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Otte KA, Fredericksen M, Fields P, Fröhlich T, Laforsch C, Ebert D. The cuticle proteome of a planktonic crustacean. Proteomics 2024:e2300292. [PMID: 38676470 DOI: 10.1002/pmic.202300292] [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: 07/27/2023] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
The cuticles of arthropods provide an interface between the organism and its environment. Thus, the cuticle's structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the moulted cuticle of the aquatic crustacean Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology. We detected a total of 278 high-confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin-modifying enzymes as the most abundant protein groups in the cuticle proteome. Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle. Finally, cuticle protein genes were also clustered as tandem gene arrays in the D. magna genome. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing genome annotations and investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
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Affiliation(s)
- Kathrin A Otte
- Institute of Cell and Systems Biology of Animals, University of Hamburg, Hamburg, Germany
| | - Maridel Fredericksen
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | | | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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2
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Zhou R, Jia H, Du Z, Jiang A, Song Z, Wang T, Du A, Gasser RB, Ma G. The non-glycosylated protein of Toxocara canis MUC-1 interacts with proteins of murine macrophages. PLoS Negl Trop Dis 2022; 16:e0010734. [PMID: 36054186 PMCID: PMC9477421 DOI: 10.1371/journal.pntd.0010734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/15/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
Toxocariasis is a neglected parasitic disease caused predominantly by larvae of Toxocara canis. While this zoonotic disease is of major importance in humans and canids, it can also affect a range of other mammalian hosts. It is known that mucins secreted by larvae play key roles in immune recognition and evasion, but very little is understood about the molecular interactions between host cells and T. canis. Here, using an integrative approach (affinity pull-down, mass spectrometry, co-immunoprecipitation and bioinformatics), we identified 219 proteins expressed by a murine macrophage cell line (RAW264.7) that interact with prokaryotically-expressed recombinant protein (rTc-MUC-1) representing the mucin Tc-MUC-1 present in the surface coat of infective larvae of T. canis. Protein-protein interactions between rTc-MUC-1 and an actin binding protein CFL1 as well as the fatty acid binding protein FABP5 of RAW264.7 macrophages were also demonstrated in a human embryonic kidney cell line (HEK 293T). By combing predicted structural information on the protein-protein interaction and functional knowledge of the related protein association networks, we inferred roles for Tc-MUC-1 protein in the regulation of actin cytoskeletal remodelling, and the migration and phagosome formation of macrophage cells. These molecular interactions now require verification in vivo. The experimental approach taken here should be readily applicable to comparative studies of other ascaridoid nematodes (e.g. T. cati, Anisakis simplex, Ascaris suum and Baylisascaris procyonis) whose larvae undergo tissue migration in accidental hosts, including humans. Toxocariasis is a neglected parasitic disease of humans caused mainly by larvae of Toxocara canis. Given that T. canis is zoonotic and can infect a range of mammals, there has been substantial interest in host-parasite relationships, with studies showing that T. canis larvae secrete abundant mucins that effect/modulate immune responses and disease pathogenesis. To improve the understanding of immunomolecular interactions, we investigated the role(s) of the protein component of a mucin (Tc-MUC-1) secreted by infective larvae using a well-defined murine macrophage line (RAW264.7). The non-glycosylated recombinant protein of Tc-MUC-1 (designated rTc-MUC-1) was shown to interact with at least 219 proteins of RAW264.7 cells, particularly with the actin binding protein (CFL1) and a fatty acid binding protein (FABP5), which are involved in cell migration and phagocytosis, respectively. Based on these findings, we propose that Tc-MUC-1 regulates cytoskeletal organisation and signal transduction in host macrophages. It would be interesting to establish, using the integrative experimental approach employed here, whether the role(s) of Tc-MUC-1 protein homologues of related ascaridoids are conserved.
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Affiliation(s)
- Rongqiong Zhou
- College of Veterinary Medicine, Southwest University, Chongqing, China
- Immunology Research Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Hongguo Jia
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Zhendong Du
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Aiyun Jiang
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Zhenhui Song
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Aifang Du
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (RBG); (GM)
| | - Guangxu Ma
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (RBG); (GM)
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Babakhanova S, Jung EE, Namikawa K, Zhang H, Wang Y, Subach OM, Korzhenevskiy DA, Rakitina TV, Xiao X, Wang W, Shi J, Drobizhev M, Park D, Eisenhard L, Tang H, Köster RW, Subach FV, Boyden ES, Piatkevich KD. Rapid directed molecular evolution of fluorescent proteins in mammalian cells. Protein Sci 2022; 31:728-751. [PMID: 34913537 PMCID: PMC8862398 DOI: 10.1002/pro.4261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 12/31/2022]
Abstract
In vivo imaging of model organisms is heavily reliant on fluorescent proteins with high intracellular brightness. Here we describe a practical method for rapid optimization of fluorescent proteins via directed molecular evolution in cultured mammalian cells. Using this method, we were able to perform screening of large gene libraries containing up to 2 × 107 independent random genes of fluorescent proteins expressed in HEK cells, completing one iteration of directed evolution in a course of 8 days. We employed this approach to develop a set of green and near-infrared fluorescent proteins with enhanced intracellular brightness. The developed near-infrared fluorescent proteins demonstrated high performance for fluorescent labeling of neurons in culture and in vivo in model organisms such as Caenorhabditis elegans, Drosophila, zebrafish, and mice. Spectral properties of the optimized near-infrared fluorescent proteins enabled crosstalk-free multicolor imaging in combination with common green and red fluorescent proteins, as well as dual-color near-infrared fluorescence imaging. The described method has a great potential to be adopted by protein engineers due to its simplicity and practicality. We also believe that the new enhanced fluorescent proteins will find wide application for in vivo multicolor imaging of small model organisms.
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Abstract
In its natural habitat, C. elegans encounters a wide variety of microbes, including food, commensals and pathogens. To be able to survive long enough to reproduce, C. elegans has developed a complex array of responses to pathogens. These activities are coordinated on scales that range from individual organelles to the entire organism. Often, the response is triggered within cells, by detection of infection-induced damage, mainly in the intestine or epidermis. C. elegans has, however, a capacity for cell non-autonomous regulation of these responses. This frequently involves the nervous system, integrating pathogen recognition, altering host biology and governing avoidance behavior. Although there are significant differences with the immune system of mammals, some mechanisms used to limit pathogenesis show remarkable phylogenetic conservation. The past 20 years have witnessed an explosion of host-pathogen interaction studies using C. elegans as a model. This review will discuss the broad themes that have emerged and highlight areas that remain to be fully explored.
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Affiliation(s)
- Céline N Martineau
- Aix Marseille Université, Inserm, CNRS, CIML, Turing Centre for Living Systems, Marseille, France
| | | | - Nathalie Pujol
- Aix Marseille Université, Inserm, CNRS, CIML, Turing Centre for Living Systems, Marseille, France.
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Liu Y, Martinez-Martinez D, Essmann CL, Cruz MR, Cabreiro F, Garsin DA. Transcriptome analysis of Caenorhabditis elegans lacking heme peroxidase SKPO-1 reveals an altered response to Enterococcus faecalis. G3 (BETHESDA, MD.) 2021; 11:jkaa055. [PMID: 33609366 PMCID: PMC8022988 DOI: 10.1093/g3journal/jkaa055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/07/2020] [Indexed: 01/01/2023]
Abstract
The nematode Caenorhabditis elegans is commonly used as a model organism in studies of the host immune response. The worm encodes twelve peroxidase-cyclooxygenase superfamily members, making it an attractive model in which to study the functions of heme peroxidases. In previous work, loss of one of these peroxidases, SKPO-1 (ShkT-containing peroxidase), rendered C. elegans more sensitive to the human, Gram-positive pathogen Enterococcus faecalis. SKPO-1 was localized to the hypodermis of the animals where it also affected cuticle development as indicated by a morphological phenotype called "dumpy." In this work, a better understanding of how loss of skpo-1 impacts both sensitivity to pathogen as well as cuticle development was sought by subjecting a deletion mutant of skpo-1 to transcriptome analysis using RNA sequencing following exposure to control (Escherichia coli) and pathogenic (E. faecalis) feeding conditions. Loss of skpo-1 caused a general upregulation of genes encoding collagens and other proteins related to cuticle development. On E. faecalis, these animals also failed to upregulate guanylyl cyclases that are often involved in environmental sensing. Hoechst straining revealed increased permeability of the cuticle and atomic force microscopy exposed the misalignment of the cuticular annuli and furrows. These findings provide a basis for better understanding of the morphological as well as the pathogen sensitivity phenotypes associated with loss of SKPO-1 function.
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Affiliation(s)
- Yi Liu
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Daniel Martinez-Martinez
- MRC London Institute of Medical Sciences,Du Cane Road, London W12 0NN, UK
- Department of Medicine, Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Clara L Essmann
- MRC London Institute of Medical Sciences,Du Cane Road, London W12 0NN, UK
- Department of Medicine, Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Melissa R Cruz
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Filipe Cabreiro
- MRC London Institute of Medical Sciences,Du Cane Road, London W12 0NN, UK
- Department of Medicine, Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Danielle A Garsin
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Martina JA, Guerrero‐Gómez D, Gómez‐Orte E, Antonio Bárcena J, Cabello J, Miranda‐Vizuete A, Puertollano R. A conserved cysteine-based redox mechanism sustains TFEB/HLH-30 activity under persistent stress. EMBO J 2021; 40:e105793. [PMID: 33314217 PMCID: PMC7849306 DOI: 10.15252/embj.2020105793] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Mammalian TFEB and TFE3, as well as their ortholog in Caenorhabditis elegans HLH-30, play an important role in mediating cellular response to a variety of stress conditions, including nutrient deprivation, oxidative stress, and pathogen infection. In this study, we identify a novel mechanism of TFEB/HLH-30 regulation through a cysteine-mediated redox switch. Under stress conditions, TFEB-C212 undergoes oxidation, allowing the formation of intermolecular disulfide bonds that result in TFEB oligomerization. TFEB oligomers display increased resistance to mTORC1-mediated inactivation and are more stable under prolonged stress conditions. Mutation of the only cysteine residue present in HLH-30 (C284) significantly reduced its activity, resulting in developmental defects and increased pathogen susceptibility in worms. Therefore, cysteine oxidation represents a new type of TFEB post-translational modification that functions as a molecular switch to link changes in redox balance with expression of TFEB/HLH-30 target genes.
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Affiliation(s)
- José A Martina
- Cell and Developmental Biology CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
| | - David Guerrero‐Gómez
- Redox Homeostasis GroupInstituto de Biomedicina de Sevilla (IBIS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Eva Gómez‐Orte
- Centro de Investigación Biomédica de la Rioja (CIBIR)LogroñoSpain
| | - José Antonio Bárcena
- Department of Biochemistry and Molecular BiologyUniversity of Córdoba and Córdoba Maimónides Institute for Biomedical Research (IMIBIC)CórdobaSpain
| | - Juan Cabello
- Centro de Investigación Biomédica de la Rioja (CIBIR)LogroñoSpain
| | - Antonio Miranda‐Vizuete
- Redox Homeostasis GroupInstituto de Biomedicina de Sevilla (IBIS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Rosa Puertollano
- Cell and Developmental Biology CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
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Han Z, Lo WS, Lightfoot JW, Witte H, Sun S, Sommer RJ. Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition in Pristionchus Nematodes. Genetics 2020; 216:947-956. [PMID: 33060138 PMCID: PMC7768246 DOI: 10.1534/genetics.120.303785] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
A lack of appropriate molecular tools is one obstacle that prevents in-depth mechanistic studies in many organisms. Transgenesis, clustered regularly interspaced short palindromic repeats (CRISPR)-associated engineering, and related tools are fundamental in the modern life sciences, but their applications are still limited to a few model organisms. In the phylum Nematoda, transgenesis can only be performed in a handful of species other than Caenorhabditis elegans, and additionally, other species suffer from significantly lower transgenesis efficiencies. We hypothesized that this may in part be due to incompatibilities of transgenes in the recipient organisms. Therefore, we investigated the genomic features of 10 nematode species from three of the major clades representing all different lifestyles. We found that these species show drastically different codon usage bias and intron composition. With these findings, we used the species Pristionchus pacificus as a proof of concept for codon optimization and native intron addition. Indeed, we were able to significantly improve transgenesis efficiency, a principle that may be usable in other nematode species. In addition, with the improved transgenes, we developed a fluorescent co-injection marker in P. pacificus for the detection of CRISPR-edited individuals, which helps considerably to reduce associated time and costs.
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Affiliation(s)
- Ziduan Han
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Wen-Sui Lo
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - James W Lightfoot
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Hanh Witte
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Shuai Sun
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Ralf J Sommer
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
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Jones LM, Chen Y, van Oosten-Hawle P. Redefining proteostasis transcription factors in organismal stress responses, development, metabolism, and health. Biol Chem 2020; 401:1005-1018. [DOI: 10.1515/hsz-2019-0385] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
AbstractEukaryotic organisms have evolved complex and robust cellular stress response pathways to ensure maintenance of proteostasis and survival during fluctuating environmental conditions. Highly conserved stress response pathways can be triggered and coordinated at the cell-autonomous and cell-nonautonomous level by proteostasis transcription factors, including HSF1, SKN-1/NRF2, HIF1, and DAF-16/FOXO that combat proteotoxic stress caused by environmental challenges. While these transcription factors are often associated with a specific stress condition, they also direct “noncanonical” transcriptional programs that serve to integrate a multitude of physiological responses required for development, metabolism, and defense responses to pathogen infections. In this review, we outline the established function of these key proteostasis transcription factors at the cell-autonomous and cell-nonautonomous level and discuss a newly emerging stress responsive transcription factor, PQM-1, within the proteostasis network. We look beyond the canonical stress response roles of proteostasis transcription factors and highlight their function in integrating different physiological stimuli to maintain cytosolic organismal proteostasis.
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Affiliation(s)
- Laura M. Jones
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yannic Chen
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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Karakuzu O, Cruz MR, Liu Y, Garsin DA. Amplex Red Assay for Measuring Hydrogen Peroxide Production from Caenorhabditis elegans. Bio Protoc 2019; 9:e3409. [PMID: 32699812 DOI: 10.21769/bioprotoc.3409] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Reagents such as Amplex® Red have been developed for detecting hydrogen peroxide (H2O2) and are used to measure the release of H2O2 from biological samples such as mammalian leukocytes undergoing the oxidative burst. Caenorhabditis elegans is commonly used as a model host in the study of interactions with microbial pathogens and releases reactive oxygen species (ROS) as a component of its defense response. We adapted the Amplex® Red Hydrogen Peroxide/Peroxidase Assay Kit to measure H2O2 output from live Caenorhabditis elegans exposed to microbial pathogens. The assay differs from other forms of ROS detection in the worm, like dihydrofluorescein dyes and genetically encoded probes such as HyPer, in that it generally detects released, extracellular ROS rather than intracellular ROS, though the distinction between the two is blurred by the fact that certain species of ROS, including H2O2, can cross membranes. The protocol involves feeding C. elegans on a lawn of the pathogen of interest for a period of time. The animals are then rinsed off the plates in buffer and washed to remove any microbes on their cuticle. Finally, the animals in buffer are distributed into 96-well plates and Amplex® Red and horseradish peroxidase (HRP) are added. Any H2O2 released into the buffer by the worms will react with the Amplex® Red reagent in a 1:1 ratio in the presence of HRP to produce the red fluorescent excitation product resorufin that can be measured fluorometrically or spectrophotometrically, and the amount of H2O2 released can be calculated by comparison to a standard curve. The assay is most appropriate for studies focused on released ROS, and its advantages include ease of use, the ability to use small numbers of animals in a plate reader assay in which measurements can be taken either fluorometrically or spectrophotometrically.
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Affiliation(s)
- Ozgur Karakuzu
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston TX, USA
| | - Melissa R Cruz
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston TX, USA
| | - Yi Liu
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston TX, USA
| | - Danielle A Garsin
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston TX, USA
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