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Valladares-Hernández IU, Hernández-Martínez JM, Cuaxospa JM, Jiménez-Vázquez EN, Sánchez-Jaramillo E, Arias JM, García U. Molecular cloning, functional characterization and differential expression of two novel GABA AR-like subunits from red swamp crayfish Procambarus clarkii. Eur J Neurosci 2024. [PMID: 39275952 DOI: 10.1111/ejn.16540] [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: 07/19/2023] [Revised: 08/09/2024] [Accepted: 08/29/2024] [Indexed: 09/16/2024]
Abstract
In this work, we cloned and functionally expressed two novel GABAA receptor subunits from Procambarus clarkii crayfish. These two new subunits, PcGABAA-α and PcGABAA-β2, revealed significant sequence homology with the PcGABAA-β subunit, previously identified in our laboratory. In addition, PcGABAA-α subunit also shared a significant degree of identity with the Drosophila melanogaster genes DmGRD (GABA and glycine-like receptor subunits of Drosophila) as well as PcGABAA-β2 subunit with DmLCCH3 (ligand-gated chloride channel homolog 3). Electrophysiological recordings showed that the expression in HEK cells of the novel subunits, either alone or in combination, failed to form functional homo- or heteromeric receptors. However, the co-expression of PcGABAA-α with PcGABAA-β evoked sodium- or chloride-dependent currents that accurately reproduced the time course of the GABA-evoked currents in the X-organ neurons from crayfish, suggesting that these GABA subunits combine to form two types of GABA receptors, one with cationic selectivity filter and the other preferentially permeates anions. On the other hand, PcGABAA-β2 and PcGABAA-β co-expression generated a chloride current that does not show desensitization. Muscimol reproduced the time course of GABA-evoked currents in all functional receptors, and picrotoxin blocked these currents; bicuculline did not block any of the recorded currents. Reverse transcription polymerae chain reaction (RT-PCR) amplifications and FISH revealed that PcGABAA-α and PcGABAA-β2 are predominantly expressed in the crayfish nervous system. Altogether, these findings provide the first evidence of a neural GABA-gated cationic channel in the crayfish, increasing our understanding of the role of these new GABAA receptor subunits in native heteromeric receptors.
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Affiliation(s)
- Iván Uriel Valladares-Hernández
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Juan Manuel Hernández-Martínez
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - José Miguel Cuaxospa
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | | | - Edith Sánchez-Jaramillo
- Laboratorio de Neuroendocrinología Molecular, Dirección de Investigaciones en Neurociencias, Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Ciudad de México, Mexico
| | - Juan Manuel Arias
- Proyecto de Neurociencias, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Ubaldo García
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
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Bissonnette N, Brousseau JP, Ollier S, Byrne AS, Ibeagha-Awemu EM, Tahlan K. Systematic assessment of the reliability of quantitative PCR assays targeting IS900 for the detection of Mycobacterium avium ssp. paratuberculosis presence in animal and environmental samples. J Dairy Sci 2024; 107:7165-7184. [PMID: 38754821 DOI: 10.3168/jds.2023-24566] [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: 12/18/2023] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the bacterium responsible for causing Johne's disease (JD), which is endemic to dairy cattle and also implicated in the etiology of Crohn's disease. The difficulty in diagnosing asymptomatic cows for JD makes this disease hard to control. Johne's disease is considered a priority under the One Health approach to prevent the spread of the causative agent to humans. Environmental screening is a strategic approach aimed at identifying dairy herds with animals infected with MAP. It serves as the initial step toward implementing more intensive actions to control the disease. Quantitative PCR (qPCR) technology is widely used for diagnosis. Given that genome sequencing is now much more accessible than ever before, it is possible to target regions of the MAP genome that allow for the greatest diagnostic sensitivity and specificity. The aim of this study was to identify among the published qPCR assays targeting IS900 the more cost-effective options to detect MAP and to validate them in the diagnostic context of JD. Mycobacterium avium ssp. paratuberculosis IS900 is a prime target because it is a multicopy genetic element. A total of 136 publications have reported on the use of IS900 qPCR assays over the past 3 decades. Among these records, 29 used the SYBR Green chemistry, and 107 used TaqMan technology. Aside from the 9 reports using commercial assays, 72 TaqMan reports cited previously published work, leaving us with 27 TaqMan qPCR designs. Upon closer examination, 5 TaqMan designs contained mismatches in primer or probe sequences. Additionally, others exhibited high similarity to environmental microorganisms or non-MAP mycobacteria. We assessed the performance of 6 IS900 qPCR designs and their sensitivity when applied to clinical or environmental samples, which varied from 4 to 56 fold overall. Additionally, we provide recommendations for testing clinical and environmental samples, as certain strategies used previously should be avoided due to poor qPCR design (e.g., the presence of mismatches) or a lack of specificity.
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Affiliation(s)
- N Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada.
| | - J-P Brousseau
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - S Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - A S Byrne
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - E M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - K Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
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Le CT, Jeung HD, Cho YG, Choi KS. Survey of trematodes in Manila clam Ruditapes philippinarum on the west coast of Korea: A preliminary study. J Invertebr Pathol 2024; 206:108172. [PMID: 39111566 DOI: 10.1016/j.jip.2024.108172] [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: 06/28/2023] [Revised: 07/13/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024]
Abstract
The Manila clam Ruditapes philippinarum on the west coast of Korea harbors several digenetic trematodes. However, most studies in this region have been restricted to a few sampling sites and the current species designation of some trematodes is largely based on morphology, leaving the molecular phylogenetic position among the Digenea unsolved. Thus, we first provide both morphology and molecular phylogeny of some components in the trematodes community in the Manila clam based on a large-scale survey of 26 sites on the west coast, where well-developed tidal flats serve as large commercial clam culture beds. Our study revealed that the trematodes community in the clams consisted of at least 5 species that belong to 3 families (Himasthlidae, Gymnophallidae, Baccigeridae) and 1 superfamily (Monorchioidea). The life mode of the 5 different species included the metacercaria and sporocyst, with one species (Parvatrema duboisi) utilizing the clams as both the first and/or second intermediate host. Trematode infection prevalences were not evenly distributed among the study sites, although the reasons behind this are yet to be determined. Morphological identification was confirmed with the molecular analyses based on ITS and 28S rDNA; phylogenetic analysis also revealed that Cercaria pectinata infecting the clam gonad should be referred to as Bacciger bacciger hereafter. The present preliminary study provides a crucial baseline that could be further developed in a future study on the digenean trematodes community in the Manila clam.
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Affiliation(s)
- Cuong Thanh Le
- Department of Marine Life Science (BK21 FOUR) and Marine Science Institute, Jeju National University, 102 Jejudaehakno, Jeju 63243, Republic of Korea; Institute for Aquaculture, Nha Trang University, 02 Nguyen Dinh Chieu, Nhatrang, Viet Nam
| | - Hee-Do Jeung
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan 54001, Republic of Korea
| | - Young-Ghan Cho
- Department of Marine Life Science (BK21 FOUR) and Marine Science Institute, Jeju National University, 102 Jejudaehakno, Jeju 63243, Republic of Korea; Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan 54001, Republic of Korea.
| | - Kwang-Sik Choi
- Department of Marine Life Science (BK21 FOUR) and Marine Science Institute, Jeju National University, 102 Jejudaehakno, Jeju 63243, Republic of Korea.
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Walther RE, Hrabak M, Bernstein DA. How advancements in molecular biology impact education and training. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024; 25:e0006124. [PMID: 38975770 PMCID: PMC11360415 DOI: 10.1128/jmbe.00061-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024]
Abstract
Molecular biology, broadly defined as the investigation of complex biomolecules in the laboratory, is a rapidly advancing field and as such the technologies available to investigators are constantly evolving. This constant advancement has obvious advantages because it allows students and researchers to perform more complex experiments in shorter periods of time. One challenge with such a rapidly advancing field is that techniques that had been vital for students to learn how to perform are now not essential for a laboratory scientist. For example, while cloning a gene in the past could have led to a publication and form the bulk of a PhD thesis project, technology has now made this process only a step toward one of these larger goals and can, in many cases, be performed by a company or core facility. As teachers and mentors, it is imperative that we understand that the technologies we teach in the lab and classroom must also evolve to match these advancements. In this perspective, we discuss how the rapid advances in gene synthesis technologies are affecting curriculum and how our classrooms should evolve to ensure our lessons prepare students for the world in which they will do science.
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Romero A, Sanchez A, Jones JD, Ledesma K, El-Halawany MS, Hamouda AK, Bill BR. Optimization of Zebrafish Larvae 6-OHDA Exposure for Neurotoxin Induced Dopaminergic Marker Reduction. Zebrafish 2024; 21:287-293. [PMID: 38608227 DOI: 10.1089/zeb.2023.0098] [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: 04/14/2024] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that is clinically assessed by motor symptoms associated with the loss of midbrain dopaminergic neurons affecting the quality of life for over 8.5 million people worldwide. The neurotoxin 6-hydroxydopamine (6-OHDA) has been used to chemically induce a PD-like state in zebrafish larvae by several laboratories; however, highly variable concentration, methodology, and reagents have resulted in conflicting results suggesting a need to investigate these issues of reproducibility. We propose a protocol that addresses the differences in methodology and induces changes in 6 days postfertilization (dpf) larvae utilizing a 24-h exposure at 3 dpf with 30 μM 6-OHDA. Despite ∼50% lethality, no morphological or development differences in surviving fish are observed. Definition of our model is defined by downregulation of the expression of th1 by reverse transcriptase-quantitative polymerase chain reaction, a marker for dopaminergic neurons and a reduction in movement. Additionally, we observed a downregulation of pink1 and an upregulation of sod1 and sod2, indicators of mitochondrial dysfunction and response to reactive oxygen species, respectively.
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Affiliation(s)
- Adrian Romero
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Armando Sanchez
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Jocelyn D Jones
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Kristel Ledesma
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Medhat S El-Halawany
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Ayman K Hamouda
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Brent R Bill
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
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Binti S, Linder AG, Edeen PT, Fay DS. A conserved protein tyrosine phosphatase, PTPN-22, functions in diverse developmental processes in C. elegans. PLoS Genet 2024; 20:e1011219. [PMID: 39173071 PMCID: PMC11373843 DOI: 10.1371/journal.pgen.1011219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 09/04/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
Protein tyrosine phosphatases non-receptor type (PTPNs) have been studied extensively in the context of the adaptive immune system; however, their roles beyond immunoregulation are less well explored. Here we identify novel functions for the conserved C. elegans phosphatase PTPN-22, establishing its role in nematode molting, cell adhesion, and cytoskeletal regulation. Through a non-biased genetic screen, we found that loss of PTPN-22 phosphatase activity suppressed molting defects caused by loss-of-function mutations in the conserved NIMA-related kinases NEKL-2 (human NEK8/NEK9) and NEKL-3 (human NEK6/NEK7), which act at the interface of membrane trafficking and actin regulation. To better understand the functions of PTPN-22, we carried out proximity labeling studies to identify candidate interactors of PTPN-22 during development. Through this approach we identified the CDC42 guanine-nucleotide exchange factor DNBP-1 (human DNMBP) as an in vivo partner of PTPN-22. Consistent with this interaction, loss of DNBP-1 also suppressed nekl-associated molting defects. Genetic analysis, co-localization studies, and proximity labeling revealed roles for PTPN-22 in several epidermal adhesion complexes, including C. elegans hemidesmosomes, suggesting that PTPN-22 plays a broad role in maintaining the structural integrity of tissues. Localization and proximity labeling also implicated PTPN-22 in functions connected to nucleocytoplasmic transport and mRNA regulation, particularly within the germline, as nearly one-third of proteins identified by PTPN-22 proximity labeling are known P granule components. Collectively, these studies highlight the utility of combined genetic and proteomic approaches for identifying novel gene functions.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Adison G Linder
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Philip T Edeen
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
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Hou S, Chen J, Feng R, Xu X, Liang N, Champer J. A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance. J Genet Genomics 2024; 51:836-843. [PMID: 38599514 DOI: 10.1016/j.jgg.2024.04.001] [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: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
CRISPR homing gene drives have considerable potential for managing populations of medically and agriculturally significant insects. They operate by Cas9 cleavage followed by homology-directed repair, copying the drive allele to the wild-type chromosome and thus increasing in frequency and spreading throughout a population. However, resistance alleles formed by end-joining repair pose a significant obstacle. To address this, we create a homing drive targeting the essential hairy gene in Drosophila melanogaster. Nonfunctional resistance alleles are recessive lethal, while drive carriers have a recoded "rescue" version of hairy. The drive inheritance rate is moderate, and multigenerational cage studies show drive spread to 96%-97% of the population. However, the drive does not reach 100% due to the formation of functional resistance alleles despite using four gRNAs. These alleles have a large deletion but likely utilize an alternate start codon. Thus, revised designs targeting more essential regions of a gene may be necessary to avoid such functional resistance. Replacement of the rescue element's native 3' UTR with a homolog from another species increases drive inheritance by 13%-24%. This was possibly because of reduced homology between the rescue element and surrounding genomic DNA, which could also be an important design consideration for rescue gene drives.
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Affiliation(s)
- Shibo Hou
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingheng Chen
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruobing Feng
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuejiao Xu
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Nan Liang
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jackson Champer
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.
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Sumathipala SH, Khan S, Kozol RA, Araki Y, Syed S, Huganir RL, Dallman JE. Context-dependent hyperactivity in syngap1a and syngap1b zebrafish models of SYNGAP1-related disorder. Front Mol Neurosci 2024; 17:1401746. [PMID: 39050824 PMCID: PMC11266194 DOI: 10.3389/fnmol.2024.1401746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/04/2024] [Indexed: 07/27/2024] Open
Abstract
Background and aims SYNGAP1-related disorder (SYNGAP1-RD) is a prevalent genetic form of Autism Spectrum Disorder and Intellectual Disability (ASD/ID) and is caused by de novo or inherited mutations in one copy of the SYNGAP1 gene. In addition to ASD/ID, SYNGAP1 disorder is associated with comorbid symptoms including treatment-resistant-epilepsy, sleep disturbances, and gastrointestinal distress. Mechanistic links between these diverse symptoms and SYNGAP1 variants remain obscure, therefore, our goal was to generate a zebrafish model in which this range of symptoms can be studied. Methods We used CRISPR/Cas9 to introduce frameshift mutations in the syngap1a and syngap1b zebrafish duplicates (syngap1ab) and validated these stable models for Syngap1 loss-of-function. Because SYNGAP1 is extensively spliced, we mapped splice variants to the two zebrafish syngap1a and b genes and identified mammalian-like isoforms. We then quantified locomotory behaviors in zebrafish syngap1ab larvae under three conditions that normally evoke different arousal states in wild-type larvae: aversive, high-arousal acoustic, medium-arousal dark, and low-arousal light stimuli. Results We show that CRISPR/Cas9 indels in zebrafish syngap1a and syngap1b produced loss-of-function alleles at RNA and protein levels. Our analyses of zebrafish Syngap1 isoforms showed that, as in mammals, zebrafish Syngap1 N- and C-termini are extensively spliced. We identified a zebrafish syngap1 α1-like variant that maps exclusively to the syngap1b gene. Quantifying locomotor behaviors showed that syngap1ab mutant larvae are hyperactive compared to wild-type but to differing degrees depending on the stimulus. Hyperactivity was most pronounced in low arousal settings, and hyperactivity was proportional to the number of mutant syngap1 alleles. Limitations Syngap1 loss-of-function mutations produce relatively subtle phenotypes in zebrafish compared to mammals. For example, while mouse Syngap1 homozygotes die at birth, zebrafish syngap1ab-/- survive to adulthood and are fertile, thus some aspects of symptoms in people with SYNGAP1-Related Disorder are not likely to be reflected in zebrafish. Conclusion Our data support mutations in zebrafish syngap1ab as causal for hyperactivity associated with elevated arousal that is especially pronounced in low-arousal environments.
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Affiliation(s)
- Sureni H. Sumathipala
- Department of Biology, University of Miami, Coral Gables, FL, United States
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Suha Khan
- Department of Biology, University of Miami, Coral Gables, FL, United States
| | - Robert A. Kozol
- Department of Biology, University of Miami, Coral Gables, FL, United States
- Department of Biological Sciences, St. John’s University, Queens, NY, United States
| | - Yoichi Araki
- Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sheyum Syed
- Department of Physics, University of Miami, Coral Gables, FL, United States
| | - Richard L. Huganir
- Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Julia E. Dallman
- Department of Biology, University of Miami, Coral Gables, FL, United States
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Kojima L, Seiriki K, Rokujo H, Nakazawa T, Kasai A, Hashimoto H. Optimization of AAV vectors for transactivator-regulated enhanced gene expression within targeted neuronal populations. iScience 2024; 27:109878. [PMID: 38799556 PMCID: PMC11126825 DOI: 10.1016/j.isci.2024.109878] [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: 09/13/2023] [Revised: 03/03/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Adeno-associated virus (AAV) vectors are potential tools for cell-type-selective gene delivery to the central nervous system. Although cell-type-specific enhancers and promoters have been identified for AAV systems, there is limited information regarding the effects of AAV genomic components on the selectivity and efficiency of gene expression. Here, we offer an alternative strategy to provide specific and efficient gene delivery to a targeted neuronal population by optimizing recombinant AAV genomic components, named TAREGET (TransActivator-Regulated Enhanced Gene Expression within Targeted neuronal populations). We established this strategy in oxytocinergic neurons and showed that the TAREGET enabled sufficient gene expression to label long-projecting axons in wild-type mice. Its application to other cell types, including serotonergic and dopaminergic neurons, was also demonstrated. These results demonstrate that optimization of AAV expression cassettes can improve the specificity and efficiency of cell-type-specific gene expression and that TAREGET can renew previously established cell-type-specific promoters with improved performance.
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Affiliation(s)
- Leo Kojima
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kaoru Seiriki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroki Rokujo
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takanobu Nakazawa
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Atsushi Kasai
- Systems Neuropharmacology, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
- Molecular Research Center for Children’s Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka 565-0871, Japan
- Institute for Datability Science, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Molecular Pharmaceutical Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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10
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Wisner SR, Chlebowski M, Mandal A, Mai D, Stein C, Petralia RS, Wang YX, Drerup CM. An initial HOPS-mediated fusion event is critical for autophagosome transport initiation from the axon terminal. Autophagy 2024:1-22. [PMID: 38899385 DOI: 10.1080/15548627.2024.2366122] [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: 12/03/2023] [Revised: 05/22/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
In neurons, macroautophagy/autophagy is a frequent and critical process. In the axon, autophagy begins in the axon terminal, where most nascent autophagosomes form. After formation, autophagosomes must initiate transport to exit the axon terminal and move toward the cell body via retrograde transport. During retrograde transport these autophagosomes mature through repetitive fusion events. Complete lysosomal cargo degradation occurs largely in the cell body. The precipitating events to stimulate retrograde autophagosome transport have been debated but their importance is clear: disrupting neuronal autophagy or autophagosome transport is detrimental to neuronal health and function. We have identified the HOPS complex as essential for early autophagosome maturation and consequent initiation of retrograde transport from the axon terminal. In yeast and mammalian cells, HOPS controls fusion between autophagosomes and late endosomes with lysosomes. Using zebrafish strains with loss-of-function mutations in vps18 and vps41, core components of the HOPS complex, we found that disruption of HOPS eliminates autophagosome maturation and disrupts retrograde autophagosome transport initiation from the axon terminal. We confirmed this phenotype was due to loss of HOPS complex formation using an endogenous deletion of the HOPS binding domain in Vps18. Finally, using pharmacological inhibition of lysosomal proteases, we show that initiation of autophagosome retrograde transport requires autophagosome maturation. Together, our data demonstrate that HOPS-mediated fusion events are critical for retrograde autophagosome transport initiation through promoting autophagosome maturation. This reveals critical roles for the HOPS complex in neuronal autophagy which deepens our understanding of the cellular pathology of HOPS-complex linked neurodegenerative diseases.Abbreviations: CORVET: Class C core vacuole/endosome tethering; gRNA: guide RNA; HOPS: homotypic fusion and protein sorting; pLL: posterior lateral line; Vps18: VPS18 core subunit of CORVET and HOPS complexes; Vps41: VPS41 subunit of HOPS complex.
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Affiliation(s)
- Serena R Wisner
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Madison Chlebowski
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Amrita Mandal
- National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Don Mai
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Stein
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ronald S Petralia
- Advanced Imaging Core, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Ya-Xian Wang
- Advanced Imaging Core, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Catherine M Drerup
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
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11
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Miles LB, Calcinotto V, Oveissi S, Serrano RJ, Sonntag C, Mulia O, Lee C, Bryson-Richardson RJ. CRIMP: a CRISPR/Cas9 insertional mutagenesis protocol and toolkit. Nat Commun 2024; 15:5011. [PMID: 38866742 PMCID: PMC11169554 DOI: 10.1038/s41467-024-49341-7] [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: 08/23/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Site-directed insertion is a powerful approach for generating mutant alleles, but low efficiency and the need for customisation for each target has limited its application. To overcome this, we developed a highly efficient targeted insertional mutagenesis system, CRIMP, and an associated plasmid toolkit, CRIMPkit, that disrupts native gene expression by inducing complete transcriptional termination, generating null mutant alleles without inducing genetic compensation. The protocol results in a high frequency of integration events and can generate very early targeted insertions, during the first cell division, producing embryos with expression in one or both halves of the body plan. Fluorescent readout of integration events facilitates selection of successfully mutagenized fish and, subsequently, visual identification of heterozygous and mutant animals. Together, these advances greatly improve the efficacy of generating and studying mutant lines. The CRIMPkit contains 24 ready-to-use plasmid vectors to allow easy and complete mutagenesis of any gene in any reading frame without requiring custom sequences, modification, or subcloning.
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Affiliation(s)
- Lee B Miles
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Vanessa Calcinotto
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Sara Oveissi
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Rita J Serrano
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Carmen Sonntag
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Orlen Mulia
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Clara Lee
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia
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Giffen KP, Liu H, Yamane KL, Li Y, Chen L, Kramer KL, Zallocchi M, He DZ. Molecular Specializations Underlying Phenotypic Differences in Inner Ear Hair Cells of Zebrafish and Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595729. [PMID: 38826418 PMCID: PMC11142236 DOI: 10.1101/2024.05.24.595729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Hair cells (HCs) are the sensory receptors of the auditory and vestibular systems in the inner ears of vertebrates that selectively transduce mechanical stimuli into electrical activity. Although all HCs have the hallmark stereocilia bundle for mechanotransduction, HCs in non-mammals and mammals differ in their molecular specialization in the apical, basolateral and synaptic membranes. HCs of non-mammals, such as zebrafish (zHCs), are electrically tuned to specific frequencies and possess an active process in the stereocilia bundle to amplify sound signals. Mammalian cochlear HCs, in contrast, are not electrically tuned and achieve amplification by somatic motility of outer HCs (OHCs). To understand the genetic mechanisms underlying differences among adult zebrafish and mammalian cochlear HCs, we compared their RNA-seq-characterized transcriptomes, focusing on protein-coding orthologous genes related to HC specialization. There was considerable shared expression of gene orthologs among the HCs, including those genes associated with mechanotransduction, ion transport/channels, and synaptic signaling. For example, both zebrafish and mouse HCs express Tmc1, Lhfpl5, Tmie, Cib2, Cacna1d, Cacnb2, Otof, Pclo and Slc17a8. However, there were some notable differences in expression among zHCs, OHCs, and inner HCs (IHCs), which likely underlie the distinctive physiological properties of each cell type. Tmc2 and Cib3 were not detected in adult mouse HCs but tmc2a and b and cib3 were highly expressed in zHCs. Mouse HCs express Kcna10, Kcnj13, Kcnj16, and Kcnq4, which were not detected in zHCs. Chrna9 and Chrna10 were expressed in mouse HCs. In contrast, chrna10 was not detected in zHCs. OHCs highly express Slc26a5 which encodes the motor protein prestin that contributes to OHC electromotility. However, zHCs have only weak expression of slc26a5, and subsequently showed no voltage dependent electromotility when measured. Notably, the zHCs expressed more paralogous genes including those associated with HC-specific functions and transcriptional activity, though it is unknown whether they have functions similar to their mammalian counterparts. There was overlap in the expressed genes associated with a known hearing phenotype. Our analyses unveil substantial differences in gene expression patterns that may explain phenotypic specialization of zebrafish and mouse HCs. This dataset also includes several protein-coding genes to further the functional characterization of HCs and study of HC evolution from non-mammals to mammals.
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Affiliation(s)
- Kimberlee P. Giffen
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
- Augusta University/University of Georgia Medical Partnership, Athens, GA, USA
| | - Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Kacey L. Yamane
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Yi Li
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
- Department of Otorhinolaryngology, Beijing Tongren Hospital, Beijing Capital Medical University, Beijing, China
| | - Lei Chen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Ken L. Kramer
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Marisa Zallocchi
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - David Z.Z. He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
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13
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Gonçalves AAM, Ribeiro AJ, Resende CAA, Couto CAP, Gandra IB, Dos Santos Barcelos IC, da Silva JO, Machado JM, Silva KA, Silva LS, Dos Santos M, da Silva Lopes L, de Faria MT, Pereira SP, Xavier SR, Aragão MM, Candida-Puma MA, de Oliveira ICM, Souza AA, Nogueira LM, da Paz MC, Coelho EAF, Giunchetti RC, de Freitas SM, Chávez-Fumagalli MA, Nagem RAP, Galdino AS. Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis. Microb Cell Fact 2024; 23:145. [PMID: 38778337 PMCID: PMC11110257 DOI: 10.1186/s12934-024-02418-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: 01/31/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes' high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits.
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Affiliation(s)
- Ana Alice Maia Gonçalves
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Anna Julia Ribeiro
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carlos Ananias Aparecido Resende
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carolina Alves Petit Couto
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isadora Braga Gandra
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isabelle Caroline Dos Santos Barcelos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Jonatas Oliveira da Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Juliana Martins Machado
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Kamila Alves Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Líria Souza Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Michelli Dos Santos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Lucas da Silva Lopes
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Teixeira de Faria
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sabrina Paula Pereira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sandra Rodrigues Xavier
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Matheus Motta Aragão
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Mayron Antonio Candida-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | | | - Amanda Araujo Souza
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Lais Moreira Nogueira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Campos da Paz
- Bioactives and Nanobiotechnology Laboratory, Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Eduardo Antônio Ferraz Coelho
- Postgraduate Program in Health Sciences, Infectious Diseases and Tropical Medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, 30130-100, Brazil
| | - Rodolfo Cordeiro Giunchetti
- Laboratory of Biology of Cell Interactions, National Institute of Science and Technology on Tropical Diseases (INCT-DT), Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Sonia Maria de Freitas
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | - Ronaldo Alves Pinto Nagem
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Alexsandro Sobreira Galdino
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil.
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Basta DW, Campbell IW, Sullivan EJ, Hotinger JA, Hullahalli K, Waldor MK. Inducible transposon mutagenesis for genome-scale forward genetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595064. [PMID: 38826325 PMCID: PMC11142078 DOI: 10.1101/2024.05.21.595064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Transposon insertion sequencing (Tn-seq) is a powerful method for genome-scale functional genetics in bacteria. However, its effectiveness is often limited by a lack of mutant diversity, caused by either inefficient transposon delivery or stochastic loss of mutants due to population bottlenecks. Here, we introduce "InducTn-seq", which leverages inducible mutagenesis for temporal control of transposition. InducTn-seq generates millions of transposon mutants from a single colony, enabling the sensitive detection of subtle fitness defects and transforming binary classifications of gene essentiality into a quantitative fitness measurement across both essential and non-essential genes. Using a mouse model of infectious colitis, we show that InducTn-seq bypasses a highly restrictive host bottleneck to generate a diverse transposon mutant population from the few cells that initiate infection, revealing the role of oxygen-related metabolic plasticity in pathogenesis. Overall, InducTn-seq overcomes the limitations of traditional Tn-seq, unlocking new possibilities for genome-scale forward genetic screens in bacteria.
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Affiliation(s)
- David W. Basta
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ian W. Campbell
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Emily J. Sullivan
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Julia A Hotinger
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Karthik Hullahalli
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
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15
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Sousa J, Santos-Pereira C, Gomes JS, Costa ÂMA, Santos AO, Franco-Duarte R, Linhares JMM, Sousa SF, Silvério SC, Rodrigues LR. Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library. Appl Microbiol Biotechnol 2024; 108:329. [PMID: 38727750 PMCID: PMC11087322 DOI: 10.1007/s00253-024-13169-4] [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: 01/10/2024] [Revised: 04/22/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Xylanases are key biocatalysts in the degradation of the β-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-β-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-β-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.
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Affiliation(s)
- Joana Sousa
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cátia Santos-Pereira
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana S Gomes
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ângela M A Costa
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andréia O Santos
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S - Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - João M M Linhares
- Physics Center of Minho and Porto Universities (CF-UM-UP), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sérgio F Sousa
- LAQV/REQUIMTE BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sara C Silvério
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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16
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Kim MJ, Simms S, Behnammanesh G, Honkura Y, Suzuki J, Park HJ, Milani M, Katori Y, Bird JE, Ikeda A, Someya S. A Mutation in Tmem135 Causes Progressive Sensorineural Hearing Loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593414. [PMID: 38766120 PMCID: PMC11100813 DOI: 10.1101/2024.05.09.593414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Transmembrane protein 135 (TMEM135) is a 52 kDa protein with five predicted transmembrane domains that is highly conserved across species. Previous studies have shown that TMEM135 is involved in mitochondrial dynamics, thermogenesis, and lipid metabolism in multiple tissues; however, its role in the inner ear or the auditory system is unknown. We investigated the function of TMEM135 in hearing using wild-type (WT) and Tmem135 FUN025/FUN025 ( FUN025 ) mutant mice on a CBA/CaJ background, a normal-hearing mouse strain. Although FUN025 mice displayed normal auditory brainstem response (ABR) at 1 month, we observed significantly elevated ABR thresholds at 8, 16, and 64 kHz by 3 months, which progressed to profound hearing loss by 12 months. Consistent with our auditory testing, 13-month-old FUN025 mice exhibited a severe loss of outer hair cells and spiral ganglion neurons in the cochlea. Our results using BaseScope in situ hybridization indicate that TMEM135 is expressed in the inner hair cells, outer hair cells, and supporting cells. Together, these results demonstrate that the FUN025 mutation in Tmem135 causes progressive sensorineural hearing loss, and suggest that TMEM135 is crucial for maintaining key cochlear cell types and normal sensory function in the aging cochlea.
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Haslam TM, Herrfurth C, Feussner I. Diverse INOSITOL PHOSPHORYLCERAMIDE SYNTHASE mutant alleles of Physcomitrium patens offer new insight into complex sphingolipid metabolism. THE NEW PHYTOLOGIST 2024; 242:1189-1205. [PMID: 38523559 DOI: 10.1111/nph.19667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
Sphingolipids are widespread, abundant, and essential lipids in plants and in other eukaryotes. Glycosyl inositol phosphorylceramides (GIPCs) are the most abundant class of plant sphingolipids, and are enriched in the plasma membrane of plant cells. They have been difficult to study due to lethal or pleiotropic mutant phenotypes. To overcome this, we developed a CRISPR/Cas9-based method for generating multiple and varied knockdown and knockout populations of mutants in a given gene of interest in the model moss Physcomitrium patens. This system is uniquely convenient due to the predominantly haploid state of the Physcomitrium life cycle, and totipotency of Physcomitrium protoplasts used for transformation. We used this approach to target the INOSITOL PHOSPHORYLCERAMIDE SYNTHASE (IPCS) gene family, which catalyzes the first, committed step in the synthesis of GIPCs. We isolated knockout single mutants and knockdown higher-order mutants showing a spectrum of deficiencies in GIPC content. Remarkably, we also identified two mutant alleles accumulating inositol phosphorylceramides, the direct products of IPCS activity, and provide our best explanation for this unexpected phenotype. Our approach is broadly applicable for studying essential genes and gene families, and for obtaining unusual lesions within a gene of interest.
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Affiliation(s)
- Tegan M Haslam
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, D-37077, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, D-37077, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, D-37077, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, D-37077, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, D-37077, Germany
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18
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Zelikson N, Ben S, Caspi M, Tarabe R, Shaleve Y, Pri-Paz Basson Y, Tayer-Shifman O, Goldberg E, Kivity S, Rosin-Arbesfeld R. Wnt signaling regulates chemokine production and cell migration of circulating human monocytes. Cell Commun Signal 2024; 22:229. [PMID: 38622714 PMCID: PMC11020454 DOI: 10.1186/s12964-024-01608-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The β-catenin dependent canonical Wnt signaling pathway plays a crucial role in maintaining normal homeostasis. However, when dysregulated, Wnt signaling is closely associated with various pathological conditions, including inflammation and different types of cancer.Here, we show a new connection between the leukocyte inflammatory response and the Wnt signaling pathway. Specifically, we demonstrate that circulating human primary monocytes express distinct Wnt signaling components and are susceptible to stimulation by the classical Wnt ligand-Wnt-3a. Although this stimulation increased the levels of β-catenin protein, the expression of the classical Wnt-target genes was not affected. Intriguingly, treating circulating human monocytes with Wnt-3a induces the secretion of cytokines and chemokines, enhancing monocyte migration. Mechanistically, the enhanced monocyte migration in response to Wnt stimuli is mediated through CCL2, a strong monocyte-chemoattractant.To further explore the physiological relevance of these findings, we conducted ex-vivo experiments using blood samples of patients with rheumatic joint diseases (RJD) - conditions where monocytes are known to be dysfunctional. Wnt-3a generated a unique cytokine expression profile, which was significantly distinct from that observed in monocytes obtained from healthy donors.Thus, our results provide the first evidence that Wnt-3a may serve as a potent stimulator of monocyte-driven immune processes. These findings contribute to our understanding of inflammatory diseases and, more importantly, shed light on the role of a core signaling pathway in the circulation.
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Affiliation(s)
- Natalie Zelikson
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaina Ben
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Raneen Tarabe
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yonatan Shaleve
- Department of Medicine F, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Pri-Paz Basson
- Rheumatology Unit, Meir Medical Center, Kfar Saba, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oshrat Tayer-Shifman
- Rheumatology Unit, Meir Medical Center, Kfar Saba, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elad Goldberg
- Department of Medicine F, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaye Kivity
- Rheumatology Unit, Meir Medical Center, Kfar Saba, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel.
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19
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Wagner C, Urquiza-Garcia U, Zurbriggen MD, Beyer HM. GMOCU: Digital Documentation, Management, and Biological Risk Assessment of Genetic Parts. Adv Biol (Weinh) 2024; 8:e2300529. [PMID: 38263723 DOI: 10.1002/adbi.202300529] [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: 09/29/2023] [Revised: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering toolkits enables the rapid design of genetic bioparts and genetically modified organisms. Although various software solutions assist with specific design tasks and challenges, lab internal documentation and ensuring compliance with governmental regulations on biosafety assessment of the generated organisms remain the responsibility of individual academic researchers. This results in inconsistent and redundant documentation regimes and a significant time and labor burden. GMOCU (GMO documentation) is a standardized semi-automatic user-oriented software approach -written in Python and freely available- that unifies lab internal data documentation on genetic parts and genetically modified organisms (GMOs). It automatizes biological risk evaluations and maintains a shared up-to-date inventory of bioparts for team-wide data navigation and sharing. GMOCU further enables data export into customizable formats suitable for scientific publications, official biosafety documents, and the research community.
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Affiliation(s)
- Christoph Wagner
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Uriel Urquiza-Garcia
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Hannes M Beyer
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
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20
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Timková I, Maliničová L, Nosáľová L, Kolesárová M, Lorková Z, Petrová N, Pristaš P, Kisková J. Genomic insights into the adaptation of Acinetobacter johnsonii RB2-047 to the heavy metal-contaminated subsurface mine environment. Biometals 2024; 37:371-387. [PMID: 37973678 PMCID: PMC11006771 DOI: 10.1007/s10534-023-00555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/21/2023] [Indexed: 11/19/2023]
Abstract
The subsurface mine environments characterized by high levels of toxic metals and low nutrient availability represent an extreme threat to bacterial persistence. In recent study, the genomic analysis of the Acinetobacter johnsonii strain RB2-047 isolated from the Rozália Gold Mine in Slovakia was performed. As expected, the studied isolate showed a high level of heavy metal tolerance (minimum inhibitory concentrations were 500 mg/L for copper and nickel, 1,500 mg/L for lead, and 250 mg/L for zinc). The RB2-047 strain also showed noticeable resistance to several antibiotics (ampicillin, kanamycin, chloramphenicol, tetracycline and ciprofloxacin). The genomic composition analysis demonstrated a low number of antibiotic and metal resistance coding genes, but a high occurrence of efflux transporter genes located on the bacterial chromosome. The experimental inhibition of efflux pumps resulted in decreased tolerance to Zn and Ni (but not to Cu and Pb) and to all antibiotics tested. In addition, the H33342 dye-accumulation assay confirmed the high efflux activity in the RB2-047 isolate. These findings showed the important role of efflux pumps in the adaptation of Acinetobacter johsonii strain RB2-047 to metal polluted mine environment as well as in development of multi-antibiotic resistance.
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Affiliation(s)
- Ivana Timková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Lenka Maliničová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Lea Nosáľová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Mariana Kolesárová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Zuzana Lorková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Nikola Petrová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Peter Pristaš
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
- Centre of Biosciences, Institute of Animal Physiology, Slovak Academy of Sciences, Šoltésovej 4-6, 04001, Košice, Slovakia
| | - Jana Kisková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia.
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21
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Zhao Z, Li W, Tran TT, Loo SCJ. Bacillus subtilis SOM8 isolated from sesame oil meal for potential probiotic application in inhibiting human enteropathogens. BMC Microbiol 2024; 24:104. [PMID: 38539071 PMCID: PMC11312844 DOI: 10.1186/s12866-024-03263-y] [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: 01/31/2024] [Accepted: 03/17/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND While particular strains within the Bacillus species, such as Bacillus subtilis, have been commercially utilised as probiotics, it is critical to implement screening assays and evaluate the safety to identify potential Bacillus probiotic strains before clinical trials. This is because some Bacillus species, including B. cereus and B. anthracis, can produce toxins that are harmful to humans. RESULTS In this study, we implemented a funnel-shaped approach to isolate and evaluate prospective probiotics from homogenised food waste - sesame oil meal (SOM). Of nine isolated strains with antipathogenic properties, B. subtilis SOM8 displayed the most promising activities against five listed human enteropathogens and was selected for further comprehensive assessment. B. subtilis SOM8 exhibited good tolerance when exposed to adverse stressors including acidity, bile salts, simulated gastric fluid (SGF), simulated intestinal fluid (SIF), and heat treatment. Additionally, B. subtilis SOM8 possesses host-associated benefits such as antioxidant and bile salt hydrolase (BSH) activity. Furthermore, B. subtilis SOM8 contains only haemolysin toxin genes but has been proved to display partial haemolysis in the test and low cytotoxicity in Caco-2 cell models for in vitro evaluation. Moreover, B. subtilis SOM8 intrinsically resists only streptomycin and lacks plasmids or other mobile genetic elements. Bioinformatic analyses also predicted B. subtilis SOM8 encodes various bioactives compound like fengycin and lichendicin that could enable further biomedical applications. CONCLUSIONS Our comprehensive evaluation revealed the substantial potential of B. subtilis SOM8 as a probiotic for targeting human enteropathogens, attributable to its exceptional performance across selection assays. Furthermore, our safety assessment, encompassing both phenotypic and genotypic analyses, showed B. subtilis SOM8 has a favourable preclinical safety profile, without significant threats to human health. Collectively, these findings highlight the promising prospects of B. subtilis SOM8 as a potent probiotic candidate for additional clinical development.
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Affiliation(s)
- Zhongtian Zhao
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Wenrui Li
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - The Thien Tran
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Say Chye Joachim Loo
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
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22
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Li W, Lim CH, Zhao Z, Wang Y, Conway PL, Loo SCJ. In Vitro Profiling of Potential Fish Probiotics, Enterococcus hirae Strains, Isolated from Jade Perch, and Safety Properties Assessed Using Whole Genome Sequencing. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10244-0. [PMID: 38498111 DOI: 10.1007/s12602-024-10244-0] [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] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The demands of intensified aquaculture production and escalating disease prevalence underscore the need for efficacious probiotic strategies to enhance fish health. This study focused on isolating and characterising potential probiotics from the gut microbiota of the emerging aquaculture species jade perch (Scortum barcoo). Eighty-seven lactic acid bacteria and 149 other bacteria were isolated from the digestive tract of five adult jade perch. The screening revealed that 24 Enterococcus hirae isolates inhibited the freshwater pathogens Aeromonas sobria and Streptococcus iniae. Co-incubating E. hirae with the host gut suspensions demonstrated a two- to five-fold increase in the size of growth inhibition zones compared to the results when using gut suspensions from tilapia (a non-host), indicating host-specificity. Genome analysis of the lead isolate, E. hirae R44, predicted the presence of antimicrobial compounds like enterolysin A, class II lanthipeptide, and terpenes, which underlay its antibacterial attributes. Isolate R44 exhibited desirable probiotic characteristics, including survival at pH values within the range of 3 to 12, bile tolerance, antioxidant activity, ampicillin sensitivity, and absence of transferable antimicrobial resistance genes and virulence factors commonly associated with hospital Enterococcus strains (IS16, hylEfm, and esp). This study offers a foundation for sourcing host-adapted probiotics from underexplored aquaculture species. Characterisation of novel probiotics like E. hirae R44 can expedite the development of disease mitigation strategies to support aquaculture intensification.
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Affiliation(s)
- Wenrui Li
- NTU Institute for Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, 61 Nanyang Drive, Singapore, 637335, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Chiun Hao Lim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Zhongtian Zhao
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yulan Wang
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Patricia Lynne Conway
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Centre for Marine Science Innovation, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Say Chye Joachim Loo
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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23
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Binti S, Linder AG, Edeen PT, Fay DS. A conserved protein tyrosine phosphatase, PTPN-22, functions in diverse developmental processes in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584557. [PMID: 38559252 PMCID: PMC10980042 DOI: 10.1101/2024.03.12.584557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein tyrosine phosphatases non-receptor type (PTPNs) have been studied extensively in the context of the adaptive immune system; however, their roles beyond immunoregulation are less well explored. Here we identify novel functions for the conserved C. elegans phosphatase PTPN-22, establishing its role in nematode molting, cell adhesion, and cytoskeletal regulation. Through a non-biased genetic screen, we found that loss of PTPN-22 phosphatase activity suppressed molting defects caused by loss-of-function mutations in the conserved NIMA-related kinases NEKL-2 (human NEK8/NEK9) and NEKL-3 (human NEK6/NEK7), which act at the interface of membrane trafficking and actin regulation. To better understand the functions of PTPN-22, we carried out proximity labeling studies to identify candidate interactors of PTPN-22 during development. Through this approach we identified the CDC42 guanine-nucleotide exchange factor DNBP-1 (human DNMBP) as an in vivo partner of PTPN-22. Consistent with this interaction, loss of DNBP-1 also suppressed nekl-associated molting defects. Genetic analysis, co-localization studies, and proximity labeling revealed roles for PTPN-22 in several epidermal adhesion complexes, including C. elegans hemidesmosomes, suggesting that PTPN-22 plays a broad role in maintaining the structural integrity of tissues. Localization and proximity labeling also implicated PTPN-22 in functions connected to nucleocytoplasmic transport and mRNA regulation, particularly within the germline, as nearly one-third of proteins identified by PTPN-22 proximity labeling are known P granule components. Collectively, these studies highlight the utility of combined genetic and proteomic approaches for identifying novel gene functions.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - Adison G Linder
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - Philip T Edeen
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
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24
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Wei J, Wu BJ, Daoud SS. Whole-Exome Sequencing (WES) Reveals Novel Sex-Specific Gene Variants in Non-Alcoholic Steatohepatitis (MASH). Genes (Basel) 2024; 15:357. [PMID: 38540416 PMCID: PMC10969913 DOI: 10.3390/genes15030357] [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: 02/13/2024] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
Non-alcoholic steatohepatitis (NASH, also known as MASH) is a severe form of non-alcoholic fatty liver disease (NAFLD, also known as MASLD). Emerging data indicate that the progression of the disease to MASH is higher in postmenopausal women and that genetic susceptibility increases the risk of MASH-related cirrhosis. This study aimed to investigate the association between genetic polymorphisms in MASH and sexual dimorphism. We applied whole-exome sequencing (WES) to identify gene variants in 8 age-adjusted matched pairs of livers from both male and female patients. Sequencing alignment, variant calling, and annotation were performed using standard methods. Polymerase chain reaction (PCR) coupled with Sanger sequencing and immunoblot analysis were used to validate specific gene variants. cBioPortal and Gene Set Enrichment Analysis (GSEA) were used for actionable target analysis. We identified 148,881 gene variants, representing 57,121 and 50,150 variants in the female and male cohorts, respectively, of which 251 were highly significant and MASH sex-specific (p < 0.0286). Polymorphisms in CAPN14, SLC37A3, BAZ1A, SRP54, MYH11, ABCC1, and RNFT1 were highly expressed in male liver samples. In female samples, Polymorphisms in RGSL1, SLC17A2, HFE, NLRC5, ACTN4, SBF1, and ALPK2 were identified. A heterozygous variant 1151G>T located on 18q21.32 for ALPK2 (rs3809983) was validated by Sanger sequencing and expressed only in female samples. Immunoblot analysis confirmed that the protein level of β-catenin in female samples was 2-fold higher than normal, whereas ALPK2 expression was 0.5-fold lower than normal. No changes in the protein levels of either ALPK2 or β-catenin were observed in male samples. Our study suggests that the perturbation of canonical Wnt/β-catenin signaling observed in postmenopausal women with MASH could be the result of polymorphisms in ALPK2.
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Affiliation(s)
| | | | - Sayed S. Daoud
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University Health Sciences, Spokane, WA 99202, USA; (J.W.); (B.J.W.)
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25
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Noguchi Y, Onodera Y, Miyamoto T, Maruoka M, Kosako H, Suzuki J. In vivo CRISPR screening directly targeting testicular cells. CELL GENOMICS 2024; 4:100510. [PMID: 38447574 PMCID: PMC10943590 DOI: 10.1016/j.xgen.2024.100510] [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: 06/21/2023] [Revised: 12/10/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
CRISPR-Cas9 short guide RNA (sgRNA) library screening is a powerful approach to understand the molecular mechanisms of biological phenomena. However, its in vivo application is currently limited. Here, we developed our previously established in vitro revival screening method into an in vivo one to identify factors involved in spermatogenesis integrity by utilizing sperm capacitation as an indicator. By introducing an sgRNA library into testicular cells, we successfully pinpointed the retinal degeneration 3 (Rd3) gene as a significant factor in spermatogenesis. Single-cell RNA sequencing (scRNA-seq) analysis highlighted the high expression of Rd3 in round spermatids, and proteomics analysis indicated that Rd3 interacts with mitochondria. To search for cell-type-specific signaling pathways based on scRNA-seq and proteomics analyses, we developed a computational tool, Hub-Explorer. Through this, we discovered that Rd3 modulates oxidative stress by regulating mitochondrial distribution upon ciliogenesis induction. Collectively, our screening system provides a valuable in vivo approach to decipher molecular mechanisms in biological processes.
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Affiliation(s)
- Yuki Noguchi
- Graduate School of Biostudies, Kyoto University, Konoe-cho, Yoshida, Sakyoku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan
| | - Yasuhito Onodera
- Global Center for Biomedical Science and Engineering, Faculty of Medicine, Hokkaido University, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Tatsuo Miyamoto
- Department of Molecular and Cellular Physiology, Yamaguchi University, Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Masahiro Maruoka
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan; Center for Integrated Biosystems, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Jun Suzuki
- Graduate School of Biostudies, Kyoto University, Konoe-cho, Yoshida, Sakyoku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan; Center for Integrated Biosystems, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
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26
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Sadeghi P, Mahnam K, Salari-Jazi A, Aspatwar A, Faghri J. Evolutionary trajectories of beta-lactamase NDM and DLST cluster in Pseudomonas aeruginosa: finding the putative ancestor. Pathog Glob Health 2024; 118:170-181. [PMID: 37464884 PMCID: PMC11141312 DOI: 10.1080/20477724.2023.2236416] [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: 07/20/2023] Open
Abstract
Pseudomonas aeruginosa has different antibiotic resistance pathways, such as broad-spectrum lactamases and metallo-β-lactamases (MBL), penicillin-binding protein (PBP) alteration, and active efflux pumps. Polymerase chain reaction (PCR) and sequencing methods were applied for double-locus sequence typing (DLST) and New Delhi metallo-β-lactamase (NDM) typing. We deduced the evolutionary pathways for DLST and NDM genes of P. aeruginosa using phylogenetic network. Among the analyzed isolates, 62.50% of the P. aeruginosa isolates were phenotypically carbapenem resistance (CARBR) isolates. Characterization of isolates revealed that the prevalence of blaNDM, blaVIM, blaIMP, undetermined carbapenemase, and MexAB-OprM were 27.5%, 2%, 2.5%, 12.5%, and 15%, respectively. The three largest clusters found were DLST t20-105, DLST t32-39, and DLST t32-52. The network phylogenic tree revealed that DLST t26-46 was a hypothetical ancestor for other DLSTs, and NDM-1 was as a hypothetical ancestor for NDMs. The combination of the NDM and DLST phylogenic trees revealed that DLST t32-39 and DLST tN2-N3 with NDM-4 potentially derived from DLST t26-46 along with NDM-1. Similarly, DLST t5-91 with NDM-5 diversified from DLST tN2-N3 with NDM-4. This is the first study in which DLST and NDM evolutionary routes were performed to investigate the origin of P. aeruginosa isolates. Our study showed that the utilization of medical equipment common to two centers, staff members common to two centers, limitations in treatment options, and prescription of unnecessary high levels of meropenem are the main agents that generate new types of resistant bacteria and spread resistance among hospitals.
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Affiliation(s)
- Parisa Sadeghi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Karim Mahnam
- Biology Department, Faculty of Sciences, Shehrekord University, Shehrekord, Iran
| | - Azhar Salari-Jazi
- Department of Drug Development and Innovation, Behban Pharmed Lotus, Tehran, Iran
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jamshid Faghri
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Torres-Haro A, Verdín J, Kirchmayr MR, Arellano-Plaza M. Combined 6-benzylaminopurine and H 2O 2 stimulate the astaxanthin biosynthesis in Xanthophyllomyces dendrorhous. Appl Microbiol Biotechnol 2024; 108:158. [PMID: 38252271 PMCID: PMC10803577 DOI: 10.1007/s00253-023-12875-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 01/23/2024]
Abstract
Astaxanthin is one of the most attractive carotenoids due to its high antioxidant activity and beneficial biological properties, while Xanthophyllomyces dendrorhous is one of its main microbial sources. Since astaxanthin is synthesized as a response to oxidative stress, several oxidative agents have been evaluated to increase X. dendrorhous astaxanthin yields. However, the extent of the stimulation is determined by the cellular damage caused by the applied oxidative agent. Phytohormones have also been reported as stimulants of astaxanthin biosynthesis acting directly on its metabolic pathway and indirectly promoting cellular resistance to reactive oxygen species. We reasoned that both oxidative agents and phytohormones lead to increased astaxanthin synthesis, but the latter could mitigate the drawbacks of the former. Thus, here, the stimulation on astaxanthin biosynthesis, as well as the cellular and transcriptional responses of wild type X. dendrorhous to phytohormones (6-benzylaminopurine, 6-BAP; abscisic acid, ABA; and indole-3-acetic acid, IAA), and oxidative agents (glutamate, menadione, H2O2, and/or Fe2+) were evaluated as a single or combined treatments. ABA and 6-BAP were the best individual stimulants leading to 2.24- and 2.60-fold astaxanthin biosynthesis increase, respectively. Nevertheless, the effect of combined 6-BAP and H2O2 led to a 3.69-fold astaxanthin synthesis increase (0.127 ± 0.018 mg astaxanthin/g biomass). Moreover, cell viability (> 82.75%) and mitochondrial activity (> 82.2%) remained almost intact in the combined treatment (6-BAP + H2O2) compared to control (< 52.17% cell viability; < 85.3% mitochondrial activity). On the other hand, mRNA levels of hmgR, idi, crtYB, crtR, and crtS, genes of the astaxanthin biosynthetic pathway, increased transiently along X. dendrorhous fermentation due to stimulations assayed in this study. KEY POINTS: • Combined 6-BAP and H2O2 is the best treatment to increase astaxanthin yields in X. dendrorhous. • 6-BAP preserves cell integrity under oxidative H2O2 stress conditions. • 6-BAP and H2O2 increase transcriptional responses of hmgR, idi, and crt family genes transiently.
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Affiliation(s)
- Alejandro Torres-Haro
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Jorge Verdín
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Manuel R Kirchmayr
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Melchor Arellano-Plaza
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico.
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28
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Bryant AS, Akimori D, Stoltzfus JDC, Hallem EA. A standard workflow for community-driven manual curation of Strongyloides genome annotations. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220443. [PMID: 38008112 PMCID: PMC10676816 DOI: 10.1098/rstb.2022.0443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/18/2023] [Indexed: 11/28/2023] Open
Abstract
Advances in the functional genomics and bioinformatics toolkits for Strongyloides species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies of Strongyloides species continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multiple Strongyloides species are broadly available via the WormBase and WormBase ParaSite online repositories. However, a recent phylogenetic analysis of the receptor-type guanylate cyclase (rGC) gene family in two Strongyloides species highlights the potential for errors in a large percentage of current Strongyloides gene models. Here, we present three examples of gene annotation updates within the Strongyloides rGC gene family; each example illustrates a type of error that may occur frequently within the annotation data for Strongyloides genomes. We also extend our analysis to 405 previously curated Strongyloides genes to confirm that gene model errors are found at high rates across gene families. Finally, we introduce a standard manual curation workflow for assessing gene annotation quality and generating corrections, and we discuss how it may be used to facilitate community-driven curation of parasitic nematode biodata. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Astra S. Bryant
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Damia Akimori
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Interdepartmental PhD Program, University of California, Los Angeles, CA 90095, USA
| | | | - Elissa A. Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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Poli MC, Rebolledo-Jaramillo B, Lagos C, Orellana J, Moreno G, Martín LM, Encina G, Böhme D, Faundes V, Zavala MJ, Hasbún T, Fischer S, Brito F, Araya D, Lira M, de la Cruz J, Astudillo C, Lay-Son G, Cares C, Aracena M, Martin ES, Coban-Akdemir Z, Posey JE, Lupski JR, Repetto GM. Decoding complex inherited phenotypes in rare disorders: the DECIPHERD initiative for rare undiagnosed diseases in Chile. Eur J Hum Genet 2024:10.1038/s41431-023-01523-5. [PMID: 38177409 DOI: 10.1038/s41431-023-01523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Rare diseases affect millions of people worldwide, and most have a genetic etiology. The incorporation of next-generation sequencing into clinical settings, particularly exome and genome sequencing, has resulted in an unprecedented improvement in diagnosis and discovery in the past decade. Nevertheless, these tools are unavailable in many countries, increasing health care gaps between high- and low-and-middle-income countries and prolonging the "diagnostic odyssey" for patients. To advance genomic diagnoses in a setting of limited genomic resources, we developed DECIPHERD, an undiagnosed diseases program in Chile. DECIPHERD was implemented in two phases: training and local development. The training phase relied on international collaboration with Baylor College of Medicine, and the local development was structured as a hybrid model, where clinical and bioinformatics analysis were performed in-house and sequencing outsourced abroad, due to lack of high-throughput equipment in Chile. We describe the implementation process and findings of the first 103 patients. They had heterogeneous phenotypes, including congenital anomalies, intellectual disabilities and/or immune system dysfunction. Patients underwent clinical exome or research exome sequencing, as solo cases or with parents using a trio design. We identified pathogenic, likely pathogenic or variants of unknown significance in genes related to the patients´ phenotypes in 47 (45.6%) of them. Half were de novo informative variants, and half of the identified variants have not been previously reported in public databases. DECIPHERD ended the diagnostic odyssey for many participants. This hybrid strategy may be useful for settings of similarly limited genomic resources and lead to discoveries in understudied populations.
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Affiliation(s)
- M Cecilia Poli
- Program for Immunogenetics and Translational Immunology, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
- Hospital Dr. Roberto del Río, Santiago, Chile
| | - Boris Rebolledo-Jaramillo
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Catalina Lagos
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Joan Orellana
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Gabriela Moreno
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Luz M Martín
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Unidad de Gestión Clínica del Niño, Hospital Padre Hurtado, Santiago, Chile
| | | | - Daniela Böhme
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Biosoluciones UDD, Santiago, Chile
| | - Víctor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | | | - Trinidad Hasbún
- Department of Dermatology, Facultad de Medicina Universidad del Desarrollo, Clínica Alemana de Santiago, Vitacura, Chile
- Department of Dermatology, Hospital Exequiel González Cortés, Vitacura, Chile
| | - Sara Fischer
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Florencia Brito
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Diego Araya
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Manuel Lira
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Javiera de la Cruz
- Program for Immunogenetics and Translational Immunology, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | | | - Guillermo Lay-Son
- Division of Pediatrics, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Cares
- Genetics Unit, Hospital Dr Luis Calvo Mackenna, Santiago, Chile
| | - Mariana Aracena
- Genetics Unit, Hospital Dr Luis Calvo Mackenna, Santiago, Chile
| | | | - Zeynep Coban-Akdemir
- University of Texas Health Science Center at Houston, School of Public Health, Department of Epidemiology, Human Genetics and Environmental Sciences, Santiago, Chile
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Gabriela M Repetto
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile.
- Unidad de Gestión Clínica del Niño, Hospital Padre Hurtado, Santiago, Chile.
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Dwyer R, Witte C, Buss P, Warren R, Miller M, Goosen W. Antemortem detection of Mycobacterium bovis in nasal swabs from African rhinoceros. Sci Rep 2024; 14:357. [PMID: 38172248 PMCID: PMC10764836 DOI: 10.1038/s41598-023-50236-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
Mycobacterium bovis (M. bovis) infection has been identified in black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros populations in Kruger National Park, South Africa. However, it is unknown whether M. bovis infected rhinoceros, like humans and cattle, can shed mycobacteria in respiratory secretions. Limited studies have suggested that rhinoceros with subclinical M. bovis infection may present minimal risk for transmission. However, recent advances that have improved detection of Mycobacterium tuberculosis complex (MTBC) members in paucibacillary samples warranted further investigation of rhinoceros secretions. In this pilot study, nasal swab samples from 75 rhinoceros with defined infection status based on M. bovis antigen-specific interferon gamma release assay (IGRA) results were analysed by GeneXpert MTB/RIF Ultra, BACTEC MGIT and TiKa-MGIT culture. Following culture, speciation was done using targeted PCRs followed by Sanger sequencing for mycobacterial species identification, and a region of difference (RD) 4 PCR. Using these techniques, MTBC was detected in secretions from 14/64 IGRA positive rhinoceros, with viable M. bovis having been isolated in 11 cases, but not in any IGRA negative rhinoceros (n = 11). This finding suggests the possibility that MTBC/M. bovis-infected rhinoceros may be a source of infection for other susceptible animals sharing the environment.
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Affiliation(s)
- Rebecca Dwyer
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Carmel Witte
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
- The Center for Wildlife Studies, P.O. Box 56, South Freeport, ME, 04078, USA
| | - Peter Buss
- Veterinary Wildlife Services, Kruger National Park, Private Bag X402, Skukuza, 1350, South Africa
| | - Robin Warren
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Michele Miller
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Wynand Goosen
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
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31
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Córdoba L, Ruiz-Padilla A, Pardo-Medina J, Rodríguez-Romero JL, Ayllón MA. Construction of a Mycoviral Infectious Clone for Reverse Genetics in Botrytis cinerea. Methods Mol Biol 2024; 2751:47-68. [PMID: 38265709 DOI: 10.1007/978-1-0716-3617-6_4] [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: 01/25/2024]
Abstract
The most important advances in our understanding of the viral life cycle, such as genome replication, packaging, transmission, and host interactions, have been made via the development of viral infectious full-length clones. Here, we describe the detailed protocols for the construction of an infectious clone derived from Botrytis virus F (BVF), a mycoflexivirus infecting the plant pathogenic fungus Botrytis cinerea, the determination of the complete sequence of the cloned mycovirus, the preparation of fungal protoplasts, and the transfection of protoplasts using transcripts derived from the BVF infectious clone.
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Affiliation(s)
- Laura Córdoba
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Ana Ruiz-Padilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Javier Pardo-Medina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Julio L Rodríguez-Romero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
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32
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Philippe N, Shukla A, Abergel C, Bisio H. Genetic manipulation of giant viruses and their host, Acanthamoeba castellanii. Nat Protoc 2024; 19:3-29. [PMID: 37964008 DOI: 10.1038/s41596-023-00910-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/25/2023] [Indexed: 11/16/2023]
Abstract
Giant viruses (GVs) provide an unprecedented source of genetic innovation in the viral world and are thus, besides their importance in basic and environmental virology, in the spotlight for bioengineering advances. Their host, Acanthamoeba castellanii, is an accidental human pathogen that acts as a natural host and environmental reservoir of other human pathogens. Tools for genetic manipulation of viruses and host were lacking. Here, we provide a detailed method for genetic manipulation of A. castellanii and the GVs it plays host to by using CRISPR-Cas9 or homologous recombination. We detail the steps of vector preparation (4 d), transfection of amoeba cells (1 h), infection (1 h), selection (5 d for viruses, 2 weeks for amoebas) and cloning of recombinant viruses (4 d) or amoebas (2 weeks). This procedure takes ~3 weeks or 1 month for the generation of recombinant viruses or amoebas, respectively. This methodology allows the generation of stable gene modifications, which was not possible by using RNA silencing, the only previously available reverse genetic tool. We also include detailed sample-preparation steps for protein localization by immunofluorescence (4 h), western blotting (4 h), quantification of viral particles by optical density (15 min), calculation of viral lethal dose 50 (7 d) and quantification of DNA replication by quantitative PCR (4 h) to allow efficient broad phenotyping of recombinant organisms. This methodology allows the function of thousands of ORFan genes present in GVs, as well as the complex pathogen-host, pathogen-pathogen or pathogen-symbiont interactions in A. castellanii, to be studied in vivo.
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Affiliation(s)
- Nadege Philippe
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), Marseille, France
| | - Avi Shukla
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), Marseille, France
| | - Chantal Abergel
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), Marseille, France.
| | - Hugo Bisio
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), Marseille, France.
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33
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Aulicino F, Raele RA, Harrison A, Berger I. Assembly of Baculovirus Vectors for Multiplexed Prime Editing. Methods Mol Biol 2024; 2829:301-327. [PMID: 38951346 DOI: 10.1007/978-1-0716-3961-0_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: 07/03/2024]
Abstract
Efficient genome editing by using CRISPR technologies requires simultaneous and efficient delivery of multiple genetically encoded components to mammalian cells. Amongst all editing approaches, prime editing (PE) has the unique potential to perform seamless genome rewriting, in the absence of DNA double-strand breaks (DSBs). The cargo capacity required for efficient PE delivery to mammalian cells stands at odd with the limited packaging capacity of traditional viral delivery vectors. By contrast, baculovirus (BV) has a large synthetic DNA capacity and can efficiently transduce mammalian cells. Here we describe a protocol for the assembly of baculovirus vectors for multiplexed prime editing in mammalian cells.
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Affiliation(s)
| | - Renata A Raele
- School of Biochemistry, University of Bristol, Bristol, UK
| | | | - Imre Berger
- School of Biochemistry, University of Bristol, Bristol, UK.
- School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck Bristol Centre for Minimal Biology, Bristol, UK.
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34
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Mali S, Zinta G. Genome-wide identification and expression analysis reveal the role of histone methyltransferase and demethylase genes in heat stress response in potato (Solanum tuberosum L.). Biochim Biophys Acta Gen Subj 2024; 1868:130507. [PMID: 37925032 DOI: 10.1016/j.bbagen.2023.130507] [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: 07/20/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Potato (Solanum tuberosum L.), the third most important non-cereal crop, is sensitive to high temperature. Histone modifications have been known to regulate various abiotic stress responses. However, the role of histone methyltransferases and demethylases remain unexplored in potato under heat stress. METHODS Potato genome database was used for genome-wide analysis of StPRMT and StHDMA gene families, which were further characterized by analyzing gene structure, conserved motif, domain organization, sub-cellular localization, promoter region and phylogenetic relationships. Additionally, expression profiling under high-temperature stress in leaf and stolon tissue of heat contrasting potato genotypes was done to study their role in response to high temperature stress. RESULTS The genome-wide analysis led to identification of nine StPRMT and eleven StHDMA genes. Structural analysis, including conserved motifs, exon/intron structure and phylogenetic relationships classified StPRMT and StHDMA gene families into two classes viz. Class I and Class II. A variety of cis-regulatory elements were explored in the promoter region associated with light, developmental, hormonal and stress responses. Prediction of sub-cellular localization of StPRMT proteins revealed their occurrence in nucleus and cytoplasm, whereas StHDMA proteins were observed in different sub-cellular compartments. Furthermore, expression profiling of StPRMT and StHDMA gene family members revealed genes responding to heat stress. Heat-inducible expression of StPRMT1, StPRMT3, StPRMT4 and StPRMT5 in leaf and stolon tissues of HS and HT cultivar indicated them as probable candidates for enhancing thermotolerance in potato. However, StHDMAs responded dynamically in leaf and stolon tissue of heat contrasting genotypes under high temperature. CONCLUSION The current study presents a detailed analysis of histone modifiers in potato and indicates their role as an important epigenetic regulators modulating heat tolerance. GENERAL SIGNIFICANCE Understanding epigenetic mechanisms underlying heat tolerance in potato will contribute towards breeding of thermotolerant potato varieties.
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Affiliation(s)
- Surbhi Mali
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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35
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Bowes DA, Henke KB, Driver EM, Newell ME, Block I, Shaffer G, Varsani A, Scotch M, Halden RU. Enhanced detection of mpox virus in wastewater using a pre-amplification approach: A pilot study informing population-level monitoring of low-titer pathogens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166230. [PMID: 37574063 PMCID: PMC10592092 DOI: 10.1016/j.scitotenv.2023.166230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
A recent outbreak of the mpox virus (MPXV) occurred in non-endemic regions of the world beginning in May 2022. Pathogen surveillance systems faced pressure to quickly establish response protocols, offering an opportunity to employ wastewater-based epidemiology (WBE) for population-level monitoring. The pilot study reported herein aimed to: (i) develop a reliable protocol for MPXV DNA detection in wastewater which would reduce false negative reporting, (ii) test this protocol on wastewater from various regions across the United States, and (iii) conduct a state of the science review of the current literature reporting on experimental methods for MPXV detection using WBE. Twenty-four-hour composite samples of untreated municipal wastewater were collected from the states of New Jersey, Georgia, Illinois, Texas, Arizona, and Washington beginning July 3rd, 2022 through October 16th, 2022 (n = 60). Samples underwent vacuum filtration, DNA extraction from captured solids, MPXV DNA pre-amplification, and qPCR analysis. Of the 60 samples analyzed, a total of eight (13%) tested positive for MPXV in the states of Washington, Texas, New Jersey, and Illinois. The presence of clade IIb MPXV DNA in these samples was confirmed via Sanger sequencing and integration of pre-amplification prior to qPCR decreased the rate of false negative detections by 87% as compared to qPCR analysis alone. Wastewater-derived detections of MPXV were compared to clinical datasets, with 50% of detections occurring as clinical cases were increasing/peaking and 50% occurring as clinical cases waned. Results from the literature review (n = 9 studies) revealed successful strategies for the detection of MPXV DNA in wastewater, however also emphasized a need for further method optimization and standardization. Overall, this work highlights the use of pre-amplification prior to qPCR detection as a means to capture the presence of MPXV DNA in community wastewater and offers guidance for monitoring low-titer pathogens via WBE.
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Affiliation(s)
- Devin A Bowes
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Katherine B Henke
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Erin M Driver
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Melanie Engstrom Newell
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Izabella Block
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Gray Shaffer
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Arvind Varsani
- The Biodesign Institute Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85281, USA; Center of Evolution and Medicine, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85281, USA
| | - Matthew Scotch
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ 85004, USA
| | - Rolf U Halden
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School for Sustainable Engineering and the Built Environment, Arizona State University, 660 S. College Ave., Tempe, AZ 85281, USA; OneWaterOneHealth, The Arizona State University Foundation, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; Global Futures Laboratory, Arizona State University, 800 S. Cady Mall, Tempe, AZ 85281, USA.
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Gregory DA, Rushford C, Hunter T, Lin CH, Darby C, Niehues N, Semkiw E, Reynolds M, Wenzel J, Johnson MC. Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater. PLoS Pathog 2023; 19:e1011688. [PMID: 38153929 PMCID: PMC10781090 DOI: 10.1371/journal.ppat.1011688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/10/2024] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Deep sequencing of wastewater to detect SARS-CoV-2 has been used during the COVID-19 pandemic to monitor viral variants as they appear and circulate in communities. SARS-CoV-2 lineages of an unknown source that have not been detected in clinical samples, referred to as cryptic lineages, are sometimes repeatedly detected from specific locations. We have continued to detect one such lineage previously seen in a Missouri site. This cryptic lineage has continued to evolve, indicating continued selective pressure similar to that observed in Omicron lineages.
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Affiliation(s)
- Devon A. Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, Missouri, United States of America
| | - Clayton Rushford
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, Missouri, United States of America
| | - Torin Hunter
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, Missouri, United States of America
| | - Chung-Ho Lin
- Center of Agroforestry, School of Natural Resources, University of Missouri, Columbia, Missouri, United States of America
| | - Christie Darby
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, Missouri, United States of America
| | - Nicole Niehues
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, Missouri, United States of America
| | - Elizabeth Semkiw
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, Missouri, United States of America
| | - Melissa Reynolds
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, Missouri, United States of America
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, Missouri, United States of America
| | - Marc C. Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, Missouri, United States of America
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Schmidt S, Wichers-Misterek JS, Behrens HM, Birnbaum J, Henshall IG, Dröge J, Jonscher E, Flemming S, Castro-Peña C, Mesén-Ramírez P, Spielmann T. The Kelch13 compartment contains highly divergent vesicle trafficking proteins in malaria parasites. PLoS Pathog 2023; 19:e1011814. [PMID: 38039338 PMCID: PMC10718435 DOI: 10.1371/journal.ppat.1011814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/13/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Single amino acid changes in the parasite protein Kelch13 (K13) result in reduced susceptibility of P. falciparum parasites to artemisinin and its derivatives (ART). Recent work indicated that K13 and other proteins co-localising with K13 (K13 compartment proteins) are involved in the endocytic uptake of host cell cytosol (HCCU) and that a reduction in HCCU results in reduced susceptibility to ART. HCCU is critical for parasite survival but is poorly understood, with the K13 compartment proteins among the few proteins so far functionally linked to this process. Here we further defined the composition of the K13 compartment by analysing more hits from a previous BioID, showing that MyoF and MCA2 as well as Kelch13 interaction candidate (KIC) 11 and 12 are found at this site. Functional analyses, tests for ART susceptibility as well as comparisons of structural similarities using AlphaFold2 predictions of these and previously identified proteins showed that vesicle trafficking and endocytosis domains were frequent in proteins involved in resistance or endocytosis (or both), comprising one group of K13 compartment proteins. While this strengthened the link of the K13 compartment to endocytosis, many proteins of this group showed unusual domain combinations and large parasite-specific regions, indicating a high level of taxon-specific adaptation of this process. Another group of K13 compartment proteins did not influence endocytosis or ART susceptibility and lacked detectable vesicle trafficking domains. We here identified the first protein of this group that is important for asexual blood stage development and showed that it likely is involved in invasion. Overall, this work identified novel proteins functioning in endocytosis and at the K13 compartment. Together with comparisons of structural predictions it provides a repertoire of functional domains at the K13 compartment that indicate a high level of adaption of endocytosis in malaria parasites.
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Affiliation(s)
- Sabine Schmidt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Jakob Birnbaum
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Jana Dröge
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ernst Jonscher
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sven Flemming
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Balmer EA, Wirdnam CD, Faso C. A core UPS molecular complement implicates unique endocytic compartments at the parasite-host interface in Giardia lamblia. Virulence 2023; 14:2174288. [PMID: 36730629 PMCID: PMC9928461 DOI: 10.1080/21505594.2023.2174288] [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] [Indexed: 02/04/2023] Open
Abstract
Unconventional protein secretion (UPS) plays important roles in cell physiology. In contrast to canonical secretory routes, UPS does not generally require secretory signal sequences and often bypasses secretory compartments such as the ER and the Golgi apparatus. Giardia lamblia is a protist parasite with reduced subcellular complexity which releases several proteins, some of them virulence factors, without canonical secretory signals. This implicates UPS at the parasite-host interface. No dedicated machinery nor mechanism(s) for UPS in Giardia are currently known, although speculations on the involvement of endocytic organelles called PV/PECs, have been put forth. To begin to address the question of whether PV/PECs are implicated in virulence-associated UPS and to define the composition of molecular machinery involved in protein release, we employed affinity purification and mass spectrometry, coupled to microscopy-based subcellular localization and signal correlation quantification to investigate the interactomes of 11 reported unconventionally secreted proteins, all predicted to be cytosolic. A subset of these are associated with PV/PECs. Extended and validated interactomes point to a core PV/PECs-associated UPS machinery, which includes uncharacterized and Giardia-specific coiled-coil proteins and NEK kinases. Finally, a subset of the alpha-giardin protein family was enriched in all PV/PECs-associated protein interactomes, highlighting a previously unappreciated role for these proteins at PV/PECs and in UPS. Taken together, our results provide the first characterization of a virulence-associated UPS protein complex in Giardia lamblia at PV/PECs, suggesting a novel link between these primarily endocytic and feeding organelles and UPS at the parasite-host interface.
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Affiliation(s)
- Erina A. Balmer
- Institute of Cell Biology, University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Carmen Faso
- Institute of Cell Biology, University of Bern, Bern, Switzerland,Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland,CONTACT Carmen Faso
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Traenkner D, Shennib O, Johnson A, Weinbrom A, Taylor MR, Williams ME. Modular Splicing Is Linked to Evolution in the Synapse-Specificity Molecule Kirrel3. eNeuro 2023; 10:ENEURO.0253-23.2023. [PMID: 37977826 DOI: 10.1523/eneuro.0253-23.2023] [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: 07/17/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023] Open
Abstract
Kirrel3 is a cell-adhesion molecule that instructs the formation of specific synapses during brain development in mouse and Kirrel3 variants may be risk factors for autism and intellectual disabilities in humans. Kirrel3 is predicted to undergo alternative splicing but brain isoforms have not been studied. Here, we present the first in-depth characterization of Kirrel3 isoform diversity in brain using targeted, long-read mRNA sequencing of mouse hippocampus. We identified 19 isoforms with predicted transmembrane and secreted forms and show that even rare isoforms generate detectable protein in the brain. We also analyzed publicly-available long-read mRNA databases from human brain tissue and found 11 Kirrel3 isoforms that, similar to mouse, encode transmembrane and secreted forms. In mice and humans, Kirrel3 diversity arises from alternative, independent use of protein-domain coding exons and alternative early translation-stop signals. Intriguingly, the alternatively spliced exons appear at branch points in the chordate phylogenetic tree, including one exon only found in humans and their closest living relatives, the great apes. Together, these results validate a simple pipeline for analyzing isoform diversity in genes with low expression and suggest that Kirrel3 function is fine-tuned by alternative splicing and may play a role in brain evolution.
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Affiliation(s)
- Dimitri Traenkner
- Department of Neurobiology, University of Utah, School of Medicine, Salt Lake City, UT 84112
| | - Omar Shennib
- Department of Neurobiology, University of Utah, School of Medicine, Salt Lake City, UT 84112
| | - Alyssa Johnson
- Department of Neurobiology, University of Utah, School of Medicine, Salt Lake City, UT 84112
| | - Adam Weinbrom
- Department of Neurobiology, University of Utah, School of Medicine, Salt Lake City, UT 84112
| | - Matthew R Taylor
- Department of Neurobiology, University of Utah, School of Medicine, Salt Lake City, UT 84112
| | - Megan E Williams
- Department of Neurobiology, University of Utah, School of Medicine, Salt Lake City, UT 84112
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40
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Canuto F, Duret S, Dubrana MP, Claverol S, Malembic-Maher S, Foissac X, Arricau-Bouvery N. A knockdown gene approach identifies an insect vector membrane protein with leucin-rich repeats as one of the receptors for the VmpA adhesin of flavescence dorée phytoplasma. Front Cell Infect Microbiol 2023; 13:1289100. [PMID: 38029232 PMCID: PMC10662966 DOI: 10.3389/fcimb.2023.1289100] [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: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The adhesion of flavescence dorée phytoplasma to the midgut epithelium cells of their insect vectors is partially mediated by the variable membrane protein A (VmpA), an adhesin which shows lectin properties. In order to identify the insect receptor for VmpA, we identified Euscelidius variegatus cell proteins interacting with recombinant VmpA-His6. Methods The E. variegatus proteins were identified by mass spectrometry analysis of VmpA-E. variegatus protein complexes formed upon in vitro interaction assays. To assess their impact in VmpA binding, we reduced the expression of the candidate genes on E. variegatus cells in culture by dsRNA-mediated RNAi. The effect of candidate gene knockdown on VmpA binding was measured by the capacity of E. variegatus cells to bind VmpA-coated fluorescent beads. Results and discussion There were 13 candidate proteins possessing potential N-glycosylation sites and predicted transmembrane domains selected. The decrease of expression of an unknown transmembrane protein with leucine-rich repeat domains (uk1_LRR) was correlated with the decreased adhesion of VmpA beads to E. variegatus cells. The uk1_LRR was more expressed in digestive tubes than salivary glands of E. variegatus. The protein uk1_LRR could be implicated in the binding with VmpA in the early stages of insect infection following phytoplasmas ingestion.
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Affiliation(s)
- Francesca Canuto
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d’Ornon, France
| | - Sybille Duret
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d’Ornon, France
| | - Marie-Pierre Dubrana
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d’Ornon, France
| | | | - Sylvie Malembic-Maher
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d’Ornon, France
| | - Xavier Foissac
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d’Ornon, France
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Sawhney SS, Vargas RC, Wallace MA, Muenks CE, Lubbers BV, Fritz SA, Burnham CAD, Dantas G. Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms. Nat Commun 2023; 14:7065. [PMID: 37923729 PMCID: PMC10624692 DOI: 10.1038/s41467-023-42694-5] [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: 02/07/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Staphylococcus pseudintermedius is historically understood as a prevalent commensal and pathogen of dogs, though modern clinical diagnostics reveal an expanded host-range that includes humans. It remains unclear whether differentiation across S. pseudintermedius populations is driven primarily by niche-type or host-species. We sequenced 501 diagnostic and commensal isolates from a hospital, veterinary diagnostic laboratory, and within households in the American Midwest, and performed a comparative genomics investigation contrasting human diagnostic, animal diagnostic, human colonizing, pet colonizing, and household-surface S. pseudintermedius isolates. Though indistinguishable by core and accessory gene architecture, diagnostic isolates harbor more encoded and phenotypic resistance, whereas colonizing and surface isolates harbor similar CRISPR defense systems likely reflective of common household phage exposures. Furthermore, household isolates that persist through anti-staphylococcal decolonization report elevated rates of base-changing mutations in - and parallel evolution of - defense genes, as well as reductions in oxacillin and trimethoprim-sulfamethoxazole susceptibility. Together we report parallel niche-specific bolstering of S. pseudintermedius defense mechanisms through gene acquisition or mutation.
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Affiliation(s)
- Sanjam S Sawhney
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Meghan A Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Carol E Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian V Lubbers
- Department of Clinical Sciences, Kansas State University, Manhattan, KS, USA
| | - Stephanie A Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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42
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Kapp FG, Kretschmer S, Beckmann CCA, Wäsch L, Molitor A, Carapito R, Schubert M, Lucas N, Conrad S, Poignant S, Isidor B, Rohlfs M, Kisaarslan AP, Schanze D, Zenker M, Schmitt-Graeff A, Strahm B, Peters A, Yoshimi A, Driever W, Zillinger T, Günther C, Maharana S, Guan K, Klein C, Ehl S, Niemeyer CM, Unal E, Bahram S, Hauck F, Lee-Kirsch MA, Speckmann C. C-terminal variants in CDC42 drive type I interferon-dependent autoinflammation in NOCARH syndrome reversible by ruxolitinib. Clin Immunol 2023; 256:109777. [PMID: 37741518 DOI: 10.1016/j.clim.2023.109777] [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: 06/21/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023]
Abstract
C-terminal variants in CDC42 encoding cell division control protein 42 homolog underlie neonatal-onset cytopenia, autoinflammation, rash, and hemophagocytic lymphohistiocytosis (NOCARH). Pyrin inflammasome hyperactivation has been shown to contribute to disease pathophysiology. However, mortality of NOCARH patients remains high despite inflammasome-focused treatments. Here, we demonstrate in four NOCARH patients from three families that cell-intrinsic activation of type I interferon (IFN) is a previously unrecognized driver of autoinflammation in NOCARH. Our data show that aberrant innate immune activation is caused by sensing of cytosolic nucleic acids released from mitochondria, which exhibit disturbances in integrity and dynamics due to CDC42 dysfunction. In one of our patients, treatment with the Janus kinase inhibitor ruxolitinib led to complete remission, indicating that inhibition of type I IFN signaling may have an important role in the management of autoinflammation in patients with NOCARH.
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Affiliation(s)
- Friedrich G Kapp
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany.
| | - Stefanie Kretschmer
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Cora C A Beckmann
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Lena Wäsch
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Anne Molitor
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France; Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Raphaël Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France; Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Mario Schubert
- Institute of Pharmacology and Toxicology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nadja Lucas
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Solène Conrad
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | | | - Meino Rohlfs
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ayşenur Paç Kisaarslan
- Erciyes University, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Rheumatology, 38039 Melikgazi, Kayseri, Türkiye
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | | | - Brigitte Strahm
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Anke Peters
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Ayami Yoshimi
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Wolfgang Driever
- Developmental Biology, Faculty of Biology, Institute of Biology 1, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Thomas Zillinger
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Claudia Günther
- Department of Dermatology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Shovamayee Maharana
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Ekrem Unal
- Erciyes University, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Hematology-Oncology, 38039 Melikgazi, Kayseri, Turkey
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France; Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Carsten Speckmann
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
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Nogueira AM, Barbosa TMC, Quadros AFF, Orílio AF, Bigão MCJ, Xavier CAD, Ferro CG, Zerbini FM. Specific Nucleotides in the Common Region of the Begomovirus Tomato Rugose Mosaic Virus (ToRMV) Are Responsible for the Negative Interference over Tomato Severe Rugose Virus (ToSRV) in Mixed Infection. Viruses 2023; 15:2074. [PMID: 37896851 PMCID: PMC10611410 DOI: 10.3390/v15102074] [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: 09/04/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Mixed infection between two or more begomoviruses is commonly found in tomato fields and can affect disease outcomes by increasing symptom severity and viral accumulation compared with single infection. Viruses that affect tomato include tomato severe rugose virus (ToSRV) and tomato rugose mosaic virus (ToRMV). Previous work showed that in mixed infection, ToRMV negatively affects the infectivity and accumulation of ToSRV. ToSRV and ToRMV share a high degree of sequence identity, including cis-elements in the common region (CR) and their specific recognition sites (iteron-related domain, IRD) within the Rep gene. Here, we investigated if divergent sites in the CR and IRD are involved in the interaction between these two begomoviruses. ToSRV clones were constructed containing the same nucleotides as ToRMV in the CR (ToSRV-A(ToR:CR)), IRD (ToSRV-A(ToR:IRD)) and in both regions (ToSRV-A(ToR:CR+IRD)). When plants were co-inoculated with ToRMV and ToSRV-A(ToR:IRD), the infectivity and accumulation of ToSRV were negatively affected. In mixed inoculation of ToRMV with ToSRV-A(ToR:CR), high infectivity of both viruses and high DNA accumulation of ToSRV-A(ToR:CR) were observed. A decrease in viral accumulation was observed in plants inoculated with ToSRV-A(ToR:CR+IRD). These results indicate that differences in the CR, but not the IRD, are responsible for the negative interference of ToRMV on ToSRV.
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Affiliation(s)
- Angélica M. Nogueira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Proteção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista (UNESP), Botucatu 18610-307, SP, Brazil
| | - Tarsiane M. C. Barbosa
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Entomologia e Acarologia, ESALQ, Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil
| | - Ayane F. F. Quadros
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Anelise F. Orílio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Marcela C. J. Bigão
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - César A. D. Xavier
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Camila G. Ferro
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Fitopatologia e Nematologia, ESALQ, Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
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Knoebel E, Dour S, Nonet M. A toolkit for assembly of targeting clones for C. elegans transgenesis. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000966. [PMID: 37854100 PMCID: PMC10580076 DOI: 10.17912/micropub.biology.000966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/23/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
Transgenic worms are a key resource for C. elegans researchers dissecting molecular pathways using this simple metazoan model system. Transgenes provide an avenue to visualize developmental events, cellular processes as well as real-time signal events in live animals using genetically encoded sensors. Generation of these tools has become increasingly efficient with the advent of numerous integration methods including transposon, CRISPR and recombinase-mediated integration. A growing limitation in transgene production is the assembly of the targeting constructs used to direct insertion of sequences into the genome. Here we present a toolkit that facilitates rapid assembly of complex reporters using a Golden Gate (GG) cloning-based approach. Co-assembly of one to eight DNA segments into an integration vector can be routinely obtained at high efficiency using a library of entry plasmids. The toolkit consists of 20 SapI GG entry vectors and 100 SapI GG insert plasmids containing a variety of promoters, FPs, tags, linkers, ORFs, 3' UTRs and numerous components for bipartite expression systems that can be mixed to create a huge repertoire of reporter constructs. The assembly process also works well with PCR products and 5' phosphorylated double stranded oligonucleotides, and such DNAs can be used to supply novel genes, promoters, and tags into the pipeline. In addition, the toolkit also provides a series of 12 empty BsaI -based GG assembly vectors that facilitate the construction of additional SapI GG plasmids containing novel inserts. A manual outlining the entire approach is provided as an appendix as well as a Microsoft® Excel based assembly tool which allows the user to choose individual inserts among the libraries of clones at each position in the assembly template and output an annotated sequence. The assembly process can easily be multiplexed and is typically over 90% efficient. The approach is sufficiently efficient to make microinjection rather than clone generation the limiting factor in transgene generation.
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Affiliation(s)
- Emma Knoebel
- Department of Neuroscience, Washington University Medical School, St. Louis, MO, USA
| | - Scott Dour
- Department of Neuroscience, Washington University Medical School, St. Louis, MO, USA
- Benson Hill, St. Louis, MO, USA
| | - Michael Nonet
- Department of Neuroscience, Washington University Medical School, St. Louis, MO, USA
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45
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Ader NR, Chen L, Surovtsev IV, Chadwick WL, Rodriguez EC, King MC, Lusk CP. An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity. Nat Cell Biol 2023; 25:1465-1477. [PMID: 37783794 PMCID: PMC11365527 DOI: 10.1038/s41556-023-01235-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The molecular mechanisms by which the endosomal sorting complexes required for transport (ESCRT) proteins contribute to the integrity of the nuclear envelope (NE) barrier are not fully defined. We leveraged the single NE hole generated by mitotic extrusion of the Schizosaccharomyces pombe spindle pole body to reveal two modes of ESCRT function executed by distinct complements of ESCRT-III proteins, both dependent on CHMP7/Cmp7. A grommet-like function is required to restrict the NE hole in anaphase B, whereas replacement of Cmp7 by a sealing module ultimately closes the NE in interphase. Without Cmp7, nucleocytoplasmic compartmentalization remains intact despite NE discontinuities of up to 540 nm, suggesting mechanisms to limit diffusion through these holes. We implicate spindle pole body proteins as key components of a diffusion barrier acting with Cmp7 in anaphase B. Thus, NE remodelling mechanisms cooperate with proteinaceous diffusion barriers beyond nuclear pore complexes to maintain the nuclear compartment.
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Affiliation(s)
- Nicholas R Ader
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Linda Chen
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Ivan V Surovtsev
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | | | - Elisa C Rodriguez
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, CT, USA.
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
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46
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Chen T, Zhou X, Wu J, Xing G, Cao H, Huang Y. Expression profile and function analysis of MsCSP17 and MsCSP18 in the larval development of Mythimna separata. BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:676-683. [PMID: 37674285 DOI: 10.1017/s0007485323000354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Chemosensory proteins (CSPs) were necessary for insect sensory system to perform important processes such as feeding, mating, spawning, and avoiding natural enemies. However, their functions in non-olfactory organs have been poorly studied. To clarify the function of CSPs in the development of Mythimna separata (Walker) larvae, two CSP genes, MsCSP17 and MsCSP18, were identified from larval integument transcriptome dataset. Both of MsCSP17 and MsCSP18 contained four conserved cysteine sites (C × (6)-C × (18)-C × (2)-C), with a signal peptide at the N-terminal. RT-qPCR analysis showed that MsCSP17 and MsCSP18 have different expression patterns among different developmental stages and tissues. MsCSP17 was highly expressed in 1st-4th instar larvae, and MsCSP18 had high expression in adults. Both genes were expressed highly in larval head, thorax, integument and mandible. Moreover, both of MsCSP17 and MsCSP18 were lowly expressed in larval integuments when larvae molted for 6 h and 9 h from 3rd to 4th instar, but highly at the beginning and end phase during molting. After injection of dsMsCSP17 and dsMsCSP18, the expression levels of two genes decreased significantly, with the body weight of larvae decreased, the mortality increased, and the eclosion rate decreased. It was suggested that MsCSP17 and MsCSP18 contributed to the development of M. separata larvae.
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Affiliation(s)
- Tingting Chen
- Anhui Province Key Laboratory of Crop Integrated Pest Management, College of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
| | - Xue Zhou
- Anhui Province Key Laboratory of Crop Integrated Pest Management, College of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
| | - Jing Wu
- Anhui Province Key Laboratory of Crop Integrated Pest Management, College of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
| | - Gaoliang Xing
- Anhui Province Key Laboratory of Crop Integrated Pest Management, College of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, College of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
| | - Yong Huang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, College of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
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Phadnis VV, Snider J, Varadharajan V, Ramachandiran I, Deik AA, Lai ZW, Kunchok T, Eaton EN, Sebastiany C, Lyakisheva A, Vaccaro KD, Allen J, Yao Z, Wong V, Geng B, Weiskopf K, Clish CB, Brown JM, Stagljar I, Weinberg RA, Henry WS. MMD collaborates with ACSL4 and MBOAT7 to promote polyunsaturated phosphatidylinositol remodeling and susceptibility to ferroptosis. Cell Rep 2023; 42:113023. [PMID: 37691145 PMCID: PMC10591818 DOI: 10.1016/j.celrep.2023.113023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023] Open
Abstract
Ferroptosis is a form of regulated cell death with roles in degenerative diseases and cancer. Excessive iron-catalyzed peroxidation of membrane phospholipids, especially those containing the polyunsaturated fatty acid arachidonic acid (AA), is central in driving ferroptosis. Here, we reveal that an understudied Golgi-resident scaffold protein, MMD, promotes susceptibility to ferroptosis in ovarian and renal carcinoma cells in an ACSL4- and MBOAT7-dependent manner. Mechanistically, MMD physically interacts with both ACSL4 and MBOAT7, two enzymes that catalyze sequential steps to incorporate AA in phosphatidylinositol (PI) lipids. Thus, MMD increases the flux of AA into PI, resulting in heightened cellular levels of AA-PI and other AA-containing phospholipid species. This molecular mechanism points to a pro-ferroptotic role for MBOAT7 and AA-PI, with potential therapeutic implications, and reveals that MMD is an important regulator of cellular lipid metabolism.
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Affiliation(s)
- Vaishnavi V Phadnis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Venkateshwari Varadharajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Amy A Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zon Weng Lai
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Elinor Ng Eaton
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Anna Lyakisheva
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kyle D Vaccaro
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Juliet Allen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Betty Geng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kipp Weiskopf
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Mediterranean Institute for Life Sciences, 21000 Split, Croatia
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA.
| | - Whitney S Henry
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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48
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Bezodis W, Prescott H, Vlad D, Dickinson H. A qPCR Method to Distinguish between Expression of Transgenic and Endogenous Copies of Genes. Bio Protoc 2023; 13:e4784. [PMID: 37575385 PMCID: PMC10415200 DOI: 10.21769/bioprotoc.4784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/21/2023] [Accepted: 06/15/2023] [Indexed: 08/15/2023] Open
Abstract
Study of gene function in eukaryotes frequently requires data on the impact of the gene when it is expressed as a transgene, such as in ectopic or overexpression studies. Currently, the use of transgenic constructs designed to achieve these aims is often hampered by the difficulty in distinguishing between the expression levels of the endogenous gene and its transgene equivalent, which may involve either laborious microdissection to isolate specific cell types or harvesting tissue at narrow timepoints. To address this challenge, we have exploited a feature of the Golden Gate cloning method to develop a simple, restriction digest-based protocol to differentiate between expression levels of transgenic and endogenous gene copies. This method is straightforward to implement when the endogenous gene contains a Bpi1 restriction site but, importantly, can be adapted for most genes and most other cloning strategies. Key features This protocol was developed to determine the expression level of an ectopically expressed transcription factor with broad native expression in all surrounding tissues. The method described is most directly compatible with Golden Gate cloning but is, in principle, compatible with any cloning method. The protocol has been developed and validated in the model plant Arabidopsis thaliana but is applicable to most eukaryotes. Graphical overview.
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Affiliation(s)
- William Bezodis
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Helen Prescott
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Daniela Vlad
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Hugh Dickinson
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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49
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Liu X, Matsumoto H, Lv T, Zhan C, Fang H, Pan Q, Xu H, Fan X, Chu T, Chen S, Qiao K, Ma Y, Sun L, Wang Q, Wang M. Phyllosphere microbiome induces host metabolic defence against rice false-smut disease. Nat Microbiol 2023; 8:1419-1433. [PMID: 37142774 DOI: 10.1038/s41564-023-01379-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/04/2023] [Indexed: 05/06/2023]
Abstract
Mutualistic interactions between host plants and their microbiota have the potential to provide disease resistance. Most research has focused on the rhizosphere, but it is unclear how the microbiome associated with the aerial surface of plants protects against infection. Here we identify a metabolic defence underlying the mutualistic interaction between the panicle and the resident microbiota in rice to defend against a globally prevalent phytopathogen, Ustilaginoidea virens, which causes false-smut disease. Analysis of the 16S ribosomal RNA gene and internal transcribed spacer sequencing data identified keystone microbial taxa enriched in the disease-suppressive panicle, in particular Lactobacillus spp. and Aspergillus spp. Integration of these data with primary metabolism profiling, host genome editing and microbial isolate transplantation experiments revealed that plants with these taxa could resist U. virens infection in a host branched-chain amino acid (BCAA)-dependent manner. Leucine, a predominant BCAA, suppressed U. virens pathogenicity by inducing apoptosis-like cell death through H2O2 overproduction. Additionally, preliminary field experiments showed that leucine could be used in combination with chemical fungicides with a 50% reduction in dose but similar efficacy to higher fungicide concentrations. These findings may facilitate protection of crops from panicle diseases prevalent at a global scale.
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Affiliation(s)
- Xiaoyu Liu
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Tianxing Lv
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hongda Fang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qianqian Pan
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haorong Xu
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyan Fan
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tianyi Chu
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kun Qiao
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Youning Ma
- China National Rice Research Institute, Hangzhou, China
| | - Li Sun
- Department of Neurobiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qiangwei Wang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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50
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Seys FM, Humphreys CM, Tomi-Andrino C, Li Q, Millat T, Yang S, Minton NP. Base editing enables duplex point mutagenesis in Clostridium autoethanogenum at the price of numerous off-target mutations. Front Bioeng Biotechnol 2023; 11:1211197. [PMID: 37496853 PMCID: PMC10366002 DOI: 10.3389/fbioe.2023.1211197] [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: 04/24/2023] [Accepted: 06/06/2023] [Indexed: 07/28/2023] Open
Abstract
Base editors are recent multiplex gene editing tools derived from the Cas9 nuclease of Streptomyces pyogenes. They can target and modify a single nucleotide in the genome without inducing double-strand breaks (DSB) of the DNA helix. As such, they hold great potential for the engineering of microbes that lack effective DSB repair pathways such as homologous recombination (HR) or non-homologous end-joining (NHEJ). However, few applications of base editors have been reported in prokaryotes to date, and their advantages and drawbacks have not been systematically reported. Here, we used the base editors Target-AID and Target-AID-NG to introduce nonsense mutations into four different coding sequences of the industrially relevant Gram-positive bacterium Clostridium autoethanogenum. While up to two loci could be edited simultaneously using a variety of multiplexing strategies, most colonies exhibited mixed genotypes and most available protospacers led to undesired mutations within the targeted editing window. Additionally, fifteen off-target mutations were detected by sequencing the genome of the resulting strain, among them seven single-nucleotide polymorphisms (SNP) in or near loci bearing some similarity with the targeted protospacers, one 15 nt duplication, and one 12 kb deletion which removed uracil DNA glycosylase (UDG), a key DNA repair enzyme thought to be an obstacle to base editing mutagenesis. A strategy to process prokaryotic single-guide RNA arrays by exploiting tRNA maturation mechanisms is also illustrated.
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Affiliation(s)
- François M. Seys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Christopher M. Humphreys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Claudio Tomi-Andrino
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
- Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Thomas Millat
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
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