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Hamrock FJ, Ryan D, Shaibah A, Ershova AS, Mogre A, Sulimani MM, Ben Taarit S, Reichardt S, Hokamp K, Westermann AJ, Kröger C. Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO. Nucleic Acids Res 2024:gkae668. [PMID: 39149883 DOI: 10.1093/nar/gkae668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies. Critical to adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. Forty sRNAs were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii. In-depth characterization uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including the transcript encoding outer membrane protein CarO. Aar initiates base-pairing with these mRNAs using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in multiple stress conditions suggesting a role in fine-tuning translation of the Aar-target molecules. Our study provides mechanistic insights into sRNA-mediated gene regulation in A. baumannii and represents a valuable resource for future RNA-centric research endeavours.
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Affiliation(s)
- Fergal J Hamrock
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Daniel Ryan
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
| | - Ali Shaibah
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Anna S Ershova
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aalap Mogre
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Maha M Sulimani
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Safa Ben Taarit
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Alexander J Westermann
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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Nevelchuk S, Brawek B, Schwarz N, Valiente-Gabioud A, Wuttke TV, Kovalchuk Y, Koch H, Höllig A, Steiner F, Figarella K, Griesbeck O, Garaschuk O. Morphotype-specific calcium signaling in human microglia. J Neuroinflammation 2024; 21:175. [PMID: 39020359 PMCID: PMC11256502 DOI: 10.1186/s12974-024-03169-6] [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: 05/25/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Key functions of Ca2+ signaling in rodent microglia include monitoring the brain state as well as the surrounding neuronal activity and sensing the danger or damage in their vicinity. Microglial Ca2+ dyshomeostasis is a disease hallmark in many mouse models of neurological disorders but the Ca2+ signal properties of human microglia remain unknown. METHODS We developed a novel genetically-encoded ratiometric Ca2+ indicator, targeting microglial cells in the freshly resected human tissue, organotypically cultured tissue slices and analyzed in situ ongoing Ca2+ signaling of decades-old microglia dwelling in their native microenvironment. RESULTS The data revealed marked compartmentalization of Ca2+ signals, with signal properties differing across the compartments and resident morphotypes. The basal Ca2+ levels were low in ramified and high in ameboid microglia. The fraction of cells with ongoing Ca2+ signaling, the fraction and the amplitude of process Ca2+ signals and the duration of somatic Ca2+ signals decreased when moving from ramified via hypertrophic to ameboid microglia. In contrast, the size of active compartments, the fraction and amplitude of somatic Ca2+ signals and the duration of process Ca2+ signals increased along this pathway.
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Affiliation(s)
- Sofia Nevelchuk
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany
| | - Bianca Brawek
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany
| | - Niklas Schwarz
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Ariel Valiente-Gabioud
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
| | - Thomas V Wuttke
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Neurosurgery, University of Tübingen, Tübingen, Germany
| | - Yury Kovalchuk
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany
| | - Henner Koch
- Department of Epileptology, Neurology, RWTH Aachen University Hospital, Aachen, Germany
| | - Anke Höllig
- Department of Neurosurgery, RWTH Aachen University, Aachen, Germany
| | - Frederik Steiner
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany
| | - Katherine Figarella
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany
- Department of Anesthesiology, Critical Care and Pain Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
| | - Olga Garaschuk
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany.
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3
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Chokshi K, Kavanagh K, Khan I, Slaveykova VI, Sieber S. Surface displayed MerR increases mercury accumulation by green microalga Chlamydomonas reinhardtii. ENVIRONMENT INTERNATIONAL 2024; 189:108813. [PMID: 38878502 DOI: 10.1016/j.envint.2024.108813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/22/2024] [Accepted: 06/10/2024] [Indexed: 06/19/2024]
Abstract
Mercury is a highly toxic trace metal that can accumulate in aquatic ecosystems and when resent at high concentrations can pose risks to both aquatic life and humans consuming contaminated fish. This research explores the use of the metalloregulatory protein MerR, known for its high affinity and selectivity toward mercury, in a novel application. Through a cell surface engineering approach, MerR was displayed on cells of green alga Chlamydomonas reinhardtii. A hydroxyproline-rich GP1 protein was used as an anchor to construct the engineered strains GP1-MerR that expresses the fluorescent protein mVenus. The surface engineered GP1-MerR strain led up to five folds higher Hg2+ accumulation compared to the WT strain at concentration range from 10-9 to 10-7 M Hg2+. The binding of Hg2+ via MerR was specific and did not get significantly affected by major freshwater water quality variables such as Ca2+ and dissolved organic matter. The presence of other trace metals (Zn2+, Cu2+, Ni2+, Pb2+, Cd2+) in a same concentration range even resulted in 30-40 % increase in the accumulated Hg. Further, the engineered cells also demonstrated the ability to accumulate Hg2+ from the water extracts of the Hg-contaminated sediment samples. These results demonstrate a novel approach utilizing the cell surface display system in C. reinhardtii for its potential application in bioremediation.
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Affiliation(s)
- Kaumeel Chokshi
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Killian Kavanagh
- Department F.A. Forel for Environmental and Aquatic Sciences, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Imran Khan
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Vera I Slaveykova
- Department F.A. Forel for Environmental and Aquatic Sciences, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland.
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4
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Isoda T, Takeda E, Hosokawa S, Hotta-Ren S, Ohsumi Y. Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast. iScience 2024; 27:109810. [PMID: 38832010 PMCID: PMC11145338 DOI: 10.1016/j.isci.2024.109810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 04/22/2024] [Indexed: 06/05/2024] Open
Abstract
The mechanisms governing autophagy of proteins and organelles have been well studied, but how other cytoplasmic components such as RNA and polysaccharides are degraded remains largely unknown. In this study, we examine autophagy of glycogen, a storage form of glucose. We find that cells accumulate glycogen in the cytoplasm during nitrogen starvation and that this carbohydrate is rarely observed within autophagosomes and autophagic bodies. However, sequestration of glycogen by autophagy is observed following prolonged nitrogen starvation. We identify a yet-uncharacterized open reading frame, Yil024c (herein Atg45), as encoding a cytosolic receptor protein that mediates autophagy of glycogen (glycophagy). Furthermore, we show that, during sporulation, Atg45 is highly expressed and is associated with an increase in glycophagy. Our results suggest that cells regulate glycophagic activity by controlling the expression level of Atg45.
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Affiliation(s)
- Takahiro Isoda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Frontier Research Center, POLA Chemical Industries, Inc, Yokohama 244-0812, Japan
| | - Eigo Takeda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Sachiko Hosokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Shukun Hotta-Ren
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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5
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Bozidis P, Markou E, Gouni A, Gartzonika K. Does Phage Therapy Need a Pan-Phage? Pathogens 2024; 13:522. [PMID: 38921819 PMCID: PMC11206709 DOI: 10.3390/pathogens13060522] [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: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
The emergence of multidrug-resistant bacteria is undoubtedly one of the most serious global health threats. One response to this threat that has been gaining momentum over the past decade is 'phage therapy'. According to this, lytic bacteriophages are used for the treatment of bacterial infections, either alone or in combination with antimicrobial agents. However, to ensure the efficacy and broad applicability of phage therapy, several challenges must be overcome. These challenges encompass the development of methods and strategies for the host range manipulation and bypass of the resistance mechanisms developed by pathogenic bacteria, as has been the case since the advent of antibiotics. As our knowledge and understanding of the interactions between phages and their hosts evolves, the key issue is to define the host range for each application. In this article, we discuss the factors that affect host range and how this determines the classification of phages into different categories of action. For each host range group, recent representative examples are provided, together with suggestions on how the different groups can be used to combat certain types of bacterial infections. The available methodologies for host range expansion, either through sequential adaptation to a new pathogen or through genetic engineering techniques, are also reviewed.
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Affiliation(s)
- Petros Bozidis
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Eleftheria Markou
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Athanasia Gouni
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Konstantina Gartzonika
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
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Pšeničnik A, Slemc L, Avbelj M, Tome M, Šala M, Herron P, Shmatkov M, Petek M, Baebler Š, Mrak P, Hranueli D, Starčević A, Hunter IS, Petković H. Oxytetracycline hyper-production through targeted genome reduction of Streptomyces rimosus. mSystems 2024; 9:e0025024. [PMID: 38564716 PMCID: PMC11097637 DOI: 10.1128/msystems.00250-24] [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: 02/20/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Most biosynthetic gene clusters (BGC) encoding the synthesis of important microbial secondary metabolites, such as antibiotics, are either silent or poorly expressed; therefore, to ensure a strong pipeline of novel antibiotics, there is a need to develop rapid and efficient strain development approaches. This study uses comparative genome analysis to instruct rational strain improvement, using Streptomyces rimosus, the producer of the important antibiotic oxytetracycline (OTC) as a model system. Sequencing of the genomes of two industrial strains M4018 and R6-500, developed independently from a common ancestor, identified large DNA rearrangements located at the chromosome end. We evaluated the effect of these genome deletions on the parental S. rimosus Type Strain (ATCC 10970) genome where introduction of a 145 kb deletion close to the OTC BGC in the Type Strain resulted in massive OTC overproduction, achieving titers that were equivalent to M4018 and R6-500. Transcriptome data supported the hypothesis that the reason for such an increase in OTC biosynthesis was due to enhanced transcription of the OTC BGC and not due to enhanced substrate supply. We also observed changes in the expression of other cryptic BGCs; some metabolites, undetectable in ATCC 10970, were now produced at high titers. This study demonstrated for the first time that the main force behind BGC overexpression is genome rearrangement. This new approach demonstrates great potential to activate cryptic gene clusters of yet unexplored natural products of medical and industrial value.IMPORTANCEThere is a critical need to develop novel antibiotics to combat antimicrobial resistance. Streptomyces species are very rich source of antibiotics, typically encoding 20-60 biosynthetic gene clusters (BGCs). However, under laboratory conditions, most are either silent or poorly expressed so that their products are only detectable at nanogram quantities, which hampers drug development efforts. To address this subject, we used comparative genome analysis of industrial Streptomyces rimosus strains producing high titers of a broad spectrum antibiotic oxytetracycline (OTC), developed during decades of industrial strain improvement. Interestingly, large-scale chromosomal deletions were observed. Based on this information, we carried out targeted genome deletions in the native strain S. rimosus ATCC 10970, and we show that a targeted deletion in the vicinity of the OTC BGC significantly induced expression of the OTC BGC, as well as some other silent BGCs, thus suggesting that this approach may be a useful way to identify new natural products.
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Affiliation(s)
- Alen Pšeničnik
- Chair of Biotechnology, Microbiology and Food Safety, University of Ljubljana Biotechnical Faculty, Ljubljana, Slovenia
| | - Lucija Slemc
- Chair of Biotechnology, Microbiology and Food Safety, University of Ljubljana Biotechnical Faculty, Ljubljana, Slovenia
| | - Martina Avbelj
- Chair of Biotechnology, Microbiology and Food Safety, University of Ljubljana Biotechnical Faculty, Ljubljana, Slovenia
| | - Miha Tome
- Chair of Biotechnology, Microbiology and Food Safety, University of Ljubljana Biotechnical Faculty, Ljubljana, Slovenia
| | - Martin Šala
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Paul Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Maksym Shmatkov
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
- Educational and Scientific Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Peter Mrak
- Antiinfectives, Sandoz, Mengeš, Slovenia
| | - Daslav Hranueli
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Antonio Starčević
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Iain S. Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Hrvoje Petković
- Chair of Biotechnology, Microbiology and Food Safety, University of Ljubljana Biotechnical Faculty, Ljubljana, Slovenia
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Kajiwara T, Miyazaki M, Yamaoka S, Yoshitake Y, Yasui Y, Nishihama R, Kohchi T. Transcription of the Antisense Long Non-Coding RNA, SUPPRESSOR OF FEMINIZATION, Represses Expression of the Female-Promoting Gene FEMALE GAMETOPHYTE MYB in the Liverwort Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2024; 65:338-349. [PMID: 38174428 PMCID: PMC11020262 DOI: 10.1093/pcp/pcad170] [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: 10/08/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/05/2024]
Abstract
Sexual differentiation is a fundamental process in the life cycles of land plants, ensuring successful sexual reproduction and thereby contributing to species diversity and survival. In the dioicous liverwort Marchantia polymorpha, this process is governed by an autosomal sex-differentiation locus comprising FEMALE GAMETOPHYTE MYB (FGMYB), a female-promoting gene, and SUPPRESSOR OF FEMINIZATION (SUF), an antisense strand-encoded long non-coding RNA (lncRNA). SUF is specifically transcribed in male plants and suppresses the expression of FGMYB, leading to male differentiation. However, the molecular mechanisms underlying this process remain elusive. Here, we show that SUF acts through its transcription to suppress FGMYB expression. Transgene complementation analysis using CRISPR/Cas9D10A-based large-deletion mutants identified a genomic region sufficient for the sex differentiation switch function in the FGMYB-SUF locus. Inserting a transcriptional terminator sequence into the SUF-transcribed region resulted in the loss of SUF function and allowed expression of FGMYB in genetically male plants, leading to conversion of the sex phenotype from male to female. Partial deletions of SUF had no obvious impact on its function. Replacement of the FGMYB sequence with that of an unrelated gene did not affect the ability of SUF transcription to suppress sense-strand expression. Taken together, our findings suggest that the process of SUF transcription, rather than the resulting transcripts, is required for controlling sex differentiation in M. polymorpha.
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Affiliation(s)
- Tomoaki Kajiwara
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Motoki Miyazaki
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yoshihiro Yoshitake
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yukiko Yasui
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
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Szczepańska A, Olek K, Kołodziejska K, Yu J, Ibrahim AT, Adamkiewicz L, Schroeder FC, Pokrzywa W, Turek M. Pheromone-based communication influences the production of somatic extracellular vesicles in C. elegans. Nat Commun 2024; 15:2715. [PMID: 38548742 PMCID: PMC10978837 DOI: 10.1038/s41467-024-47016-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Extracellular vesicles (EVs) are integral to numerous biological processes, yet it is unclear how environmental factors or interactions among individuals within a population affect EV-regulated systems. In Caenorhabditis elegans, the evolutionarily conserved large EVs, known as exophers, are part of a maternal somatic tissue resource management system. Consequently, the offspring of individuals exhibiting active exopher biogenesis (exophergenesis) develop faster. Our research focuses on unraveling the complex inter-tissue and social dynamics that govern exophergenesis. We found that ascr#10, the primary male pheromone, enhances exopher production in hermaphrodites, mediated by the G-protein-coupled receptor STR-173 in ASK sensory neurons. In contrast, pheromone produced by other hermaphrodites, ascr#3, diminishes exophergenesis within the population. This process is regulated via the neuropeptides FLP-8 and FLP-21, which originate from the URX and AQR/PQR/URX neurons, respectively. Our results reveal a regulatory network that controls the production of somatic EV by the nervous system in response to social signals.
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Affiliation(s)
- Agata Szczepańska
- Laboratory of Animal Molecular Physiology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Olek
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Klaudia Kołodziejska
- Laboratory of Animal Molecular Physiology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jingfang Yu
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Abdulrahman Tudu Ibrahim
- Laboratory of Animal Molecular Physiology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Laura Adamkiewicz
- Laboratory of Animal Molecular Physiology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
| | - Michał Turek
- Laboratory of Animal Molecular Physiology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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9
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Karbelkar AA, Font M, Smith TJ, Sondermann H, O’Toole GA. Reconstitution of a biofilm adhesin system from a sulfate-reducing bacterium in Pseudomonas fluorescens. Proc Natl Acad Sci U S A 2024; 121:e2320410121. [PMID: 38498718 PMCID: PMC10990149 DOI: 10.1073/pnas.2320410121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Biofilms of sulfate-reducing bacterium (SRB) like Desulfovibrio vulgaris Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses. Although the mechanisms of biofilm formation by DvH are not yet well understood, recent studies indicate the large adhesin, DvhA, is a key determinant of biofilm formation. The dvhA gene neighborhood resembles the biofilm-regulating Lap system of Pseudomonas fluorescens but is curiously missing the c-di-GMP-binding regulator LapD. Instead, DvH encodes an evolutionarily unrelated c-di-GMP-binding protein (DVU1020) that we hypothesized is functionally analogous to LapD. To study this unusual Lap system and overcome experimental limitations with the slow-growing anaerobe DvH, we reconstituted its predicted SRB Lap system in a P. fluorescens strain lacking its native Lap regulatory components (ΔlapGΔlapD). Our data support the model that DvhA is a cell surface-associated LapA-like adhesin with a N-terminal "retention module" and that DvhA is released from the cell surface upon cleavage by the LapG-like protease DvhG. Further, we demonstrate DVU1020 (named here DvhD) represents a distinct class of c-di-GMP-binding, biofilm-regulating proteins that regulates DvhG activity in response to intracellular levels of this second messenger. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.
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Affiliation(s)
- Amruta A. Karbelkar
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
| | - Maria Font
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, D-22607Hamburg, Germany
| | - T. Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, D-22607Hamburg, Germany
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
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10
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Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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11
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Levrier A, Karpathakis I, Nash B, Bowden SD, Lindner AB, Noireaux V. PHEIGES: all-cell-free phage synthesis and selection from engineered genomes. Nat Commun 2024; 15:2223. [PMID: 38472230 PMCID: PMC10933291 DOI: 10.1038/s41467-024-46585-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Bacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.
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Affiliation(s)
- Antoine Levrier
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
- Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006, Paris, France
| | - Ioannis Karpathakis
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
- Facultatea de Biotehnologii, USAMV Bucuresti, Sector 1, Cod 011464, Bucureşti, Romania
| | - Bruce Nash
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Steven D Bowden
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Ariel B Lindner
- Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006, Paris, France.
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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12
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Vojnovic I, Caspari OD, Hoşkan MA, Endesfelder U. Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level. Open Biol 2024; 14:230414. [PMID: 38320620 PMCID: PMC10846934 DOI: 10.1098/rsob.230414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024] Open
Abstract
In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, abbreviated as SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets (e.g. nuclear proteins such as cbp1 and mis16, and the centromere-specific histone protein cnp1). The SExY protocol optimizations increasing protein yield could be beneficial for many studies, when targeting low abundance proteins, or for studies that rely on genetic labelling for various reasons (e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality).
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Affiliation(s)
- Ilijana Vojnovic
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oliver D. Caspari
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Microbiology, Institute Pasteur, Paris, France
| | - Mehmet Ali Hoşkan
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
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13
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Su T, Pang Q, Qi Q. In Vivo DNA Assembly Using the PEDA Method. Methods Mol Biol 2024; 2760:437-445. [PMID: 38468102 DOI: 10.1007/978-1-0716-3658-9_24] [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: 03/13/2024]
Abstract
Simple and efficient DNA assembly methods have been widely used in synthetic biology. Here, we provide the protocol for the recently developed PEDA (phage enzyme-assisted in vivo DNA assembly) method for direct in vivo assembly of individual DNA parts in multiple microorganisms, such as Escherichia coli, Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. PEDA allows in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and the efficiency is comparable to the prevailing in vitro DNA assembly, which will broadly boost the rapid progress of synthetic biology.
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Affiliation(s)
- Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qingxiao Pang
- Shandong Lishan Biotechnology Co. LTD, Jinan, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.
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14
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Eddins AJ, Bednar RM, Jana S, Pung AH, Mbengi L, Meyer K, Perona JJ, Cooley RB, Karplus PA, Mehl RA. Truncation-Free Genetic Code Expansion with Tetrazine Amino Acids for Quantitative Protein Ligations. Bioconjug Chem 2023; 34:2243-2254. [PMID: 38047550 DOI: 10.1021/acs.bioconjchem.3c00380] [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] [Indexed: 12/05/2023]
Abstract
Quantitative labeling of biomolecules is necessary to advance areas of antibody-drug conjugation, super-resolution microscopy imaging of molecules in live cells, and determination of the stoichiometry of protein complexes. Bio-orthogonal labeling to genetically encodable noncanonical amino acids (ncAAs) offers an elegant solution; however, their suboptimal reactivity and stability hinder the utility of this method. Previously, we showed that encoding stable 1,2,4,5-tetrazine (Tet)-containing ncAAs enables rapid, complete conjugation, yet some expression conditions greatly limited the quantitative reactivity of the Tet-protein. Here, we demonstrate that reduction of on-protein Tet ncAAs impacts their reactivity, while the leading cause of the unreactive protein is near-cognate suppression (NCS) of UAG codons by endogenous aminoacylated tRNAs. To overcome incomplete conjugation due to NCS, we developed a more catalytically efficient tRNA synthetase and developed a series of new machinery plasmids harboring the aminoacyl tRNA synthetase/tRNA pair (aaRS/tRNA pair). These plasmids enable robust production of homogeneously reactive Tet-protein in truncation-free cell lines, eliminating the contamination caused by NCS and protein truncation. Furthermore, these plasmid systems utilize orthogonal synthetic origins, which render these machinery vectors compatible with any common expression system. Through developing these new machinery plasmids, we established that the aaRS/tRNA pair plasmid copy-number greatly affects the yields and quality of the protein produced. We then produced quantitatively reactive soluble Tet-Fabs, demonstrating the utility of this system for rapid, homogeneous conjugations of biomedically relevant proteins.
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Affiliation(s)
- Alex J Eddins
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Abigail H Pung
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Lea Mbengi
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - Kyle Meyer
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - John J Perona
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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15
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Sun R, Okabe M, Miyazaki S, Ishida T, Mashiguchi K, Inoue K, Yoshitake Y, Yamaoka S, Nishihama R, Kawaide H, Nakajima M, Yamaguchi S, Kohchi T. Biosynthesis of gibberellin-related compounds modulates far-red light responses in the liverwort Marchantia polymorpha. THE PLANT CELL 2023; 35:4111-4132. [PMID: 37597168 PMCID: PMC10615216 DOI: 10.1093/plcell/koad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/21/2023]
Abstract
Gibberellins (GAs) are key phytohormones that regulate growth, development, and environmental responses in angiosperms. From an evolutionary perspective, all major steps of GA biosynthesis are conserved among vascular plants, while GA biosynthesis intermediates such as ent-kaurenoic acid (KA) are also produced by bryophytes. Here, we show that in the liverwort Marchantia polymorpha, KA and GA12 are synthesized by evolutionarily conserved enzymes, which are required for developmental responses to far-red light (FR). Under FR-enriched conditions, mutants of various biosynthesis enzymes consistently exhibited altered thallus growth allometry, delayed initiation of gametogenesis, and abnormal morphology of gamete-bearing structures (gametangiophores). By chemical treatments and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses, we confirmed that these phenotypes were caused by the deficiency of some GA-related compounds derived from KA, but not bioactive GAs from vascular plants. Transcriptome analysis showed that FR enrichment induced the up-regulation of genes related to stress responses and secondary metabolism in M. polymorpha, which was largely dependent on the biosynthesis of GA-related compounds. Due to the lack of canonical GA receptors in bryophytes, we hypothesize that GA-related compounds are commonly synthesized in land plants but were co-opted independently to regulate responses to light quality change in different plant lineages during the past 450 million years of evolution.
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Affiliation(s)
- Rui Sun
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | - Maiko Okabe
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | - Sho Miyazaki
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, 183-8509,Japan
| | - Toshiaki Ishida
- Institute for Chemical Research, Kyoto University, Uji 611-0011,Japan
| | | | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda 278-8510,Japan
| | - Hiroshi Kawaide
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509,Japan
| | - Masatoshi Nakajima
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo 113-8657,Japan
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
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16
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Valiente-Gabioud AA, Garteizgogeascoa Suñer I, Idziak A, Fabritius A, Basquin J, Angibaud J, Nägerl UV, Singh SP, Griesbeck O. Fluorescent sensors for imaging of interstitial calcium. Nat Commun 2023; 14:6220. [PMID: 37798285 PMCID: PMC10556026 DOI: 10.1038/s41467-023-41928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
Calcium in interstitial fluids is central to systemic physiology and a crucial ion pool for entry into cells through numerous plasma membrane channels. Its study has been limited by the scarcity of methods that allow monitoring in tight inter-cell spaces of living tissues. Here we present high performance ultra-low affinity genetically encoded calcium biosensors named GreenT-ECs. GreenT-ECs combine large fluorescence changes upon calcium binding and binding affinities (Kds) ranging from 0.8 mM to 2.9 mM, making them tuned to calcium concentrations in extracellular organismal fluids. We validated GreenT-ECs in rodent hippocampal neurons and transgenic zebrafish in vivo, where the sensors enabled monitoring homeostatic regulation of tissue interstitial calcium. GreenT-ECs may become useful for recording very large calcium transients and for imaging calcium homeostasis in inter-cell structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Inés Garteizgogeascoa Suñer
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Agata Idziak
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Arne Fabritius
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Julie Angibaud
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - U Valentin Nägerl
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Sumeet Pal Singh
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Oliver Griesbeck
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany.
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17
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Naseri G, Raasch H, Charpentier E, Erhardt M. A versatile regulatory toolkit of arabinose-inducible artificial transcription factors for Enterobacteriaceae. Commun Biol 2023; 6:1005. [PMID: 37789111 PMCID: PMC10547716 DOI: 10.1038/s42003-023-05363-3] [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: 05/31/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
The Gram-negative bacteria Salmonella enterica and Escherichia coli are important model organisms, powerful prokaryotic expression platforms for biotechnological applications, and pathogenic strains constitute major public health threats. To facilitate new approaches for research and biotechnological applications, we here develop a set of arabinose-inducible artificial transcription factors (ATFs) using CRISPR/dCas9 and Arabidopsis-derived DNA-binding proteins to control gene expression in E. coli and Salmonella over a wide inducer concentration range. The transcriptional output of the different ATFs, in particular when expressed in Salmonella rewired for arabinose catabolism, varies over a wide spectrum (up to 35-fold gene activation). As a proof-of-concept, we use the developed ATFs to engineer a Salmonella two-input biosensor strain, SALSOR 0.2 (SALmonella biosenSOR 0.2), which detects and quantifies alkaloid drugs through a measurable fluorescent output. Moreover, we use plant-derived ATFs to regulate β-carotene biosynthesis in E. coli, resulting in ~2.1-fold higher β-carotene production compared to expression of the biosynthesis pathway using a strong constitutive promoter.
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Affiliation(s)
- Gita Naseri
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
| | - Hannah Raasch
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Marc Erhardt
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
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18
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Bharathan G, Mundra S, Darwich DM, Saeed MM, Al Hafri ASA, Alsalmi MMSM, Maqsood S, Mudgil P, Fanning S, Srikumar S. Regulation of iron metabolism is critical for the survival of Salmonella Typhimurium in pasteurized milk. Food Microbiol 2023; 115:104326. [PMID: 37567619 DOI: 10.1016/j.fm.2023.104326] [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: 02/06/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/13/2023]
Abstract
Salmonella is known to survive in raw/pasteurized milk and cause foodborne outbreaks. Lactoferrin, present in milk from all animal sources, is an iron-binding glycoprotein that limits the availability of iron to pathogenic bacteria. Despite the presence of lactoferrins, Salmonella can grow in milk obtained from different animal sources. However, the mechanism by which Salmonella overcomes iron scarcity induced by lactoferrin in milk is not evaluated yet. Salmonella employs the DNA binding transcriptional regulator Fur (ferric update regulator) to mediate iron uptake during survival in iron deplete conditions. To understand the importance of Fur in Salmonella milk growth, we profiled the growth of Salmonella Typhimurium Δfur (ST4/74Δfur) in both bovine and camel milk. ST4/74Δfur was highly inhibited in milk compared to wild-type ST4/74, confirming the importance of Fur mediated regulation of iron metabolism in Salmonella milk growth. We further studied the biology of ST4/74Δfur to understand the importance of iron metabolism in Salmonella milk survival. Using increasing concentrations of FeCl3, and the antibiotic streptonigrin we show that iron accumulates in the cytoplasm of ST4/74Δfur. We hypothesized that the accumulated iron could activate oxidative stress via Fenton's reaction leading to growth inhibition. However, the inhibition of ST4/74Δfur in milk was not due to Fenton's reaction, but due to the 'iron scarce' conditions of milk and microaerophilic incubation conditions which made the presence of the fur gene indispensable for Salmonella milk growth. Subsequently, survival studies of 14 other transcriptional mutants of ST4/74 in milk confirmed that RpoE-mediated response to extracytoplasmic stress is also important for the survival of Salmonella in milk. Though we have data only for fur and rpoE, many other Salmonella transcriptional factors could play important roles in the growth of Salmonella in milk, a theme for future research on Salmonella milk biology. Nevertheless, our data provide early insights into the biology of milk-associated Salmonella.
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Affiliation(s)
- Greeshma Bharathan
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Dania Mustafa Darwich
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Maitha Mohammad Saeed
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Ahad Saeed Ali Al Hafri
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | | | - Sajid Maqsood
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Priti Mudgil
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, D04 N2E5, Ireland
| | - Shabarinath Srikumar
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates.
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19
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Sun M, Gao AX, Liu X, Yang Y, Ledesma-Amaro R, Bai Z. High-throughput process development from gene cloning to protein production. Microb Cell Fact 2023; 22:182. [PMID: 37715258 PMCID: PMC10503041 DOI: 10.1186/s12934-023-02184-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/19/2023] [Indexed: 09/17/2023] Open
Abstract
In the post-genomic era, the demand for faster and more efficient protein production has increased, both in public laboratories and industry. In addition, with the expansion of protein sequences in databases, the range of possible enzymes of interest for a given application is also increasing. Faced with peer competition, budgetary, and time constraints, companies and laboratories must find ways to develop a robust manufacturing process for recombinant protein production. In this review, we explore high-throughput technologies for recombinant protein expression and present a holistic high-throughput process development strategy that spans from genes to proteins. We discuss the challenges that come with this task, the limitations of previous studies, and future research directions.
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Affiliation(s)
- Manman Sun
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Alex Xiong Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China.
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
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20
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Pourjafar M, Saidijam M, Miehe M, Najafi R, Soleimani M, Spillner E. Surfaceome Profiling Suggests Potential of Anti-MUC1×EGFR Bispecific Antibody for Breast Cancer Targeted Therapy. J Immunother 2023; 46:245-261. [PMID: 37493044 DOI: 10.1097/cji.0000000000000482] [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: 01/11/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023]
Abstract
Breast cancer (BC) treatment has traditionally been challenging due to tumor heterogeneity. Bispecific antibodies (bsAbs) offer a promising approach for overcoming these challenges by targeting multiple specific epitopes. In the current study, we designed a new bsAb against the most common BC cell surface proteins (SPs). To achieve this, we analyzed RNA-sequencing data to identify differentially expressed genes, which were further evaluated using Gene Ontology enrichment, Hidden Markov Models, clinical trial data, and survival analysis to identify druggable gene-encoding cell SPs. Based on these analyses, we constructed and expressed a bsAb targeting the mucin 1 (MUC1) and epidermal growth factor receptor (EGFR) proteins, which are the dominant druggable gene-encoding cell SPs in BC. The recombinant anti-MUC1×EGFR bsAb demonstrated efficient production and high specificity for MUC1 and EGFR + cell lines and BC tissue. Furthermore, the bsAb significantly reduced the proliferation and migration of BC cells. Our results suggested that simultaneous targeting with bsAbs could be a promising targeted therapy for improving the overall efficacy of BC treatment.
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Affiliation(s)
- Mona Pourjafar
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences
- Department of Biological and Chemical Engineering, Immunological Biotechnology, Aarhus University, Aarhus, Denmark
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences
| | - Michaela Miehe
- Department of Biological and Chemical Engineering, Immunological Biotechnology, Aarhus University, Aarhus, Denmark
| | - Rezvan Najafi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Edzard Spillner
- Department of Biological and Chemical Engineering, Immunological Biotechnology, Aarhus University, Aarhus, Denmark
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21
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He B, Ma Y, Tian F, Zhao GR, Wu Y, Yuan YJ. YLC-assembly: large DNA assembly via yeast life cycle. Nucleic Acids Res 2023; 51:8283-8292. [PMID: 37486765 PMCID: PMC10450165 DOI: 10.1093/nar/gkad599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023] Open
Abstract
As an enabling technique of synthetic biology, the scale of DNA assembly largely determines the scale of genetic manipulation. However, large DNA assembly technologies are generally cumbersome and inefficient. Here, we developed a YLC (yeast life cycle)-assembly method that enables in vivo iterative assembly of large DNA by nesting cell-cell transfer of assembled DNA in the cycle of yeast mating and sporulation. Using this method, we successfully assembled a hundred-kilobase (kb)-sized endogenous yeast DNA and a megabase (Mb)-sized exogenous DNA. For each round, over 104 positive colonies per 107 cells could be obtained, with an accuracy ranging from 67% to 100%. Compared with other Mb-sized DNA assembly methods, this method exhibits a higher success rate with an easy-to-operate workflow that avoid in vitro operations of large DNA. YLC-assembly lowers the technical difficulty of Mb-sized DNA assembly and could be a valuable tool for large-scale genome engineering and synthetic genomics.
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Affiliation(s)
- Bo He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yuan Ma
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Fangfang Tian
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Guang-Rong Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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22
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Cui Y, Hisanaga T, Kajiwara T, Yamaoka S, Kohchi T, Goh T, Nakajima K. Three-Dimensional Morphological Analysis Revealed the Cell Patterning Bases for the Sexual Dimorphism Development in the Liverwort Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2023; 64:866-879. [PMID: 37225421 DOI: 10.1093/pcp/pcad048] [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: 01/24/2023] [Revised: 04/21/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023]
Abstract
In land plants, sexual dimorphism can develop in both diploid sporophytes and haploid gametophytes. While developmental processes of sexual dimorphism have been extensively studied in the sporophytic reproductive organs of model flowering plants such as stamens and carpels of Arabidopsis thaliana, those occurring in gametophyte generation are less well characterized due to the lack of amenable model systems. In this study, we performed three-dimensional morphological analyses of gametophytic sexual branch differentiation in the liverwort Marchantia polymorpha, using high-depth confocal imaging and a computational cell segmentation technique. Our analysis revealed that the specification of germline precursors initiates in a very early stage of sexual branch development, where incipient branch primordia are barely recognizable in the apical notch region. Moreover, spatial distribution patterns of germline precursors differ between males and females from the initial stage of primordium development in a manner dependent on the master sexual differentiation regulator MpFGMYB. At later stages, distribution patterns of germline precursors predict the sex-specific gametangia arrangement and receptacle morphologies seen in mature sexual branches. Taken together, our data suggest a tightly coupled progression of germline segregation and sexual dimorphism development in M. polymorpha.
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Affiliation(s)
- Yihui Cui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
| | - Tetsuya Hisanaga
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tomoaki Kajiwara
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502 Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502 Japan
| | - Tatsuaki Goh
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
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23
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Liu AY, Koga H, Goya C, Kitabatake M. Quick and affordable DNA cloning by reconstitution of Seamless Ligation Cloning Extract using defined factors. Genes Cells 2023; 28:553-562. [PMID: 37132531 DOI: 10.1111/gtc.13034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/04/2023]
Abstract
The cloning of DNA fragments to plasmid vectors is at the heart of molecular biology. Recent developments have led to various methods utilizing homologous recombination of homology arms. Among them, Seamless Ligation Cloning Extract (SLiCE) is an affordable alternative solution that uses simple Escherichia coli lysates. However, the underlying molecular mechanisms remain unclear and the reconstitution of the extract by defined factors has not yet been reported. We herein show that the key factor in SLiCE is Exonuclease III (ExoIII), a double-strand (ds) DNA-dependent 3'-5' exonuclease, encoded by XthA. SLiCE prepared from the xthAΔ strain is devoid of recombination activity, whereas purified ExoIII alone is sufficient to assemble two blunt-ended dsDNA fragments with homology arms. In contrast to SLiCE, ExoIII is unable to digest (or assemble) fragments with 3' protruding ends; however, the addition of single-strand DNA-targeting Exonuclease T overcomes this issue. Through the combination of commercially available enzymes under optimized conditions, we achieved the efficient, reproducible, and affordable cocktail, "XE cocktail," for seamless DNA cloning. By reducing the cost and time required for DNA cloning, researchers will devote more resources to advanced studies and the careful validation of their own findings.
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Affiliation(s)
- Alexander Y Liu
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroto Koga
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Chihiro Goya
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Makoto Kitabatake
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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24
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Sivelle C, Sierocki R, Lesparre Y, Lomet A, Quintilio W, Dubois S, Correia E, Moro AM, Maillère B, Nozach H. Combining deep mutational scanning to heatmap of HLA class II binding of immunogenic sequences to preserve functionality and mitigate predicted immunogenicity. Front Immunol 2023; 14:1197919. [PMID: 37575221 PMCID: PMC10416631 DOI: 10.3389/fimmu.2023.1197919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Removal of CD4 T cell epitopes from therapeutic antibody sequences is expected to mitigate their potential immunogenicity, but its application is complicated by the location of their T cell epitopes, which mainly overlap with complementarity-determining regions. We therefore evaluated the flexibility of antibody sequences to reduce the predicted affinity of corresponding peptides for HLA II molecules and to maintain antibody binding to its target in order to guide antibody engineering for mitigation of predicted immunogenicity. Permissive substitutions to reduce affinity of peptides for HLA II molecules were identified by establishing a heatmap of HLA class II binding using T-cell epitope prediction tools, while permissive substitutions preserving binding to the target were identified by means of deep mutational scanning and yeast surface display. Combinatorial libraries were then designed to identify active clones. Applied to adalimumab, an anti-TNFα human antibody, this approach identified 200 mutants with a lower HLA binding score than adalimumab. Three mutants were produced as full-length antibodies and showed a higher affinity for TNFα and neutralization ability than adalimumab. This study also sheds light on the permissiveness of antibody sequences with regard to functionality and predicted T cell epitope content.
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Affiliation(s)
- Coline Sivelle
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Raphael Sierocki
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
- Deeptope SAS, Orsay, France
| | | | - Aurore Lomet
- CEA List, Université Paris-Saclay, Palaiseau, France
| | - Wagner Quintilio
- Biopharmaceuticals Laboratory, Butantan Institute, Sao Paulo, Brazil
| | - Steven Dubois
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Evelyne Correia
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Ana Maria Moro
- Biopharmaceuticals Laboratory, Butantan Institute, Sao Paulo, Brazil
| | - Bernard Maillère
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Hervé Nozach
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
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25
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Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [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: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
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Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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26
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Hachani A, Giulieri SG, Guérillot R, Walsh CJ, Herisse M, Soe YM, Baines SL, Thomas DR, Cheung SD, Hayes AS, Cho E, Newton HJ, Pidot S, Massey RC, Howden BP, Stinear TP. A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence. eLife 2023; 12:84778. [PMID: 37289634 DOI: 10.7554/elife.84778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.
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Affiliation(s)
- Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Stefano G Giulieri
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Calum J Walsh
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ye Mon Soe
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - David R Thomas
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Shane Doris Cheung
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Hayley J Newton
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sacha Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ruth C Massey
- School of Microbiology, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
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27
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Bernauw AJ, Crabbe V, Ryssegem F, Willaert R, Bervoets I, Peeters E. Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis. Microbiologyopen 2023; 12:e1356. [PMID: 37379425 DOI: 10.1002/mbo3.1356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 06/30/2023] Open
Abstract
The leucine-responsive regulatory protein (Lrp) family of transcriptional regulators is widespread among prokaryotes and especially well-represented in archaea. It harbors members with diverse functional mechanisms and physiological roles, often linked to the regulation of amino acid metabolism. BarR is an Lrp-type regulator that is conserved in thermoacidophilic Thermoprotei belonging to the order Sulfolobales and is responsive to the non-proteinogenic amino acid β-alanine. In this work, we unravel molecular mechanisms of the Acidianus hospitalis BarR homolog, Ah-BarR. Using a heterologous reporter gene system in Escherichia coli, we demonstrate that Ah-BarR is a dual-function transcription regulator that is capable of repressing transcription of its own gene and activating transcription of an aminotransferase gene, which is divergently transcribed from a common intergenic region. Atomic force microscopy (AFM) visualization reveals a conformation in which the intergenic region appears wrapped around an octameric Ah-BarR protein. β-alanine causes small conformational changes without affecting the oligomeric state of the protein, resulting in a relief of regulation while the regulator remains bound to the DNA. This regulatory and ligand response is different from the orthologous regulators in Sulfolobus acidocaldarius and Sulfurisphaera tokodaii, which is possibly explained by a distinct binding site organization and/or by the presence of an additional C-terminal tail in Ah-BarR. By performing site-directed mutagenesis, this tail is shown to be involved in ligand-binding response.
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Affiliation(s)
- Amber J Bernauw
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vincent Crabbe
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fraukje Ryssegem
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ronnie Willaert
- Research Group Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Alliance Research Group VUB-UGent NanoMicrobiology, International Joint Research Group VUB-EFPL NanoBiotechnology & NanoMedicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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28
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Nagao A, Nakanishi Y, Yamaguchi Y, Mishina Y, Karoji M, Toya T, Fujita T, Iwasaki S, Miyauchi K, Sakaguchi Y, Suzuki T. Quality control of protein synthesis in the early elongation stage. Nat Commun 2023; 14:2704. [PMID: 37198183 PMCID: PMC10192219 DOI: 10.1038/s41467-023-38077-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
In the early stage of bacterial translation, peptidyl-tRNAs frequently dissociate from the ribosome (pep-tRNA drop-off) and are recycled by peptidyl-tRNA hydrolase. Here, we establish a highly sensitive method for profiling of pep-tRNAs using mass spectrometry, and successfully detect a large number of nascent peptides from pep-tRNAs accumulated in Escherichia coli pthts strain. Based on molecular mass analysis, we found about 20% of the peptides bear single amino-acid substitutions of the N-terminal sequences of E. coli ORFs. Detailed analysis of individual pep-tRNAs and reporter assay revealed that most of the substitutions take place at the C-terminal drop-off site and that the miscoded pep-tRNAs rarely participate in the next round of elongation but dissociate from the ribosome. These findings suggest that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yui Nakanishi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yutaro Yamaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshifumi Mishina
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Minami Karoji
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takafumi Toya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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29
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Zhu P, Stanisheuski S, Franklin R, Vogel A, Vesely CH, Reardon P, Sluchanko NN, Beckman JS, Karplus PA, Mehl RA, Cooley RB. Autonomous Synthesis of Functional, Permanently Phosphorylated Proteins for Defining the Interactome of Monomeric 14-3-3ζ. ACS CENTRAL SCIENCE 2023; 9:816-835. [PMID: 37122473 PMCID: PMC10141581 DOI: 10.1021/acscentsci.3c00191] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/03/2023]
Abstract
14-3-3 proteins are dimeric hubs that bind hundreds of phosphorylated "clients" to regulate their function. Installing stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study 14-3-3 function in cellular-like environments, but a previous genetic code expansion (GCE) system to translationally install nonhydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with CH2, site-specifically into proteins has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a six-step biosynthetic pathway that produces nhpSer from phosphoenolpyruvate. Using this autonomous "PermaPhos" expression system, we produce three biologically relevant proteins with nhpSer and confirm that nhpSer mimics the effects of phosphoserine for activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein, promoting 14-3-3/client complexation, and monomerizing 14-3-3 dimers. Then, to understand the biological function of these phosphorylated 14-3-3ζ monomers (containing nhpSer at Ser58), we isolate its interactome from HEK293T lysates and compare it with that of wild-type 14-3-3ζ. These data identify two new subsets of 14-3-3 client proteins: (i) those that selectively bind dimeric 14-3-3ζ and (ii) those that selectively bind monomeric 14-3-3ζ. We discover that monomeric-but not dimeric-14-3-3ζ interacts with cereblon, an E3 ubiquitin-ligase adaptor protein of pharmacological interest.
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Affiliation(s)
- Phillip Zhu
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Stanislau Stanisheuski
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Rachel Franklin
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Amber Vogel
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Cat Hoang Vesely
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Patrick Reardon
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Nikolai N. Sluchanko
- A.N.
Bach Institute of Biochemistry, Federal Research Center of Biotechnology
of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Joseph S. Beckman
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- e-MSion
Inc., 2121 NE Jack London
St., Corvallis, Oregon 97330, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Richard B. Cooley
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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30
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Liu SM, Ifebi B, Johnson F, Xu A, Ho J, Yang Y, Schwartz G, Jo YH, Chua S. The gut signals to AGRP-expressing cells of the pituitary to control glucose homeostasis. J Clin Invest 2023; 133:e164185. [PMID: 36787185 PMCID: PMC10065075 DOI: 10.1172/jci164185] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Glucose homeostasis can be improved after bariatric surgery, which alters bile flow and stimulates gut hormone secretion, particularly FGF15/19. FGFR1 expression in AGRP-expressing cells is required for bile acids' ability to improve glucose control. We show that the mouse Agrp gene has 3 promoter/enhancer regions that direct transcription of each of their own AGRP transcripts. One of these Agrp promoters/enhancers, Agrp-B, is regulated by bile acids. We generated an Agrp-B knockin FLP/knockout allele. AGRP-B-expressing cells are found in endocrine cells of the pars tuberalis and coexpress diacylglycerol lipase B - an endocannabinoid biosynthetic enzyme - distinct from pars tuberalis thyrotropes. AGRP-B expression is also found in the folliculostellate cells of the pituitary's anterior lobe. Mice without AGRP-B were protected from glucose intolerance induced by high-fat feeding but not from excess weight gain. Chemogenetic inhibition of AGRP-B cells improved glucose tolerance by enhancing glucose-stimulated insulin secretion. Inhibition of the AGRP-B cells also caused weight loss. The improved glucose tolerance and reduced body weight persisted up to 6 weeks after cessation of the DREADD-mediated inhibition, suggesting the presence of a biological switch for glucose homeostasis that is regulated by long-term stability of food availability.
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Affiliation(s)
| | | | | | | | | | - Yunlei Yang
- Department of Medicine
- Department of Neuroscience, and
| | - Gary Schwartz
- Department of Medicine
- Department of Neuroscience, and
| | - Young Hwan Jo
- Department of Medicine
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, New York, USA
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31
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Kawano T, Kashiwagi M, Kanuka M, Chen CK, Yasugaki S, Hatori S, Miyazaki S, Tanaka K, Fujita H, Nakajima T, Yanagisawa M, Nakagawa Y, Hayashi Y. ER proteostasis regulators cell-non-autonomously control sleep. Cell Rep 2023; 42:112267. [PMID: 36924492 DOI: 10.1016/j.celrep.2023.112267] [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: 07/01/2022] [Revised: 01/17/2023] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Sleep is regulated by peripheral tissues under fatigue. The molecular pathways in peripheral cells that trigger systemic sleep-related signals, however, are unclear. Here, a forward genetic screen in C. elegans identifies 3 genes that strongly affect sleep amount: sel-1, sel-11, and mars-1. sel-1 and sel-11 encode endoplasmic reticulum (ER)-associated degradation components, whereas mars-1 encodes methionyl-tRNA synthetase. We find that these machineries function in non-neuronal tissues and that the ER unfolded protein response components inositol-requiring enzyme 1 (IRE1)/XBP1 and protein kinase R-like ER kinase (PERK)/eukaryotic initiation factor-2α (eIF2α)/activating transcription factor-4 (ATF4) participate in non-neuronal sleep regulation, partly by reducing global translation. Neuronal epidermal growth factor receptor (EGFR) signaling is also required. Mouse studies suggest that this mechanism is conserved in mammals. Considering that prolonged wakefulness increases ER proteostasis stress in peripheral tissues, our results suggest that peripheral ER proteostasis factors control sleep homeostasis. Moreover, based on our results, peripheral tissues likely cope with ER stress not only by the well-established cell-autonomous mechanisms but also by promoting the individual's sleep.
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Affiliation(s)
- Taizo Kawano
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
| | - Mitsuaki Kashiwagi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mika Kanuka
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
| | - Chung-Kuan Chen
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Shinnosuke Yasugaki
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Sena Hatori
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; PhD Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Shinichi Miyazaki
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; PhD Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kaeko Tanaka
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
| | - Hidetoshi Fujita
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Toshiro Nakajima
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8575, Japan; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yoshimi Nakagawa
- Department of Complex Biosystem Research, Institute of Natural Medicine, University of Toyama, Toyama, Toyama 930-0194, Japan
| | - Yu Hayashi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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32
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Hinzmann M, Yavuzer H, Hinzmann A, Gröger H. Database-driven In Silico-Identification and Characterization of Novel Aldoxime Dehydratases. J Biotechnol 2023; 367:81-88. [PMID: 36907356 DOI: 10.1016/j.jbiotec.2023.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
Aldoxime dehydratases (Oxds) are a unique class of enzymes, which catalyzes the dehydration of aldoximes to nitriles in an aqueous environment. Recently, they gained attention as a catalyst for a green and cyanide-free alternative to established nitrile syntheses, which often require the use of toxic cyanides and harsh reaction conditions. Up to now only thirteen aldoxime dehydratases have been discovered and biochemically characterized. This raised the interest for identifying further Oxds with, e.g., complementary properties in terms of substrate scope. In this study, 16 novel genes, presumably encoding aldoxime dehydratases, were selected by using a commercially available 3DM database based on OxdB an Oxd from Bacillus sp. OxB-1. Out of 16 proteins, six enzymes with aldoxime dehydratases activity were identified, which differ in their substrate scope and activity. While some novel Oxds showed better performance for aliphatic substrate such as n-octanaloxime compared to the well characterized OxdRE from Rhodococcus sp. N-771, some showed activity for aromatic aldoximes, leading to an overall high usability of these enzymes in organic chemistry. The applicability for organic synthesis was underlined by converting 100 mM n-octanaloxime at a 10 mL scale within 5 h with the novel aldoxime dehydratase OxdHR as whole-cell catalyst (33 mgbww/mL).
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Affiliation(s)
- Michael Hinzmann
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Hilmi Yavuzer
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Alessa Hinzmann
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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33
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Enhancement of Inhibition of the Pseudomonas sp. Biofilm Formation on Bacterial Cellulose-Based Wound Dressing by the Combined Action of Alginate Lyase and Gentamicin. Int J Mol Sci 2023; 24:ijms24054740. [PMID: 36902169 PMCID: PMC10002595 DOI: 10.3390/ijms24054740] [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: 02/05/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Bacterial biofilms generally contribute to chronic infections, including wound infections. Due to the antibiotic resistance mechanisms protecting bacteria living in the biofilm, they are a serious problem in the wound healing process. To accelerate the wound healing process and avoid bacterial infection, it is necessary to select the appropriate dressing material. In this study, the promising therapeutic properties of alginate lyase (AlgL) immobilised on BC membranes for protecting wounds from Pseudomonas aeruginosa infection were investigated. The AlgL was immobilised on never dried BC pellicles via physical adsorption. The maximum adsorption capacity of AlgL was 6.0 mg/g of dry BC, and the equilibrium was reached after 2 h. The adsorption kinetics was studied, and it has been proven that the adsorption was consistent with Langmuir isotherm. In addition, the impact of enzyme immobilisation on bacterial biofilm stability and the effect of simultaneous immobilisation of AlgL and gentamicin on the viability of bacterial cells was investigated. The obtained results showed that the AlgL immobilisation significantly reduced the amount of polysaccharides component of the P. aeruginosa biofilm. Moreover, the biofilm disruption by AlgL immobilised on BC membranes exhibited synergism with the gentamicin, resulting in 86.5% more dead P. aeruginosa PAO-1 cells.
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34
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Zhu P, Nguyen KT, Estelle AB, Sluchanko NN, Mehl RA, Cooley RB. Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation. Protein Sci 2023; 32:e4574. [PMID: 36691781 PMCID: PMC9926477 DOI: 10.1002/pro.4574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
14-3-3 proteins are central hub regulators of hundreds of phosphorylated "client" proteins. They are subject to over 60 post-translational modifications (PTMs), yet little is known how these PTMs alter 14-3-3 function and its ability to regulate downstream signaling pathways. An often neglected, but well-documented 14-3-3 PTM found under physiological and immune-stimulatory conditions is the conversion of tyrosine to 3-nitro-tyrosine at several Tyr sites, two of which are located at sites considered important for 14-3-3 function: Y130 (β-isoform numbering) is located in the primary phospho-client peptide-binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14-3-3/client complex formation and client regulation. By genetically encoding 3-nitro-tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14-3-3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14-3-3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14-3-3. But, in contrast to other client-binding deficient variants, it did not localize to the nucleus. The 1.9 Å resolution structure of 14-3-3 nitrated at Y213 revealed unusual flexibility of its C-terminal α-helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14-3-3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14-3-3 interactome.
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Affiliation(s)
- Phillip Zhu
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Kyle T. Nguyen
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Aidan B. Estelle
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of SciencesA.N. Bach Institute of BiochemistryMoscowRussia
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
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Late Embryogenesis Abundant Proteins Contribute to the Resistance of Toxoplasma gondii Oocysts against Environmental Stresses. mBio 2023; 14:e0286822. [PMID: 36809045 PMCID: PMC10128015 DOI: 10.1128/mbio.02868-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Toxoplasma gondii oocysts, which are shed in large quantities in the feces from infected felines, are very stable in the environment, resistant to most inactivation procedures, and highly infectious. The oocyst wall provides an important physical barrier for sporozoites contained inside oocysts, protecting them from many chemical and physical stressors, including most inactivation procedures. Furthermore, sporozoites can withstand large temperature changes, even freeze-thawing, as well as desiccation, high salinity, and other environmental insults; however, the genetic basis for this environmental resistance is unknown. Here, we show that a cluster of four genes encoding Late Embryogenesis Abundant (LEA)-related proteins are required to provide Toxoplasma sporozoites resistance to environmental stresses. Toxoplasma LEA-like genes (TgLEAs) exhibit the characteristic features of intrinsically disordered proteins, explaining some of their properties. Our in vitro biochemical experiments using recombinant TgLEA proteins show that they have cryoprotective effects on the oocyst-resident lactate dehydrogenase enzyme and that induced expression in E. coli of two of them leads to better survival after cold stress. Oocysts from a strain in which the four LEA genes were knocked out en bloc were significantly more susceptible to high salinity, freezing, and desiccation compared to wild-type oocysts. We discuss the evolutionary acquisition of LEA-like genes in Toxoplasma and other oocyst-producing apicomplexan parasites of the Sarcocystidae family and discuss how this has likely contributed to the ability of sporozoites within oocysts to survive outside the host for extended periods. Collectively, our data provide a first molecular detailed view on a mechanism that contributes to the remarkable resilience of oocysts against environmental stresses. IMPORTANCE Toxoplasma gondii oocysts are highly infectious and may survive in the environment for years. Their resistance against disinfectants and irradiation has been attributed to the oocyst and sporocyst walls by acting as physical and permeability barriers. However, the genetic basis for their resistance against stressors like changes in temperature, salinity, or humidity, is unknown. We show that a cluster of four genes encoding Toxoplasma Late Embryogenesis Abundant (TgLEA)-related proteins are important for this resistance to environmental stresses. TgLEAs have features of intrinsically disordered proteins, explaining some of their properties. Recombinant TgLEA proteins show cryoprotective effects on the parasite's lactate dehydrogenase, an abundant enzyme in oocysts, and expression in E. coli of two TgLEAs has a beneficial effect on growth after cold stress. Moreover, oocysts from a strain lacking all four TgLEA genes were more susceptible to high salinity, freezing, and desiccation compared to wild-type oocysts, highlighting the importance of the four TgLEAs for oocyst resilience.
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36
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Buchko GW, Zhou M, Vesely CH, Tao J, Shaw WJ, Mehl RA, Cooley RB. High-yield recombinant bacterial expression of 13 C-, 15 N-labeled, serine-16 phosphorylated, murine amelogenin using a modified third generation genetic code expansion protocol. Protein Sci 2023; 32:e4560. [PMID: 36585836 PMCID: PMC9850436 DOI: 10.1002/pro.4560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/21/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Amelogenin constitutes ~90% of the enamel matrix in the secretory stage of amelogenesis, a still poorly understood process that results in the formation of the hardest and most mineralized tissue in vertebrates-enamel. Most biophysical research with amelogenin uses recombinant protein expressed in Escherichia coli. In addition to providing copious amounts of protein, recombinant expression allows 13 C- and 15 N-labeling for detailed structural studies using NMR spectroscopy. However, native amelogenin is phosphorylated at one position, Ser-16 in murine amelogenin, and there is mounting evidence that Ser-16 phosphorylation is important. Using a modified genetic code expansion protocol we have expressed and purified uniformly 13 C-, 15 N-labeled murine amelogenin (pS16M179) with ~95% of the protein being correctly phosphorylated. Homogeneous phosphorylation was achieved using commercially available, enriched, 13 C-, 15 N-labeled media, and protein expression was induced with isopropyl β-D-1-thiogalactopyranoside at 310 K. Phosphoserine incorporation was verified from one-dimensional 31 P NMR spectra, comparison of 1 H-15 N HSQC spectra, Phos-tag SDS PAGE, and mass spectrometry. Phosphorus-31 NMR spectra for pS16M179 under conditions known to trigger amelogenin self-assembly into nanospheres confirm nanosphere models with buried N-termini. Lambda phosphatase treatment of these nanospheres results in the dephosphorylation of pS16M179, confirming that smaller oligomers and monomers with exposed N-termini are in equilibrium with nanospheres. Such 13 C-, 15 N-labeling of amelogenin with accurately encoded phosphoserine incorporation will accelerate biomineralization research to understand amelogenesis and stimulate the expanded use of genetic code expansion protocols to introduce phosphorylated amino acids into proteins.
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Affiliation(s)
- Garry W. Buchko
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA,School of Molecular BiosciencesWashington State UniversityPullmanWashingtonUSA
| | - Mowei Zhou
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Cat Hoang Vesely
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Jinhui Tao
- Physical and Computational Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Wendy J. Shaw
- Physical and Computational Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Ryan A. Mehl
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
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Wang X, Teng C, Wei H, Liu S, Xuan H, Peng W, Li Q, Hao H, Lyu Q, Lyu S, Fan Y. Development of a set of novel binary expression vectors for plant gene function analysis and genetic transformation. FRONTIERS IN PLANT SCIENCE 2023; 13:1104905. [PMID: 36714700 PMCID: PMC9877630 DOI: 10.3389/fpls.2022.1104905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/21/2022] [Indexed: 05/29/2023]
Abstract
With the advent of multiple omics and Genome-Wide Association Studies (GWAS) technology, genome-scale functional analysis of candidate genes is to be conducted in diverse plant species. Construction of plant binary expression vectors is the prerequisite for gene function analysis. Therefore, it is of significance to develop a set of plant binary expression vectors with highly efficient, inexpensive, and convenient cloning method, and easy-to-use in screening of positive recombinant in Escherichia coli. In this study, we developed a set of plant binary expression vectors, termed pBTR vectors, based on Golden Gate cloning using BsaI restriction site. Foreign DNA fragment of interest (FDI) can be cloned into the destination pBTR by one-step digestion-ligation reaction in a single tube, and even the FDI contains internal BsaI site(s). Markedly, in one digestion-ligation reaction, multiple FDIs (exemplified by cloning four soybean Glyma.02g025400, Glyma.05g201700, Glyma.06g165700, and Glyma.17g095000 genes) can be cloned into the pBTR vector to generate multiple corresponding expression constructs (each expression vector carrying an FDI). In addition, the pBTR vectors carry the visual marker, a brightness monomeric red fluorescent protein mScarlet-I, that can be observed with the unaided eye in screening of positive recombinants without the use of additional reagents/equipment. The reliability of the pBTR vectors was validated in plants by overexpression of AtMyb75/PAP1 in tomato and GUSPlus in soybean roots via Agrobacterium rhizogenes-mediated transformation, promoter activity analysis of AtGCSpro in Arabidopsis via A. tumefaciens-mediated transformation, and protein subcellular localization of the Vitis vinifera VvCEB1opt in tobacco, respectively. These results demonstrated that the pBTR vectors can be used in analysis of gene (over)expression, promoter activity, and protein subcellular localization. These vectors will contribute to speeding up gene function analysis and the process of plant molecular breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shanhua Lyu
- *Correspondence: Shanhua Lyu, ; ; Yinglun Fan,
| | - Yinglun Fan
- *Correspondence: Shanhua Lyu, ; ; Yinglun Fan,
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38
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Weber VM, Doucet AJ, Cristofari G. Precise and Scarless Insertion of Transposable Elements by Cas9-Mediated Genome Engineering. Methods Mol Biol 2023; 2607:329-353. [PMID: 36449169 DOI: 10.1007/978-1-0716-2883-6_15] [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: 06/17/2023]
Abstract
Transposable element insertions can have broad effects on gene expression, ranging from new regulatory functions to pathogenic consequences by transplanting new cis-regulating elements or perturbing existing ones. Genetic manipulation of such DNA sequences can help decipher their mechanism of action. Here, we describe a CRISPR-Cas9-mediated two-step approach to precisely insert transposable elements into into the genome of cultured human cells, without scar or reporter gene. First, a double-selection cassette is inserted into the desired target locus. Once a clone containing a single copy of this cassette has been isolated, a second editing step is performed to exchange the double-selection cassette with a markerless transposable element sequence. More generally, this method can be used for knocking in any large insert without genetic markers.
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39
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Juhas M. Synthetic Biology in Microbiology. BRIEF LESSONS IN MICROBIOLOGY 2023:79-91. [DOI: 10.1007/978-3-031-29544-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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40
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Gong K, Wang M, Duan Q, Li G, Yong D, Ren C, Li Y, Zhang Q, Wang Z, Sun T, Zhang H, Tu Q, Wu C, Fu J, Li A, Song C, Zhang Y, Li R. High-yield production of FK228 and new derivatives in a Burkholderia chassis. Metab Eng 2023; 75:131-142. [PMID: 36528227 DOI: 10.1016/j.ymben.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
FK228 (romidepsin) is the only natural histone deacetylases (HDACs) inhibitor approved by FDA to treat cutaneous and peripheral T-cell lymphoma. However, the limited supply and severe cardiotoxicity of FK228 underscore the importance to develop an effective synthetic biology platform for the manufacturing and fine-tuning of this drug lead. In this work, we constructed a Burkholderia chassis for the high-yield production of FK228-family (unnatural) natural products. By virtue of the optimized Burkholderia-specific recombineering system, the biosynthetic gene cluster (BGC) encoding the FK228-like skeleton thailandepsins (tdp) in Burkholderia thailandensis E264 was replaced with an attB integration site to afford the basal chassis KOGC1. The tdp BGC directly captured from E264 was hybridized with the FK228-encoding BGC (dep) using the versatile Red/ET technology. The hybrid BGC (tdp-dep) was integrated into the attB site of KOGC1, resulting in the heterologous expression of FK228. Remarkably, the titer reached 581 mg/L, which is 30-fold higher than that of native producer Chromobacterium violaceum No. 968. This success encouraged us to further engineer the NRPS modules 4 or 6 of hybrid tdp-dep BGC by domain units swapping strategy, and eight new FK228 derivatives (1-8) varying in the composition of amino acids were generated. Especially, the titers of 2 and 3 in KOGC1 were up to 985 mg/L and 453 mg/L, respectively. 2 and 3 displayed stronger cytotoxic activity than FK228. All in all, this work established a robust platform to produce FK228 and its new derivatives in sufficient quantities for anticancer drug development.
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Affiliation(s)
- Kai Gong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Maoqin Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiong Duan
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Gang Li
- Department of Natural Medicinal Chemistry and Pharmacognosy, Qingdao University, Qingdao, Shandong, China
| | - Daojing Yong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Cailing Ren
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Yue Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qijun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Zongjie Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Tao Sun
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Huanyun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiang Tu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Changsheng Wu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
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Avila-Crump S, Hemshorn ML, Jones CM, Mbengi L, Meyer K, Griffis JA, Jana S, Petrina GE, Pagar VV, Karplus PA, Petersson EJ, Perona JJ, Mehl RA, Cooley RB. Generating Efficient Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetases for Structurally Diverse Non-Canonical Amino Acids. ACS Chem Biol 2022; 17:3458-3469. [PMID: 36383641 PMCID: PMC9833845 DOI: 10.1021/acschembio.2c00639] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Genetic code expansion (GCE) technologies commonly use the pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs from Methanosarcina mazei (Mm) and Methanosarcina barkeri (Mb) for site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. Recently a homologous PylRS/tRNAPyl pair from Candidatus Methanomethylophilus alvus Mx1201 (Ma) was developed that, lacking the N-terminal tRNA-recognition domain of most PylRSs, overcomes insolubility, instability, and proteolysis issues seen with Mb/Mm PylRSs. An open question is how to alter Ma PylRS specificity to encode specific ncAAs with high efficiency. Prior work focused on "transplanting" ncAA substrate specificity by reconstructing the same active site mutations found in functional Mm/Mb PylRSs in Ma PylRS. Here, we found that this strategy produced low-efficiency Ma PylRSs for encoding three structurally diverse ncAAs: acridonyl-alanine (Acd), 3-nitro-tyrosine, and m-methyl-tetrazinyl-phenylalanine (Tet3.0-Me). On the other hand, efficient Ma PylRS variants were generated by a conventional life/death selection process from a large library of active site mutants: for Acd encoding, one variant was highly functional in HEK293T cells at just 10 μM Acd; for nitroY encoding, two variants also encoded 3-chloro, 3-bromo-, and 3-iodo-tyrosine at high efficiency; and for Tet-3.0-Me, all variants were more functional at lower ncAA concentrations. All Ma PylRS variants identified through selection had at least two different active site residues when compared with their Mb PylRS counterparts. We conclude that Ma and Mm/Mb PylRSs are sufficiently different that "active site transplantation" yields suboptimal Ma GCE systems. This work establishes a paradigm for expanding the utility of the promising Ma PylRS/tRNAPyl GCE platform.
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Affiliation(s)
- Savanna Avila-Crump
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Marcus L. Hemshorn
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Chloe M. Jones
- Biochemistry and Molecular Biophysics Graduate Group; University of Pennsylvania; 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Lea Mbengi
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Kyle Meyer
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Joshua A. Griffis
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Subhashis Jana
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Grace E. Petrina
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Vinayak V. Pagar
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - John J. Perona
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
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Vicente M, Salgado-Almario J, Valiente-Gabioud AA, Collins MM, Vincent P, Domingo B, Llopis J. Early calcium and cardiac contraction defects in a model of phospholamban R9C mutation in zebrafish. J Mol Cell Cardiol 2022; 173:127-140. [PMID: 36273660 DOI: 10.1016/j.yjmcc.2022.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/28/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
The phospholamban mutation Arg 9 to Cys (R9C) has been found to cause a dilated cardiomyopathy in humans and in transgenic mice, with ventricular dilation and premature death. Emerging evidence suggests that phospholamban R9C is a loss-of-function mutation with dominant negative effect on SERCA2a activity. We imaged calcium and cardiac contraction simultaneously in 3 and 9 days-post-fertilization (dpf) zebrafish larvae expressing plnbR9C in the heart to unveil the early pathological pathway that triggers the disease. We generated transgenic zebrafish lines expressing phospholamban wild-type (Tg(myl7:plnbwt)) and phospholamban R9C (Tg(myl7:plnbR9C)) in the heart of zebrafish. To measure calcium and cardiac contraction in 3 and 9 dpf larvae, Tg(myl7:plnbwt) and Tg(myl7:plnbR9C) fish were outcrossed with a transgenic line expressing the ratiometric fluorescent calcium biosensor mCyRFP1-GCaMP6f. We found that PlnbR9C raised calcium transient amplitude, induced positive inotropy and lusitropy, and blunted the β-adrenergic response to isoproterenol in 3 dpf larvae. These effects can be attributed to enhanced SERCA2a activity induced by the PlnbR9C mutation. In contrast, Tg(myl7:plnbR9C) larvae at 9 dpf exhibited ventricular dilation, systolic dysfunction and negative lusitropy, hallmarks of a dilated cardiomyopathy in humans. Importantly, N-acetyl-L-cysteine rescued this deleterious phenotype, suggesting that reactive oxygen species contribute to the pathological pathway. These results also imply that dysregulation of calcium homeostasis during embryo development contributes to the disease progression at later stages. Our in vivo model in zebrafish allows characterization of pathophysiological mechanisms leading to heart disease, and can be used for screening of potential therapeutical agents.
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Affiliation(s)
- Manuel Vicente
- Physiology and Cell Dynamics Group, Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, C/Almansa 14, 02006 Albacete, Spain.
| | - Jussep Salgado-Almario
- Physiology and Cell Dynamics Group, Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, C/Almansa 14, 02006 Albacete, Spain
| | - Ariel A Valiente-Gabioud
- Tools for Bio-Imaging, Max-Planck-Institut für biologische Intelligenz, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Michelle M Collins
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, College of Medicine, SK S7N 5E5, Canada
| | - Pierre Vincent
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Beatriz Domingo
- Physiology and Cell Dynamics Group, Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, C/Almansa 14, 02006 Albacete, Spain.
| | - Juan Llopis
- Physiology and Cell Dynamics Group, Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, C/Almansa 14, 02006 Albacete, Spain.
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Liyanagedera SBW, Williams J, Wheatley JP, Biketova AY, Hasan M, Sagona AP, Purdy KJ, Puxty RJ, Feher T, Kulkarni V. SpyPhage: A Cell-Free TXTL Platform for Rapid Engineering of Targeted Phage Therapies. ACS Synth Biol 2022; 11:3330-3342. [PMID: 36194543 DOI: 10.1021/acssynbio.2c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The past decade has seen the emergence of multidrug resistant pathogens as a leading cause of death worldwide, reigniting interest in the field of phage therapy. Modern advances in the genetic engineering of bacteriophages have enabled several useful results including host range alterations, constitutive lytic growth, and control over phage replication. However, the slow licensing process of genetically modified organisms clearly inhibits the rapid therapeutic application of novel engineered variants necessary to fight mutant pathogens that emerge throughout the course of a pandemic. As a solution to this problem, we propose the SpyPhage system where a "scaffold" bacteriophage is engineered to incorporate a SpyTag moiety on its capsid head to enable rapid postsynthetic modification of their surfaces with SpyCatcher-fused therapeutic proteins. As a proof of concept, through CRISPR/Cas-facilitated phage engineering and whole genome assembly, we targeted a SpyTag capsid fusion to K1F, a phage targeting the pathogenic strain Escherichia coli K1. We demonstrate for the first time the cell-free assembly and decoration of the phage surface with two alternative fusion proteins, SpyCatcher-mCherry-EGF and SpyCatcher-mCherry-Rck, both of which facilitate the endocytotic uptake of the phages by a urinary bladder epithelial cell line. Overall, our work presents a cell-free phage production pipeline for the generation of multiple phenotypically distinct phages with a single underlying "scaffold" genotype. These phages could become the basis of next-generation phage therapies where the knowledge-based engineering of numerous phage variants would be quickly achievable without the use of live bacteria or the need to repeatedly license novel genetic alterations.
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Affiliation(s)
| | - Joshua Williams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Joseph P Wheatley
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alona Yu Biketova
- Institute of Biochemistry, Eötvös Lóránd Research Network, Szeged Biological Research Centre, Szeged 6726, Hungary.,Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Muhammad Hasan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tamas Feher
- Institute of Biochemistry, Eötvös Lóránd Research Network, Szeged Biological Research Centre, Szeged 6726, Hungary
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Vesely CH, Reardon PN, Yu Z, Barbar E, Mehl RA, Cooley RB. Accessing isotopically labeled proteins containing genetically encoded phosphoserine for NMR with optimized expression conditions. J Biol Chem 2022; 298:102613. [PMID: 36265582 PMCID: PMC9678770 DOI: 10.1016/j.jbc.2022.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Phosphoserine (pSer) sites are primarily located within disordered protein regions, making it difficult to experimentally ascertain their effects on protein structure and function. Therefore, the production of 15N- (and 13C)-labeled proteins with site-specifically encoded pSer for NMR studies is essential to uncover molecular mechanisms of protein regulation by phosphorylation. While genetic code expansion technologies for the translational installation of pSer in Escherichia coli are well established and offer a powerful strategy to produce site-specifically phosphorylated proteins, methodologies to adapt them to minimal or isotope-enriched media have not been described. This shortcoming exists because pSer genetic code expansion expression hosts require the genomic ΔserB mutation, which increases pSer bioavailability but also imposes serine auxotrophy, preventing growth in minimal media used for isotopic labeling of recombinant proteins. Here, by testing different media supplements, we restored normal BL21(DE3) ΔserB growth in labeling media but subsequently observed an increase of phosphatase activity and mis-incorporation not typically seen in standard rich media. After rounds of optimization and adaption of a high-density culture protocol, we were able to obtain ≥10 mg/L homogenously labeled, phosphorylated superfolder GFP. To demonstrate the utility of this method, we also produced the intrinsically disordered serine/arginine-rich region of the SARS-CoV-2 Nucleocapsid protein labeled with 15N and pSer at the key site S188 and observed the resulting peak shift due to phosphorylation by 2D and 3D heteronuclear single quantum correlation analyses. We propose this cost-effective methodology will pave the way for more routine access to pSer-enriched proteins for 2D and 3D NMR analyses.
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Affiliation(s)
- Cat Hoang Vesely
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Patrick N. Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon, USA
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Ryan A. Mehl
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Richard B. Cooley
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA,For correspondence: Richard B. Cooley
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45
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Cibelli A, Scemes E, Spray DC. Activity and Stability of Panx1 Channels in Astrocytes and Neuroblastoma Cells Are Enhanced by Cholesterol Depletion. Cells 2022; 11:3219. [PMID: 36291086 PMCID: PMC9600160 DOI: 10.3390/cells11203219] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/01/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Pannexin1 (Panx1) is expressed in both neurons and glia where it forms ATP-permeable channels that are activated under pathological conditions such as epilepsy, migraine, inflammation, and ischemia. Membrane lipid composition affects proper distribution and function of receptors and ion channels, and defects in cholesterol metabolism are associated with neurological diseases. In order to understand the impact of membrane cholesterol on the distribution and function of Panx1 in neural cells, we used fluorescence recovery after photobleaching (FRAP) to evaluate its mobility and electrophysiology and dye uptake to assess channel function. We observed that cholesterol extraction (using methyl-β-cyclodextrin) and inhibition of its synthesis (lovastatin) decreased the lateral diffusion of Panx1 in the plasma membrane. Panx1 channel activity (dye uptake, ATP release and ionic current) was enhanced in cholesterol-depleted Panx1 transfected cells and in wild-type astrocytes compared to non-depleted or Panx1 null cells. Manipulation of cholesterol levels may, therefore, offer a novel strategy by which Panx1 channel activation might modulate various pathological conditions.
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Affiliation(s)
- Antonio Cibelli
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Eliana Scemes
- Department of Cell Biology and Anatomy, NY Medical College, Valhalla, NY10595, USA
| | - David C. Spray
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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46
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Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, Weixlbaumer A. Structural insights into RNA-mediated transcription regulation in bacteria. Mol Cell 2022; 82:3885-3900.e10. [DOI: 10.1016/j.molcel.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/07/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
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47
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Iqbal Z, Sadaf S. A patent-based consideration of latest platforms in the art of directed evolution: a decade long untold story. Biotechnol Genet Eng Rev 2022; 38:133-246. [PMID: 35200115 DOI: 10.1080/02648725.2021.2017638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Directed (or in vitro) evolution of proteins and metabolic pathways requires tools for creating genetic diversity and identifying protein variants with new or improved functional properties. Besides simplicity, reliability, speed, versatility, universal applicability and economy of the technique, the new science of synthetic biology requires improved means for construction of smart and high-quality mutant libraries to better navigate the sequence diversity. In vitro CRISPR/Cas9-mediated mutagenic (ICM) system and machine-learning (ML)-assisted approaches to directed evolution are now in the field to achieve the goal. This review describes the gene diversification strategies, screening and selection methods, in silico (computer-aided), Cas9-mediated and ML-based approaches to mutagenesis, developed especially in the last decade, and their patent position. The objective behind is to emphasize researchers the need for noting which mutagenesis, screening or selection method is patented and then selecting a suitable restriction-free approach to sequence diversity. Techniques and evolved products subject to patent rights need commercial license if their use is for purposes other than private or experimental research.
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Affiliation(s)
- Zarina Iqbal
- IP Litigation Department, PakPat World Intellectual Property Protection Services, Lahore, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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48
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Jiang H, Meng F, Lu D, Chen Y, Luo G, Chen Y, Chen J, Chen C, Zhang X, Su D. High-throughput FastCloning technology: A low-cost method for parallel cloning. PLoS One 2022; 17:e0273873. [PMID: 36084059 PMCID: PMC9462701 DOI: 10.1371/journal.pone.0273873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
FastCloning, a reliable cloning technique for plasmid construction, is a widely used protocol in biomedical research laboratories. Only two-step molecular manipulations are required to add a gene (cDNA) of interest into the desired vector. However, parallel cloning of the gene into multiple vectors is still a labor-intensive operation, which requires a range of primers for different vectors in high-throughput cloning projects. The situation could even be worse if multiple fragments of DNA are required to be added into one plasmid. Here, we describe a high-throughput FastCloning (HTFC) method, a protocol for parallel cloning by adding an adaptor sequence into all vectors. The target gene and vectors were PCR amplified separately to obtain the insert product and linear vectors with 18-base overlapping at each end of the DNAs required for FastCloning. Furthermore, a method for generating polycistronic bacterial constructs based on the same strategy as that used for HTFC was developed. Thus, the HTFC technique is a simple, effective, reliable, and low-cost tool for parallel cloning.
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Affiliation(s)
- Hua Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Fan Meng
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Deren Lu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yanjuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Guilin Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yuejun Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Jun Chen
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Cheng Chen
- Department of Gynecology and Obstetrics, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P.R. China
| | - Xi Zhang
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, P.R. China
| | - Dan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, P.R. China
- * E-mail:
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49
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Pillay LM, Yano JJ, Davis AE, Butler MG, Ezeude MO, Park JS, Barnes KA, Reyes VL, Castranova D, Gore AV, Swift MR, Iben JR, Kenton MI, Stratman AN, Weinstein BM. In vivo dissection of Rhoa function in vascular development using zebrafish. Angiogenesis 2022; 25:411-434. [PMID: 35320450 DOI: 10.1007/s10456-022-09834-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 02/22/2022] [Indexed: 12/27/2022]
Abstract
The small monomeric GTPase RHOA acts as a master regulator of signal transduction cascades by activating effectors of cellular signaling, including the Rho-associated protein kinases ROCK1/2. Previous in vitro cell culture studies suggest that RHOA can regulate many critical aspects of vascular endothelial cell (EC) biology, including focal adhesion, stress fiber formation, and angiogenesis. However, the specific in vivo roles of RHOA during vascular development and homeostasis are still not well understood. In this study, we examine the in vivo functions of RHOA in regulating vascular development and integrity in zebrafish. We use zebrafish RHOA-ortholog (rhoaa) mutants, transgenic embryos expressing wild type, dominant negative, or constitutively active forms of rhoaa in ECs, pharmacological inhibitors of RHOA and ROCK1/2, and Rock1 and Rock2a/b dgRNP-injected zebrafish embryos to study the in vivo consequences of RHOA gain- and loss-of-function in the vascular endothelium. Our findings document roles for RHOA in vascular integrity, developmental angiogenesis, and vascular morphogenesis in vivo, showing that either too much or too little RHOA activity leads to vascular dysfunction.
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Affiliation(s)
- Laura M Pillay
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Joseph J Yano
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
- Department of Cell and Molecular Biology, University of Pennsylvania, 440 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Andrew E Davis
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Matthew G Butler
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Megan O Ezeude
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Jong S Park
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Keith A Barnes
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Vanessa L Reyes
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Daniel Castranova
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Aniket V Gore
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Matthew R Swift
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - James R Iben
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Madeleine I Kenton
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
| | - Amber N Stratman
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brant M Weinstein
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Dr. Bethesda, Bethesda, MD, 20892, USA.
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50
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Simple and reliable in situ CRISPR-Cas9 nuclease visualization tool is ensuring efficient editing in Streptomyces species. METHODS IN MICROBIOLOGY 2022; 200:106545. [DOI: 10.1016/j.mimet.2022.106545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022]
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