatment.
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Affiliation(s)
- Li Qu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhou Chi
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhen-Ping Zou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ying Zhou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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2
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Abundo MP, Tifrea AT, Buss MT, Barturen-Larrea P, Jin Z, Malounda D, Shapiro MG. Acoustic percolation switches enable targeted drug delivery controlled by diagnostic ultrasound. Proc Natl Acad Sci U S A 2025; 122:e2423078122. [PMID: 40366696 DOI: 10.1073/pnas.2423078122] [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: 11/06/2024] [Accepted: 04/09/2025] [Indexed: 05/15/2025] Open
Abstract
Delivering biomedicines to specific sites of disease using remote-controlled devices is a long-standing vision in biomedical research. However, most existing externally triggered delivery systems are based on complex micromachines that are controlled with electromagnetic waves and require custom external instrumentation. Here, we present a drug delivery platform based on a simple protein-containing hydrogel that can be both imaged and triggered to release drugs at specific locations using widely available diagnostic ultrasound devices. This technology is based on the addition of air-filled protein nanostructures called gas vesicles (GVs) to hydrogel delivery vehicles. While intact, GVs sterically block the release of drug payloads and allow the vehicle to be imaged with ultrasound. An increase in ultrasound pressure causes the collapse of GVs within the delivery vehicles at the desired anatomical location, instantly creating percolation channels in the hydrogel, massively increasing diffusivity, and leading to rapid drug release. Unlike previous ultrasound-actuated delivery approaches, both the imaging and release are performed using a simple diagnostic ultrasound probe ubiquitously available in clinical settings. We implement this concept by quantifying ultrasound-controlled drug diffusion and release in vitro and demonstrating image-guided protein delivery in vivo in the gastrointestinal (GI) tract following oral administration. We further validate this technology by using it to deliver anti-inflammatory antibodies to effectively treat a rat model of colitis. Targeted acoustic percolation switches (TAPS) open a conduit for local, image-guided drug delivery with a simple formulation and commonplace ultrasound equipment.
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Affiliation(s)
- Maria Paulene Abundo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Anna T Tifrea
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Marjorie T Buss
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Pierina Barturen-Larrea
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Zhiyang Jin
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125
- Howard Hughes Medical Institute, Pasadena, CA 91125
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3
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Liu W, Liu T, Huang S, Yan F, Liu JZ. Excavation of acoustic nanostructures biosynthesis gene clusters by combinatorial strategy. ADVANCED BIOTECHNOLOGY 2025; 3:15. [PMID: 40372536 DOI: 10.1007/s44307-025-00069-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 04/15/2025] [Accepted: 04/24/2025] [Indexed: 05/16/2025]
Abstract
Gas vesicles (GVs) produced by microorganisms are genetically engineered, air-filled protein nanostructures that have widespread applications in ultrasound imaging and ultrasound-mediated drug delivery. However, constrained by the shape and size, most of them are difficult to be imaged by clinical ultrasound machines, which limits their biomedical applications. Here, we constructed a hybrid gene cluster of the structural gene cluster from Serratia sp. ATCC 39006 and the accessory gene cluster from Bacillus megaterium in Escherichia coli to synthesize a novel gene-encoded gas vesicle with a width of approximately 70 nm and a length of about 100 nm, using a synthetic biology strategy, termed as ARGS1B. This new type of GVs can be stably produced in bacteria and is able to be imaged by clinical ultrasound machines in vivo and in vitro. Furthermore, the novel nanostructure can be easily engineered for different particle sizes through point saturation mutation, expanding the sources of GVs and providing new insights into the biosynthesis mechanism of GVs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Tingting Liu
- Department of Ultrasound, The Second People's Hospital of Shenzhen, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518061, China
| | - Shenxi Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Fei Yan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jian-Zhong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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4
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Quan MC, Mai DJ. Biomolecular Actuators for Soft Robots. Chem Rev 2025. [PMID: 40331746 DOI: 10.1021/acs.chemrev.4c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2025]
Abstract
Biomolecules present promising stimuli-responsive mechanisms to revolutionize soft actuators. Proteins, peptides, and nucleic acids foster specific intermolecular interactions, and their boundless sequence design spaces encode precise actuation capabilities. Drawing inspiration from nature, biomolecular actuators harness existing stimuli-responsive properties to meet the needs of diverse applications. This review features biomolecular actuators that respond to a wide variety of stimuli to drive both user-directed and autonomous actuation. We discuss how advances in biomaterial fabrication accelerate prototyping of precise, custom actuators, and we identify biomolecules with untapped actuation potential. Finally, we highlight opportunities for multifunctional and reconfigurable biomolecules to improve the versatility and sustainability of next-generation soft actuators.
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Affiliation(s)
- Michelle C Quan
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Danielle J Mai
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
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5
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Iburg M, Anderson AP, Wong VT, Anton ED, He A, Lu GJ. Elucidating the assembly of gas vesicles by systematic protein-protein interaction analysis. EMBO J 2024; 43:4156-4172. [PMID: 39227754 PMCID: PMC11445434 DOI: 10.1038/s44318-024-00178-2] [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: 10/04/2023] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 09/05/2024] Open
Abstract
Gas vesicles (GVs) are gas-filled microbial organelles formed by unique 3-nm thick, amphipathic, force-bearing protein shells, which can withstand multiple atmospheric pressures and maintain a physically stable air bubble with megapascal surface tension. However, the molecular process of GV assembly remains elusive. To begin understanding this process, we have devised a high-throughput in vivo assay to determine the interactions of all 11 proteins in the pNL29 GV operon. Complete or partial deletions of the operon establish interdependent relationships among GV proteins during assembly. We also examine the tolerance of the GV assembly process to protein mutations and the cellular burdens caused by GV proteins. Clusters of GV protein interactions are revealed, proposing plausible protein complexes that are important for GV assembly. We anticipate our findings will set the stage for designing GVs that efficiently assemble in heterologous hosts during biomedical applications.
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Affiliation(s)
- Manuel Iburg
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Andrew P Anderson
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Vivian T Wong
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Erica D Anton
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Art He
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - George J Lu
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
- Department of BioSciences, Rice University, Houston, TX, 77005, USA.
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6
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Fu M, Wang Y, Wang J, Hao Y, Zeng F, Zhang Z, Du J, Long H, Yan F. Genetic Modulation of Biosynthetic Gas Vesicles for Ultrasound Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310008. [PMID: 38533968 DOI: 10.1002/smll.202310008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Gas vesicles (GVs) from microorganisms are genetically air-filled protein nanostructures, and serve as a new class of nanoscale contrast agents for ultrasound imaging. Recently, the genetically encoded GV gene clusters have been heterologously expressed in Escherichia coli, allowing these genetically engineered bacteria to be visualized in vivo in a real-time manner by ultrasound. However, most of the GV genes remained functionally uncharacterized, which makes it difficult to regulate and modify GVs for broad medical applications. Here, the impact of GV proteins on GV formation is systematically investigated. The results first uncovered that the deletions of GvpR or GvpU resulted in the formation of a larger proportion of small, biconical GVs compared to the full-length construct, and the deletion of GvpT resulted in a larger portion of large GVs. Meanwhile, the combination of gene deletions has resulted in several genotypes of ultrasmall GVs that span from 50 to 20 nm. Furthermore, the results showed that E. coli carrying the ΔGvpCRTU mutant can produce strong ultrasound contrast signals in mouse liver. In conclusion, the study provides new insights into the roles of GV proteins in GV formation and produce ultrasmall GVs with a wide range of in vivo research.
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Affiliation(s)
- Meijun Fu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jieqiong Wang
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, 201206, China
| | - Yongsheng Hao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengyi Zeng
- Department of Ultrasound, The Second People's Hospital of Shenzhen, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518061, China
| | | | - Jianxiong Du
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Fei Yan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Feng R, Lan J, Goh MC, Du M, Chen Z. Advances in the application of gas vesicles in medical imaging and disease treatment. J Biol Eng 2024; 18:41. [PMID: 39044273 PMCID: PMC11267810 DOI: 10.1186/s13036-024-00426-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/18/2024] [Indexed: 07/25/2024] Open
Abstract
The gas vesicle (GV) is like a hollow nanoparticle consisting of an internal gas and a protein shell, which mainly consists of hydrophobic gas vesicle protein A (GvpA) and GvpC attached to the surface. GVs, first discovered in cyanobacteria, are mainly produced by photosynthetic bacteria (PSB) and halophilic archaea. After being modified and engineered, GVs can be utilized as contrast agents, delivery carriers, and immunological boosters for disease prevention, diagnosis, and treatment with good results due to their tiny size, strong stability and non-toxicity advantages. Many diagnostic and therapeutic approaches based on GV are currently under development. In this review, we discuss the source, function, physical and chemical properties of GV, focus on the current application progress of GV, and put forward the possible application prospect and development direction of GV in the future.
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Affiliation(s)
- Renjie Feng
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, the Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, China
- The Seventh Affiliated Hospital, Hunan Veterans Administration Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Jie Lan
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, China
- The Seventh Affiliated Hospital, Hunan Veterans Administration Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Meei Chyn Goh
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, China
| | - Meng Du
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, the Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China.
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, China.
| | - Zhiyi Chen
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, the Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China.
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, China.
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8
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Hurt R, Jin Z, Soufi M, Wong KK, Sawyer DP, Shen HK, Dutka P, Deshpande R, Zhang R, Mittelstein DR, Shapiro MG. Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening. ACS Synth Biol 2024; 13:2215-2226. [PMID: 38981096 PMCID: PMC11264329 DOI: 10.1021/acssynbio.4c00283] [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: 04/22/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024]
Abstract
A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 μm. Within the past decade, reporter genes for US have been introduced and engineered to link cellular functions to US signals via heterologous expression in commensal bacteria and mammalian cells. These acoustic reporter genes (ARGs) represent a novel class of genetically encoded US contrast agent, and are based on air-filled protein nanostructures called gas vesicles (GVs). Just as the discovery of fluorescent proteins was followed by the improvement and diversification of their optical properties through directed evolution, here we describe the evolution of GVs as acoustic reporters. To accomplish this task, we establish high-throughput, semiautomated acoustic screening of ARGs in bacterial cultures and use it to screen mutant libraries for variants with increased nonlinear US scattering. Starting with scanning site saturation libraries for two homologues of the primary GV structural protein, GvpA/B, two rounds of evolution resulted in GV variants with 5- and 14-fold stronger acoustic signals than the parent proteins. We anticipate that this and similar approaches will help high-throughput protein engineering play as large a role in the development of acoustic biomolecules as it has for their fluorescent counterparts.
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Affiliation(s)
- Robert
C. Hurt
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Zhiyang Jin
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Mohamed Soufi
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Katie K. Wong
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Daniel P. Sawyer
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Hao K. Shen
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Przemysław Dutka
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Ramya Deshpande
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Ruby Zhang
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - David R. Mittelstein
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Mikhail G. Shapiro
- Division
of Biology and Biological Engineering, Andrew and Peggy Cherng Department
of Medical Engineering, Division of Chemistry and Chemical Engineering, Howard Hughes Medical
Institute, California Institute of Technology, Pasadena, California 91125, United States
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9
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Duan M, Dev I, Lu A, Ayrapetyan G, You MY, Shapiro MG. SEMPER: Stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes for compact, ratio-tunable multi-gene expression. Cell Syst 2024; 15:597-609.e4. [PMID: 38971149 PMCID: PMC11298409 DOI: 10.1016/j.cels.2024.06.001] [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: 06/07/2023] [Revised: 04/01/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
Here, we present a method for expressing multiple open reading frames (ORFs) from single transcripts using the leaky scanning model of translation initiation. In this approach termed "stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes" (SEMPER), adjacent ORFs are translated from a single mRNA at tunable ratios determined by their order in the sequence and the strength of their translation initiation sites. We validate this approach by expressing up to three fluorescent proteins from one plasmid in two different cell lines. We then use it to encode a stoichiometrically tuned polycistronic construct encoding gas vesicle acoustic reporter genes that enables efficient formation of the multi-protein complex while minimizing cellular toxicity. We also demonstrate that SEMPER enables polycistronic expression of recombinant monoclonal antibodies from plasmid DNA and of two fluorescent proteins from single mRNAs made through in vitro transcription. Finally, we provide a probabilistic model to elucidate the mechanisms underlying SEMPER. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Mengtong Duan
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Ishaan Dev
- Division of Chemistry and Chemical Engineering, Caltech, Pasadena, CA 91125, USA
| | - Andrew Lu
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA; UCLA-Caltech Medical Scientist Training Program, UCLA, Los Angeles, CA 90095, USA
| | - Goar Ayrapetyan
- Division of Chemistry and Chemical Engineering, Caltech, Pasadena, CA 91125, USA
| | - Mei Yi You
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, Caltech, Pasadena, CA 91125, USA; Andrew and Peggy Cherng Department of Medical Engineering, Caltech, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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10
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Jazbec V, Varda N, Šprager E, Meško M, Vidmar S, Romih R, Podobnik M, Kežar A, Jerala R, Benčina M. Protein Gas Vesicles of Bacillus megaterium as Enhancers of Ultrasound-Induced Transcriptional Regulation. ACS NANO 2024; 18:16692-16700. [PMID: 38952323 PMCID: PMC11223475 DOI: 10.1021/acsnano.4c01498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Gas vesicles (GVs) are large cylindrical gas-filled protein assemblies found in diverse aquatic bacteria that enable their adaptation of buoyancy. GVs have already been used as ultrasound contrasting agents. Here, we investigate GVs derived from Bacillus megaterium, aiming to minimize the number of accessory Gvps within the GV gene cluster and demonstrate the use of GVs as enhancers of acoustic radiation force administered by ultrasound. Three (GvpR, GvpT, and GvpU) out of 11 genes in the cluster were found to be dispensable for functional GV formation, and their omission resulted in narrower GVs. Two essential proteins GvpJ and GvpN were absent from recently determined GV structures, but GvpJ was nevertheless found to be tightly bound to the cylindrical part of GVs in this study. Additionally, the N-terminus of GvpN was observed to play an important role in the formation of mature GVs. The binding of engineered GvpC fromAnabaena flos-aquae to HEK293 cells via integrins enhanced the acoustic force delivered by ultrasound and resulted in an increased Ca2+ influx into cells. Coupling with a synthetic Ca2+-dependent signaling pathway GVs efficiently enhanced cell stimulation by ultrasound, which expands the potentials of noninvasive sonogenetics cell stimulation.
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Affiliation(s)
- Vid Jazbec
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Nina Varda
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Ernest Šprager
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Maja Meško
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Sara Vidmar
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Rok Romih
- Institute
of Cell Biology, Faculty of Medicine, University
of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Andreja Kežar
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- CTGCT,
Centre for the Technologies of Gene and Cell Therapy, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- CTGCT,
Centre for the Technologies of Gene and Cell Therapy, Hajdrihova 19, 1000 Ljubljana, Slovenia
- University
of Ljubljana, Kongresni
trg 12, 1000 Ljubljana, Slovenia
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11
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Shen Q, Li Z, Wang Y, Meyer MD, De Guzman MT, Lim JC, Xiao H, Bouchard RR, Lu GJ. 50-nm Gas-Filled Protein Nanostructures to Enable the Access of Lymphatic Cells by Ultrasound Technologies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307123. [PMID: 38533973 PMCID: PMC11550859 DOI: 10.1002/adma.202307123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 03/14/2024] [Indexed: 03/28/2024]
Abstract
Ultrasound imaging and ultrasound-mediated gene and drug delivery are rapidly advancing diagnostic and therapeutic methods; however, their use is often limited by the need for microbubbles, which cannot transverse many biological barriers due to their large size. Here, the authors introduce 50-nm gas-filled protein nanostructures derived from genetically engineered gas vesicles(GVs) that are referred to as 50 nmGVs. These diamond-shaped nanostructures have hydrodynamic diameters smaller than commercially available 50-nm gold nanoparticles and are, to the authors' knowledge, the smallest stable, free-floating bubbles made to date. 50 nmGVs can be produced in bacteria, purified through centrifugation, and remain stable for months. Interstitially injected 50 nmGVs can extravasate into lymphatic tissues and gain access to critical immune cell populations, and electron microscopy images of lymph node tissues reveal their subcellular location in antigen-presenting cells adjacent to lymphocytes. The authors anticipate that 50 nmGVs can substantially broaden the range of cells accessible to current ultrasound technologies and may generate applications beyond biomedicine as ultrasmall stable gas-filled nanomaterials.
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Affiliation(s)
- Qionghua Shen
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Zongru Li
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Yixian Wang
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX, 77005, USA
| | - Marc T De Guzman
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Janie C Lim
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Han Xiao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
- SynthX Center, Rice University, Houston, TX, 77005, USA
| | - Richard R Bouchard
- Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - George J Lu
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
- Rice Synthetic Biology Institute, Rice University, Houston, TX, 77005, USA
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12
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Ling B, Gungoren B, Yao Y, Dutka P, Vassallo R, Nayak R, Smith CAB, Lee J, Swift MB, Shapiro MG. Truly Tiny Acoustic Biomolecules for Ultrasound Imaging and Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307106. [PMID: 38409678 PMCID: PMC11602542 DOI: 10.1002/adma.202307106] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/01/2024] [Indexed: 02/28/2024]
Abstract
Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography is challenging due to the size and stability constraints of conventional bubble-based agents. Here bicones, truly tiny acoustic contrast agents based on gas vesicles (GVs), a unique class of air-filled protein nanostructures naturally produced in buoyant microbes, are described. It is shown that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.
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Affiliation(s)
- Bill Ling
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Bilge Gungoren
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yuxing Yao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Reid Vassallo
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Rohit Nayak
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Cameron A. B. Smith
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Justin Lee
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Margaret B. Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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13
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Wang J, Wang Y, Zhong L, Yan F, Zheng H. Nanoscale contrast agents: A promising tool for ultrasound imaging and therapy. Adv Drug Deliv Rev 2024; 207:115200. [PMID: 38364906 DOI: 10.1016/j.addr.2024.115200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/31/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Nanoscale contrast agents have emerged as a versatile platform in the field of biomedical research, offering great potential for ultrasound imaging and therapy. Various kinds of nanoscale contrast agents have been extensively investigated in preclinical experiments to satisfy diverse biomedical applications. This paper provides a comprehensive review of the structure and composition of various nanoscale contrast agents, as well as their preparation and functionalization, encompassing both chemosynthetic and biosynthetic strategies. Subsequently, we delve into recent advances in the utilization of nanoscale contrast agents in various biomedical applications, including ultrasound molecular imaging, ultrasound-mediated drug delivery, and cell acoustic manipulation. Finally, the challenges and prospects of nanoscale contrast agents are also discussed to promote the development of this innovative nanoplatform in the field of biomedicine.
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Affiliation(s)
- Jieqiong Wang
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai 201206, China
| | - Yuanyuan Wang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lin Zhong
- School of public health, Nanchang University, Nanchang, Jiangxi, 330019, China
| | - Fei Yan
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hairong Zheng
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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14
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Yan H, Liu JH, Lu Y, Wu YH, Chen Z, Hu HY. Do all algae grow faster in environments replenished by reclaimed water? Examples of two effluents produced in Beijing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170784. [PMID: 38340834 DOI: 10.1016/j.scitotenv.2024.170784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Reclaimed water with nitrogen, phosphorus, and other contaminants may trigger algal blooms during its ecological utilization in replenishing rivers or lakes. However, the effect of reclaimed water on algal growth rates is not well understood. In this study, the growth potentials of algae in terms of Cyanophyta, Chlorophyta, and Bacillariophyta, as well as mixed algae in both regular culture medium and reclaimed water produced from treatment plants in Beijing with similar N and P concentrations, were compared to evaluate whether reclaimed water could facilitate algal growth. In addition, reclaimed water was also sterilized to verify the impact of bacteria's presence on algal growth. The results indicated that most algae grew faster in reclaimed water, among which the growth rate of Microcystis aeruginosa even increased by 5.5 fold. The growth of mixed algae in reclaimed water was not enhanced due to the strong adaptive ability of the community structure. Residual bacteria in the reclaimed water were found to be important contributors to algal growth. This work provided theoretical support for the safe and efficient utilization of reclaimed water.
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Affiliation(s)
- Han Yan
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, China
| | - Jun-Han Liu
- Baowu Clean Energy Co., Ltd, Shanghai 201999, China
| | - Yun Lu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, China; Beijing Laboratory for Environmental Frontier Technologies, Beijing 100084, China.
| | - Yin-Hu Wu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, China; Beijing Laboratory for Environmental Frontier Technologies, Beijing 100084, China
| | - Zhuo Chen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, China; Beijing Laboratory for Environmental Frontier Technologies, Beijing 100084, China.
| | - Hong-Ying Hu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, China; Beijing Laboratory for Environmental Frontier Technologies, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou), Tsinghua University, Suzhou 215163, China
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15
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Li Z, Shen Q, Usher ET, Anderson AP, Iburg M, Lin R, Zimmer B, Meyer MD, Holehouse AS, You L, Chilkoti A, Dai Y, Lu GJ. Phase transition of GvpU regulates gas vesicle clustering in bacteria. Nat Microbiol 2024; 9:1021-1035. [PMID: 38553608 DOI: 10.1038/s41564-024-01648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy. GV engineering has multiple applications, including reporter gene imaging, acoustic control and payload delivery. GVs often cluster into a honeycomb pattern to minimize occupancy of the cytosol. The underlying molecular mechanism and the influence on cellular physiology remain unknown. Using genetic, biochemical and imaging approaches, here we identify GvpU from Priestia megaterium as a protein that regulates GV clustering in vitro and upon expression in Escherichia coli. GvpU binds to the C-terminal tail of the core GV shell protein and undergoes a phase transition to form clusters in subsaturated solution. These properties of GvpU tune GV clustering and directly modulate bacterial fitness. GV variants can be designed with controllable sensitivity to GvpU-mediated clustering, enabling design of genetically tunable biosensors. Our findings elucidate the molecular mechanisms and functional roles of GV clustering, enabling its programmability for biomedical applications.
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Affiliation(s)
- Zongru Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Qionghua Shen
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Emery T Usher
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | | | - Manuel Iburg
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Richard Lin
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Brandon Zimmer
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Quantitative BioDesign, Duke University, Durham, NC, USA.
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - George J Lu
- Department of Bioengineering, Rice University, Houston, TX, USA.
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16
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Hurt RC, Jin Z, Soufi M, Wong KK, Sawyer DP, Shen HK, Dutka P, Deshpande R, Zhang R, Mittelstein DR, Shapiro MG. Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.30.587094. [PMID: 38617214 PMCID: PMC11014471 DOI: 10.1101/2024.03.30.587094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 µm. 1 Within the past decade, reporter genes for US have been introduced 2,3 and engineered 4,5 to link cellular functions to US signals via heterologous expression in commensal bacteria and mammalian cells. These acoustic reporter genes (ARGs) represent a novel class of genetically encoded US contrast agent, and are based on air-filled protein nanostructures called gas vesicles (GVs). 6 Just as the discovery of fluorescent proteins was followed by the improvement and diversification of their optical properties through directed evolution, here we describe the evolution of GVs as acoustic reporters. To accomplish this task, we establish high-throughput, semi-automated acoustic screening of ARGs in bacterial cultures and use it to screen mutant libraries for variants with increased nonlinear US scattering. Starting with scanning site saturation libraries for two homologs of the primary GV structural protein, GvpA/B, two rounds of evolution resulted in GV variants with 5- and 14-fold stronger acoustic signals than the parent proteins. We anticipate that this and similar approaches will help high-throughput protein engineering play as large a role in the development of acoustic biomolecules as it has for their fluorescent counterparts.
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17
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Hahmann J, Ishaqat A, Lammers T, Herrmann A. Sonogenetics for Monitoring and Modulating Biomolecular Function by Ultrasound. Angew Chem Int Ed Engl 2024; 63:e202317112. [PMID: 38197549 DOI: 10.1002/anie.202317112] [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: 11/10/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/11/2024]
Abstract
Ultrasound technology, synergistically harnessed with genetic engineering and chemistry concepts, has started to open the gateway to the remarkable realm of sonogenetics-a pioneering paradigm for remotely orchestrating cellular functions at the molecular level. This fusion not only enables precisely targeted imaging and therapeutic interventions, but also advances our comprehension of mechanobiology to unparalleled depths. Sonogenetic tools harness mechanical force within small tissue volumes while preserving the integrity of the surrounding physiological environment, reaching depths of up to tens of centimeters with high spatiotemporal precision. These capabilities circumvent the inherent physical limitations of alternative in vivo control methods such as optogenetics and magnetogenetics. In this review, we first discuss mechanosensitive ion channels, the most commonly utilized sonogenetic mediators, in both mammalian and non-mammalian systems. Subsequently, we provide a comprehensive overview of state-of-the-art sonogenetic approaches that leverage thermal or mechanical features of ultrasonic waves. Additionally, we explore strategies centered around the design of mechanochemically reactive macromolecular systems. Furthermore, we delve into the realm of ultrasound imaging of biomolecular function, encompassing the utilization of gas vesicles and acoustic reporter genes. Finally, we shed light on limitations and challenges of sonogenetics and present a perspective on the future of this promising technology.
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Affiliation(s)
- Johannes Hahmann
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074, Aachen, Germany
- Max Planck School Matter to Life, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Aman Ishaqat
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074, Aachen, Germany
| | - Twan Lammers
- Institute for Experimental Molecular Imaging (ExMI), Center for Biohybrid Medical Systems (CBMS), RWTH Aachen University Clinic, Forckenbeckstr. 55, 52074, Aachen, Germany
| | - Andreas Herrmann
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074, Aachen, Germany
- Max Planck School Matter to Life, Jahnstr. 29, 69120, Heidelberg, Germany
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18
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Schrunk E, Dutka P, Hurt RC, Wu D, Shapiro MG. Bioorthogonal Labeling Enables In Situ Fluorescence Imaging of Expressed Gas Vesicle Nanostructures. Bioconjug Chem 2024; 35:333-339. [PMID: 38346316 PMCID: PMC10961726 DOI: 10.1021/acs.bioconjchem.3c00518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/27/2024]
Abstract
Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nanocages, and other macromolecular assemblies, are being developed for potential biomedical applications. To facilitate such development, it would be valuable to characterize these nanostructures' subcellular assembly and localization. However, traditional fluorescent protein fusions are not tolerated by GVs' primary constituent protein, making optical microscopy a challenge. Here, we introduce a method for fluorescently visualizing intracellular GVs using the bioorthogonal label FlAsH, which becomes fluorescent upon reaction with the six-amino acid tetracysteine (TC) tag. We engineered the GV subunit protein, GvpA, to display the TC tag and showed that GVs bearing TC-tagged GvpA can be successfully assembled and fluorescently visualized in HEK 293T cells. Importantly, this was achieved by replacing only a fraction of GvpA with the tagged version. We used fluorescence images of the tagged GVs to study the GV size and distance distributions within these cells. This bioorthogonal and fractional labeling approach will enable research to provide a greater understanding of GVs and could be adapted to similar proteinaceous nanostructures.
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Affiliation(s)
- Erik Schrunk
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology; Pasadena, California 91125, United States
| | - Przemysław Dutka
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology; Pasadena, California 91125, United States
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Robert C. Hurt
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Di Wu
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology; Pasadena, California 91125, United States
| | - Mikhail G. Shapiro
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology; Pasadena, California 91125, United States
- Andrew
and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Howard
Hughes Medical Institute, Pasadena, California 91125, United States
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19
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Huber ST, Jakobi AJ. Structural biology of microbial gas vesicles: historical milestones and current knowledge. Biochem Soc Trans 2024; 52:205-215. [PMID: 38329160 PMCID: PMC10903477 DOI: 10.1042/bst20230396] [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: 12/14/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024]
Abstract
Gas vesicles mediate buoyancy-based motility in aquatic bacteria and archaea and are the only protein-based structures known to enclose a gas-filled volume. Their unique physicochemical properties and ingenious architecture rank them among the most intriguing macromolecular assemblies characterised to date. This review covers the 60-year journey in quest for a high-resolution structural model of gas vesicles, first highlighting significant strides made in establishing the detailed ultrastructure of gas vesicles through transmission electron microscopy, X-ray fibre diffraction, atomic force microscopy, and NMR spectroscopy. We then survey the recent progress in cryogenic electron microscopy studies of gas vesicles, which eventually led to a comprehensive atomic model of the mature assembly. Synthesising insight from these structures, we examine possible mechanisms of gas vesicle biogenesis and growth, presenting a testable model to guide future experimental work. We conclude by discussing future directions in the structural biology of gas vesicles, particularly considering advancements in AI-driven structure prediction.
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Affiliation(s)
- Stefan T. Huber
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Arjen J. Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
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20
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Schrunk E, Dutka P, Hurt RC, Wu D, Shapiro MG. Bioorthogonal labeling enables in situ fluorescence imaging of expressed gas vesicle nanostructures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569486. [PMID: 38077067 PMCID: PMC10705464 DOI: 10.1101/2023.11.30.569486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nano-cages, and other macromolecular assemblies are being developed for potential biomedical applications. To facilitate such development, it would be valuable to characterize these nanostructures' sub-cellular assembly and localization. However, traditional fluorescent protein fusions are not tolerated by GVs' primary constituent protein, making optical microscopy a challenge. Here, we introduce a method for fluorescently visualizing intracellular GVs using the bioorthogonal label FlAsH, which becomes fluorescent upon binding the six-amino acid tetracysteine (TC) tag. We engineered the GV subunit protein, GvpA, to display the TC tag, and showed that GVs bearing TC-tagged GvpA can be successfully assembled and fluorescently visualized in HEK 293T cells. We used fluorescence images of the tagged GVs to study GV size and distance distributions within these cells. This bioorthogonal labeling approach will enable research to provide a greater understanding of GVs and could be adapted to similar proteinaceous nanostructures.
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21
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Jin Z, Lakshmanan A, Zhang R, Tran TA, Rabut C, Dutka P, Duan M, Hurt RC, Malounda D, Yao Y, Shapiro MG. Ultrasonic reporters of calcium for deep tissue imaging of cellular signals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566364. [PMID: 37986929 PMCID: PMC10659314 DOI: 10.1101/2023.11.09.566364] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Calcium imaging has enabled major biological discoveries. However, the scattering of light by tissue limits the use of standard fluorescent calcium indicators in living animals. To address this limitation, we introduce the first genetically encoded ultrasonic reporter of calcium (URoC). Based on a unique class of air-filled protein nanostructures called gas vesicles, we engineered URoC to produce elevated nonlinear ultrasound signal upon binding to calcium ions. With URoC expressed in mammalian cells, we demonstrate noninvasive ultrasound imaging of calcium signaling in vivo during drug-induced receptor activation. URoC brings the depth and resolution advantages of ultrasound to the in vivo imaging of dynamic cellular function and paves the way for acoustic biosensing of a broader variety of biological signals.
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22
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Wang H, Zhang J, Toso D, Liao S, Sedighian F, Gunsalus R, Zhou ZH. Hierarchical organization and assembly of the archaeal cell sheath from an amyloid-like protein. Nat Commun 2023; 14:6720. [PMID: 37872154 PMCID: PMC10593813 DOI: 10.1038/s41467-023-42368-2] [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: 03/30/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023] Open
Abstract
Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei. Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 Å-resolution structure reveals that the sheath cylinder consists of axially stacked β-hoops, each of which is comprised of two to six 400 nm-diameter rings of β-strand arches (β-rings). With both similarities to and differences from amyloid cross-β fibril architecture, each β-ring contains two giant β-sheets contributed by ~ 450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into β-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent β-hoops into the immature sheath cylinder at the junction of two daughter cells.
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Affiliation(s)
- Hui Wang
- Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Jiayan Zhang
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Daniel Toso
- Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Shiqing Liao
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Farzaneh Sedighian
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Robert Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
- The UCLA-DOE Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Z Hong Zhou
- Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA.
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23
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Yao Y, McFadden ME, Luo SM, Barber RW, Kang E, Bar-Zion A, Smith CAB, Jin Z, Legendre M, Ling B, Malounda D, Torres A, Hamza T, Edwards CER, Shapiro MG, Robb MJ. Remote control of mechanochemical reactions under physiological conditions using biocompatible focused ultrasound. Proc Natl Acad Sci U S A 2023; 120:e2309822120. [PMID: 37725651 PMCID: PMC10523651 DOI: 10.1073/pnas.2309822120] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/01/2023] [Indexed: 09/21/2023] Open
Abstract
External control of chemical reactions in biological settings with spatial and temporal precision is a grand challenge for noninvasive diagnostic and therapeutic applications. While light is a conventional stimulus for remote chemical activation, its penetration is severely attenuated in tissues, which limits biological applicability. On the other hand, ultrasound is a biocompatible remote energy source that is highly penetrant and offers a wide range of functional tunability. Coupling ultrasound to the activation of specific chemical reactions under physiological conditions, however, remains a challenge. Here, we describe a synergistic platform that couples the selective mechanochemical activation of mechanophore-functionalized polymers with biocompatible focused ultrasound (FUS) by leveraging pressure-sensitive gas vesicles (GVs) as acousto-mechanical transducers. The power of this approach is illustrated through the mechanically triggered release of covalently bound fluorogenic and therapeutic cargo molecules from polymers containing a masked 2-furylcarbinol mechanophore. Molecular release occurs selectively in the presence of GVs upon exposure to FUS under physiological conditions. These results showcase the viability of this system for enabling remote control of specific mechanochemical reactions with spatiotemporal precision in biologically relevant settings and demonstrate the translational potential of polymer mechanochemistry.
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Affiliation(s)
- Yuxing Yao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Molly E. McFadden
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Stella M. Luo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Ross W. Barber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Elin Kang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Avinoam Bar-Zion
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Cameron A. B. Smith
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Zhiyang Jin
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA91125
| | - Mark Legendre
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Bill Ling
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Andrea Torres
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Tiba Hamza
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Chelsea E. R. Edwards
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA91125
- HHMI, Pasadena, CA91125
| | - Maxwell J. Robb
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
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24
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Shen Q, Li Z, Meyer MD, De Guzman MT, Lim JC, Bouchard RR, Lu GJ. 50-nm gas-filled protein nanostructures to enable the access of lymphatic cells by ultrasound technologies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546433. [PMID: 37425762 PMCID: PMC10327079 DOI: 10.1101/2023.06.27.546433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Ultrasound imaging and ultrasound-mediated gene and drug delivery are rapidly advancing diagnostic and therapeutic methods; however, their use is often limited by the need of microbubbles, which cannot transverse many biological barriers due to their large size. Here we introduce 50-nm gas-filled protein nanostructures derived from genetically engineered gas vesicles that we referred to as 50nm GVs. These diamond-shaped nanostructures have hydrodynamic diameters smaller than commercially available 50-nm gold nanoparticles and are, to our knowledge, the smallest stable, free-floating bubbles made to date. 50nm GVs can be produced in bacteria, purified through centrifugation, and remain stable for months. Interstitially injected 50nm GVs can extravasate into lymphatic tissues and gain access to critical immune cell populations, and electron microscopy images of lymph node tissues reveal their subcellular location in antigen-presenting cells adjacent to lymphocytes. We anticipate that 50nm GVs can substantially broaden the range of cells accessible to current ultrasound technologies and may generate applications beyond biomedicine as ultrasmall stable gas-filled nanomaterials.
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25
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Ling B, Gungoren B, Yao Y, Dutka P, Smith CAB, Lee J, Swift MB, Shapiro MG. Truly tiny acoustic biomolecules for ultrasound imaging and therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546773. [PMID: 37425749 PMCID: PMC10327013 DOI: 10.1101/2023.06.27.546773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography has been challenging due to the size and stability constraints of conventional bubble-based agents. Here we describe bicones, truly tiny acoustic contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures naturally produced in buoyant microbes. We show that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.
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Affiliation(s)
- Bill Ling
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Bilge Gungoren
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Yuxing Yao
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Cameron A. B. Smith
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Justin Lee
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Margaret B. Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
- Division of Engineering and Applied Science, California Institute of Technology; Pasadena, CA 91125, USA
- Howard Hughes Medical Institute; Pasadena, CA 91125, USA
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