1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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 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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
|
9
|
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] [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.
Collapse
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
| |
Collapse
|
10
|
Jiang H, Cao Z, Liu Y, Liu R, Zhou Y, Liu J. Bacteria-Based Living Probes: Preparation and the Applications in Bioimaging and Diagnosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306480. [PMID: 38032119 PMCID: PMC10811517 DOI: 10.1002/advs.202306480] [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: 09/08/2023] [Revised: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Bacteria can colonize a variety of in vivo biointerfaces, particularly the skin, nasal, and oral mucosa, the gastrointestinal tract, and the reproductive tract, but also target specific lesion sites, such as tumor and wound. By virtue of their prominent characteristics in motility, editability, and targeting ability, bacteria carrying imageable agents are widely developed as living probes for bioimaging and diagnosis of different diseases. This review first introduces the strategies used for preparing bacteria-based living probes, including biological engineering, chemical modification, intracellular loading, and optical manipulation. It then summarizes the recent progress of these living probes for fluorescence imaging, near-infrared imaging, ultrasonic imaging, photoacoustic imaging, magnetic resonance imaging, and positron emission tomography imaging. The biomedical applications of bacteria-based living probes are also reviewed particularly in the bioimaging and diagnosis of bacterial infections, cancers, and intestine-associated diseases. In addition, the advantages and challenges of bacteria-based living probes are discussed and future perspectives are also proposed. This review provides an updated overview of bacteria-based living probes, highlighting their great potential as a unique yet versatile platform for developing next-generation imageable agents for intelligent bioimaging, diagnosis, and even therapy.
Collapse
Affiliation(s)
- Hejin Jiang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineInstitute of Molecular MedicineState Key Laboratory of Systems Medicine for CancerRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Zhenping Cao
- Shanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineInstitute of Molecular MedicineState Key Laboratory of Systems Medicine for CancerRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Ying Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineInstitute of Molecular MedicineState Key Laboratory of Systems Medicine for CancerRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Rui Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineInstitute of Molecular MedicineState Key Laboratory of Systems Medicine for CancerRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yan Zhou
- Department of RadiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Jinyao Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineInstitute of Molecular MedicineState Key Laboratory of Systems Medicine for CancerRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| |
Collapse
|
11
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
|
12
|
Wang R, Liu X, Lv B, Sun W, Li C. Designing Intracellular Compartments for Efficient Engineered Microbial Cell Factories. ACS Synth Biol 2023; 12:1378-1395. [PMID: 37083286 DOI: 10.1021/acssynbio.2c00671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
With the rapid development of synthetic biology, various kinds of microbial cell factories (MCFs) have been successfully constructed to produce high-value-added compounds. However, the complexity of metabolic regulation and pathway crosstalk always cause issues such as intermediate metabolite accumulation, byproduct generation, and metabolic burden in MCFs, resulting in low efficiencies and low yields of industrial biomanufacturing. Such issues could be solved by spatially rearranging the pathways using intracellular compartments. In this review, design strategies are summarized and discussed based on the types and characteristics of natural and artificial subcellular compartments. This review systematically presents information for the construction of efficient MCFs with intracellular compartments in terms of four aspects of design strategy goals: (1) improving local reactant concentration; (2) intercepting and isolating competing pathways; (3) providing specific reaction substances and environments; and (4) storing and accumulating products.
Collapse
Affiliation(s)
- Ruwen Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xin Liu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Wentao Sun
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
- Center for Synthetic and System Biology, Tsinghua University, Beijing, 100084, PR China
| |
Collapse
|
13
|
Huber ST, Terwiel D, Evers WH, Maresca D, Jakobi AJ. Cryo-EM structure of gas vesicles for buoyancy-controlled motility. Cell 2023; 186:975-986.e13. [PMID: 36868215 PMCID: PMC9994262 DOI: 10.1016/j.cell.2023.01.041] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/14/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
Abstract
Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, we report the 3.2 Å cryo-EM structure of the gas vesicle shell made from the structural protein GvpA that self-assembles into hollow helical cylinders closed off by cone-shaped tips. Two helical half shells connect through a characteristic arrangement of GvpA monomers, suggesting a mechanism of gas vesicle biogenesis. The fold of GvpA features a corrugated wall structure typical for force-bearing thin-walled cylinders. Small pores enable gas molecules to diffuse across the shell, while the exceptionally hydrophobic interior surface effectively repels water. Comparative structural analysis confirms the evolutionary conservation of gas vesicle assemblies and demonstrates molecular features of shell reinforcement by GvpC. Our findings will further research into gas vesicle biology and facilitate molecular engineering of gas vesicles for ultrasound imaging.
Collapse
Affiliation(s)
- Stefan T Huber
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2628CD, the Netherlands
| | - Dion Terwiel
- Department of Imaging Physics, Delft University of Technology, Delft 2628CD, the Netherlands
| | - Wiel H Evers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2628CD, the Netherlands
| | - David Maresca
- Department of Imaging Physics, Delft University of Technology, Delft 2628CD, the Netherlands.
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2628CD, the Netherlands.
| |
Collapse
|
14
|
Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria. Nat Biotechnol 2023:10.1038/s41587-022-01581-y. [PMID: 36593411 DOI: 10.1038/s41587-022-01581-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/20/2022] [Indexed: 01/03/2023]
Abstract
Ultrasound allows imaging at a much greater depth than optical methods, but existing genetically encoded acoustic reporters for in vivo cellular imaging have been limited by poor sensitivity, specificity and in vivo expression. Here we describe two acoustic reporter genes (ARGs)-one for use in bacteria and one for use in mammalian cells-identified through a phylogenetic screen of candidate gas vesicle gene clusters from diverse bacteria and archaea that provide stronger ultrasound contrast, produce non-linear signals distinguishable from background tissue and have stable long-term expression. Compared to their first-generation counterparts, these improved bacterial and mammalian ARGs produce 9-fold and 38-fold stronger non-linear contrast, respectively. Using these new ARGs, we non-invasively imaged in situ tumor colonization and gene expression in tumor-homing therapeutic bacteria, tracked the progression of tumor gene expression and growth in a mouse model of breast cancer, and performed gene-expression-guided needle biopsies of a genetically mosaic tumor, demonstrating non-invasive access to dynamic biological processes at centimeter depth.
Collapse
|
15
|
Recent Advances in the Study of Gas Vesicle Proteins and Application of Gas Vesicles in Biomedical Research. Life (Basel) 2022; 12:life12091455. [PMID: 36143491 PMCID: PMC9501494 DOI: 10.3390/life12091455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022] Open
Abstract
The formation of gas vesicles has been investigated in bacteria and haloarchaea for more than 50 years. These air-filled nanostructures allow cells to stay at a certain height optimal for growth in their watery environment. Several gvp genes are involved and have been studied in Halobacterium salinarum, cyanobacteria, Bacillus megaterium, and Serratia sp. ATCC39006 in more detail. GvpA and GvpC form the gas vesicle shell, and additional Gvp are required as minor structural proteins, chaperones, an ATP-hydrolyzing enzyme, or as gene regulators. We analyzed the Gvp proteins of Hbt. salinarum with respect to their protein–protein interactions, and developed a model for the formation of these nanostructures. Gas vesicles are also used in biomedical research. Since they scatter waves and produce ultrasound contrast, they could serve as novel contrast agent for ultrasound or magnetic resonance imaging. Additionally, gas vesicles were engineered as acoustic biosensors to determine enzyme activities in cells. These applications are based on modifications of the surface protein GvpC that alter the mechanical properties of the gas vesicles. In addition, gas vesicles have been decorated with GvpC proteins fused to peptides of bacterial or viral pathogens and are used as tools for vaccine development.
Collapse
|
16
|
Kim S, Yoon S, Zhang S. Multiplexed Ultrasound Imaging Using Spectral Analysis on Gas Vesicles. Adv Healthc Mater 2022; 11:e2200568. [PMID: 35765741 PMCID: PMC9463101 DOI: 10.1002/adhm.202200568] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/18/2022] [Indexed: 01/27/2023]
Abstract
Current advances in ultrasound imaging techniques combined with the next generation contrast agents such as gas vesicles (GV) revolutionize the visualization of biological tissues with spatiotemporal precision. In optics, fluorescent proteins enable understanding of molecular and cellular functions in biological systems due to their multiplexed imaging capability. Here, a panel of GVs is investigated using mid-band fit (MBF) spectral imaging to realize multiplexed ultrasound imaging to uniquely visualize locations of different types of stationary GVs. The MBF spectral imaging technique demonstrates that stationary clustered GVs are efficiently localized and distinguished from unclustered GVs in agarose gel phantom and 3D vessel structures are visualized in ex vivo mouse liver specimens. Mouse macrophages serve as carriers of clustered and unclustered GVs and multiplexing beacons to report cells' spatial locations by emitting distinct spectral signals. 2D MBF spectral images are reconstructed, and pixels in these images are classified depending on MBF values by comparing predetermined filters that predict the existence of cells with clustered and unclustered GVs. This pseudo-coloring scheme clearly distinguishes the locations of two classes of cells like pseudo-color images in fluorescence microscopy.
Collapse
Affiliation(s)
- Sangnam Kim
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana, USA
| | - Sangpil Yoon
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana, USA
| | - Siyuan Zhang
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| |
Collapse
|
17
|
Jost A, Pfeifer F. Interaction of the gas vesicle proteins GvpA, GvpC, GvpN, and GvpO of Halobacterium salinarum. Front Microbiol 2022; 13:971917. [PMID: 35966690 PMCID: PMC9372576 DOI: 10.3389/fmicb.2022.971917] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
|
18
|
Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome. Cell 2022; 185:1297-1307.e11. [PMID: 35325592 PMCID: PMC9018610 DOI: 10.1016/j.cell.2022.02.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/23/2022] [Accepted: 02/15/2022] [Indexed: 11/22/2022]
Abstract
Spindle- or lemon-shaped viruses infect archaea in diverse environments. Due to the highly pleomorphic nature of these virions, which can be found with cylindrical tails emanating from the spindle-shaped body, structural studies of these capsids have been challenging. We have determined the atomic structure of the capsid of Sulfolobus monocaudavirus 1, a virus that infects hosts living in nearly boiling acid. A highly hydrophobic protein, likely integrated into the host membrane before the virions assemble, forms 7 strands that slide past each other in both the tails and the spindle body. We observe the discrete steps that occur as the tail tubes expand, and these are due to highly conserved quasiequivalent interactions with neighboring subunits maintained despite significant diameter changes. Our results show how helical assemblies can vary their diameters, becoming nearly spherical to package a larger genome and suggest how all spindle-shaped viruses have evolved from archaeal rod-like viruses.
Collapse
|
19
|
Jung H, Ling H, Tan YQ, Chua NH, Yew WS, Chang MW. Heterologous expression of cyanobacterial gas vesicle proteins in Saccharomyces cerevisiae. Biotechnol J 2021; 16:e2100059. [PMID: 34499423 DOI: 10.1002/biot.202100059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/11/2022]
Abstract
Given the potential applications of gas vesicles (GVs) in multiple fields including antigen-displaying and imaging, heterologous reconstitution of synthetic GVs is an attractive and interesting study that has translational potential. Here, we attempted to express and assemble GV proteins (GVPs) into GVs using the model eukaryotic organism Saccharomyces cerevisiae. We first selected and expressed two core structural proteins, GvpA and GvpC from cyanobacteria Anabaena flos-aquae and Planktothrix rubescens, respectively. We then optimized the protein production conditions and validated GV assembly in the context of GV shapes. We found that when two copies of anaA were integrated into the genome, the chromosomal expression of AnaA resulted in GV production regardless of GvpC expression. Next, we co-expressed chaperone-RFP with the GFP-AnaA to aid the AnaA aggregation. The co-expression of individual chaperones (Hsp42, Sis1, Hsp104, and GvpN) with AnaA led to the formation of larger inclusions and enhanced the sequestration of AnaA into the perivacuolar site. To our knowledge, this represents the first study on reconstitution of GVs in S. cerevisiae. Our results could provide insights into optimizing conditions for heterologous protein production as well as the reconstitution of other synthetic microcompartments in yeast.
Collapse
Affiliation(s)
- Harin Jung
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Wilmar-NUS Corporate Laboratory, National University of Singapore, Singapore, Singapore
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Wilmar-NUS Corporate Laboratory, National University of Singapore, Singapore, Singapore
| | - Yong Quan Tan
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Wilmar-NUS Corporate Laboratory, National University of Singapore, Singapore, Singapore
| | - Nam-Hai Chua
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Wilmar-NUS Corporate Laboratory, National University of Singapore, Singapore, Singapore.,Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Wen Shan Yew
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Wilmar-NUS Corporate Laboratory, National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Wilmar-NUS Corporate Laboratory, National University of Singapore, Singapore, Singapore
| |
Collapse
|
20
|
Wang R, Zhang L, Xie M, Wang L, Jin Q, Chen Y, Xie Y, He M, Zhu Y, Xu L, Han Z, Chen D. Biogenic Gas Vesicles for Ultrasound Imaging and Targeted Therapeutics. Curr Med Chem 2021; 29:1316-1330. [PMID: 34225604 DOI: 10.2174/0929867328666210705145642] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/01/2021] [Accepted: 05/15/2021] [Indexed: 11/22/2022]
Abstract
Ultrasound is not only the most widely used medical imaging mode for diagnostics owing to its real-time, non-radiation, portable, and low-cost merits, but also a promising targeted drug/gene delivery technique by exhibiting a series of powerful bioeffects. The development of micron-sized or nanometer-sized ultrasound agents or delivery carriers further makes ultrasound a distinctive modality in accurate diagnosis and effective treatment. In this review, we introduce one kind of unique biogenic gas-filled protein nanostructures called gas vesicles, presenting some unique characteristics than the conventional microbubbles. Gas vesicles can not only serve as ultrasound contrast agents with innovative imaging methods such as cross-amplitude modulation harmonic imaging but also can further be adjusted and optimized via genetic engineering techniques. Moreover, they could not only serve as acoustic gene reporters, acoustic biosensors to monitor the cell metabolism, but also serve as cavitation nuclei and drug carriers for therapeutic purposes. In this study, we focus on the latest development and applications in the area of ultrasound imaging and targeted therapeutics, and also provide a brief introduction of the corresponding mechanisms. In summary, these biogenic gas vesicles show some advantages over conventional MBs that deserve more efforts to promote their development.
Collapse
Affiliation(s)
- Rui Wang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zhang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingxing Xie
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lufang Wang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiaofeng Jin
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yihan Chen
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuji Xie
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengrong He
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ye Zhu
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lingling Xu
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhengyang Han
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dandan Chen
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
21
|
Jiang F, Yang H, Wang L, Wang Y, Tang Y, Wang D, Wang Q, Zou J. [ Escherichia coli expressing gas vesicles is safe for enhancing the ablation effect of highintensity focused ultrasound in tumor-bearing mice]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:649-656. [PMID: 34134950 DOI: 10.12122/j.issn.1673-4254.2021.05.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the effect and safety of Escherichia coli (E.coli) expressing gas vesicle (GVs) for enhancing the efficacy of tumor ablation by high intensity focused ultrasound (HIFU) in tumor-bearing mice. OBJECTIVE Thirty-two female BALB/c mice were used to establish mouse models bearing 4T1 tumor, which were randomized into GVs group [E.coli BL21 (AI)-PET28a-Arg1] and control group (PBS), and the efficacy of HIFU ablation was evaluated by examining coagulative necrotic volume and pathology of the tumors. Another 104 BALB/c mice were also randomly divided into GVs group and control group, and body weight changes of the mice were recorded on days 1, 4 and 15 after intravenous injection of E.coli containing GVs or PBS. White blood cells, red blood cells, hemoglobin and platelet counts and liver and renal function parameters of the mice were detected, and serum levels of TNF-α and IL-1β were examined using ELISA. The pathological changes in the liver and spleen were evaluated using HE staining to assess the safety of the treatments. OBJECTIVE HIFU ablation resulted in a significantly greater volume of coagulative necrosis and severer tissue damage in GVs group than in the control group (P < 0.001). In the 104 BALB/c mice without tumor cell inoculation, intravenous injection of E.coli expressing GVs, as compared with PBS, did not significantly affect body weight or cause changes in white blood cell, red blood cell and platelet counts or hemoglobin level (P1=0.59, P2=0.27, P3=0.76, P4=0.81). The liver and kidney function parameters (P1=0.12, P2=0.46, P3=0.62, P4=0.86) and serum levels of TNF-α and IL-1β (P1=0.48, P2=0.56) were all comparable between GVs group and control group. No obvious pathological changes were detected in the liver and spleen tissues in either GVs group or the control group. OBJECTIVE E.coli expressing GVs is safe for enhancing the ablation effect of HIFU in tumor-bearing mice.
Collapse
Affiliation(s)
- F Jiang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - H Yang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - L Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Y Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Y Tang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - D Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Q Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - J Zou
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| |
Collapse
|
22
|
Dutka P, Malounda D, Metskas LA, Chen S, Hurt RC, Lu GJ, Jensen GJ, Shapiro MG. Measuring gas vesicle dimensions by electron microscopy. Protein Sci 2021; 30:1081-1086. [PMID: 33641210 PMCID: PMC8040859 DOI: 10.1002/pro.4056] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/22/2021] [Indexed: 11/08/2022]
Abstract
Gas vesicles (GVs) are cylindrical or spindle-shaped protein nanostructures filled with air and used for flotation by various cyanobacteria, heterotrophic bacteria, and Archaea. Recently, GVs have gained interest in biotechnology applications due to their ability to serve as imaging agents and actuators for ultrasound, magnetic resonance and several optical techniques. The diameter of GVs is a crucial parameter contributing to their mechanical stability, buoyancy function and evolution in host cells, as well as their properties in imaging applications. Despite its importance, reported diameters for the same types of GV differ depending on the method used for its assessment. Here, we provide an explanation for these discrepancies and utilize electron microscopy (EM) techniques to accurately estimate the diameter of the most commonly studied types of GVs. We show that during air drying on the EM grid, GVs flatten, leading to a ~1.5-fold increase in their apparent diameter. We demonstrate that GVs' diameter can be accurately determined by direct measurements from cryo-EM samples or alternatively indirectly derived from widths of flat collapsed and negatively stained GVs. Our findings help explain the inconsistency in previously reported data and provide accurate methods to measure GVs dimensions.
Collapse
Affiliation(s)
- Przemysław Dutka
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Dina Malounda
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Lauren Ann Metskas
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Songye Chen
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
- Beckman InstituteCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Robert C. Hurt
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - George J. Lu
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
- Present address:
Department of BioengineeringRice UniversityHoustonTX77030USA
| | - Grant J. Jensen
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
- Department of Chemistry and BiochemistryBrigham Young UniversityProvoUtahUSA
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| |
Collapse
|
23
|
Martijn J, Schön ME, Lind AE, Vosseberg J, Williams TA, Spang A, Ettema TJG. Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition. Nat Commun 2020; 11:5490. [PMID: 33127909 PMCID: PMC7599335 DOI: 10.1038/s41467-020-19200-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/01/2020] [Indexed: 01/09/2023] Open
Abstract
Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.
Collapse
Affiliation(s)
- Joran Martijn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Max E Schön
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anders E Lind
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Julian Vosseberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Anja Spang
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Thijs J G Ettema
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| |
Collapse
|
24
|
Jayapaul J, Schröder L. Molecular Sensing with Host Systems for Hyperpolarized 129Xe. Molecules 2020; 25:E4627. [PMID: 33050669 PMCID: PMC7587211 DOI: 10.3390/molecules25204627] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/27/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.
Collapse
Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
| |
Collapse
|
25
|
Hill AM, Salmond GPC. Microbial gas vesicles as nanotechnology tools: exploiting intracellular organelles for translational utility in biotechnology, medicine and the environment. MICROBIOLOGY (READING, ENGLAND) 2020; 166:501-509. [PMID: 32324529 PMCID: PMC7376271 DOI: 10.1099/mic.0.000912] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/21/2020] [Indexed: 12/12/2022]
Abstract
A range of bacteria and archaea produce gas vesicles as a means to facilitate flotation. These gas vesicles have been purified from a number of species and their applications in biotechnology and medicine are reviewed here. Halobacterium sp. NRC-1 gas vesicles have been engineered to display antigens from eukaryotic, bacterial and viral pathogens. The ability of these recombinant nanoparticles to generate an immune response has been quantified both in vitro and in vivo. These gas vesicles, along with those purified from Anabaena flos-aquae and Bacillus megaterium, have been developed as an acoustic reporter system. This system utilizes the ability of gas vesicles to retain gas within a stable, rigid structure to produce contrast upon exposure to ultrasound. The susceptibility of gas vesicles to collapse when exposed to excess pressure has also been proposed as a biocontrol mechanism to disperse cyanobacterial blooms, providing an environmental function for these structures.
Collapse
Affiliation(s)
- Amy M. Hill
- Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
| | - George P. C. Salmond
- Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
| |
Collapse
|
26
|
Cai K, Xu BY, Jiang YL, Wang Y, Chen Y, Zhou CZ, Li Q. The model cyanobacteria Anabaena sp. PCC 7120 possess an intact but partially degenerated gene cluster encoding gas vesicles. BMC Microbiol 2020; 20:110. [PMID: 32375647 PMCID: PMC7204071 DOI: 10.1186/s12866-020-01805-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
Background Bacterial gas vesicles, composed of two major gas vesicle proteins and filled with gas, are a unique class of intracellular bubble-like nanostructures. They provide buoyancy for cells, and thus play an essential role in the growth and survival of aquatic and soil microbes. Moreover, the gas vesicle could be applied to multimodal and noninvasive biological imaging as a potential nanoscale contrast agent. To date, cylinder-shaped gas vesicles have been found in several strains of cyanobacteria. However, whether the functional gas vesicles could be produced in the model filamentous cyanobacteria Anabaena sp. PCC 7120 remains controversial. Results In this study, we found that an intact gvp gene cluster indeed exists in the model filamentous cyanobacteria Anabaena sp. PCC 7120. Real-time PCR assays showed that the gvpA gene is constitutively transcribed in vivo, and its expression level is upregulated at low light intensity and/or high growth temperature. Functional expression of this intact gvp gene cluster enables the recombinant Escherichia coli to gain the capability of floatation in the liquid medium, thanks to the assembly of irregular gas vesicles. Furthermore, crystal structure of GvpF in combination with enzymatic activity assays of GvpN suggested that these two auxiliary proteins of gas vesicle are structurally and enzymatically conserved, respectively. Conclusions Our findings show that the laboratory strain of model filamentous cyanobacteria Anabaena sp. PCC 7120 possesses an intact but partially degenerated gas vesicle gene cluster, indicating that the natural isolate might be able to produce gas vesicles under some given environmental stimuli for better floatation.
Collapse
Affiliation(s)
- Kun Cai
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Bo-Ying Xu
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Ying Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| |
Collapse
|
27
|
Nascimento FX, Hernández AG, Glick BR, Rossi MJ. Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 25:e00406. [PMID: 31886139 PMCID: PMC6920507 DOI: 10.1016/j.btre.2019.e00406] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/05/2019] [Accepted: 12/01/2019] [Indexed: 12/14/2022]
Abstract
In this work, the stress-resistant Bacillus megaterium STB1 is characterized and its ability to promote plant growth under normal and stress conditions is demonstrated. The genomic sequence of this bacterium, and a detailed analysis of the genes involved in facilitating its stress resistance and plant growth-promoting activities is also reported. The B. megaterium STB1 genome is rich in genetic elements involved in multiple stress resistance, xenobiotic degradation, pathogen antagonistic activities, and other traits related to soil and rhizosphere colonization. Moreover, genes participating in the biosynthesis of auxins and cytokinins, the modulation of polyamines, GABA, brassinosteroids and ethylene levels were also found. Ultimately, this study brings new insights into the role of B. megaterium as a plant growth-promoting bacterium and opens new opportunities for the development of novel strategies for agriculture and biotechnology.
Collapse
Affiliation(s)
- Francisco X. Nascimento
- IBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, 2780-157, Portugal
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Anabel G. Hernández
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Márcio J. Rossi
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| |
Collapse
|
28
|
Huang R, Lin J, Gao D, Zhang F, Yi L, Huang Y, Yan X, Duan Y, Zhu X. Discovery of gas vesicles in Streptomyces sp. CB03234-S and potential effects of gas vesicle gene overexpression on morphological and metabolic changes in streptomycetes. Appl Microbiol Biotechnol 2019; 103:5751-5761. [DOI: 10.1007/s00253-019-09891-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 12/24/2022]
|
29
|
Kunth M, Lu GJ, Witte C, Shapiro MG, Schröder L. Protein Nanostructures Produce Self-Adjusting Hyperpolarized Magnetic Resonance Imaging Contrast through Physical Gas Partitioning. ACS NANO 2018; 12:10939-10948. [PMID: 30204404 DOI: 10.1021/acsnano.8b04222] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Signal amplification strategies are critical for overcoming the intrinsically poor sensitivity of nuclear magnetic resonance (NMR) reporters in noninvasive molecular detection. A mechanism widely used for signal enhancement is chemical exchange saturation transfer (CEST) of nuclei between a dilute sensing pool and an abundant detection pool. However, the dependence of CEST amplification on the relative size of these spin pools confounds quantitative molecular detection with a larger detection pool typically making saturation transfer less efficient. Here we show that a recently discovered class of genetically encoded nanoscale reporters for 129Xe magnetic resonance overcomes this fundamental limitation through an elastic binding capacity for NMR-active nuclei. This approach pairs high signal amplification from hyperpolarized spins with ideal, self-adjusting saturation transfer behavior as the overall spin ensemble changes in size. These reporters are based on gas vesicles, i.e., microbe-derived, gas-filled protein nanostructures. We show that the xenon fraction that partitions into gas vesicles follows the ideal gas law, allowing the signal transfer under hyperpolarized xenon chemical exchange saturation transfer (Hyper-CEST) imaging to scale linearly with the total xenon ensemble. This conceptually distinct elastic response allows the production of quantitative signal contrast that is robust to variability in the concentration of xenon, enabling virtually unlimited improvement in absolute contrast with increased xenon delivery, and establishing a unique principle of operation for contrast agent development in emerging biochemical and in vivo applications of hyperpolarized NMR and magnetic resonance imaging.
Collapse
Affiliation(s)
- Martin Kunth
- California Institute of Technology , Division of Chemistry and Chemical Engineering , Pasadena , California 91125 , United States
- Leibniz-Forschungsinstitut für Molekulare Pharmarkologie (FMP) , 13125 Berlin , Germany
| | - George J Lu
- California Institute of Technology , Division of Chemistry and Chemical Engineering , Pasadena , California 91125 , United States
| | - Christopher Witte
- Leibniz-Forschungsinstitut für Molekulare Pharmarkologie (FMP) , 13125 Berlin , Germany
| | - Mikhail G Shapiro
- California Institute of Technology , Division of Chemistry and Chemical Engineering , Pasadena , California 91125 , United States
| | - Leif Schröder
- Leibniz-Forschungsinstitut für Molekulare Pharmarkologie (FMP) , 13125 Berlin , Germany
| |
Collapse
|
30
|
Farhadi A, Ho G, Kunth M, Ling B, Lakshmanan A, Lu GJ, Bourdeau RW, Schröder L, Shapiro MG. Recombinantly Expressed Gas Vesicles as Nanoscale Contrast Agents for Ultrasound and Hyperpolarized MRI. AIChE J 2018; 64:2927-2933. [PMID: 30555168 DOI: 10.1002/aic.16138] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrasound and hyperpolarized magnetic resonance imaging enable the visualization of biological processes in deep tissues. However, few molecular contrast agents are available to connect these modalities to specific aspects of biological function. We recently discovered that a unique class of gas-filled protein nanostructures known as gas vesicles could serve as nanoscale molecular reporters for these modalities. However, the need to produce these nanostructures via expression in specialized cultures of cyanobacteria or haloarchaea limits their broader adoption by other laboratories and hinders genetic engineering of their properties. Here, we describe recombinant expression and purification of Bacillus megaterium gas vesicles using a common laboratory strain of Escherichia coli, and characterize the physical, acoustic and magnetic resonance properties of these nanostructures. Recombinantly expressed gas vesicles produce ultrasound and hyperpolarized 129Xe MRI contrast at sub-nanomolar concentrations, thus validating a simple platform for their production and engineering.
Collapse
Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering; California Institute of Technology; Pasadena CA 91125
| | - Gabrielle Ho
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Martin Kunth
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
- Dept. of Structural Biology, Molecular Imaging; Leibniz-Forschungsinstitute für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Bill Ling
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering; California Institute of Technology; Pasadena CA 91125
| | - George J Lu
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Raymond W. Bourdeau
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Leif Schröder
- Dept. of Structural Biology, Molecular Imaging; Leibniz-Forschungsinstitute für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| |
Collapse
|
31
|
Lu GJ, Farhadi A, Mukherjee A, Shapiro MG. Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging. Curr Opin Chem Biol 2018; 45:57-63. [PMID: 29549770 PMCID: PMC6076850 DOI: 10.1016/j.cbpa.2018.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 12/31/2022]
Abstract
A long-standing goal of molecular imaging is to visualize cellular function within the context of living animals, necessitating the development of reporter genes compatible with deeply penetrant imaging modalities such as ultrasound and magnetic resonance imaging (MRI). Until recently, no reporter genes for ultrasound were available, and most genetically encoded reporters for MRI were limited by metal availability or relatively low sensitivity. Here we review how these limitations are being addressed by recently introduced reporter genes based on air-filled and water-transporting biomolecules. We focus on gas-filled protein nanostructures adapted from buoyant microbes, which scatter sound waves, perturb magnetic fields and interact with hyperpolarized nuclei, as well as transmembrane water channels that alter the effective diffusivity of water in tissue.
Collapse
Affiliation(s)
- George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
32
|
Maresca D, Lakshmanan A, Abedi M, Bar-Zion A, Farhadi A, Lu GJ, Szablowski JO, Wu D, Yoo S, Shapiro MG. Biomolecular Ultrasound and Sonogenetics. Annu Rev Chem Biomol Eng 2018; 9:229-252. [PMID: 29579400 PMCID: PMC6086606 DOI: 10.1146/annurev-chembioeng-060817-084034] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Visualizing and modulating molecular and cellular processes occurring deep within living organisms is fundamental to our study of basic biology and disease. Currently, the most sophisticated tools available to dynamically monitor and control cellular events rely on light-responsive proteins, which are difficult to use outside of optically transparent model systems, cultured cells, or surgically accessed regions owing to strong scattering of light by biological tissue. In contrast, ultrasound is a widely used medical imaging and therapeutic modality that enables the observation and perturbation of internal anatomy and physiology but has historically had limited ability to monitor and control specific cellular processes. Recent advances are beginning to address this limitation through the development of biomolecular tools that allow ultrasound to connect directly to cellular functions such as gene expression. Driven by the discovery and engineering of new contrast agents, reporter genes, and bioswitches, the nascent field of biomolecular ultrasound carries a wave of exciting opportunities.
Collapse
Affiliation(s)
- David Maresca
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mohamad Abedi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Avinoam Bar-Zion
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Jerzy O Szablowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Di Wu
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California 91125, USA
| | - Sangjin Yoo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| |
Collapse
|
33
|
Bourdeau RW, Lee-Gosselin A, Lakshmanan A, Farhadi A, Kumar SR, Nety SP, Shapiro MG. Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts. Nature 2018; 553:86-90. [PMID: 29300010 PMCID: PMC5920530 DOI: 10.1038/nature25021] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 11/09/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Raymond W Bourdeau
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sripriya Ravindra Kumar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Suchita P Nety
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
34
|
Lu GJ, Farhadi A, Szablowski JO, Lee-Gosselin A, Barnes SR, Lakshmanan A, Bourdeau RW, Shapiro MG. Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures. NATURE MATERIALS 2018; 17:456-463. [PMID: 29483636 PMCID: PMC6015773 DOI: 10.1038/s41563-018-0023-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/17/2018] [Indexed: 05/11/2023]
Abstract
Non-invasive biological imaging requires materials capable of interacting with deeply penetrant forms of energy such as magnetic fields and sound waves. Here, we show that gas vesicles (GVs), a unique class of gas-filled protein nanostructures with differential magnetic susceptibility relative to water, can produce robust contrast in magnetic resonance imaging (MRI) at sub-nanomolar concentrations, and that this contrast can be inactivated with ultrasound in situ to enable background-free imaging. We demonstrate this capability in vitro, in cells expressing these nanostructures as genetically encoded reporters, and in three model in vivo scenarios. Genetic variants of GVs, differing in their magnetic or mechanical phenotypes, allow multiplexed imaging using parametric MRI and differential acoustic sensitivity. Additionally, clustering-induced changes in MRI contrast enable the design of dynamic molecular sensors. By coupling the complementary physics of MRI and ultrasound, this nanomaterial gives rise to a distinct modality for molecular imaging with unique advantages and capabilities.
Collapse
Affiliation(s)
- George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jerzy O Szablowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Samuel R Barnes
- Department of Radiology, Loma Linda University, Loma Linda, CA, USA
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Raymond W Bourdeau
- 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.
| |
Collapse
|
35
|
Hydrodynamic Impedance of Bacteria and Bacteria-Inspired Micro-Swimmers: A New Strategy to Predict Power Consumption of Swimming Micro-Robots for Real-Time Applications. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201700013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
36
|
Piraner DI, Farhadi A, Davis HC, Wu D, Maresca D, Szablowski JO, Shapiro MG. Going Deeper: Biomolecular Tools for Acoustic and Magnetic Imaging and Control of Cellular Function. Biochemistry 2017; 56:5202-5209. [PMID: 28782927 PMCID: PMC6058970 DOI: 10.1021/acs.biochem.7b00443] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most cellular phenomena of interest to mammalian biology occur within the context of living tissues and organisms. However, today's most advanced tools for observing and manipulating cellular function, based on fluorescent or light-controlled proteins, work best in cultured cells, transparent model species, or small, surgically accessed anatomical regions. Their reach into deep tissues and larger animals is limited by photon scattering. To overcome this limitation, we must design biochemical tools that interface with more penetrant forms of energy. For example, sound waves and magnetic fields easily permeate most biological tissues, allowing the formation of images and delivery of energy for actuation. These capabilities are widely used in clinical techniques such as diagnostic ultrasound, magnetic resonance imaging, focused ultrasound ablation, and magnetic particle hyperthermia. Each of these modalities offers spatial and temporal precision that could be used to study a multitude of cellular processes in vivo. However, connecting these techniques to cellular functions such as gene expression, proliferation, migration, and signaling requires the development of new biochemical tools that can interact with sound waves and magnetic fields as optogenetic tools interact with photons. Here, we discuss the exciting challenges this poses for biomolecular engineering and provide examples of recent advances pointing the way to greater depth in in vivo cell biology.
Collapse
Affiliation(s)
- Dan I. Piraner
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hunter C. Davis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Di Wu
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - David Maresca
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jerzy O. Szablowski
- 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
| |
Collapse
|
37
|
Lakshmanan A, Lu GJ, Farhadi A, Nety SP, Kunth M, Lee-Gosselin A, Maresca D, Bourdeau RW, Yin M, Yan J, Witte C, Malounda D, Foster FS, Schröder L, Shapiro MG. Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI. Nat Protoc 2017; 12:2050-2080. [PMID: 28880278 DOI: 10.1038/nprot.2017.081] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Gas vesicles (GVs) are a unique class of gas-filled protein nanostructures that are detectable at subnanomolar concentrations and whose physical properties allow them to serve as highly sensitive imaging agents for ultrasound and MRI. Here we provide a protocol for isolating GVs from native and heterologous host organisms, functionalizing these nanostructures with moieties for targeting and fluorescence, characterizing their biophysical properties and imaging them using ultrasound and MRI. GVs can be isolated from natural cyanobacterial and haloarchaeal host organisms or from Escherichia coli expressing a heterologous GV gene cluster and purified using buoyancy-assisted techniques. They can then be modified by replacing surface-bound proteins with engineered, heterologously expressed variants or through chemical conjugation, resulting in altered mechanical, surface and targeting properties. Pressurized absorbance spectroscopy is used to characterize their mechanical properties, whereas dynamic light scattering (DLS)and transmission electron microscopy (TEM) are used to determine nanoparticle size and morphology, respectively. GVs can then be imaged with ultrasound in vitro and in vivo using pulse sequences optimized for their detection versus background. They can also be imaged with hyperpolarized xenon MRI using chemical exchange saturation transfer between GV-bound and dissolved xenon-a technique currently implemented in vitro. Taking 3-8 d to prepare, these genetically encodable nanostructures enable multimodal, noninvasive biological imaging with high sensitivity and potential for molecular targeting.
Collapse
Affiliation(s)
- Anupama Lakshmanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Suchita P Nety
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Martin Kunth
- Molecular Imaging, Department of Structural Biology, Leibniz-Forschungsinstitute für Molekulare Pharmakologie, Berlin, Germany
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - David Maresca
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Raymond W Bourdeau
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Melissa Yin
- Sunnybrook Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Judy Yan
- Sunnybrook Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Witte
- Molecular Imaging, Department of Structural Biology, Leibniz-Forschungsinstitute für Molekulare Pharmakologie, Berlin, Germany
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - F Stuart Foster
- Sunnybrook Research Institute, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Leif Schröder
- Molecular Imaging, Department of Structural Biology, Leibniz-Forschungsinstitute für Molekulare Pharmakologie, Berlin, Germany
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| |
Collapse
|
38
|
Monson RE, Tashiro Y, Salmond GPC. Overproduction of individual gas vesicle proteins perturbs flotation, antibiotic production and cell division in the enterobacterium Serratia sp. ATCC 39006. Microbiology (Reading) 2016; 162:1595-1607. [DOI: 10.1099/mic.0.000347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rita E. Monson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Yosuke Tashiro
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu 432-8561, Japan
| | | |
Collapse
|
39
|
Polka JK, Hays SG, Silver PA. Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a024018. [PMID: 27270297 DOI: 10.1101/cshperspect.a024018] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular function: not only metabolic, but also physical and mechanical. Here, we discuss a variety of perturbations available to biologists in controlling protein, nucleotide, and membrane localization. These range from simple tags, fusions, and scaffolds to heterologous expression of compartments and other structures that confer unique physical properties to cells. Next, we relate these principles to those guiding the spatial environments outside of cells such as the extracellular matrix. Finally, we discuss new directions in building intercellular organizations to create novel symbioses.
Collapse
Affiliation(s)
- Jessica K Polka
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
| | - Stephanie G Hays
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
| |
Collapse
|
40
|
Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree. Appl Environ Microbiol 2016; 82:2854-2861. [PMID: 26944845 DOI: 10.1128/aem.00483-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. IMPORTANCE Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.
Collapse
|
41
|
Tashiro Y, Monson RE, Ramsay JP, Salmond GPC. Molecular genetic and physical analysis of gas vesicles in buoyant enterobacteria. Environ Microbiol 2016; 18:1264-76. [PMID: 26743231 PMCID: PMC4982088 DOI: 10.1111/1462-2920.13203] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/29/2015] [Indexed: 11/29/2022]
Abstract
Different modes of bacterial taxis play important roles in environmental adaptation, survival, colonization and dissemination of disease. One mode of taxis is flotation due to the production of gas vesicles. Gas vesicles are proteinaceous intracellular organelles, permeable only to gas, that enable flotation in aquatic niches. Gene clusters for gas vesicle biosynthesis are partially conserved in various archaea, cyanobacteria, and some proteobacteria, such as the enterobacterium, Serratia sp. ATCC 39006 (S39006). Here we present the first systematic analysis of the genes required to produce gas vesicles in S39006, identifying how this differs from the archaeon Halobacterium salinarum. We define 11 proteins essential for gas vesicle production. Mutation of gvpN or gvpV produced small bicone gas vesicles, suggesting that the cognate proteins are involved in the morphogenetic assembly pathway from bicones to mature cylindrical forms. Using volumetric compression, gas vesicles were shown to comprise 17% of S39006 cells, whereas in Escherichia coli heterologously expressing the gas vesicle cluster in a deregulated environment, gas vesicles can occupy around half of cellular volume. Gas vesicle production in S39006 and E. coli was exploited to calculate the instantaneous turgor pressure within cultured bacterial cells; the first time this has been performed in either strain.
Collapse
Affiliation(s)
- Yosuke Tashiro
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.,Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, 432-8561, Japan
| | - Rita E Monson
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Joshua P Ramsay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.,Curtin Health Innovation Research Institute Biosciences Precinct, Faculty of Health Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| |
Collapse
|
42
|
Abstract
Many plasmids have been described in Euryarchaeota, one of the three major archaeal phyla, most of them in salt-loving haloarchaea and hyperthermophilic Thermococcales. These plasmids resemble bacterial plasmids in terms of size (from small plasmids encoding only one gene up to large megaplasmids) and replication mechanisms (rolling circle or theta). Some of them are related to viral genomes and form a more or less continuous sequence space including many integrated elements. Plasmids from Euryarchaeota have been useful for designing efficient genetic tools for these microorganisms. In addition, they have also been used to probe the topological state of plasmids in species with or without DNA gyrase and/or reverse gyrase. Plasmids from Euryarchaeota encode both DNA replication proteins recruited from their hosts and novel families of DNA replication proteins. Euryarchaeota form an interesting playground to test evolutionary hypotheses on the origin and evolution of viruses and plasmids, since a robust phylogeny is available for this phylum. Preliminary studies have shown that for different plasmid families, plasmids share a common gene pool and coevolve with their hosts. They are involved in gene transfer, mostly between plasmids and viruses present in closely related species, but rarely between cells from distantly related archaeal lineages. With few exceptions (e.g., plasmids carrying gas vesicle genes), most archaeal plasmids seem to be cryptic. Interestingly, plasmids and viral genomes have been detected in extracellular membrane vesicles produced by Thermococcales, suggesting that these vesicles could be involved in the transfer of viruses and plasmids between cells.
Collapse
|
43
|
Ishikawa T, Tanaka T, Imai Y, Omori T, Matsunaga D. Deformation of a micro-torque swimmer. Proc Math Phys Eng Sci 2016; 472:20150604. [PMID: 26997893 PMCID: PMC4786038 DOI: 10.1098/rspa.2015.0604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/15/2015] [Indexed: 11/25/2022] Open
Abstract
The membrane tension of some kinds of ciliates has been suggested to regulate upward and downward swimming velocities under gravity. Despite its biological importance, deformation and membrane tension of a ciliate have not been clarified fully. In this study, we numerically investigated the deformation of a ciliate swimming freely in a fluid otherwise at rest. The cell body was modelled as a capsule with a hyperelastic membrane enclosing a Newtonian fluid. Thrust forces due to the ciliary beat were modelled as torques distributed above the cell body. The effects of membrane elasticity, the aspect ratio of the cell's reference shape, and the density difference between the cell and the surrounding fluid were investigated. The results showed that the cell deformed like a heart shape, when the capillary number was sufficiently large. Under the influence of gravity, the membrane tension at the anterior end decreased in the upward swimming while it increased in the downward swimming. Moreover, gravity-induced deformation caused the cells to move gravitationally downwards or upwards, which resulted in a positive or negative geotaxis-like behaviour with a physical origin. These results are important in understanding the physiology of a ciliate's biological responses to mechanical stimuli.
Collapse
Affiliation(s)
- Takuji Ishikawa
- Department of Bioengineering and Robotics, Tohoku University, 6-6-01, Aoba, Sendai 980-8579, Japan
| | | | | | | | | |
Collapse
|
44
|
DasSarma S, DasSarma P. Gas Vesicle Nanoparticles for Antigen Display. Vaccines (Basel) 2015; 3:686-702. [PMID: 26350601 PMCID: PMC4586473 DOI: 10.3390/vaccines3030686] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/17/2015] [Accepted: 08/31/2015] [Indexed: 11/16/2022] Open
Abstract
Microorganisms like the halophilic archaeon Halobacterium sp. NRC-1 produce gas-filled buoyant organelles, which are easily purified as protein nanoparticles (called gas vesicles or GVNPs). GVNPs are non-toxic, exceptionally stable, bioengineerable, and self-adjuvanting. A large gene cluster encoding more than a dozen proteins has been implicated in their biogenesis. One protein, GvpC, found on the exterior surface of the nanoparticles, can accommodate insertions near the C-terminal region and results in GVNPs displaying the inserted sequences on the surface of the nanoparticles. Here, we review the current state of knowledge on GVNP structure and biogenesis as well as available studies on immunogenicity of pathogenic viral, bacterial, and eukaryotic proteins and peptides displayed on the nanoparticles. Recent improvements in genetic tools for bioengineering of GVNPs are discussed, along with future opportunities and challenges for development of vaccines and other applications.
Collapse
Affiliation(s)
- Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD 21202, USA.
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD 21202, USA.
| |
Collapse
|
45
|
General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
46
|
Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging. Nat Chem 2014; 6:629-34. [PMID: 24950334 DOI: 10.1038/nchem.1934] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 03/24/2014] [Indexed: 01/17/2023]
Abstract
Magnetic resonance imaging (MRI) enables high-resolution non-invasive observation of the anatomy and function of intact organisms. However, previous MRI reporters of key biological processes tied to gene expression have been limited by the inherently low molecular sensitivity of conventional (1)H MRI. This limitation could be overcome through the use of hyperpolarized nuclei, such as in the noble gas xenon, but previous reporters acting on such nuclei have been synthetic. Here, we introduce the first genetically encoded reporters for hyperpolarized (129)Xe MRI. These expressible reporters are based on gas vesicles (GVs), gas-binding protein nanostructures expressed by certain buoyant microorganisms. We show that GVs are capable of chemical exchange saturation transfer interactions with xenon, which enables chemically amplified GV detection at picomolar concentrations (a 100- to 10,000-fold improvement over comparable constructs for (1)H MRI). We demonstrate the use of GVs as heterologously expressed indicators of gene expression and chemically targeted exogenous labels in MRI experiments performed on living cells.
Collapse
|
47
|
Shapiro MG, Goodwill PW, Neogy A, Yin M, Foster FS, Schaffer DV, Conolly SM. Biogenic gas nanostructures as ultrasonic molecular reporters. NATURE NANOTECHNOLOGY 2014; 9:311-6. [PMID: 24633522 PMCID: PMC4023545 DOI: 10.1038/nnano.2014.32] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/28/2014] [Indexed: 05/04/2023]
Abstract
Ultrasound is among the most widely used non-invasive imaging modalities in biomedicine, but plays a surprisingly small role in molecular imaging due to a lack of suitable molecular reporters on the nanoscale. Here, we introduce a new class of reporters for ultrasound based on genetically encoded gas nanostructures from microorganisms, including bacteria and archaea. Gas vesicles are gas-filled protein-shelled compartments with typical widths of 45-250 nm and lengths of 100-600 nm that exclude water and are permeable to gas. We show that gas vesicles produce stable ultrasound contrast that is readily detected in vitro and in vivo, that their genetically encoded physical properties enable multiple modes of imaging, and that contrast enhancement through aggregation permits their use as molecular biosensors.
Collapse
Affiliation(s)
- Mikhail G. Shapiro
- Miller Research Institute, University of California at Berkeley, Berkeley, CA, USA 94720
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA 94720
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA 94720
- Correspondence to: M.G.S.:
| | - Patrick W. Goodwill
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA 94720
- Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, USA 94720
| | - Arkosnato Neogy
- Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, USA 94720
| | - Melissa Yin
- Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada, M4N 3M5
| | - F. Stuart Foster
- Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada, M4N 3M5
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada, M4N 3M5
| | - David V. Schaffer
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA 94720
- Department of Chemical and Biomolecular Engineering, University of California at Berkeley, Berkeley, CA, USA 94720
| | - Steven M. Conolly
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA 94720
- Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, USA 94720
| |
Collapse
|
48
|
Genomic sequence of Heliothis virescens ascovirus 3g isolated from Spodoptera exigua. J Virol 2013; 86:12467-8. [PMID: 23087124 DOI: 10.1128/jvi.02342-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heliothis virescens ascovirus 3a (HvAV-3a), a member of the family Ascoviridae, has the highest diversity among ascovirus species that have been reported in Australia, Indonesia, China, and the United States. To understand the diversity and origin of this important ascovirus, the complete genome of the HvAV Indonesia strain (HvAV-3g), isolated from Spodoptera exigua, was determined to be 199,721 bp, with a G+C content of 45.9%. Therefore, HvAV-3g has the largest genome among the reported ascovirus genomes to date. There are 194 predicted open reading frames (ORFs) encoding proteins of 50 or more amino acid residues. In comparison to HvAV-3e reported from Australia, HvAV-3g has all the ORFs in HvAV-3e with 6 additional ORFs unique to HvAV-3g, including 1 peptidase C26 gene with the highest identity to Drosophila spp. and 2 gas vesicle protein U (GvpU) genes with identities to Bacillus megaterium. The five unique homologous regions (hrs) and 25 baculovirus repeat ORFs (bro) of HvAV-3g are highly variable.
Collapse
|
49
|
Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci U S A 2012. [PMID: 23184964 DOI: 10.1073/pnas.1209119109] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Archaebacterial halophiles (Haloarchaea) are oxygen-respiring heterotrophs that derive from methanogens--strictly anaerobic, hydrogen-dependent autotrophs. Haloarchaeal genomes are known to have acquired, via lateral gene transfer (LGT), several genes from eubacteria, but it is yet unknown how many genes the Haloarchaea acquired in total and, more importantly, whether independent haloarchaeal lineages acquired their genes in parallel, or as a single acquisition at the origin of the group. Here we have studied 10 haloarchaeal and 1,143 reference genomes and have identified 1,089 haloarchaeal gene families that were acquired by a methanogenic recipient from eubacteria. The data suggest that these genes were acquired in the haloarchaeal common ancestor, not in parallel in independent haloarchaeal lineages, nor in the common ancestor of haloarchaeans and methanosarcinales. The 1,089 acquisitions include genes for catabolic carbon metabolism, membrane transporters, menaquinone biosynthesis, and complexes I-IV of the eubacterial respiratory chain that functions in the haloarchaeal membrane consisting of diphytanyl isoprene ether lipids. LGT on a massive scale transformed a strictly anaerobic, chemolithoautotrophic methanogen into the heterotrophic, oxygen-respiring, and bacteriorhodopsin-photosynthetic haloarchaeal common ancestor.
Collapse
|
50
|
Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 2012; 14:3122-45. [PMID: 23057602 DOI: 10.1111/j.1462-2920.2012.02893.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 01/21/2023]
Abstract
The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
Collapse
Affiliation(s)
- Anja Spang
- Department of Genetics in Ecology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|