1
|
Hu G, Cooke MB, Wen AX, Yu X, Wang J, Herman C, Wang MC. Chemical Induction of Longevity-Promoting Colanic Acid in the Host's Microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604802. [PMID: 39211270 PMCID: PMC11360898 DOI: 10.1101/2024.07.23.604802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Microbiota-derived metabolites have emerged as key regulators of longevity. The metabolic activity of the gut microbiota, influenced by dietary components and ingested chemical compounds, profoundly impacts host fitness. While the benefits of dietary prebiotics are well-known, chemically targeting the gut microbiota to enhance host fitness remains largely unexplored. Here, we report a novel chemical approach to induce a pro-longevity bacterial metabolite in the host gut. We discovered that specific Escherichia coli strains overproduce colanic acids (CAs) when exposed to a low dose of cephaloridine, leading to an increased lifespan in host Caenorhabditis elegans . In the mouse gut, oral administration of low-dose cephaloridine induces the transcription of the capsular biosynthesis operon responsible for CA biosynthesis in commensal E. coli , which overcomes the inhibition of CA biosynthesis above 30°C and enables its induction directly from the microbiota. Importantly, low-dose cephaloridine induces CA independently of its antibiotic properties through a previously unknown mechanism mediated by the membrane-bound histidine kinase ZraS. Our work lays the foundation for microbiota-based therapeutics through the chemical modulation of bacterial metabolism and reveals the promising potential of bacteria-targeting drugs in promoting host longevity.
Collapse
|
2
|
Tsvetikova SA, Zabavkina AA, Ivankova O, Koshel EI. Cellular Effects of Enterobacteriaceae Polysaccharide Colanic Acid. Int J Mol Sci 2024; 25:8017. [PMID: 39125588 PMCID: PMC11312057 DOI: 10.3390/ijms25158017] [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: 05/30/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024] Open
Abstract
Colanic acid (CA) is an exopolysaccharide found in Enterobacteriaceae. Recently, its ability to stimulate physical activity in mice and to prolong the lifespan of invertebrates has been described. In the current work, we use standard MTT assay, fluorescence microscopy, and flow cytometry to describe CA action on several cell lines of different origins. We observed slight antiproliferative activity against colorectal cancer (HCT-116), neuroblastoma (IMR-32), and myoblast (C2C12) cell lines at a concentration of 256 μg/mL, while other cell lines of non-cancerous origin (Vero, HPF) did not show any decrease in the MTT assay. In all cell lines, we observed a rearrangement of mitochondria localization using fluorescence microscopy. CA induces cell differentiation in the myoblast cell line (C2C12) at concentrations of 50-200 μg/mL. Briefly, we observed that the number of apoptotic cells increased and the metabolic activity in the MTT assay decreased, which was accompanied by changes in cell morphology, the quantity of ROS, and the potential of the mitochondrial membrane. Taken together, these results indicate that CA is specific in cytotoxicity to cell lines of different origins and can impact mitochondria and differentiation, consistent with its potential geroprotective function.
Collapse
Affiliation(s)
- Sofia A. Tsvetikova
- SCAMT Laboratory, National Research University ITMO, St. Petersburg 197101, Russia; (A.A.Z.); (O.I.)
| | | | | | - Elena I. Koshel
- SCAMT Laboratory, National Research University ITMO, St. Petersburg 197101, Russia; (A.A.Z.); (O.I.)
| |
Collapse
|
3
|
Zhao J, Sun H, Wang G, Wang Q, Wang Y, Li Q, Bi S, Qi Q, Wang Q. Engineering Chimeric Chemoreceptors and Two-Component Systems for Orthogonal and Leakless Biosensing of Extracellular γ-Aminobutyric Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14216-14228. [PMID: 38860925 DOI: 10.1021/acs.jafc.4c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Two-component systems (TCSs) sensing and responding to various stimuli outside and inside cells are valuable resources for developing biosensors with synthetic biology applications. However, the use of TCS-based biosensors suffers from a limited effector spectrum, hypersensitivity, low dynamic range, and unwanted signal crosstalk. Here, we developed a tailor-made Escherichia coli whole-cell γ-aminobutyric acid (GABA) biosensor by engineering a chimeric GABA chemoreceptor PctC and TCS. By testing different TCSs, the chimeric PctC/PhoQ showed the response to GABA. Chimera-directed evolution and introduction of the insulated chimeric pair PctC/PhoQ*PhoP* produced biosensors with up to 3.50-fold dynamic range and good orthogonality. To further enhance the dynamic range and lower the basal leakage, three strategies, engineering of PhoP DNA binding sites, fine-tuning reporter expression by optimizing transcription/translation components, and a tobacco etch virus protease-controlled protein degradation, were integrated. This chimeric biosensor displayed a low basal leakage, a large dynamic range (15.8-fold), and a high threshold level (22.7 g L-1). Finally, the optimized biosensor was successfully applied in the high-throughput microdroplet screening of GABA-overproducing Corynebacterium glutamicum, demonstrating its desired properties for extracellular signal biosensing.
Collapse
Affiliation(s)
- Jingyu Zhao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Huanhuan Sun
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Gege Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Qi Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingbin Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| |
Collapse
|
4
|
Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
Collapse
Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| |
Collapse
|
5
|
Meier SSM, Multamäki E, Ranzani AT, Takala H, Möglich A. Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling. Nat Commun 2024; 15:4876. [PMID: 38858359 PMCID: PMC11164954 DOI: 10.1038/s41467-024-49251-8] [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: 02/07/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Bacteria must constantly probe their environment for rapid adaptation, a crucial need most frequently served by two-component systems (TCS). As one component, sensor histidine kinases (SHK) control the phosphorylation of the second component, the response regulator (RR). Downstream responses hinge on RR phosphorylation and can be highly stringent, acute, and sensitive because SHKs commonly exert both kinase and phosphatase activity. With a bacteriophytochrome TCS as a paradigm, we here interrogate how this catalytic duality underlies signal responses. Derivative systems exhibit tenfold higher red-light sensitivity, owing to an altered kinase-phosphatase balance. Modifications of the linker intervening the SHK sensor and catalytic entities likewise tilt this balance and provide TCSs with inverted output that increases under red light. These TCSs expand synthetic biology and showcase how deliberate perturbations of the kinase-phosphatase duality unlock altered signal-response regimes. Arguably, these aspects equally pertain to the engineering and the natural evolution of TCSs.
Collapse
Affiliation(s)
| | - Elina Multamäki
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | - Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- Department of Anatomy, University of Helsinki, Helsinki, Finland.
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
- Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, Bayreuth, Germany.
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany.
| |
Collapse
|
6
|
Gao B, Ruiz D, Case H, Jinkerson RE, Sun Q. Engineering bacterial warriors: harnessing microbes to modulate animal physiology. Curr Opin Biotechnol 2024; 87:103113. [PMID: 38564969 DOI: 10.1016/j.copbio.2024.103113] [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: 12/10/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
A central goal of synthetic biology is the reprogramming of living systems for predetermined biological functions. While many engineering efforts have been made in living systems, these innovations have been mainly employed with microorganisms or cell lines. The engineering of multicellular organisms including animals remains challenging owing to the complexity of these systems. In this context, microbes, with their intricate impact on animals, have opened new opportunities. Through the utilization of the symbiotic relationships between microbes and animals, researchers have effectively manipulated animals in various ways using engineered microbes. This focused approach has demonstrated its significance in scientific exploration and engineering with model animals, coral preservation and restoration, and advancements in human health.
Collapse
Affiliation(s)
- Baizhen Gao
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77840, United States
| | - Daniela Ruiz
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77840, United States; Program of Genetics and Genomics, Texas A&M University, College Station, TX 77840, United States
| | - Hayden Case
- Department of Biology, Texas A&M University, College Station, TX 77840, United States
| | - Robert E Jinkerson
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, United States; Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, United States
| | - Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77840, United States; Program of Genetics and Genomics, Texas A&M University, College Station, TX 77840, United States.
| |
Collapse
|
7
|
Quispe Haro JJ, Chen F, Los R, Shi S, Sun W, Chen Y, Idema T, Wegner SV. Optogenetic Control of Bacterial Cell-Cell Adhesion Dynamics: Unraveling the Influence on Biofilm Architecture and Functionality. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310079. [PMID: 38613837 PMCID: PMC11187914 DOI: 10.1002/advs.202310079] [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: 12/21/2023] [Revised: 03/22/2024] [Indexed: 04/15/2024]
Abstract
The transition of bacteria from an individualistic to a biofilm lifestyle profoundly alters their biology. During biofilm development, the bacterial cell-cell adhesions are a major determinant of initial microcolonies, which serve as kernels for the subsequent microscopic and mesoscopic structure of the biofilm, and determine the resulting functionality. In this study, the significance of bacterial cell-cell adhesion dynamics on bacterial aggregation and biofilm maturation is elucidated. Using photoswitchable adhesins between bacteria, modifying the dynamics of bacterial cell-cell adhesions with periodic dark-light cycles is systematic. Dynamic cell-cell adhesions with liquid-like behavior improve bacterial aggregation and produce more compact microcolonies than static adhesions with solid-like behavior in both experiments and individual-based simulations. Consequently, dynamic cell-cell adhesions give rise to earlier quorum sensing activation, better intermixing of different bacterial populations, improved biofilm maturation, changes in the growth of cocultures, and higher yields in fermentation. The here presented approach of tuning bacterial cell-cell adhesion dynamics opens the door for regulating the structure and function of biofilms and cocultures with potential biotechnological applications.
Collapse
Affiliation(s)
- Juan José Quispe Haro
- Institute of Physiological Chemistry and PathobiochemistryUniversity of MünsterMünsterGermany
| | - Fei Chen
- Institute of Physiological Chemistry and PathobiochemistryUniversity of MünsterMünsterGermany
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaChina
| | - Rachel Los
- Department of BionanoscienceKavli Institute of NanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Shuqi Shi
- National Engineering Research Center for BiotechnologyCollege of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
- State Key Laboratory of Materials‐Oriented Chemical EngineeringCollege of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Wenjun Sun
- National Engineering Research Center for BiotechnologyCollege of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
- State Key Laboratory of Materials‐Oriented Chemical EngineeringCollege of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Yong Chen
- National Engineering Research Center for BiotechnologyCollege of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
- State Key Laboratory of Materials‐Oriented Chemical EngineeringCollege of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Timon Idema
- Department of BionanoscienceKavli Institute of NanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Seraphine V. Wegner
- Institute of Physiological Chemistry and PathobiochemistryUniversity of MünsterMünsterGermany
| |
Collapse
|
8
|
Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
Collapse
Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| |
Collapse
|
9
|
Elahi Y, Baker MAB. Light Control in Microbial Systems. Int J Mol Sci 2024; 25:4001. [PMID: 38612810 PMCID: PMC11011852 DOI: 10.3390/ijms25074001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Light is a key environmental component influencing many biological processes, particularly in prokaryotes such as archaea and bacteria. Light control techniques have revolutionized precise manipulation at molecular and cellular levels in recent years. Bacteria, with adaptability and genetic tractability, are promising candidates for light control studies. This review investigates the mechanisms underlying light activation in bacteria and discusses recent advancements focusing on light control methods and techniques for controlling bacteria. We delve into the mechanisms by which bacteria sense and transduce light signals, including engineered photoreceptors and light-sensitive actuators, and various strategies employed to modulate gene expression, protein function, and bacterial motility. Furthermore, we highlight recent developments in light-integrated methods of controlling microbial responses, such as upconversion nanoparticles and optical tweezers, which can enhance the spatial and temporal control of bacteria and open new horizons for biomedical applications.
Collapse
|
10
|
Benisch M, Aoki SK, Khammash M. Unlocking the potential of optogenetics in microbial applications. Curr Opin Microbiol 2024; 77:102404. [PMID: 38039932 DOI: 10.1016/j.mib.2023.102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/07/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
Optogenetics is a powerful approach that enables researchers to use light to dynamically manipulate cellular behavior. Since the first published use of optogenetics in synthetic biology, the field has expanded rapidly, yielding a vast array of tools and applications. Despite its immense potential for achieving high spatiotemporal precision, optogenetics has predominantly been employed as a substitute for conventional chemical inducers. In this short review, we discuss key features of microbial optogenetics and highlight applications for understanding biology, cocultures, bioproduction, biomaterials, and therapeutics, in which optogenetics is more fully utilized to realize goals not previously possible by other methods.
Collapse
Affiliation(s)
- Moritz Benisch
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Stephanie K Aoki
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| |
Collapse
|
11
|
Chen X, Wang Z, Zheng P, Dongol A, Xie Y, Ge X, Zheng M, Dang X, Seyhan ZB, Nagaratnam N, Yu Y, Huang X. Impaired mitophagosome-lysosome fusion mediates olanzapine-induced aging. Aging Cell 2023; 22:e14003. [PMID: 37828862 PMCID: PMC10652317 DOI: 10.1111/acel.14003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
The lifespan of schizophrenia patients is significantly shorter than the general population. Olanzapine is one of the most commonly used antipsychotic drugs (APDs) for treating patients with psychosis, including schizophrenia and bipolar disorder. Despite their effectiveness in treating positive and negative symptoms, prolonged exposure to APDs may lead to accelerated aging and cognitive decline, among other side effects. Here we report that dysfunctional mitophagy is a fundamental mechanism underlying accelerated aging induced by olanzapine, using in vitro and in vivo (Caenorhabditis elegans) models. We showed that the aberrant mitophagy caused by olanzapine was via blocking mitophagosome-lysosome fusion. Furthermore, olanzapine can induce mitochondrial damage and hyperfragmentation of the mitochondrial network. The mitophagosome-lysosome fusion in olanzapine-induced aging models can be restored by a mitophagy inducer, urolithin A, which alleviates defective mitophagy, mitochondrial damage, and fragmentation of the mitochondrial network. Moreover, the mitophagy inducer ameliorated behavioral changes induced by olanzapine, including shortened lifespan, and impaired health span, learning, and memory. These data indicate that olanzapine impairs mitophagy, leading to the shortened lifespan, impaired health span, and cognitive deficits. Furthermore, this study suggests the potential application of mitophagy inducers as therapeutic strategies to reverse APD-induced adverse effects associated with accelerated aging.
Collapse
Affiliation(s)
- Xi Chen
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Zhizhen Wang
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Peng Zheng
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Anjila Dongol
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Yuanyi Xie
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Xing Ge
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and ImmunologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Mingxuan Zheng
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and ImmunologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Xuemei Dang
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and ImmunologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Zehra Boz Seyhan
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Nathan Nagaratnam
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Yinghua Yu
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and ImmunologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Xu‐Feng Huang
- School of Medical, Indigenous and Health SciencesUniversity of WollongongWollongongNew South WalesAustralia
| |
Collapse
|
12
|
Wang Q, Yang Q, Liu X. The microbiota-gut-brain axis and neurodevelopmental disorders. Protein Cell 2023; 14:762-775. [PMID: 37166201 PMCID: PMC10599644 DOI: 10.1093/procel/pwad026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 04/27/2023] [Indexed: 05/12/2023] Open
Abstract
The gut microbiota has been found to interact with the brain through the microbiota-gut-brain axis, regulating various physiological processes. In recent years, the impacts of the gut microbiota on neurodevelopment through this axis have been increasingly appreciated. The gut microbiota is commonly considered to regulate neurodevelopment through three pathways, the immune pathway, the neuronal pathway, and the endocrine/systemic pathway, with overlaps and crosstalks in between. Accumulating studies have identified the role of the microbiota-gut-brain axis in neurodevelopmental disorders including autism spectrum disorder, attention deficit hyperactivity disorder, and Rett Syndrome. Numerous researchers have examined the physiological and pathophysiological mechanisms influenced by the gut microbiota in neurodevelopmental disorders (NDDs). This review aims to provide a comprehensive overview of advancements in research pertaining to the microbiota-gut-brain axis in NDDs. Furthermore, we analyzed both the current state of research progress and discuss future perspectives in this field.
Collapse
Affiliation(s)
- Qinwen Wang
- State Key Laboratory of Reproductive Medicine and offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China
| | - Qianyue Yang
- State Key Laboratory of Reproductive Medicine and offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China
| | - Xingyin Liu
- State Key Laboratory of Reproductive Medicine and offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
- Department of Microbiota Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 211166, China
| |
Collapse
|
13
|
Mim MS, Knight C, Zartman JJ. Quantitative insights in tissue growth and morphogenesis with optogenetics. Phys Biol 2023; 20:061001. [PMID: 37678266 PMCID: PMC10594237 DOI: 10.1088/1478-3975/acf7a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/09/2023]
Abstract
Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.
Collapse
Affiliation(s)
- Mayesha Sahir Mim
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Caroline Knight
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Jeremiah J Zartman
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| |
Collapse
|
14
|
Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [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] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
Collapse
Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| |
Collapse
|
15
|
Wu J, Huang M, Zhan Y, Liu M, Hu X, Wu Y, Qiao J, Wang Z, Li H, Wang J, Wang X. Regulating Cardiolipin Biosynthesis for Efficient Production of Colanic Acid in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37235531 DOI: 10.1021/acs.jafc.3c01414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Colanic acid has broad application prospects in the food and healthcare market due to its excellent physical properties and biological activities. In this study, we discovered that colonic acid production in Escherichia coli could be enhanced by regulating cardiolipin biosynthesis. Single deletion of clsA, clsB, or clsC related to cardiolipin biosynthesis in E. coli MG1655 only slightly increased colonic acid production, but double or triple deletion of these three genes in E. coli MG1655 increased colonic acid production up to 2.48-fold. Previously, we have discovered that truncating lipopolysaccharide by deletion of the waaLUZYROBSPGQ gene cluster and enhancing RcsA by deletion of genes lon and hns can increase colonic acid production in E. coli. Therefore, these genes together with clsA, clsB, or/and clsC were deleted in E. coli, and all the resulting mutants showed increased colonic acid production. The best colonic acid production was observed in the mutant WWM16, which is 126-fold higher than in the control MG1655. To further improve colonic acid production, the genes rcsA and rcsD1-466 were overexpressed in WWM16, and the resulting recombinant E. coli WWM16/pWADT could produce 44.9 g/L colonic acid, which is the highest titer reported to date.
Collapse
Affiliation(s)
- Jiaxin Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Ming Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Yi Zhan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Minmin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Yuanming Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jun Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Hedan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
16
|
Chemical synthesis of oligosaccharides and their application in new drug research. Eur J Med Chem 2023; 249:115164. [PMID: 36758451 DOI: 10.1016/j.ejmech.2023.115164] [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: 12/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
Oligosaccharides are the ubiquitous molecules of life. In order to translate human bioglycosylation into clinical applications, homogeneous samples of oligosaccharides and glycoconjugates can be obtained by chemical, enzymatic or other biological methods for systematic studies. However, the structural complexity and diversity of glycans and their conjugates present a major challenge for the synthesis of such molecules. This review summarizes the chemical synthesis methods of oligosaccharides, the application of oligosaccharides in the field of medicinal chemistry according to their related biological activities, and shows the great prospect of oligosaccharides in the field of pharmaceutical chemistry.
Collapse
|
17
|
A red light-controlled probiotic bio-system for in-situ gut-brain axis regulation. Biomaterials 2023; 294:122005. [PMID: 36701997 DOI: 10.1016/j.biomaterials.2023.122005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 12/27/2022] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
Microbes regulate brain function through the gut-brain axis, deriving the technology to modulate the gut-brain axis in situ by engineered probiotics. Optogenetics offers precise and flexible strategies for controlling the functions of probiotics in situ. However, the poor penetration of most frequently used short wavelength light has limited the application of optogenetic probiotics in the gut. Herein, a red-light optogenetic gut probiotic was applied for drug production and delivery and regulation of the host behaviors. Firstly, a Red-light Optogenetic E. coli Nissle 1917 strain (ROEN) that could respond to red light and release drug product by light-controlled lysis was constructed. The remaining optical power of red light after 3 cm tissue was still able to initiate gene expression of ROEN and produce about approximately 3-fold induction efficiency. To give full play to the in vivo potential of ROEN, its responsive ability of the penetrated red light was tested, and its encapsulation was realized by PH-sensitive alginate microcapsules for further oral administration. The function of ROEN for gut-brain regulation was realized by releasing Exendin-4 fused with anti-neonatal Fc receptor affibody. Neuroprotection and behavioral regulation effects were evaluated in the Parkinson's disease mouse model, after orally administration of ROEN delivering Exendin-4 under optogenetic control in the murine gut. The red-light optogenetic probiotic might be a perspective platform for in situ drug delivery and gut-brain axis regulation.
Collapse
|
18
|
Sheets MB, Tague N, Dunlop MJ. An optogenetic toolkit for light-inducible antibiotic resistance. Nat Commun 2023; 14:1034. [PMID: 36823420 PMCID: PMC9950086 DOI: 10.1038/s41467-023-36670-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Antibiotics are a key control mechanism for synthetic biology and microbiology. Resistance genes are used to select desired cells and regulate bacterial populations, however their use to-date has been largely static. Precise spatiotemporal control of antibiotic resistance could enable a wide variety of applications that require dynamic control of susceptibility and survival. Here, we use light-inducible Cre recombinase to activate expression of drug resistance genes in Escherichia coli. We demonstrate light-activated resistance to four antibiotics: carbenicillin, kanamycin, chloramphenicol, and tetracycline. Cells exposed to blue light survive in the presence of lethal antibiotic concentrations, while those kept in the dark do not. To optimize resistance induction, we vary promoter, ribosome binding site, and enzyme variant strength using chromosome and plasmid-based constructs. We then link inducible resistance to expression of a heterologous fatty acid enzyme to increase production of octanoic acid. These optogenetic resistance tools pave the way for spatiotemporal control of cell survival.
Collapse
Affiliation(s)
- Michael B Sheets
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Nathan Tague
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Biological Design Center, Boston University, Boston, MA, 02215, USA.
| |
Collapse
|
19
|
The Crosstalk between Microbiome and Mitochondrial Homeostasis in Neurodegeneration. Cells 2023; 12:cells12030429. [PMID: 36766772 PMCID: PMC9913973 DOI: 10.3390/cells12030429] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Mitochondria are highly dynamic organelles that serve as the primary cellular energy-generating system. Apart from ATP production, they are essential for many biological processes, including calcium homeostasis, lipid biogenesis, ROS regulation and programmed cell death, which collectively render them invaluable for neuronal integrity and function. Emerging evidence indicates that mitochondrial dysfunction and altered mitochondrial dynamics are crucial hallmarks of a wide variety of neurodevelopmental and neurodegenerative conditions. At the same time, the gut microbiome has been implicated in the pathogenesis of several neurodegenerative disorders due to the bidirectional communication between the gut and the central nervous system, known as the gut-brain axis. Here we summarize new insights into the complex interplay between mitochondria, gut microbiota and neurodegeneration, and we refer to animal models that could elucidate the underlying mechanisms, as well as novel interventions to tackle age-related neurodegenerative conditions, based on this intricate network.
Collapse
|
20
|
Abstract
Chemical biosensors are an increasingly ubiquitous part of our lives. Beyond enzyme-coupled assays, recent synthetic biology advances now allow us to hijack more complex biosensing systems to respond to difficult to detect analytes, such as chemical small molecules. Here, we briefly overview recent advances in the biosensing of small molecules, including nucleic acid aptamers, allosteric transcription factors, and two-component systems. We then look more closely at a recently developed chemical sensing system, G protein-coupled receptor (GPCR)-based sensors. Finally, we consider the chemical sensing capabilities of the largest GPCR subfamily, olfactory receptors (ORs). We examine ORs' role in nature, their potential as a biomedical target, and their ability to detect compounds not amenable for detection using other biological scaffolds. We conclude by evaluating the current challenges, opportunities, and future applications of GPCR- and OR-based sensors.
Collapse
Affiliation(s)
- Amisha Patel
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Pamela Peralta-Yahya
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States,School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States,E-mail:
| |
Collapse
|
21
|
Multamäki E, García de Fuentes A, Sieryi O, Bykov A, Gerken U, Ranzani A, Köhler J, Meglinski I, Möglich A, Takala H. Optogenetic Control of Bacterial Expression by Red Light. ACS Synth Biol 2022; 11:3354-3367. [PMID: 35998606 PMCID: PMC9594775 DOI: 10.1021/acssynbio.2c00259] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In optogenetics, as in nature, sensory photoreceptors serve to control cellular processes by light. Bacteriophytochrome (BphP) photoreceptors sense red and far-red light via a biliverdin chromophore and, in response, cycle between the spectroscopically, structurally, and functionally distinct Pr and Pfr states. BphPs commonly belong to two-component systems that control the phosphorylation of cognate response regulators and downstream gene expression through histidine kinase modules. We recently demonstrated that the paradigm BphP from Deinococcus radiodurans exclusively acts as a phosphatase but that its photosensory module can control the histidine kinase activity of homologous receptors. Here, we apply this insight to reprogram two widely used setups for bacterial gene expression from blue-light to red-light control. The resultant pREDusk and pREDawn systems allow gene expression to be regulated down and up, respectively, uniformly under red light by 100-fold or more. Both setups are realized as portable, single plasmids that encode all necessary components including the biliverdin-producing machinery. The triggering by red light affords high spatial resolution down to the single-cell level. As pREDusk and pREDawn respond sensitively to red light, they support multiplexing with optogenetic systems sensitive to other light colors. Owing to the superior tissue penetration of red light, the pREDawn system can be triggered at therapeutically safe light intensities through material layers, replicating the optical properties of the skin and skull. Given these advantages, pREDusk and pREDawn enable red-light-regulated expression for diverse use cases in bacteria.
Collapse
Affiliation(s)
- Elina Multamäki
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland
| | | | - Oleksii Sieryi
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Alexander Bykov
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Uwe Gerken
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | | | - Jürgen Köhler
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | - Igor Meglinski
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland,College
of Engineering and Physical Sciences, Aston
University, Birmingham B4 7ET, U.K.
| | - Andreas Möglich
- Lehrstuhl
für Biochemie, Photobiochemie, Universität
Bayreuth, Bayreuth 95447, Germany,. Phone: +49 921 55
7835
| | - Heikki Takala
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland,Department
of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla 40014, Finland,. Phone: +358 46 923 6211
| |
Collapse
|
22
|
Ranzani AT, Wehrmann M, Kaiser J, Juraschitz M, Weber AM, Pietruschka G, Gerken U, Mayer G, Möglich A. Light-Dependent Control of Bacterial Expression at the mRNA Level. ACS Synth Biol 2022; 11:3482-3492. [PMID: 36129831 DOI: 10.1021/acssynbio.2c00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sensory photoreceptors mediate numerous light-dependent adaptations across organisms. In optogenetics, photoreceptors achieve the reversible, non-invasive, and spatiotemporally precise control by light of gene expression and other cellular processes. The light-oxygen-voltage receptor PAL binds to small RNA aptamers with sequence specificity upon blue-light illumination. By embedding the responsive aptamer in the ribosome-binding sequence of genes of interest, their expression can be downregulated by light. We developed the pCrepusculo and pAurora optogenetic systems that are based on PAL and allow to down- and upregulate, respectively, bacterial gene expression using blue light. Both systems are realized as compact, single plasmids that exhibit stringent blue-light responses with low basal activity and up to several 10-fold dynamic range. As PAL exerts light-dependent control at the RNA level, it can be combined with other optogenetic circuits that control transcription initiation. By integrating regulatory mechanisms operating at the DNA and mRNA levels, optogenetic circuits with emergent properties can thus be devised. As a case in point, the pEnumbra setup permits to upregulate gene expression under moderate blue light whereas strong blue light shuts off expression again. Beyond providing novel signal-responsive expression systems for diverse applications in biotechnology and synthetic biology, our work also illustrates how the light-dependent PAL-aptamer interaction can be harnessed for the control and interrogation of RNA-based processes.
Collapse
Affiliation(s)
- Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Markus Wehrmann
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Jennifer Kaiser
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Marc Juraschitz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Anna M Weber
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany
| | - Georg Pietruschka
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany
| | - Uwe Gerken
- Lehrstuhl für Spektroskopie weicher Materie, University of Bayreuth, 95447 Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany.,Center of Aptamer Research & Development, University of Bonn, 53121 Bonn, Germany
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.,Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447 Bayreuth, Germany.,North-Bavarian NMR Center, Universität Bayreuth, 95447 Bayreuth, Germany
| |
Collapse
|
23
|
Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
Collapse
Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
| |
Collapse
|
24
|
Robinson CM, Short NE, Riglar DT. Achieving spatially precise diagnosis and therapy in the mammalian gut using synthetic microbial gene circuits. Front Bioeng Biotechnol 2022; 10:959441. [PMID: 36118573 PMCID: PMC9478464 DOI: 10.3389/fbioe.2022.959441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian gut and its microbiome form a temporally dynamic and spatially heterogeneous environment. The inaccessibility of the gut and the spatially restricted nature of many gut diseases translate into difficulties in diagnosis and therapy for which novel tools are needed. Engineered bacterial whole-cell biosensors and therapeutics have shown early promise at addressing these challenges. Natural and engineered sensing systems can be repurposed in synthetic genetic circuits to detect spatially specific biomarkers during health and disease. Heat, light, and magnetic signals can also activate gene circuit function with externally directed spatial precision. The resulting engineered bacteria can report on conditions in situ within the complex gut environment or produce biotherapeutics that specifically target host or microbiome activity. Here, we review the current approaches to engineering spatial precision for in vivo bacterial diagnostics and therapeutics using synthetic circuits, and the challenges and opportunities this technology presents.
Collapse
Affiliation(s)
| | | | - David T. Riglar
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| |
Collapse
|
25
|
Bencurova E, Shityakov S, Schaack D, Kaltdorf M, Sarukhanyan E, Hilgarth A, Rath C, Montenegro S, Roth G, Lopez D, Dandekar T. Nanocellulose Composites as Smart Devices With Chassis, Light-Directed DNA Storage, Engineered Electronic Properties, and Chip Integration. Front Bioeng Biotechnol 2022; 10:869111. [PMID: 36105598 PMCID: PMC9465592 DOI: 10.3389/fbioe.2022.869111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of green and sustainable materials opens up new possibilities in the field of applied research. Such materials include nanocellulose composites that can integrate many components into composites and provide a good chassis for smart devices. In our study, we evaluate four approaches for turning a nanocellulose composite into an information storage or processing device: 1) nanocellulose can be a suitable carrier material and protect information stored in DNA. 2) Nucleotide-processing enzymes (polymerase and exonuclease) can be controlled by light after fusing them with light-gating domains; nucleotide substrate specificity can be changed by mutation or pH change (read-in and read-out of the information). 3) Semiconductors and electronic capabilities can be achieved: we show that nanocellulose is rendered electronic by iodine treatment replacing silicon including microstructures. Nanocellulose semiconductor properties are measured, and the resulting potential including single-electron transistors (SET) and their properties are modeled. Electric current can also be transported by DNA through G-quadruplex DNA molecules; these as well as classical silicon semiconductors can easily be integrated into the nanocellulose composite. 4) To elaborate upon miniaturization and integration for a smart nanocellulose chip device, we demonstrate pH-sensitive dyes in nanocellulose, nanopore creation, and kinase micropatterning on bacterial membranes as well as digital PCR micro-wells. Future application potential includes nano-3D printing and fast molecular processors (e.g., SETs) integrated with DNA storage and conventional electronics. This would also lead to environment-friendly nanocellulose chips for information processing as well as smart nanocellulose composites for biomedical applications and nano-factories.
Collapse
Affiliation(s)
- Elena Bencurova
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russia
| | - Dominik Schaack
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Kaltdorf
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Edita Sarukhanyan
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alexander Hilgarth
- Aerospace Information Technology, University of Würzburg, Würzburg, Germany
| | - Christin Rath
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
| | - Sergio Montenegro
- Aerospace Information Technology, University of Würzburg, Würzburg, Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
- BioCopy GmbH, Emmendingen, Germany
| | - Daniel Lopez
- Centro Nacional de Biotecnologia CNB, Universidad Autonoma de Madrid, Madrid, Spain
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- *Correspondence: Thomas Dandekar,
| |
Collapse
|
26
|
The microbiota-gut-brain axis in sleep disorders. Sleep Med Rev 2022; 65:101691. [DOI: 10.1016/j.smrv.2022.101691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/04/2022] [Accepted: 08/19/2022] [Indexed: 12/25/2022]
|
27
|
Han C, Zhang X, Pang G, Zhang Y, Pan H, Li L, Cui M, Liu B, Kang R, Xue X, Sun T, Liu J, Chang J, Zhao P, Wang H. Hydrogel microcapsules containing engineered bacteria for sustained production and release of protein drugs. Biomaterials 2022; 287:121619. [PMID: 35700622 DOI: 10.1016/j.biomaterials.2022.121619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 12/18/2022]
Abstract
Subcutaneous administration of sustained-release formulations is a common strategy for protein drugs, which avoids first pass effect and has high bioavailability. However, conventional sustained-release strategies can only load a limited amount of drug, leading to insufficient durability. Herein, we developed microcapsules based on engineered bacteria for sustained release of protein drugs. Engineered bacteria were carried in microcapsules for subcutaneous administration, with a production-lysis circuit for sustained protein production and release. Administrated in diabetic rats, engineered bacteria microcapsules was observed to smoothly release Exendin-4 for 2 weeks and reduce blood glucose. In another example, by releasing subunit vaccines with bacterial microcomponents as vehicles, engineered bacterial microcapsules activated specific immunity in mice and achieved tumor prevention. The engineered bacteria microcapsules have potential to durably release protein drugs and show versatility on the size of drugs. It might be a promising design strategy for long-acting in situ drug factory.
Collapse
Affiliation(s)
- Chunli Han
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Xinyu Zhang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Gaoju Pang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Yingying Zhang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Huizhuo Pan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Lianyue Li
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Meihui Cui
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Baona Liu
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Ruru Kang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Xin Xue
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Tao Sun
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, China; Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Jing Liu
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Jin Chang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Peiqi Zhao
- Department of Lymphoma, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, China.
| | - Hanjie Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China; Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China.
| |
Collapse
|
28
|
Chen B, Cui M, Wang Y, Shi P, Wang H, Wang F. Recent advances in cellular optogenetics for photomedicine. Adv Drug Deliv Rev 2022; 188:114457. [PMID: 35843507 DOI: 10.1016/j.addr.2022.114457] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/13/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
Since the successful introduction of exogenous photosensitive proteins, channelrhodopsin, to neurons, optogenetics has enabled substantial understanding of profound brain function by selectively manipulating neural circuits. In an optogenetic system, optical stimulation can be precisely delivered to brain tissue to achieve regulation of cellular electrical activity with unprecedented spatio-temporal resolution in living organisms. In recent years, the development of various optical actuators and novel light-delivery techniques has greatly expanded the scope of optogenetics, enabling the control of other signal pathways in non-neuronal cells for different biomedical applications, such as phototherapy and immunotherapy. This review focuses on the recent advances in optogenetic regulation of cellular activities for photomedicine. We discuss emerging optogenetic tools and light-delivery platforms, along with a survey of optogenetic execution in mammalian and microbial cells.
Collapse
Affiliation(s)
- Bing Chen
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Meihui Cui
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yuan Wang
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Peng Shi
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
| | - Hanjie Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China.
| | - Feng Wang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.
| |
Collapse
|
29
|
Mazraeh D, Di Ventura B. Synthetic microbiology applications powered by light. Curr Opin Microbiol 2022; 68:102158. [PMID: 35660240 DOI: 10.1016/j.mib.2022.102158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
Synthetic biology is a field of research in which molecular parts (mostly nucleic acids and proteins) are de novo created or modified and then used either alone or in combination to achieve new functions that can help solve the problems of our modern society. In synthetic microbiology, microbes are employed rather than other organisms or cell-free systems. Optogenetics, a relatively recently established technology that relies on the use of genetically encoded photosensitive proteins to control biological processes with high spatiotemporal precision, offers the possibility to empower synthetic (micro)biology applications due to the many positive features that light has as an external trigger. In this review, we describe recent synthetic microbiology applications that made use of optogenetics after briefly introducing the molecular mechanism behind some of the most employed optogenetic tools. We highlight the power and versatility of this technique, which opens up new horizons for both research and industry.
Collapse
Affiliation(s)
- Daniel Mazraeh
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
30
|
Li S, Xu X, Lv X, Liu Y, Li J, Du G, Liu L. Combinatorial Metabolic Engineering and Enzymatic Catalysis Enable Efficient Production of Colanic Acid. Microorganisms 2022; 10:877. [PMID: 35630322 PMCID: PMC9143390 DOI: 10.3390/microorganisms10050877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Abstract
Colanic acid can promote the lifespan of humans by regulating mitochondrial homeostasis, and it has widespread applications in the field of health. However, colanic acid is produced at a low temperature (20 °C) with low titer. Using Escherichia coli K-12 MG1655, we constructed the SRP-4 strain with high colanic acid production at 30 °C by enhancing the precursor supply and relieving the regulation of transcription for colanic acid synthesis genes by the RCS system. After media optimization, the colanic acid titer increased by 579.9-fold and reached 12.2 g/L. Subsequently, we successfully purified the colanic acid hydrolase and reduced the molecular weight of colanic acid (106.854 kDa), thereby eliminating the inhibition of high-molecular-weight colanic acid on strain growth. Finally, after adding the colanic acid hydrolase (4000 U/L), the colanic acid with low molecular weight reached 24.99 g/L in 3-L bioreactor, the highest titer reported so far. This high-producing strain of colanic acid will promote the application of low-molecular-weight colanic acid in the field of health.
Collapse
Affiliation(s)
- Suwei Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (S.L.); (X.X.); (X.L.); (Y.L.); (J.L.); (G.D.)
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xianhao Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (S.L.); (X.X.); (X.L.); (Y.L.); (J.L.); (G.D.)
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (S.L.); (X.X.); (X.L.); (Y.L.); (J.L.); (G.D.)
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (S.L.); (X.X.); (X.L.); (Y.L.); (J.L.); (G.D.)
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (S.L.); (X.X.); (X.L.); (Y.L.); (J.L.); (G.D.)
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (S.L.); (X.X.); (X.L.); (Y.L.); (J.L.); (G.D.)
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (S.L.); (X.X.); (X.L.); (Y.L.); (J.L.); (G.D.)
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
31
|
Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
|
32
|
Abedi MH, Yao MS, Mittelstein DR, Bar-Zion A, Swift MB, Lee-Gosselin A, Barturen-Larrea P, Buss MT, Shapiro MG. Ultrasound-controllable engineered bacteria for cancer immunotherapy. Nat Commun 2022; 13:1585. [PMID: 35332124 PMCID: PMC8948203 DOI: 10.1038/s41467-022-29065-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 02/16/2022] [Indexed: 12/25/2022] Open
Abstract
Rapid advances in synthetic biology are driving the development of genetically engineered microbes as therapeutic agents for a multitude of human diseases, including cancer. The immunosuppressive microenvironment of solid tumors, in particular, creates a favorable niche for systemically administered bacteria to engraft and release therapeutic payloads. However, such payloads can be harmful if released outside the tumor in healthy tissues where the bacteria also engraft in smaller numbers. To address this limitation, we engineer therapeutic bacteria to be controlled by focused ultrasound, a form of energy that can be applied noninvasively to specific anatomical sites such as solid tumors. This control is provided by a temperature-actuated genetic state switch that produces lasting therapeutic output in response to briefly applied focused ultrasound hyperthermia. Using a combination of rational design and high-throughput screening we optimize the switching circuits of engineered cells and connect their activity to the release of immune checkpoint inhibitors. In a clinically relevant cancer model, ultrasound-activated therapeutic microbes successfully turn on in situ and induce a marked suppression of tumor growth. This technology provides a critical tool for the spatiotemporal targeting of potent bacterial therapeutics in a variety of biological and clinical scenarios.
Collapse
Affiliation(s)
- Mohamad H Abedi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Michael S Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - David R Mittelstein
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Avinoam Bar-Zion
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Margaret B Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Pierina Barturen-Larrea
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Marjorie T Buss
- 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.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
| |
Collapse
|
33
|
Hoffman SM, Tang AY, Avalos JL. Optogenetics Illuminates Applications in Microbial Engineering. Annu Rev Chem Biomol Eng 2022; 13:373-403. [PMID: 35320696 DOI: 10.1146/annurev-chembioeng-092120-092340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe-host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Finally, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Shannon M Hoffman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - Allison Y Tang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , , .,The Andlinger Center for Energy and the Environment, Department of Molecular Biology, and High Meadows Environmental Institute, Princeton University, Princeton, New Jersey, USA
| |
Collapse
|
34
|
Ronda C, Wang HH. Engineering temporal dynamics in microbial communities. Curr Opin Microbiol 2022; 65:47-55. [PMID: 34739926 PMCID: PMC10659046 DOI: 10.1016/j.mib.2021.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/05/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022]
Abstract
Microbial communities are a key part to tackling global challenges in human health, environmental conservation, and sustainable agriculture in the coming decade. Recent advances in synthetic biology to study and modify microbial communities have led to important insights into their physiology and ecology. Understanding how targeted changes to microbial communities result in reproducible alterations of the community's intrinsic fluctuations and function is important for mechanistic reconstruction of microbiomes. Studies of synthetic microbial consortia and comparative analysis of communities in normal and disrupted states have revealed ecological principles that can be leveraged to engineer communities towards desired functions. Tools enabling temporal modulation and sensing of the community dynamics offer precise spatiotemporal control of functions, help to dissect microbial interaction networks, and improve predictions of population temporal dynamics. Here we discuss recent advances to manipulate microbiome dynamics through control of specific strain engraftment and abundance, modulation of cell-cell signaling for tuning population dynamics, infiltration of new functions in the existing community with in situ engineering, and in silico modeling of microbial consortia to predict community function and ecology.
Collapse
Affiliation(s)
- Carlotta Ronda
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
| |
Collapse
|
35
|
Hernandez CM, Hernandez AR, Hoffman JM, King PH, McMahon LL, Buford TW, Carter C, Bizon JL, Burke SN. A Neuroscience Primer for Integrating Geroscience With the Neurobiology of Aging. J Gerontol A Biol Sci Med Sci 2022; 77:e19-e33. [PMID: 34623396 PMCID: PMC8751809 DOI: 10.1093/gerona/glab301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Indexed: 11/13/2022] Open
Abstract
Neuroscience has a rich history of studies focusing on neurobiology of aging. However, much of the aging studies in neuroscience occur outside of the gerosciences. The goal of this primer is 2-fold: first, to briefly highlight some of the history of aging neurobiology and second, to introduce to geroscientists the broad spectrum of methodological approaches neuroscientists use to study the neurobiology of aging. This primer is accompanied by a corresponding geroscience primer, as well as a perspective on the current challenges and triumphs of the current divide across these 2 fields. This series of manuscripts is intended to foster enhanced collaborations between neuroscientists and geroscientists with the intent of strengthening the field of cognitive aging through inclusion of parameters from both areas of expertise.
Collapse
Affiliation(s)
- Caesar M Hernandez
- Department of Cellular, Development, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Evelyn F. McKnight Brain Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Abigail R Hernandez
- Evelyn F. McKnight Brain Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Medicine, Division of Gerontology, Geriatrics, and Palliative Care, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jessica M Hoffman
- Department of Medicine, Division of Gerontology, Geriatrics, and Palliative Care, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Peter H King
- Department of Cellular, Development, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, USA
| | - Lori L McMahon
- Department of Cellular, Development, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Evelyn F. McKnight Brain Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,UAB Nathan Shock Center for the Basic Biology of Aging, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,UAB Integrative Center for Aging Research, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Thomas W Buford
- Evelyn F. McKnight Brain Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Medicine, Division of Gerontology, Geriatrics, and Palliative Care, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,UAB Nathan Shock Center for the Basic Biology of Aging, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,UAB Integrative Center for Aging Research, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Geriatric Research Education and Clinical Center, Birmingham VA Medical Center, Birmingham, Alabama, USA
| | - Christy Carter
- Evelyn F. McKnight Brain Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Medicine, Division of Gerontology, Geriatrics, and Palliative Care, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jennifer L Bizon
- Department of Neuroscience, Center for Cognitive Aging and Memory, and the McKnight Brain Institute, The University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Sara N Burke
- Department of Neuroscience, Center for Cognitive Aging and Memory, and the McKnight Brain Institute, The University of Florida, College of Medicine, Gainesville, Florida, USA
| |
Collapse
|
36
|
Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
Collapse
Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
| |
Collapse
|
37
|
Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
Collapse
Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| |
Collapse
|
38
|
Lindner F, Diepold A. Optogenetics in bacteria - applications and opportunities. FEMS Microbiol Rev 2021; 46:6427354. [PMID: 34791201 PMCID: PMC8892541 DOI: 10.1093/femsre/fuab055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Optogenetics holds the promise of controlling biological processes with superb temporal and spatial resolution at minimal perturbation. Although many of the light-reactive proteins used in optogenetic systems are derived from prokaryotes, applications were largely limited to eukaryotes for a long time. In recent years, however, an increasing number of microbiologists use optogenetics as a powerful new tool to study and control key aspects of bacterial biology in a fast and often reversible manner. After a brief discussion of optogenetic principles, this review provides an overview of the rapidly growing number of optogenetic applications in bacteria, with a particular focus on studies venturing beyond transcriptional control. To guide future experiments, we highlight helpful tools, provide considerations for successful application of optogenetics in bacterial systems, and identify particular opportunities and challenges that arise when applying these approaches in bacteria.
Collapse
Affiliation(s)
- Florian Lindner
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.,SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
| |
Collapse
|
39
|
A collective analysis of lifespan-extending compounds in diverse model organisms, and of species whose lifespan can be extended the most by the application of compounds. Biogerontology 2021; 22:639-653. [PMID: 34687363 DOI: 10.1007/s10522-021-09941-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/17/2021] [Indexed: 12/13/2022]
Abstract
Research on aging and lifespan-extending compounds has been carried out using diverse model organisms, including yeast, worms, flies and mice. Many studies reported the identification of novel lifespan-extending compounds in different species, some of which may have the potential to translate to the clinic. However, studies collectively and comparatively analyzing all the data available in these studies are highly limited. Here, by using data from the DrugAge database, we first identified top compounds in terms of their effects on percent change in average lifespan of diverse organisms, collectively (n = 1728). We found that, when data from all organisms studied were combined for each compound, aspirin resulted in the highest percent increase in average lifespan (52.01%), followed by minocycline (27.30%), N-acetyl cysteine (17.93%), nordihydroguaiaretic acid (17.65%) and rapamycin (15.66%), in average. We showed that minocycline led to the highest percent increase in average lifespan among other compounds, in both Drosophila melanogaster (28.09%) and Caenorhabditis elegans (26.67%), followed by curcumin (11.29%) and gluconic acid (5.51%) for D. melanogaster and by metformin (26.56%), resveratrol (15.82%) and quercetin (9.58%) for C. elegans. Moreover, we found that top 5 species whose lifespan can be extended the most by compounds with lifespan-extending properties are Philodina acuticornis, Acheta domesticus, Aeolosoma viride, Mytilina brevispina and Saccharomyces cerevisiae (211.80%, 76%, 70.26%, 55.18% and 45.71% in average, respectively). This study provides novel insights on lifespan extension in model organisms, and highlights the importance of databases with high quality content curated by researchers from multiple resources, in aging research.
Collapse
|
40
|
Zhou Y, Hu G, Wang MC. Host and microbiota metabolic signals in aging and longevity. Nat Chem Biol 2021; 17:1027-1036. [PMID: 34552221 DOI: 10.1038/s41589-021-00837-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023]
Abstract
Aging is an inevitable biochemical process that adversely affects personal health and poses ever-increasing challenges to society. Recent research has revealed the crucial role of metabolism in regulating aging and longevity. During diverse metabolic processes, the host organism and their symbiotic partners-the microbiota-produce thousands of chemical products (metabolites). Emerging studies have uncovered specific metabolites that act as signaling molecules to actively regulate longevity. Here we review the latest progress in understanding the molecular mechanisms by which metabolites from the host and/or microbiota promote longevity. We also highlight state-of-the-art technologies for discovering, profiling and imaging aging- and longevity-regulating metabolites and for deciphering the molecular basis of their actions. The broad application of these technologies in aging research, together with future advances, will foster the systematic discovery of aging- and longevity-regulating metabolites and their signaling pathways. These metabolite signals should provide promising targets for developing new interventions to promote longevity and healthy aging.
Collapse
Affiliation(s)
- Yue Zhou
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Guo Hu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Graduate Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
41
|
Abstract
Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.
Collapse
|
42
|
Wang Z, Zhao Y, Jiang Y, Chu W. Prebiotic, Antioxidant, and Immunomodulatory Properties of Acidic Exopolysaccharide From Marine Rhodotorula RY1801. Front Nutr 2021; 8:710668. [PMID: 34497821 PMCID: PMC8419279 DOI: 10.3389/fnut.2021.710668] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/23/2021] [Indexed: 12/26/2022] Open
Abstract
In this study, an extracellular acidic polysaccharide (EAPS) from marine Rhodotorula sp. RY1801 was extracted, and its biological properties were investigated. EAPS is mainly composed of monosaccharides, including mannose, rhamnose, glucose, galactose, and fucose, had an average molecular weight of 5.902 × 107 Da. The results indicated that EAPS can promote the growth of Lactobacillus acidophilus and L. acidophilus plantarum. EAPS is capable of scavenging both superoxide anion and hydroxyl radicals in vitro. The highest scavenging rate of superoxide anion and hydroxyl radicals is 29 and 84%, respectively. Using in vivo model, we found that the EAPS can expand the lifespan and increase the disease resistance of Caenorhabditis elegans against Klebsiella pneumoniae infection via the DAF-2/DAF-16 pathway. These results suggested that EAPS from marine Rhodotorula sp. RY1801 could promote the growth of beneficial bacteria and can be used as an antioxidant and immunomodulator, which had considerable potential in the food and health industry.
Collapse
Affiliation(s)
- Zheng Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yanchen Zhao
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yan Jiang
- Animal, Plant and Food Inspection Center of Nanjing Customs, Nanjing, China
| | - Weihua Chu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
43
|
Backes C, Martinez-Martinez D, Cabreiro F. C. elegans: A biosensor for host-microbe interactions. Lab Anim (NY) 2021; 50:127-135. [PMID: 33649581 DOI: 10.1038/s41684-021-00724-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Microbes are an integral part of life on this planet. Microbes and their hosts influence each other in an endless dance that shapes how the meta-organism interacts with its environment. Although great advances have been made in microbiome research over the past 20 years, the mechanisms by which both hosts and their microbes interact with each other and the environment are still not well understood. The nematode Caenorhabditis elegans has been widely used as a model organism to study a remarkable number of human-like processes. Recent evidence shows that the worm is a powerful tool to investigate in fine detail the complexity that exists in microbe-host interactions. By combining the large array of genetic tools available for both organisms together with deep phenotyping approaches, it has been possible to uncover key effectors in the complex relationship between microbes and their hosts. In this perspective, we survey the literature for insightful discoveries in the microbiome field using the worm as a model. We discuss the latest conceptual and technological advances in the field and highlight the strengths that make C. elegans a valuable biosensor tool for the study of microbe-host interactions.
Collapse
Affiliation(s)
- Cassandra Backes
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | | | - Filipe Cabreiro
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
| |
Collapse
|
44
|
Wu J, Dellal D, Wasserman S. Prokaryote playhouse: A low-cost, laser-cut acrylic incubator for optogenetic bacterial culture. HARDWAREX 2021; 9:e00184. [PMID: 35492052 PMCID: PMC9041274 DOI: 10.1016/j.ohx.2021.e00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/03/2021] [Accepted: 02/21/2021] [Indexed: 06/14/2023]
Abstract
Bacterial photography is a printing technique that replaces conventional photochemistry with a living film of engineered Escherichia coli. Many biology teaching labs have adopted monochrome bacterial photography because it offers a captivating playground for illustrating central concepts and lab techniques in biological engineering, particularly in the fields of synthetic biology and optogenetics. Recent improvements have increased the number of color channels from one to three. A key practical challenge in three-color printing is to expose a Petri dish loaded with engineered bacteria to a trichromatic image while maintaining it at 37 °C. Prokaryote Playhouse is a compact, inexpensive, open-source, benchtop incubator for light-sensitive bacterial cultures that makes bacterial photography and similar bacterial optogenetic methods more accessible to teaching labs, makerspaces, and research labs. The system includes a laser-cut, light-tight enclosure; digital thermostat; heated sample shelf; single-board computer; and miniature projector. We built a fleet of Prokaryote Playhouses that students have used to produce hundreds of bacterial photographs in a wide range of educational experiences, ranging from a four-hour introduction to synthetic biology and wet lab techniques to a six-week exploratory class for first-year students at MIT.
Collapse
Affiliation(s)
- Jin Wu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of System Design and Management, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Dellal
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Steven Wasserman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|