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Alav I, Pordelkhaki P, de Resende PE, Partington H, Gibbons S, Lord RM, Buckner MMC. Cobalt complexes modulate plasmid conjugation in Escherichia coli and Klebsiella pneumoniae. Sci Rep 2024; 14:8103. [PMID: 38582880 PMCID: PMC10998897 DOI: 10.1038/s41598-024-58895-x] [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: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 04/08/2024] Open
Abstract
Antimicrobial resistance genes (ARG), such as extended-spectrum β-lactamase (ESBL) and carbapenemase genes, are commonly carried on plasmids. Plasmids can transmit between bacteria, disseminate globally, and cause clinically important resistance. Therefore, targeting plasmids could reduce ARG prevalence, and restore the efficacy of existing antibiotics. Cobalt complexes possess diverse biological activities, including antimicrobial and anticancer properties. However, their effect on plasmid conjugation has not been explored yet. Here, we assessed the effect of four previously characterised bis(N-picolinamido)cobalt(II) complexes lacking antibacterial activity on plasmid conjugation in Escherichia coli and Klebsiella pneumoniae. Antimicrobial susceptibility testing of these cobalt complexes confirmed the lack of antibacterial activity in E. coli and K. pneumoniae. Liquid broth and solid agar conjugation assays were used to screen the activity of the complexes on four archetypical plasmids in E. coli J53. The cobalt complexes significantly reduced the conjugation of RP4, R6K, and R388 plasmids, but not pKM101, on solid agar in E. coli J53. Owing to their promising activity, the impact of cobalt complexes was tested on the conjugation of fluorescently tagged extended-spectrum β-lactamase encoding pCTgfp plasmid in E. coli and carbapenemase encoding pKpQILgfp plasmid in K. pneumoniae, using flow cytometry. The complexes significantly reduced the conjugation of pKpQILgfp in K. pneumoniae but had no impact on pCTgfp conjugation in E. coli. The cobalt complexes did not have plasmid-curing activity, suggesting that they target conjugation rather than plasmid stability. To our knowledge, this is the first study to report reduced conjugation of clinically relevant plasmids with cobalt complexes. These cobalt complexes are not cytotoxic towards mammalian cells and are not antibacterial, therefore they could be optimised and employed as inhibitors of plasmid conjugation.
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Affiliation(s)
- Ilyas Alav
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Parisa Pordelkhaki
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pedro Ernesto de Resende
- School of Pharmacy, Faculty of Science, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Hannah Partington
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Simon Gibbons
- Natural & Medical Sciences Research Center, University of Nizwa, Birkat Al Mauz, P.O. Box 33, Nizwa, 616, Oman
| | - Rianne M Lord
- School of Chemistry, Faculty of Science, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Michelle M C Buckner
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, Yasir M, Holden E, Al-Khanaq H, Webber M, Adriaenssens EM, Kingsley RA. Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica. J Virol 2024; 98:e0147623. [PMID: 38376991 PMCID: PMC10949491 DOI: 10.1128/jvi.01476-23] [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: 09/20/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica was used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.IMPORTANCEAs antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse Salmonella enterica and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.
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Affiliation(s)
- Luke Acton
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Hannah V. Pye
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Gaëtan Thilliez
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Rafał Kolenda
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Michaela Matthews
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - A. Keith Turner
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Muhammad Yasir
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Emma Holden
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Haider Al-Khanaq
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Mark Webber
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | | | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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3
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Yao T, Liu X, Li D, Huang Y, Yang W, Liu R, Wang Q, Li X, Zhou J, Jin C, Liu Y, Yang B, Pang Y. Two-component system RstAB promotes the pathogenicity of adherent-invasive Escherichia coli in response to acidic conditions within macrophages. Gut Microbes 2024; 16:2356642. [PMID: 38769708 PMCID: PMC11135836 DOI: 10.1080/19490976.2024.2356642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strain LF82, isolated from patients with Crohn's disease, invades gut epithelial cells, and replicates in macrophages contributing to chronic inflammation. In this study, we found that RstAB contributing to the colonization of LF82 in a mouse model of chronic colitis by promoting bacterial replication in macrophages. By comparing the transcriptomes of rstAB mutant- and wild-type when infected macrophages, 83 significant differentially expressed genes in LF82 were identified. And we identified two possible RstA target genes (csgD and asr) among the differentially expressed genes. The electrophoretic mobility shift assay and quantitative real-time PCR confirmed that RstA binds to the promoters of csgD and asr and activates their expression. csgD deletion attenuated LF82 intracellular biofilm formation, and asr deletion reduced acid tolerance compared with the wild-type. Acidic pH was shown by quantitative real-time PCR to be the signal sensed by RstAB to activate the expression of csgD and asr. We uncovered a signal transduction pathway whereby LF82, in response to the acidic environment within macrophages, activates transcription of the csgD to promote biofilm formation, and activates transcription of the asr to promote acid tolerance, promoting its replication within macrophages and colonization of the intestine. This finding deepens our understanding of the LF82 replication regulation mechanism in macrophages and offers new perspectives for further studies on AIEC virulence mechanisms.
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Affiliation(s)
- Ting Yao
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Xingmei Liu
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Dan Li
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Yu Huang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Wen Yang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Ruiying Liu
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Qian Wang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Xueping Li
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Jiarui Zhou
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Chen Jin
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Yutao Liu
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Bin Yang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Yu Pang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
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Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church G. Strategies to identify and edit improvements in synthetic genome segments episomally. Nucleic Acids Res 2023; 51:10094-10106. [PMID: 37615546 PMCID: PMC10570025 DOI: 10.1093/nar/gkad692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/30/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Genome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments at low copy number. However, all stages of whole-genome engineering have the potential to impose mutations on the synthetic genome that can reduce or eliminate the fitness of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to recoding an Escherichia coli strain to replace seven codons with synonymous alternatives genome wide. Ten 44 402-47 179 bp de novo synthesized DNA segments contained in a BAC from the recoded strain were unable to complement deletion of the corresponding 33-61 wild-type genes using a single antibiotic resistance marker. Next-generation sequencing (NGS) was used to identify 1-7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the recoded segment contained in the BAC when both the recoded and wild-type copies of the mutated genes had to exist by necessity during the repair process. Finally, two web-based tools were used to predict the impact of a subset of non-recoding missense mutations on strain fitness using protein structure and function calls.
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Affiliation(s)
- Alexandra Rudolph
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anush Chiappino-Pepe
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Matthieu Landon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
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Element SJ, Moran RA, Beattie E, Hall RJ, van Schaik W, Buckner MM. Growth in a biofilm promotes conjugation of a bla NDM-1-bearing plasmid between Klebsiella pneumoniae strains. mSphere 2023; 8:e0017023. [PMID: 37417759 PMCID: PMC10449501 DOI: 10.1128/msphere.00170-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 07/08/2023] Open
Abstract
Antimicrobial resistance (AMR) is a growing problem, especially in Gram-negative Enterobacteriaceae such as Klebsiella pneumoniae. Horizontal transfer of conjugative plasmids contributes to AMR gene dissemination. Bacteria such as K. pneumoniae commonly exist in biofilms, yet most studies focus on planktonic cultures. Here we studied the transfer of a multi-drug resistance plasmid in planktonic and biofilm populations of K. pneumoniae. We determined plasmid transfer from a clinical isolate, CPE16, which carried four plasmids, including the 119-kbp blaNDM-1-bearing F-type plasmid pCPE16_3, in planktonic and biofilm conditions. We found that transfer frequency of pCPE16_3 in a biofilm was orders-of-magnitude higher than between planktonic cells. In 5/7 sequenced transconjugants (TCs) multiple plasmids had transferred. Plasmid acquisition had no detectable growth impact on TCs. Gene expression of the recipient and a transconjugant was investigated by RNA-sequencing in three lifestyles: planktonic exponential growth, planktonic stationary phase, and biofilm. We found that lifestyle had a substantial impact on chromosomal gene expression, and plasmid carriage affected chromosomal gene expression most in stationary planktonic and biofilm lifestyles. Furthermore, expression of plasmid genes was lifestyle-dependent, with distinct signatures across the three conditions. Our study shows that growth in biofilm greatly increased the risk of conjugative transfer of a carbapenem resistance plasmid in K. pneumoniae without fitness costs and minimal transcriptional rearrangements, thus highlighting the importance of biofilms in the spread of AMR in this opportunistic pathogen. IMPORTANCE Carbapenem-resistant K. pneumoniae is particularly problematic in hospital settings. Carbapenem resistance genes can transfer between bacteria via plasmid conjugation. Alongside drug resistance, K. pneumoniae can form biofilms on hospital surfaces, at infection sites and on implanted devices. Biofilms are naturally protected and can be inherently more tolerant to antimicrobials than their free-floating counterparts. There have been indications that plasmid transfer may be more likely in biofilm populations, thus creating a conjugation "hotspot". However, there is no clear consensus on the effect of the biofilm lifestyle on plasmid transfer. Therefore, we aimed to explore the transfer of a plasmid in planktonic and biofilm conditions, and the impact of plasmid acquisition on a new bacterial host. Our data show transfer of a resistance plasmid is increased in a biofilm, which may be a significant contributing factor to the rapid dissemination of resistance plasmids in K. pneumoniae.
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Affiliation(s)
- Sarah J. Element
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Robert A. Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Emilie Beattie
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Rebecca J. Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Michelle M.C. Buckner
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
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Ragunathan PT, Ng Kwan Lim E, Ma X, Massé E, Vanderpool CK. Mechanisms of Regulation of Cryptic Prophage-Encoded Gene Products in Escherichia coli. J Bacteriol 2023; 205:e0012923. [PMID: 37439671 PMCID: PMC10448788 DOI: 10.1128/jb.00129-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
The dicBF operon of Qin cryptic prophage in Escherichia coli K-12 encodes the small RNA (sRNA) DicF and small protein DicB, which regulate host cell division and are toxic when overexpressed. While new functions of DicB and DicF have been identified in recent years, the mechanisms controlling the expression of the dicBF operon have remained unclear. Transcription from dicBp, the major promoter of the dicBF operon, is repressed by DicA. In this study, we discovered that transcription of the dicBF operon and processing of the polycistronic mRNA is regulated by multiple mechanisms. DicF sRNA accumulates during stationary phase and is processed from the polycistronic dicBF mRNA by the action of both RNase III and RNase E. DicA-mediated transcriptional repression of dicBp can be relieved by an antirepressor protein, Rem, encoded on the Qin prophage. Ectopic production of Rem results in cell filamentation due to strong induction of the dicBF operon, and filamentation is mediated by DicF and DicB. Spontaneous derepression of dicBp occurs in a subpopulation of cells independent of the antirepressor. This phenomenon is reminiscent of the bistable switch of λ phage with DicA and DicC performing functions similar to those of CI and Cro, respectively. Additional experiments demonstrate stress-dependent induction of the dicBF operon. Collectively, our results illustrate that toxic genes carried on cryptic prophages are subject to layered mechanisms of control, some that are derived from the ancestral phage and some that are likely later adaptations. IMPORTANCE Cryptic or defective prophages have lost genes necessary to excise from the bacterial chromosome and produce phage progeny. In recent years, studies have found that cryptic prophage gene products influence diverse aspects of bacterial host cell physiology. However, to obtain a complete understanding of the relationship between cryptic prophages and the host bacterium, identification of the environmental, host, or prophage-encoded factors that induce the expression of cryptic prophage genes is crucial. In this study, we examined the regulation of a cryptic prophage operon in Escherichia coli encoding a small RNA and a small protein that are involved in inhibiting bacterial cell division, altering host metabolism, and protecting the host bacterium from phage infections.
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Affiliation(s)
- Preethi T. Ragunathan
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Evelyne Ng Kwan Lim
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Québec, Canada
| | - Xiangqian Ma
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Eric Massé
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Québec, Canada
| | - Carin K. Vanderpool
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Morra R, Pratama F, Butterfield T, Tomazetto G, Young K, Lopez R, Dixon N. arfA antisense RNA regulates MscL excretory activity. Life Sci Alliance 2023; 6:e202301954. [PMID: 37012050 PMCID: PMC10070815 DOI: 10.26508/lsa.202301954] [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: 01/27/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Excretion of cytoplasmic protein (ECP) is a commonly observed phenomenon in bacteria, and this partial extracellular localisation of the intracellular proteome has been implicated in a variety of stress response mechanisms. In response to hypoosmotic shock and ribosome stalling in Escherichia coli, ECP is dependent upon the presence of the large-conductance mechanosensitive channel and the alternative ribosome-rescue factor A gene products. However, it is not known if a mechanistic link exists between the corresponding genes and the respective stress response pathways. Here, we report that the corresponding mscL and arfA genes are commonly co-located on the genomes of Gammaproteobacteria and display overlap in their respective 3' UTR and 3' CDS. We show this unusual genomic arrangement permits an antisense RNA-mediated regulatory control between mscL and arfA, and this modulates MscL excretory activity in E. coli These findings highlight a mechanistic link between osmotic, translational stress responses and ECP in E. coli, further elucidating the previously unknown regulatory function of arfA sRNA.
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Affiliation(s)
- Rosa Morra
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Fenryco Pratama
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Institut Teknologi Bandung, Bandung, Indonesia
| | - Thomas Butterfield
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Geizecler Tomazetto
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Kate Young
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Ruth Lopez
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Neil Dixon
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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Demeter A, Jacomin AC, Gul L, Lister A, Lipscombe J, Invernizzi R, Branchu P, Macaulay I, Nezis IP, Kingsley RA, Korcsmaros T, Hautefort I. Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells. Front Cell Infect Microbiol 2022; 12:834895. [PMID: 36061866 PMCID: PMC9428466 DOI: 10.3389/fcimb.2022.834895] [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: 12/13/2021] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Macroautophagy is a ubiquitous homeostasis and health-promoting recycling process of eukaryotic cells, targeting misfolded proteins, damaged organelles and intracellular infectious agents. Some intracellular pathogens such as Salmonella enterica serovar Typhimurium hijack this process during pathogenesis. Here we investigate potential protein-protein interactions between host transcription factors and secreted effector proteins of Salmonella and their effect on host gene transcription. A systems-level analysis identified Salmonella effector proteins that had the potential to affect core autophagy gene regulation. The effect of a SPI-1 effector protein, SopE, that was predicted to interact with regulatory proteins of the autophagy process, was investigated to validate our approach. We then confirmed experimentally that SopE can directly bind to SP1, a host transcription factor, which modulates the expression of the autophagy gene MAP1LC3B. We also revealed that SopE might have a double role in the modulation of autophagy: Following initial increase of MAP1LC3B transcription triggered by Salmonella infection, subsequent decrease in MAP1LC3B transcription at 6h post-infection was SopE-dependent. SopE also played a role in modulation of the autophagy flux machinery, in particular MAP1LC3B and p62 autophagy proteins, depending on the level of autophagy already taking place. Upon typical infection of epithelial cells, the autophagic flux is increased. However, when autophagy was chemically induced prior to infection, SopE dampened the autophagic flux. The same was also observed when most of the intracellular Salmonella cells were not associated with the SCV (strain lacking sifA) regardless of the autophagy induction status before infection. We demonstrated how regulatory network analysis can be used to better characterise the impact of pathogenic effector proteins, in this case, Salmonella. This study complements previous work in which we had demonstrated that specific pathogen effectors can affect the autophagy process through direct interaction with autophagy proteins. Here we show that effector proteins can also influence the upstream regulation of the process. Such interdisciplinary studies can increase our understanding of the infection process and point out targets important in intestinal epithelial cell defense.
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Affiliation(s)
- Amanda Demeter
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | | | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ashleigh Lister
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - James Lipscombe
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Rachele Invernizzi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- *Correspondence: Tamas Korcsmaros,
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Rinaldi MA, Tait S, Toogood HS, Scrutton NS. Bioproduction of Linalool From Paper Mill Waste. Front Bioeng Biotechnol 2022; 10:892896. [PMID: 35711639 PMCID: PMC9195575 DOI: 10.3389/fbioe.2022.892896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
A key challenge in chemicals biomanufacturing is the maintenance of stable, highly productive microbial strains to enable cost-effective fermentation at scale. A “cookie-cutter” approach to microbial engineering is often used to optimize host stability and productivity. This can involve identifying potential limitations in strain characteristics followed by attempts to systematically optimize production strains by targeted engineering. Such targeted approaches however do not always lead to the desired traits. Here, we demonstrate both ‘hit and miss’ outcomes of targeted approaches in attempts to generate a stable Escherichia coli strain for the bioproduction of the monoterpenoid linalool, a fragrance molecule of industrial interest. First, we stabilized linalool production strains by eliminating repetitive sequences responsible for excision of pathway components in plasmid constructs that encode the pathway for linalool production. These optimized pathway constructs were then integrated within the genome of E. coli in three parts to eliminate a need for antibiotics to maintain linalool production. Additional strategies were also employed including: reduction in cytotoxicity of linalool by adaptive laboratory evolution and modification or homologous gene replacement of key bottleneck enzymes GPPS/LinS. Our study highlights that a major factor influencing linalool titres in E. coli is the stability of the genetic construct against excision or similar recombination events. Other factors, such as decreasing linalool cytotoxicity and changing pathway genes, did not lead to improvements in the stability or titres obtained. With the objective of reducing fermentation costs at scale, the use of minimal base medium containing paper mill wastewater secondary paper fiber as sole carbon source was also investigated. This involved simultaneous saccharification and fermentation using either supplemental cellulase blends or by co-expressing secretable cellulases in E. coli containing the stabilized linalool production pathway. Combined, this study has demonstrated a stable method for linalool production using an abundant and low-cost feedstock and improved production strains, providing an important proof-of-concept for chemicals production from paper mill waste streams. For scaled production, optimization will be required, using more holistic approaches that involve further rounds of microbial engineering and fermentation process development.
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Affiliation(s)
- Mauro A Rinaldi
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Shirley Tait
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Helen S Toogood
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,C3 Biotechnologies (Maritime and Aerospace) Ltd, Lancaster, United Kingdom
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10
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Enterobacteria impair host p53 tumor suppressor activity through mRNA destabilization. Oncogene 2022; 41:2173-2186. [PMID: 35197571 PMCID: PMC8993692 DOI: 10.1038/s41388-022-02238-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/25/2022]
Abstract
Increasing evidence highlights the role of bacteria in the physiopathology of cancer. However, the underlying molecular mechanisms remains poorly understood. Several cancer-associated bacteria have been shown to produce toxins which interfere with the host defense against tumorigenesis. Here, we show that lipopolysaccharides from Klebsiella pneumoniae and other Enterobacteria strongly inhibit the host tumor suppressor p53 pathway through a novel mechanism of p53 regulation. We found that lipopolysaccharides destabilize TP53 mRNA through a TLR4-NF-κB-mediated inhibition of the RNA-binding factor Wig-1. Importantly, we show that K. pneumoniae disables two major tumor barriers, oncogene-induced DNA damage signaling and senescence, by impairing p53 transcriptional activity upon DNA damage and oncogenic stress. Furthermore, we found an inverse correlation between the levels of TLR4 and p53 mutation in colorectal tumors. Hence, our data suggest that the repression of p53 by Enterobacteria via TLR4 alleviates the selection pressure for p53 oncogenic mutations and shapes the genomic evolution of cancer.
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11
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Qian C, Huang M, Du Y, Song J, Mu H, Wei Y, Zhang S, Yin Z, Yuan C, Liu B, Liu B. Chemotaxis and Shorter O-Antigen Chain Length Contribute to the Strong Desiccation Tolerance of a Food-Isolated Cronobacter sakazakii Strain. Front Microbiol 2022; 12:779538. [PMID: 35058898 PMCID: PMC8764414 DOI: 10.3389/fmicb.2021.779538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen causing a lethality rate as high as 80% in infants. Desiccation tolerance ensures its survival in powdered infant formula (PIF) and contributes to the increased exposure to neonates, resulting in neonatal meningitis, septicemia, and necrotizing enterocolitis. This study showed that a food-isolated C. sakazakii G4023 strain exhibited a stronger desiccation tolerance than C. sakazakii ATCC 29544 strain. Considering the proven pathogenicity of G4023, it could be a big threat to infants. Transcriptome and proteome were performed to provide new insights into the desiccation adaptation mechanisms of G4023. Integrated analyses of these omics suggested that 331 genes were found regulated at both transcriptional and protein levels (≥2.0- and ≥1.5-fold, respectively). Deletion of chemotaxis system encoded genes cheA and cheW resulted in decreased tolerance in both short- and long-term desiccation. Reduced O-antigen chain length contributed to the biofilm formation and desiccation tolerance in the short term rather than the long term. In addition, biosynthesis of flagella, arginine and its transport system, and Fe/S cluster were also observed regulated in desiccated G4023. A better understanding of desiccation adaptation mechanisms of G4023 could in turn guide the operations during production and preservation of PIF or other food to reduce survival odds of G4023 and lower its exposure to get to infants.
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Affiliation(s)
- Chengqian Qian
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Min Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yuhui Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Jingjie Song
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Huiqian Mu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yi Wei
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Si Zhang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Zhiqiu Yin
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an, China
| | - Chao Yuan
- Department of Sanitary Toxicology and Chemistry, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
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12
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Efficient retroelement-mediated DNA writing in bacteria. Cell Syst 2021; 12:860-872.e5. [PMID: 34358440 DOI: 10.1016/j.cels.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 11/03/2020] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
The ability to efficiently and dynamically change information stored in genomes would enable powerful strategies for studying cell biology and controlling cellular phenotypes. Current recombineering-mediated DNA writing platforms in bacteria are limited to specific laboratory conditions, often suffer from suboptimal editing efficiencies, and are not suitable for in situ applications. To overcome these limitations, we engineered a retroelement-mediated DNA writing system that enables efficient and precise editing of bacterial genomes without the requirement for target-specific elements or selection. We demonstrate that this DNA writing platform enables a broad range of applications, including efficient, scarless, and cis-element-independent editing of targeted microbial genomes within complex communities, the high-throughput mapping of spatial information and cellular interactions into DNA memory, and the continuous evolution of cellular traits.
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13
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Li W, Jiang L, Liu X, Guo R, Ma S, Wang J, Ma S, Li S, Li H. YhjC is a novel transcriptional regulator required for Shigella flexneri virulence. Virulence 2021; 12:1661-1671. [PMID: 34152261 PMCID: PMC8218686 DOI: 10.1080/21505594.2021.1936767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Shigella is an intracellular pathogen that primarily infects the human colon and causes shigellosis. Shigella virulence relies largely on the type III secretion system (T3SS) and secreted effectors. VirF, the master Shigella virulence regulator, is essential for the expression of T3SS-related genes. In this study, we found that YhjC, a LysR-type transcriptional regulator, is required for Shigella virulence through activating the transcription of virF. Pathogenicity of the yhjC mutant, including colonization in the colons of guinea pigs as well as its ability for host cell adhesion and invasion, was significantly lowered. Expression levels of virF and nearly all VirF-dependent genes were downregulated by yhjC deletion, indicating that YhjC can activate virF transcription. Electrophoretic mobility shift assay analysis demonstrated that YhjC could bind directly to the virF promoter region. Therefore, YhjC is a novel virulence regulator that positively regulates the virF expression and promotes Shigella virulence. Additionally, genome-wide expression analysis identified the presence of other genes in the large virulence plasmid and a genome exhibiting differential expression in response to yhjC deletion, with 169 downregulated and 99 upregulated genes, indicating that YhjC also functioned as a global regulatory factor.
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Affiliation(s)
- Wanwu Li
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China.,Shandong Center for Food and Drug Evaluation & Certification, Jinan, China
| | - Lingyan Jiang
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Xiaoqian Liu
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Rui Guo
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China
| | - Shuai Ma
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Jingting Wang
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Shuangshuang Ma
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Shujie Li
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Huiying Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China.,School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
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14
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Liu S, Zhang B, Rowan BG, Jazwinski SM, Abdel-Mageed AB, Steele C, Wang AR, Sartor O, Niu T, Zhang Q. A Novel Controlled PTEN-Knockout Mouse Model for Prostate Cancer Study. Front Mol Biosci 2021; 8:696537. [PMID: 34150854 PMCID: PMC8211560 DOI: 10.3389/fmolb.2021.696537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is associated with advanced age, but how age contributes to prostate carcinogenesis remains unknown. The prostate-specific Pten conditional knockout mouse model closely imitates human PCa initiation and progression. To better understand how age impacts PCa in an experimental model, we have generated a spatially and temporally controlled Pten-null PCa murine model at different ages (aged vs. non-aged) of adult mice. Here, we present a protocol to inject the Cre-expressing adenovirus with luciferin tag, intraductally, into the prostate anterior lobes of Pten-floxed mice; Pten-loss will be triggered post-Cre expression at different ages. In vivo imaging of luciferin signal following viral infection confirmed successful delivery of the virus and Cre activity. Immunohistochemical staining confirmed prostate epithelial-specific expression of Cre recombinase and the loss of Pten and activation of P-Akt, P-S6, and P-4E-BP1. The Cre-expression, Pten ablation, and activated PI3K/AKT/mTOR pathways were limited to the prostate epithelium. All mice developed prostatic epithelial hyperplasia within 4 weeks after Pten ablation and prostatic intraepithelial neoplasia (PIN) within 8 weeks post-Pten ablation. Some PINs had progressed to invasive adenocarcinoma at 8-16 weeks post-Pten ablation. Aged mice exhibited significantly accelerated PI3K/AKT/mTOR signaling and increased PCa onset and progression compared to young mice. The viral infection success rate is ∼80%. This model will be beneficial for investigations of cancer-related to aging.
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Affiliation(s)
- Sen Liu
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Bing Zhang
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
- Medical Laboratory of ShenZhen LuoHu People’s Hospital, Shenzhen, China
| | - Brian G. Rowan
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - S. Michal Jazwinski
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA, United States
| | - Asim B. Abdel-Mageed
- Department of Urology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Chad Steele
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Alun R. Wang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Oliver Sartor
- Department of Urology, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Tianhua Niu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Qiuyang Zhang
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
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15
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Jervis AJ, Hanko EK, Dunstan MS, Robinson CJ, Takano E, Scrutton NS. A plasmid toolset for CRISPR-mediated genome editing and CRISPRi gene regulation in Escherichia coli. Microb Biotechnol 2021; 14:1120-1129. [PMID: 33710766 PMCID: PMC8085919 DOI: 10.1111/1751-7915.13780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
CRISPR technologies have become standard laboratory tools for genetic manipulations across all kingdoms of life. Despite their origins in bacteria, the development of CRISPR tools for engineering bacteria has been slower than for eukaryotes; nevertheless, their function and application for genome engineering and gene regulation via CRISPR interference (CRISPRi) has been demonstrated in various bacteria, and adoption has become more widespread. Here, we provide simple plasmid-based systems for genome editing (gene knockouts/knock-ins, and genome integration of large DNA fragments) and CRISPRi in E. coli using a CRISPR-Cas12a system. The described genome engineering protocols allow markerless deletion or genome integration in just seven working days with high efficiency (> 80% and 50%, respectively), and the CRISPRi protocols allow robust transcriptional repression of target genes (> 90%) with a single cloning step. The presented minimized plasmids and their associated design and experimental protocols provide efficient and effective CRISPR-Cas12 genome editing, genome integration and CRISPRi implementation. These simple-to-use systems and protocols will allow the easy adoption of CRISPR technology by any laboratory.
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Affiliation(s)
- Adrian J. Jervis
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Erik K.R. Hanko
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Mark S. Dunstan
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Christopher J. Robinson
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Eriko Takano
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Nigel S. Scrutton
- Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM)Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
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16
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Howitz N, Su T, Lazazzera BA. Meta-Tyrosine Induces Cytotoxic Misregulation of Metabolism in Escherichia coli. J Mol Biol 2020; 432:166716. [PMID: 33220263 DOI: 10.1016/j.jmb.2020.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022]
Abstract
The non-protein amino acid meta-Tyrosine (m-Tyr) is produced in cells under conditions of oxidative stress, and m-Tyr has been shown to be toxic to a broad range of biological systems. However, the mechanism by which m-Tyr damages cells is unclear. In E. coli, the quality control (QC) function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to m-Tyr. To determine the mechanism of m-Tyr toxicity, we utilitized a strain of E. coli that expresses a QC-defective PheRS. The global responses of E. coli cells to m-Tyr were assessed by RNA-seq, and >500 genes were differentially expressed after the addition of m-Tyr. The most strongly up-regulated genes are involved in unfolded-protein stress response, and cells exposed to m-Tyr contained large, electron-dense protein aggregates, indicating that m-Tyr destabilized a large fraction of the proteome. Additionally, we observed that amino acid biosynthesis and transport regulons, controlled by ArgR, TrpR, and TyrR, and the stringent-response regulon, controlled by DksA/ppGpp, were differentially expressed. m-Tyr resistant mutants were isolated and found to have altered a promoter to increase expression of the enzymes for Phe production or to have altered transporters, which likely result in less uptake or increased efflux of m-Tyr. These findings indicate that when m-Tyr has passed the QC checkpoint by the PheRS, this toxicity of m-Tyr may result from interfering with amino acid metabolism, destabalizing a large number of proteins, and the formation of protein aggregates.
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Affiliation(s)
- Nathaniel Howitz
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA 90095, USA
| | - Beth A Lazazzera
- 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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17
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Tassinari E, Bawn M, Thilliez G, Charity O, Acton L, Kirkwood M, Petrovska L, Dallman T, Burgess CM, Hall N, Duffy G, Kingsley RA. Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone. Microb Genom 2020; 6:mgen000456. [PMID: 33112226 PMCID: PMC7725340 DOI: 10.1099/mgen.0.000456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/01/2020] [Indexed: 01/10/2023] Open
Abstract
Epidemic and pandemic clones of bacterial pathogens with distinct characteristics continually emerge, replacing those previously dominant through mechanisms that remain poorly characterized. Here, whole-genome-sequencing-powered epidemiology linked horizontal transfer of a virulence gene, sopE, to the emergence and clonal expansion of a new epidemic Salmonella enterica serovar Typhimurium (S. Typhimurium) clone. The sopE gene is sporadically distributed within the genus Salmonella and rare in S. enterica Typhimurium lineages, but was acquired multiple times during clonal expansion of the currently dominant pandemic monophasic S. Typhimurium sequence type (ST) 34 clone. Ancestral state reconstruction and time-scaled phylogenetic analysis indicated that sopE was not present in the common ancestor of the epidemic clade, but later acquisition resulted in increased clonal expansion of sopE-containing clones that was temporally associated with emergence of the epidemic, consistent with increased fitness. The sopE gene was mainly associated with a temperate bacteriophage mTmV, but recombination with other bacteriophage and apparent horizontal gene transfer of the sopE gene cassette resulted in distribution among at least four mobile genetic elements within the monophasic S. enterica Typhimurium ST34 epidemic clade. The mTmV prophage lysogenic transfer to other S. enterica serovars in vitro was limited, but included the common pig-associated S. enterica Derby (S. Derby). This may explain mTmV in S. Derby co-circulating on farms with monophasic S. Typhimurium ST34, highlighting the potential for further transfer of the sopE virulence gene in nature. We conclude that whole-genome epidemiology pinpoints potential drivers of evolutionary and epidemiological dynamics during pathogen emergence, and identifies targets for subsequent research in epidemiology and bacterial pathogenesis.
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Affiliation(s)
- Eleonora Tassinari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gaetan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Oliver Charity
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Luke Acton
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mark Kirkwood
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Timothy Dallman
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
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18
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Clairfeuille T, Buchholz KR, Li Q, Verschueren E, Liu P, Sangaraju D, Park S, Noland CL, Storek KM, Nickerson NN, Martin L, Dela Vega T, Miu A, Reeder J, Ruiz-Gonzalez M, Swem D, Han G, DePonte DP, Hunter MS, Gati C, Shahidi-Latham S, Xu M, Skelton N, Sellers BD, Skippington E, Sandoval W, Hanan EJ, Payandeh J, Rutherford ST. Structure of the essential inner membrane lipopolysaccharide-PbgA complex. Nature 2020; 584:479-483. [PMID: 32788728 DOI: 10.1038/s41586-020-2597-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Lipopolysaccharide (LPS) resides in the outer membrane of Gram-negative bacteria where it is responsible for barrier function1,2. LPS can cause death as a result of septic shock, and its lipid A core is the target of polymyxin antibiotics3,4. Despite the clinical importance of polymyxins and the emergence of multidrug resistant strains5, our understanding of the bacterial factors that regulate LPS biogenesis is incomplete. Here we characterize the inner membrane protein PbgA and report that its depletion attenuates the virulence of Escherichia coli by reducing levels of LPS and outer membrane integrity. In contrast to previous claims that PbgA functions as a cardiolipin transporter6-9, our structural analyses and physiological studies identify a lipid A-binding motif along the periplasmic leaflet of the inner membrane. Synthetic PbgA-derived peptides selectively bind to LPS in vitro and inhibit the growth of diverse Gram-negative bacteria, including polymyxin-resistant strains. Proteomic, genetic and pharmacological experiments uncover a model in which direct periplasmic sensing of LPS by PbgA coordinates the biosynthesis of lipid A by regulating the stability of LpxC, a key cytoplasmic biosynthetic enzyme10-12. In summary, we find that PbgA has an unexpected but essential role in the regulation of LPS biogenesis, presents a new structural basis for the selective recognition of lipids, and provides opportunities for future antibiotic discovery.
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Affiliation(s)
| | - Kerry R Buchholz
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Qingling Li
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Erik Verschueren
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Peter Liu
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Dewakar Sangaraju
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA, USA
| | - Summer Park
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Cameron L Noland
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | | | - Lynn Martin
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Trisha Dela Vega
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Anh Miu
- Biochemical & Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Janina Reeder
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Maria Ruiz-Gonzalez
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Danielle Swem
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cornelius Gati
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Stanford University, Department of Structural Biology, Stanford, CA, USA
| | | | - Min Xu
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Elizabeth Skippington
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Emily J Hanan
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Structural Biology, Genentech Inc., South San Francisco, CA, USA. .,Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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19
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Tian H, Huo Y, Zhang J, Ding S, Wang Z, Li H, Wang L, Lu M, Liu S, Qiu S, Zhang Q. Disruption of ubiquitin specific protease 26 gene causes male subfertility associated with spermatogenesis defects in mice†. Biol Reprod 2020; 100:1118-1128. [PMID: 30561524 DOI: 10.1093/biolre/ioy258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 11/01/2017] [Accepted: 12/15/2018] [Indexed: 11/14/2022] Open
Abstract
Ubiquitin-specific protease 26 (USP26) is an X-linked gene exclusively expressed in the testis and codes for the USP26, a peptidase enzyme that belongs to the deubiquitinating enzyme family. Recent studies have indicated that mutations in USP26 affect spermatogenesis and are associated with male infertility in humans and mice. However, the exact role of USP26 in spermatogenesis and how it affects male reproduction remains unknown. In this study, we generated a conventional Usp26 knockout mouse model and found that deletion of Usp26 in male mice (Usp26-/Y) leads to significantly reduced pup numbers per litter and significantly increased intervals between two consecutive offspring. We also found that the serum follicle stimulating hormone and testosterone levels of adult Usp26-/Y mice were significantly decreased compared to those of Usp26+/Y mice. Histological examination results showed that Usp26-/Y mice had significantly increased percentage of abnormal seminiferous tubules at different ages. Flow cytometry results exhibited that Usp26-/Y mice had significantly reduced percentage of mature haploid cells in the testes compared to Usp26+/Y mice. Sperm counts in epididymis were also significantly declined in Usp26-/Y mice compared to those in Usp26+/Y mice. Immunohistochemistry and immunofluorescence staining and immunoprecipitation analysis results showed that USP26 and androgen receptor were co-localized in mouse testicular cells at different ages and they both had physiological interactions. All these results demonstrated that the loss of Usp26 affects spermatogenesis and hormone secretion and causes male subfertility. Our study also provides the evidence on the interactions between USP26 and androgen receptor in mouse testis, whereby pointing to a potential mechanism.
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Affiliation(s)
- Hong Tian
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,Research Center of Reproductive Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Yongwei Huo
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,Research Center of Reproductive Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Jie Zhang
- Dalian Municipal Women and Children's Medical Center, Dalian, Liaoning, China
| | - Shangshu Ding
- Research Center of Reproductive Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Zhiyong Wang
- Research Center of Reproductive Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hecheng Li
- Research Center of Reproductive Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lirong Wang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,Research Center of Reproductive Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Ming Lu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Sen Liu
- Department of Structural & Cellular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Shudong Qiu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,Research Center of Reproductive Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Qiuyang Zhang
- Department of Structural & Cellular Biology, Tulane University School of Medicine, New Orleans, LA, USA.,Tulane Center for Aging.,Tulane Cancer Center, Louisiana Cancer Research Consortium
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20
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Transposon Insertion Site Sequencing of Providencia stuartii: Essential Genes, Fitness Factors for Catheter-Associated Urinary Tract Infection, and the Impact of Polymicrobial Infection on Fitness Requirements. mSphere 2020; 5:5/3/e00412-20. [PMID: 32461277 PMCID: PMC7253602 DOI: 10.1128/msphere.00412-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Providencia stuartii is a common cause of polymicrobial catheter-associated urinary tract infection (CAUTI), and yet literature describing the molecular mechanisms of its pathogenesis is limited. To identify factors important for colonization during single-species infection and during polymicrobial infection with a common cocolonizer, Proteus mirabilis, we created a saturating library of ∼50,000 transposon mutants and conducted transposon insertion site sequencing (Tn-Seq) in a murine model of CAUTI. P. stuartii strain BE2467 carries 4,398 genes, 521 of which were identified as essential for growth in laboratory medium and therefore could not be assessed for contribution to infection. Using an input/output fold change cutoff value of 20 and P values of <0.05, 340 genes were identified as important for establishing single-species infection only and 63 genes as uniquely important for polymicrobial infection with P. mirabilis, and 168 genes contributed to both single-species and coinfection. Seven mutants were constructed for experimental validation of the primary screen that corresponded to flagella (fliC mutant), twin arginine translocation (tatC), an ATP-dependent protease (clpP), d-alanine-d-alanine ligase (ddlA), type 3 secretion (yscI and sopB), and type VI secretion (impJ). Infection-specific phenotypes validated 6/7 (86%) mutants during direct cochallenge with wild-type P. stuartii and 3/5 (60%) mutants during coinfection with P. mirabilis, for a combined validation rate of 9/12 (75%). Tn-Seq therefore successfully identified genes that contribute to fitness of P. stuartii within the urinary tract, determined the impact of coinfection on fitness requirements, and added to the identification of a collection of genes that may contribute to fitness of multiple urinary tract pathogens.IMPORTANCE Providencia stuartii is a common cause of polymicrobial catheter-associated urinary tract infections (CAUTIs), particularly during long-term catheterization. However, little is known regarding the pathogenesis of this organism. Using transposon insertion site sequencing (Tn-Seq), we performed a global assessment of P. stuartii fitness factors for CAUTI while simultaneously determining how coinfection with another pathogen alters fitness requirements. This approach provides four important contributions to the field: (i) the first global estimation of P. stuartii genes essential for growth in laboratory medium, (ii) identification of novel fitness factors for P. stuartii colonization of the catheterized urinary tract, (iii) identification of core fitness factors for both single-species and polymicrobial CAUTI, and (iv) assessment of conservation of fitness factors between common uropathogens. Genomewide assessment of the fitness requirements for common uropathogens during single-species and polymicrobial CAUTI thus elucidates complex interactions that contribute to disease severity and will uncover conserved targets for therapeutic intervention.
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21
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Buckner MMC, Ciusa ML, Meek RW, Moorey AR, McCallum GE, Prentice EL, Reid JP, Alderwick LJ, Di Maio A, Piddock LJV. HIV Drugs Inhibit Transfer of Plasmids Carrying Extended-Spectrum β-Lactamase and Carbapenemase Genes. mBio 2020; 11:e03355-19. [PMID: 32098822 PMCID: PMC7042701 DOI: 10.1128/mbio.03355-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial-resistant (AMR) infections pose a serious risk to human and animal health. A major factor contributing to this global crisis is the sharing of resistance genes between different bacteria via plasmids. The WHO lists Enterobacteriaceae, such as Escherichia coli and Klebsiella pneumoniae, producing extended-spectrum β-lactamases (ESBL) and carbapenemases as "critical" priorities for new drug development. These resistance genes are most often shared via plasmid transfer. However, finding methods to prevent resistance gene sharing has been hampered by the lack of screening systems for medium-/high-throughput approaches. Here, we have used an ESBL-producing plasmid, pCT, and a carbapenemase-producing plasmid, pKpQIL, in two different Gram-negative bacteria, E. coli and K. pneumoniae Using these critical resistance-pathogen combinations, we developed an assay using fluorescent proteins, flow cytometry, and confocal microscopy to assess plasmid transmission inhibition within bacterial populations in a medium-throughput manner. Three compounds with some reports of antiplasmid properties were tested; chlorpromazine reduced transmission of both plasmids and linoleic acid reduced transmission of pCT. We screened the Prestwick library of over 1,200 FDA-approved drugs/compounds. From this, we found two nucleoside analogue drugs used to treat HIV, abacavir and azidothymidine (AZT), which reduced plasmid transmission (AZT, e.g., at 0.25 μg/ml reduced pCT transmission in E. coli by 83.3% and pKpQIL transmission in K. pneumoniae by 80.8% compared to untreated controls). Plasmid transmission was reduced by concentrations of the drugs which are below peak serum concentrations and are achievable in the gastrointestinal tract. These drugs could be used to decolonize humans, animals, or the environment from AMR plasmids.IMPORTANCE More and more bacterial infections are becoming resistant to antibiotics. This has made treatment of many infections very difficult. One of the reasons this is such a large problem is that bacteria are able to share their genetic material with other bacteria, and these shared genes often include resistance to a variety of antibiotics, including some of our drugs of last resort. We are addressing this problem by using a fluorescence-based system to search for drugs that will stop bacteria from sharing resistance genes. We uncovered a new role for two drugs used to treat HIV and show that they are able to prevent the sharing of two different types of resistance genes in two unique bacterial strains. This work lays the foundation for future work to reduce the prevalence of resistant infections.
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Affiliation(s)
- Michelle M C Buckner
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - M Laura Ciusa
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Richard W Meek
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Alice R Moorey
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Gregory E McCallum
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Emma L Prentice
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Jeremy P Reid
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Alessandro Di Maio
- Birmingham Advanced Light Microscopy, School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Laura J V Piddock
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
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22
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Domínguez-Medina CC, Pérez-Toledo M, Schager AE, Marshall JL, Cook CN, Bobat S, Hwang H, Chun BJ, Logan E, Bryant JA, Channell WM, Morris FC, Jossi SE, Alshayea A, Rossiter AE, Barrow PA, Horsnell WG, MacLennan CA, Henderson IR, Lakey JH, Gumbart JC, López-Macías C, Bavro VN, Cunningham AF. Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface. Nat Commun 2020; 11:851. [PMID: 32051408 PMCID: PMC7015928 DOI: 10.1038/s41467-020-14655-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/23/2020] [Indexed: 11/28/2022] Open
Abstract
Lipopolysaccharide (LPS) O-antigen (O-Ag) is known to limit antibody binding to surface antigens, although the relationship between antibody, O-Ag and other outer-membrane antigens is poorly understood. Here we report, immunization with the trimeric porin OmpD from Salmonella Typhimurium (STmOmpD) protects against infection. Atomistic molecular dynamics simulations indicate this is because OmpD trimers generate footprints within the O-Ag layer sufficiently sized for a single IgG Fab to access. While STmOmpD differs from its orthologue in S. Enteritidis (SEn) by a single amino-acid residue, immunization with STmOmpD confers minimal protection to SEn. This is due to the OmpD-O-Ag interplay restricting IgG binding, with the pairing of OmpD with its native O-Ag being essential for optimal protection after immunization. Thus, both the chemical and physical structure of O-Ag are key for the presentation of specific epitopes within proteinaceous surface-antigens. This enhances combinatorial antigenic diversity in Gram-negative bacteria, while reducing associated fitness costs. The O-antigen of LPS is known to limit the binding of antibody to bacterial surface antigens. Here the AUs show that the chemical and physical structure of the O-antigen are central factors in limiting the exposure of surface antigens to antibodies during Salmonella infection, thus defining their protective qualities.
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Affiliation(s)
- C Coral Domínguez-Medina
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Marisol Pérez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.,Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Anna E Schager
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jennifer L Marshall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Charlotte N Cook
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Saeeda Bobat
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Byeong Jae Chun
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Erin Logan
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Will M Channell
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Faye C Morris
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sian E Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Areej Alshayea
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - William G Horsnell
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Constantino López-Macías
- Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK. .,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
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23
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Cryptic-Prophage-Encoded Small Protein DicB Protects Escherichia coli from Phage Infection by Inhibiting Inner Membrane Receptor Proteins. J Bacteriol 2019; 201:JB.00475-19. [PMID: 31527115 PMCID: PMC6832061 DOI: 10.1128/jb.00475-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Temperate bacteriophages can integrate their genomes into the bacterial host chromosome and exist as prophages whose gene products play key roles in bacterial fitness and interactions with eukaryotic host organisms. Most bacterial chromosomes contain “cryptic” prophages that have lost genes required for production of phage progeny but retain genes of unknown function that may be important for regulating bacterial host physiology. This study provides such an example, where a cryptic-prophage-encoded product can perform multiple roles in the bacterial host and influence processes, including metabolism, cell division, and susceptibility to phage infection. Further functional characterization of cryptic-prophage-encoded functions will shed new light on host-phage interactions and their cellular physiological implications. Bacterial genomes harbor cryptic prophages that have lost genes required for induction, excision from host chromosomes, or production of phage progeny. Escherichia coli K-12 strains contain a cryptic prophage, Qin, that encodes a small RNA, DicF, and a small protein, DicB, that have been implicated in control of bacterial metabolism and cell division. Since DicB and DicF are encoded in the Qin immunity region, we tested whether these gene products could protect the E. coli host from bacteriophage infection. Transient expression of the dicBF operon yielded cells that were ∼100-fold more resistant to infection by λ phage than control cells, and the phenotype was DicB dependent. DicB specifically inhibited infection by λ and other phages that use ManYZ membrane proteins for cytoplasmic entry of phage DNA. In addition to blocking ManYZ-dependent phage infection, DicB also inhibited the canonical sugar transport activity of ManYZ. Previous studies demonstrated that DicB interacts with MinC, an FtsZ polymerization inhibitor, causing MinC localization to midcell and preventing Z ring formation and cell division. In strains producing mutant MinC proteins that do not interact with DicB, both DicB-dependent phenotypes involving ManYZ were lost. These results suggest that DicB is a pleiotropic regulator of bacterial physiology and cell division and that these effects are mediated by a key molecular interaction with the cell division protein MinC. IMPORTANCE Temperate bacteriophages can integrate their genomes into the bacterial host chromosome and exist as prophages whose gene products play key roles in bacterial fitness and interactions with eukaryotic host organisms. Most bacterial chromosomes contain “cryptic” prophages that have lost genes required for production of phage progeny but retain genes of unknown function that may be important for regulating bacterial host physiology. This study provides such an example, where a cryptic-prophage-encoded product can perform multiple roles in the bacterial host and influence processes, including metabolism, cell division, and susceptibility to phage infection. Further functional characterization of cryptic-prophage-encoded functions will shed new light on host-phage interactions and their cellular physiological implications.
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24
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Khoja S, Nitzahn M, Truong B, Lambert J, Willis B, Allegri G, Rüfenacht V, Häberle J, Lipshutz GS. A constitutive knockout of murine carbamoyl phosphate synthetase 1 results in death with marked hyperglutaminemia and hyperammonemia. J Inherit Metab Dis 2019; 42:1044-1053. [PMID: 30835861 PMCID: PMC6728231 DOI: 10.1002/jimd.12048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/31/2018] [Indexed: 12/25/2022]
Abstract
The enzyme carbamoyl phosphate synthetase 1 (CPS1; EC 6.3.4.16) forms carbamoyl phosphate from bicarbonate, ammonia, and adenosine triphosphate (ATP) and is activated allosterically by N-acetylglutamate. The neonatal presentation of bi-allelic mutations of CPS1 results in hyperammonemia with reduced citrulline and is reported as the most challenging nitrogen metabolism disorder to treat. As therapeutic interventions are limited, patients often develop neurological injury or die from hyperammonemia. Survivors remain vulnerable to nitrogen overload, being at risk for repetitive neurological injury. With transgenic technology, our lab developed a constitutive Cps1 mutant mouse and reports its characterization herein. Within 24 hours of birth, all Cps1 -/- mice developed hyperammonemia and expired. No CPS1 protein by Western blot or immunostaining was detected in livers nor was Cps1 mRNA present. CPS1 enzymatic activity was markedly decreased in knockout livers and reduced in Cps1+/- mice. Plasma analysis found markedly reduced citrulline and arginine and markedly increased glutamine and alanine, both intermolecular carriers of nitrogen, along with elevated ammonia, taurine, and lysine. Derangements in multiple other amino acids were also detected. While hepatic amino acids also demonstrated markedly reduced citrulline, arginine, while decreased, was not statistically significant; alanine and lysine were markedly increased while glutamine was trending towards significance. In conclusion we have determined that this constitutive neonatal mouse model of CPS1 deficiency replicates the neonatal human phenotype and demonstrates the key biochemical features of the disorder. These mice will be integral for addressing the challenges of developing new therapeutic approaches for this, at present, poorly treated disorder.
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Affiliation(s)
- Suhail Khoja
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Matthew Nitzahn
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Brian Truong
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jenna Lambert
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Brandon Willis
- Mouse Biology Program, University of California, Davis, California
| | - Gabriella Allegri
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Gerald S Lipshutz
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, California
- Intellectual and Developmental Disabilities Research Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, California
- Semel Institute for Neuroscience, David Geffen School of Medicine at UCLA, Los Angeles, California
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25
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Isogai Y, Wu Z, Love MI, Ahn MHY, Bambah-Mukku D, Hua V, Farrell K, Dulac C. Multisensory Logic of Infant-Directed Aggression by Males. Cell 2019; 175:1827-1841.e17. [PMID: 30550786 DOI: 10.1016/j.cell.2018.11.032] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 10/11/2018] [Accepted: 11/20/2018] [Indexed: 12/24/2022]
Abstract
Newborn mice emit signals that promote parenting from mothers and fathers but trigger aggressive responses from virgin males. Although pup-directed attacks by males require vomeronasal function, the specific infant cues that elicit this behavior are unknown. We developed a behavioral paradigm based on reconstituted pup cues and showed that discrete infant morphological features combined with salivary chemosignals elicit robust male aggression. Seven vomeronasal receptors were identified based on infant-mediated activity, and the involvement of two receptors, Vmn2r65 and Vmn2r88, in infant-directed aggression was demonstrated by genetic deletion. Using the activation of these receptors as readouts for biochemical fractionation, we isolated two pheromonal compounds, the submandibular gland protein C and hemoglobins. Unexpectedly, none of the identified vomeronasal receptors and associated cues were specific to pups. Thus, infant-mediated aggression by virgin males relies on the recognition of pup's physical traits in addition to parental and infant chemical cues.
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Affiliation(s)
- Yoh Isogai
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK.
| | - Zheng Wu
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael I Love
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Michael Ho-Young Ahn
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dhananjay Bambah-Mukku
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vivian Hua
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Karolina Farrell
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
| | - Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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26
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Huang J, Zhao L, Fan Y, Liao L, Ma PX, Xiao G, Chen D. The microRNAs miR-204 and miR-211 maintain joint homeostasis and protect against osteoarthritis progression. Nat Commun 2019; 10:2876. [PMID: 31253842 PMCID: PMC6599052 DOI: 10.1038/s41467-019-10753-5] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/24/2019] [Indexed: 12/19/2022] Open
Abstract
Osteoarthritis (OA) is a common, painful disease. Currently OA is incurable, and its etiology largely unknown, partly due to limited understanding of OA as a whole-joint disease. Here we report that two homologous microRNAs, miR-204 and miR-211, maintain joint homeostasis to suppress OA pathogenesis. Specific knockout of miR-204/-211 in mesenchymal progenitor cells (MPCs) results in Runx2 accumulation in multi-type joint cells, causing whole-joint degeneration. Specifically, miR-204/-211 loss-of-function induces matrix-degrading proteases in articular chondrocytes and synoviocytes, stimulating articular cartilage destruction. Moreover, miR-204/-211 ablation enhances NGF expression in a Runx2-dependent manner, and thus hyper-activates Akt signaling and MPC proliferation, underlying multiplex non-cartilaginous OA conditions including synovial hyperplasia, osteophyte outgrowth and subchondral sclerosis. Importantly, miR-204/-211-deficiency-induced OA is largely rescued by Runx2 insufficiency, confirming the miR-204/-211-Runx2 axis. Further, intraarticular administration of miR-204-expressing adeno-associated virus significantly decelerates OA progression. Collectively, miR-204/-211 are essential in maintaining healthy homeostasis of mesenchymal joint cells to counteract OA pathogenesis. Osteoarthritis involves whole-joint tissue degeneration. Here, the authors show that miR-204 and miR-211 in mesenchymal joint cells regulate their proliferation, catabolic and osteogenic responses, and that disease progression is ameliorated by intra-articular miR-204 delivery in mice.
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Affiliation(s)
- Jian Huang
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Lan Zhao
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Yunshan Fan
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Lifan Liao
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Peter X Ma
- Department of Biologic and Materials Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Guozhi Xiao
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Di Chen
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL, 60612, USA.
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27
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Storek KM, Chan J, Vij R, Chiang N, Lin Z, Bevers J, Koth CM, Vernes JM, Meng YG, Yin J, Wallweber H, Dalmas O, Shriver S, Tam C, Schneider K, Seshasayee D, Nakamura G, Smith PA, Payandeh J, Koerber JT, Comps-Agrar L, Rutherford ST. Massive antibody discovery used to probe structure-function relationships of the essential outer membrane protein LptD. eLife 2019; 8:46258. [PMID: 31237236 PMCID: PMC6592684 DOI: 10.7554/elife.46258] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/17/2019] [Indexed: 12/17/2022] Open
Abstract
Outer membrane proteins (OMPs) in Gram-negative bacteria dictate permeability of metabolites, antibiotics, and toxins. Elucidating the structure-function relationships governing OMPs within native membrane environments remains challenging. We constructed a diverse library of >3000 monoclonal antibodies to assess the roles of extracellular loops (ECLs) in LptD, an essential OMP that inserts lipopolysaccharide into the outer membrane of Escherichia coli. Epitope binning and mapping experiments with LptD-loop-deletion mutants demonstrated that 7 of the 13 ECLs are targeted by antibodies. Only ECLs inaccessible to antibodies were required for the structure or function of LptD. Our results suggest that antibody-accessible loops evolved to protect key extracellular regions of LptD, but are themselves dispensable. Supporting this hypothesis, no α-LptD antibody interfered with essential functions of LptD. Our experimental workflow enables structure-function studies of OMPs in native cellular environments, provides unexpected insight into LptD, and presents a method to assess the therapeutic potential of antibody targeting. The overuse and misuse of antibiotics has led to the rise of multi-drug resistant bacteria which threaten global public health. Antibiotics interfere with essential processes in bacteria so they are unable to divide or survive, but over time, the microbes have found ways to become immune to the drugs. New antibiotics are now desperately needed. Gram-negative bacteria are wrapped in an outer membrane made of large molecules called lipopolysaccharides. This structure is an extra barrier to molecules (such as drugs) that try to enter the cell, but it could also hold new targets for antibiotics to exploit. A protein called LptD is embedded in the outer membrane, where it inserts new lipopolysaccharides. It is critical for bacteria to grow and survive, and is a relatively new potential target for antibiotic development. The protein has a number of ‘extracellular loops’ that extend into the environment, but their roles in the structure and the activity of LptD are still largely unknown. This is partly due to a lack of tools to investigate these elements. In response, Storek et al. built a library of over 3,000 custom antibodies, which are small Y-shaped proteins that can each recognise a specific portion in one of the extracellular loops and potentially incapacitate LptD. The antibodies were used to target LptD in its native environment, when it is embedded in the bacteria. In parallel, mutant bacteria were created in which the loops were genetically removed one by one to assess their importance for LptD activity. The experiments revealed that although the antibodies could target most extracellular loops, they could not target the few loops that were essential for LptD to work properly. This suggests that antibody-accessible loops are expendable and that these structures could serve to shield other regions of LptD which are critical for survival. The findings will help to prioritise research that develops other approaches to inhibit LptD. Finally, the antibody workflow designed by Storek et al. can serve as a road map to study other membrane proteins in their native cellular environment.
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Affiliation(s)
- Kelly M Storek
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Joyce Chan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Rajesh Vij
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Nancy Chiang
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Jack Bevers
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Christopher M Koth
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Jean-Michel Vernes
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Y Gloria Meng
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - JianPing Yin
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Heidi Wallweber
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Olivier Dalmas
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Stephanie Shriver
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Christine Tam
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Peter A Smith
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Laetitia Comps-Agrar
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
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FBX8 degrades GSTP1 through ubiquitination to suppress colorectal cancer progression. Cell Death Dis 2019; 10:351. [PMID: 31024008 PMCID: PMC6484082 DOI: 10.1038/s41419-019-1588-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 12/25/2018] [Accepted: 01/18/2019] [Indexed: 12/19/2022]
Abstract
F-box only protein 8 (FBX8), as a critical component of the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligases, has been associated with several malignancies through interacting with a member of proteins. However, the substrates of FBX8 for destruction in the progression of colorectal carcinoma (CRC) need to be explored. Here, we show that loss of FBX8 accelerates chemical-induced colon tumorigenesis. FBX8 directly targets GSTP1 for ubiquitin-mediated proteasome degradation in CRC. GSTP1 promotes the proliferation, invasion, and metastasis of CRC cells. Furthermore, GSTP1 is upregulated in CRC tissue samples and predicts poor prognosis of CRC patients. The inactivation of FBX8 negatively correlated with increased levels and stability of GSTP1 in clinical CRC tissues and FBX8 knockout transgenic mice. These findings identify a novel ubiquitination pathway as FBX8-GSTP1 axis that regulates the progression of CRC, which might be a potential prognostic biomarker for CRC patients.
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29
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Qian N, Ichimura A, Takei D, Sakaguchi R, Kitani A, Nagaoka R, Tomizawa M, Miyazaki Y, Miyachi H, Numata T, Kakizawa S, Nishi M, Mori Y, Takeshima H. TRPM7 channels mediate spontaneous Ca 2+ fluctuations in growth plate chondrocytes that promote bone development. Sci Signal 2019; 12:12/576/eaaw4847. [PMID: 30967513 DOI: 10.1126/scisignal.aaw4847] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
During endochondral ossification of long bones, the proliferation and differentiation of chondrocytes cause them to be arranged into layered structures constituting the epiphyseal growth plate, where they secrete the cartilage matrix that is subsequently converted into trabecular bone. Ca2+ signaling has been implicated in chondrogenesis in vitro. Through fluorometric imaging of bone slices from embryonic mice, we demonstrated that live growth plate chondrocytes generated small, cell-autonomous Ca2+ fluctuations that were associated with weak and intermittent Ca2+ influx. Several genes encoding Ca2+-permeable channels were expressed in growth plate chondrocytes, but only pharmacological inhibitors of transient receptor potential cation channel subfamily M member 7 (TRPM7) reduced the spontaneous Ca2+ fluctuations. The TRPM7-mediated Ca2+ influx was likely activated downstream of basal phospholipase C activity and was potentiated upon cell hyperpolarization induced by big-conductance Ca2+-dependent K+ channels. Bones from embryos in which Trpm7 was conditionally knocked out during ex vivo culture exhibited reduced outgrowth and displayed histological abnormalities accompanied by insufficient autophosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) in the growth plate. The link between TRPM7-mediated Ca2+ fluctuations and CaMKII-dependent chondrogenesis was further supported by experiments with chondrocyte-specific Trpm7 knockout mice. Thus, growth plate chondrocytes generate spontaneous, TRPM7-mediated Ca2+ fluctuations that promote self-maturation and bone development.
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Affiliation(s)
- Nianchao Qian
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan
| | - Atsuhiko Ichimura
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan.,Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto 606-8501, Japan
| | - Daisuke Takei
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan
| | - Reiko Sakaguchi
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 615-8510, Japan
| | - Akihiro Kitani
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan
| | - Ryohei Nagaoka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan
| | - Masato Tomizawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan
| | - Yuu Miyazaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan
| | - Hitoshi Miyachi
- Reproductive Engineering Team, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Tomohiro Numata
- Graduate School of Medical Sciences, Fukuoka University, Fukuoka 814-0180, Japan.,Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Sho Kakizawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan
| | - Miyuki Nishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan.,Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yasuo Mori
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Takeshima
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 615-8501, Japan.
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30
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Buckley KM, Ettensohn CA. Techniques for analyzing gene expression using BAC-based reporter constructs. Methods Cell Biol 2019; 151:197-218. [PMID: 30948008 PMCID: PMC7215881 DOI: 10.1016/bs.mcb.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To characterize the complex regulatory control of gene expression using fluorescent protein reporters, it is often necessary to analyze large genomic regions. Bacteria artificial chromosome (BAC) vectors, which are able to support DNA fragments of up to 300kb, provide stable platforms for experimental manipulation. Using phage-based systems of homologous recombination, BACs can be efficiently engineered for a variety of aims. These include expressing fluorescent proteins to delineate gene expression boundaries using high-resolution, in vivo microscopy, tracing cell lineages using stable fluorescent proteins, perturbing endogenous protein function by expressing dominant negative forms, interfering with development by mis-expressing transcription factors, and identifying regulatory regions through deletion analysis. Here, we present a series of protocols for identifying BAC clones that contain genes of interest, modifying BACs for use as reporter constructs, and preparing BAC DNA for microinjection into fertilized eggs. Although the protocols here are tailored for use in echinoderm embryonic and larval stages, these methods are easily adaptable for use in other transgenic systems. As fluorescent protein technology continues to expand, so do the potential applications for recombinant BACs.
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Affiliation(s)
- Katherine M Buckley
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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31
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Horga LG, Halliwell S, Castiñeiras TS, Wyre C, Matos CFRO, Yovcheva DS, Kent R, Morra R, Williams SG, Smith DC, Dixon N. Tuning recombinant protein expression to match secretion capacity. Microb Cell Fact 2018; 17:199. [PMID: 30577801 PMCID: PMC6303999 DOI: 10.1186/s12934-018-1047-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/14/2018] [Indexed: 03/08/2023] Open
Abstract
Background The secretion of recombinant disulfide-bond containing proteins into the periplasm of Gram-negative bacterial hosts, such as E. coli, has many advantages that can facilitate product isolation, quality and activity. However, the secretion machinery of E. coli has a limited capacity and can become overloaded, leading to cytoplasmic retention of product; which can negatively impact cell viability and biomass accumulation. Fine control over recombinant gene expression offers the potential to avoid this overload by matching expression levels to the host secretion capacity. Results Here we report the application of the RiboTite gene expression control system to achieve this by finely controlling cellular expression levels. The level of control afforded by this system allows cell viability to be maintained, permitting production of high-quality, active product with enhanced volumetric titres. Conclusions The methods and systems reported expand the tools available for the production of disulfide-bond containing proteins, including antibody fragments, in bacterial hosts. Electronic supplementary material The online version of this article (10.1186/s12934-018-1047-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luminita Gabriela Horga
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Samantha Halliwell
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | | | | | | | | | - Ross Kent
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Rosa Morra
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | | | | | - Neil Dixon
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK.
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32
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Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion. Nat Commun 2018; 9:4187. [PMID: 30305622 PMCID: PMC6180029 DOI: 10.1038/s41467-018-06701-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 09/14/2018] [Indexed: 12/31/2022] Open
Abstract
Niche-adaptation of a bacterial pathogen hinges on the ability to recognize the complexity of signals from the environment and integrate that information with the regulation of genes critical for infection. Here we report the transcriptome of the attaching and effacing pathogen Citrobacter rodentium during infection of its natural murine host. Pathogen gene expression in vivo was heavily biased towards the virulence factor repertoire and was found to be co-ordinated uniquely in response to the host. Concordantly, we identified the host-specific induction of a metabolic pathway that overlapped with the regulation of virulence. The essential type 3 secretion system and an associated suite of distinct effectors were found to be modulated co-ordinately through a unique mechanism involving metabolism of microbiota-derived 1,2-propanediol, which dictated the ability to colonize the host effectively. This study provides novel insights into how host-specific metabolic adaptation acts as a cue to fine-tune virulence. Infection of mice with Citrobacter rodentium is a common model of infection with attaching-and-effacing pathogens. Here, Connolly et al. analyse the transcriptome of C. rodentium during mouse infection, showing host-induced coordinated upregulation of virulence factors and 1,2-propanediol metabolism.
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33
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Zhao Y, Song G, Ren J, Li Q, Zhong S, Cui Z. Sleeping beauty transposon-mediated poly(A)-trapping and insertion mutagenesis in mouse embryonic stem cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:687-697. [PMID: 30280432 DOI: 10.1002/em.22234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Saturation mutagenesis of all endogenous genes within the mouse genome remains a challenging task, although a plenty of gene-editing approaches are available for this purpose. Here, a poly(A)-trap vector was generated for insertion mutagenesis in mouse embryonic stem (mES) cells. This vector contains an expression cassette of neomycin (Neo)-resistant gene lacking a poly(A) signal and flanked by two inverted terminal repeats of the Sleeping Beauty (SB) transposon. The whole poly(A)-trap cassette can transpose into target TA dinucleotides, properly splice with endogenous genes and effectively interrupt the transcription of trapped genes in mES cells after transient induction of SB expression by doxycycline (DOX)-treatment at 1 μg/ml, leading to the formation of multiple geneticin (G418)-resistant cell clones. In the first round of mutation screening, we identified six transposition events from 23 cell clones, including four inserted into an endogenous gene and two landed between endogenous genes. The abilities of self-renewal, totipotency, genetic stability and differentiation of syngap1+/- cells were not affected by DOX-treatment and G418-selection. These findings suggest that this SB transposon-mediated poly(A)-trap vector can be used as an alternative tool for a large-scale screening of mES cells with a gene mutation and for further generation of mutant mouse strains. Environ. Mol. Mutagen. 59:687-697, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yi Zhao
- Department of Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jing Ren
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shan Zhong
- Department of Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, Hubei, China
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, Hubei, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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34
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Johnson BA, Coutts M, Vo HM, Hao X, Fatima N, Rivera MJ, Sims RJ, Neel MJ, Kang YJ, Monuki ES. Accurate, strong, and stable reporting of choroid plexus epithelial cells in transgenic mice using a human transthyretin BAC. Fluids Barriers CNS 2018; 15:22. [PMID: 30111340 PMCID: PMC6094443 DOI: 10.1186/s12987-018-0107-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Choroid plexus epithelial cells express high levels of transthyretin, produce cerebrospinal fluid and many of its proteins, and make up the blood-cerebrospinal fluid barrier. Choroid plexus epithelial cells are vital to brain health and may be involved in neurological diseases. Transgenic mice containing fluorescent and luminescent reporters of these cells would facilitate their study in health and disease, but prior transgenic reporters lost expression over the early postnatal period. METHODS Human bacterial artificial chromosomes in which the transthyretin coding sequence was replaced with DNA for tdTomato or luciferase 2 were used in pronuclear injections to produce transgenic mice. These mice were characterized by visualizing red fluorescence, immunostaining, real-time reverse transcription polymerase chain reaction, and luciferase enzyme assay. RESULTS Reporters were faithfully expressed in cells that express transthyretin constitutively, including choroid plexus epithelial cells, retinal pigment epithelium, pancreatic islets, and liver. Expression of tdTomato in choroid plexus began at the appropriate embryonic age, being detectable by E11.5. Relative levels of tdTomato transcript in the liver and choroid plexus paralleled relative levels of transcripts for transthyretin. Expression remained robust over the first postnatal year, although choroid plexus transcripts of tdTomato declined slightly with age whereas transthyretin remained constant. TdTomato expression patterns were consistent across three founder lines, displayed no sex differences, and were stable across several generations. Two of the tdTomato lines were bred to homozygosity, and homozygous mice are healthy and fertile. The usefulness of tdTomato reporters in visualizing and analyzing live Transwell cultures was demonstrated. Luciferase activity was very high in homogenates of choroid plexus and continued to be expressed through adulthood. Luciferase also was detectable in eye and pancreas. CONCLUSIONS Transgenic mice bearing fluorescent and luminescent reporters of transthyretin should prove useful for tracking transplanted choroid plexus epithelial cells, for purifying the cells, and for reporting their derivation from stem cells. They also should prove useful for studying transthyretin synthesis by other cell types, as transthyretin has been implicated in many functions and conditions, including clearance of β-amyloid peptides associated with Alzheimer's disease, heat shock in neurons, processing of neuropeptides, nerve regeneration, astrocyte metabolism, and transthyretin amyloidosis.
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Affiliation(s)
- Brett A Johnson
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA
| | - Margaret Coutts
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA
| | - Hillary M Vo
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA
| | - Xinya Hao
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA
| | - Nida Fatima
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA
| | - Maria J Rivera
- Department of Biological Sciences, California State University, Long Beach, USA
| | - Robert J Sims
- Department of Biological Sciences, California State University, Long Beach, USA
| | - Michael J Neel
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA
| | - Young-Jin Kang
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA
| | - Edwin S Monuki
- Department of Pathology and Laboratory Medicine, UC Irvine, Irvine, USA. .,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, USA. .,Department of Developmental and Cell Biology, UC Irvine, Irvine, USA.
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35
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Seo GY, Shui JW, Takahashi D, Song C, Wang Q, Kim K, Mikulski Z, Chandra S, Giles DA, Zahner S, Kim PH, Cheroutre H, Colonna M, Kronenberg M. LIGHT-HVEM Signaling in Innate Lymphoid Cell Subsets Protects Against Enteric Bacterial Infection. Cell Host Microbe 2018; 24:249-260.e4. [PMID: 30092201 PMCID: PMC6132068 DOI: 10.1016/j.chom.2018.07.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/19/2018] [Accepted: 07/16/2018] [Indexed: 01/25/2023]
Abstract
Innate lymphoid cells (ILCs) are important regulators of early infection at mucosal barriers. ILCs are divided into three groups based on expression profiles, and are activated by cytokines and neuropeptides. Yet, it remains unknown if ILCs integrate other signals in providing protection. We show that signaling through herpes virus entry mediator (HVEM), a member of the tumor necrosis factor (TNF) receptor superfamily, in ILC3 is important for host defense against oral infection with the bacterial pathogen Yersinia enterocolitica. HVEM stimulates protective interferon-γ (IFN-γ) secretion from ILCs, and mice with HVEM-deficient ILC3 exhibit reduced IFN-γ production, higher bacterial burdens and increased mortality. In addition, IFN-γ production is critical as adoptive transfer of wild-type but not IFN-γ-deficient ILC3 can restore protection to mice lacking ILCs. We identify the TNF superfamily member, LIGHT, as the ligand inducing HVEM signals in ILCs. Thus HVEM signaling mediated by LIGHT plays a critical role in regulating ILC3-derived IFN-γ production for protection following infection. VIDEO ABSTRACT.
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MESH Headings
- Adoptive Transfer
- Adult
- Animals
- Cytokines/metabolism
- Disease Models, Animal
- Enterobacteriaceae Infections/pathology
- Enterobacteriaceae Infections/prevention & control
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Host-Pathogen Interactions/immunology
- Host-Pathogen Interactions/physiology
- Humans
- Interferon-gamma/metabolism
- Lymphocytes/immunology
- Lymphocytes/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Neuropeptides/metabolism
- Protein Transport
- Receptors, CCR6/genetics
- Receptors, CCR6/metabolism
- Receptors, Tumor Necrosis Factor/metabolism
- Receptors, Tumor Necrosis Factor, Member 14/immunology
- Receptors, Tumor Necrosis Factor, Member 14/metabolism
- Signal Transduction
- Spleen/microbiology
- Spleen/pathology
- Tumor Necrosis Factor Ligand Superfamily Member 14/metabolism
- Yersinia enterocolitica/pathogenicity
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Affiliation(s)
- Goo-Young Seo
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA; Department of Molecular Bioscience, School of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jr-Wen Shui
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Daisuke Takahashi
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Christina Song
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Qingyang Wang
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Kenneth Kim
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Shilpi Chandra
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Daniel A Giles
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Sonja Zahner
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Pyeung-Hyeun Kim
- Department of Molecular Bioscience, School of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hilde Cheroutre
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mitchell Kronenberg
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA; Division of Biology, University of California San Diego, La Jolla, CA 92037, USA.
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Khoja S, Nitzahn M, Hermann K, Truong B, Borzone R, Willis B, Rudd M, Palmer DJ, Ng P, Brunetti-Pierri N, Lipshutz GS. Conditional disruption of hepatic carbamoyl phosphate synthetase 1 in mice results in hyperammonemia without orotic aciduria and can be corrected by liver-directed gene therapy. Mol Genet Metab 2018; 124:243-253. [PMID: 29801986 PMCID: PMC6076338 DOI: 10.1016/j.ymgme.2018.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/02/2018] [Accepted: 04/02/2018] [Indexed: 02/06/2023]
Abstract
Carbamoyl phosphate synthetase 1 (CPS1) is a urea cycle enzyme that forms carbamoyl phosphate from bicarbonate, ammonia and ATP. Bi-allelic mutations of the CPS1 gene result in a urea cycle disorder presenting with hyperammonemia, often with reduced citrulline, and without orotic aciduria. CPS1 deficiency is particularly challenging to treat and lack of early recognition typically results in early neonatal death. Therapeutic interventions have limited efficacy and most patients develop long-term neurologic sequelae. Using transgenic techniques, we generated a conditional Cps1 knockout mouse. By loxP/Cre recombinase technology, deletion of the Cps1 locus was achieved in adult transgenic animals using a Cre recombinase-expressing adeno-associated viral vector. Within four weeks from vector injection, all animals developed hyperammonemia without orotic aciduria and died. Minimal CPS1 protein was detectable in livers. To investigate the efficacy of gene therapy for CPS deficiency following knock-down of hepatic endogenous CPS1 expression, we injected these mice with a helper-dependent adenoviral vector (HDAd) expressing the large murine CPS1 cDNA under control of the phosphoenolpyruvate carboxykinase promoter. Liver-directed HDAd-mediated gene therapy resulted in survival, normalization of plasma ammonia and glutamine, and 13% of normal Cps1 expression. A gender difference in survival suggests that female mice may require higher hepatic CPS1 expression. We conclude that this conditional murine model recapitulates the clinical and biochemical phenotype detected in human patients with CPS1 deficiency and will be useful to investigate ammonia-mediated neurotoxicity and for the development of cell- and gene-based therapeutic approaches.
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Affiliation(s)
- Suhail Khoja
- Departments of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States
| | - Matt Nitzahn
- Departments of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States
| | - Kip Hermann
- Departments of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States
| | - Brian Truong
- Departments of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States
| | | | - Brandon Willis
- Mouse Biology Program (MBP), University of California, Davis, United States
| | - Mitchell Rudd
- Departments of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States
| | - Donna J Palmer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Philip Ng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Naples, Italy; Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Gerald S Lipshutz
- Departments of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Intellectual and Developmental Disabilities Research Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States; Semel Institute for Neuroscience, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States.
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Hunt AJ, Dasgupta R, Rajamanickam S, Jiang Z, Beierlein M, Chan CS, Justice NJ. Paraventricular hypothalamic and amygdalar CRF neurons synapse in the external globus pallidus. Brain Struct Funct 2018; 223:2685-2698. [PMID: 29569009 PMCID: PMC5997534 DOI: 10.1007/s00429-018-1652-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 03/16/2018] [Indexed: 12/16/2022]
Abstract
Stress evokes directed movement to escape or hide from potential danger. Corticotropin-releasing factor (CRF) neurons are highly activated by stress; however, it remains unclear how this activity participates in stress-evoked movement. The external globus pallidus (GPe) expresses high levels of the primary receptor for CRF, CRFR1, suggesting the GPe may serve as an entry point for stress-relevant information to reach basal ganglia circuits, which ultimately gate motor output. Indeed, projections from CRF neurons are present within the GPe, making direct contact with CRFR1-positive neurons. CRFR1 expression is heterogenous in the GPe; prototypic GPe neurons selectively express CRFR1, while arkypallidal neurons do not. Moreover, CRFR1-positive GPe neurons are excited by CRF via activation of CRFR1, while nearby CRFR1-negative neurons do not respond to CRF. Using monosynaptic rabies viral tracing techniques, we show that CRF neurons in the stress-activated paraventricular nucleus of the hypothalamus (PVN), central nucleus of the amygdala (CeA), and bed nucleus of the stria terminalis (BST) make synaptic connections with CRFR1-positive neurons in the GPe an unprecedented circuit connecting the limbic system with the basal ganglia. CRF neurons also make synapses on Npas1 neurons, although the majority of Npas1 neurons are arkypallidal and do not express CRFR1. Interestingly, prototypic and arkypallidal neurons receive different patterns of innervation from CRF-rich nuclei. Hypothalamic CRF neurons preferentially target prototypic neurons, while amygdalar CRF neurons preferentially target arkypallidal neurons, suggesting that these two inputs to the GPe may have different impacts on GPe output. Together, these data describe a novel neural circuit by which stress-relevant information carried by the limbic system signals in the GPe via CRF to influence motor output.
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Affiliation(s)
- Albert J Hunt
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, Center for Metabolic and Degenerative Diseases, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Graduate Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Rajan Dasgupta
- Department of Neurobiology and Anatomy, McGovern Medical School, Houston, TX, 77030, USA
- Graduate Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Shivakumar Rajamanickam
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, Center for Metabolic and Degenerative Diseases, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zhiying Jiang
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, Center for Metabolic and Degenerative Diseases, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Michael Beierlein
- Department of Neurobiology and Anatomy, McGovern Medical School, Houston, TX, 77030, USA
- Graduate Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - C Savio Chan
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Nicholas J Justice
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, Center for Metabolic and Degenerative Diseases, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Graduate Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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Severe Intestinal Inflammation in the Small Intestine of Mice Induced by Controllable Deletion of Claudin-7. Dig Dis Sci 2018; 63:1200-1209. [PMID: 29488037 PMCID: PMC5897149 DOI: 10.1007/s10620-018-4973-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 02/07/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND As a potential tumor suppressor gene, Claudin-7 (Cldn7), which is a component of tight junctions, may play an important role in colorectal cancer occurrence and development. AIMS To generate a knockout mouse model of inducible conditional Cldn7 in the intestine and analyze the phenotype of the mice after induction with tamoxifen. METHODS We constructed Cldn7-flox transgenic mice and crossed them with Villin-CreERT2 mice. The Cldn7 inducible conditional knockout mice appeared normal and were well developed at birth. We induced Cldn7 gene deletion by injecting different dosages of tamoxifen into the mice and then conducted a further phenotypic analysis. RESULTS After induction for 5 days in succession at a dose of 200 µl tamoxifen in sunflower oil at 10 mg/ml per mouse every time, the mice appeared dehydrated, had a lower temperature, and displayed inactivity or death. The results of hematoxylin-eosin staining showed that the intestines of the Cldn7 inducible conditional knockout mice had severe intestinal defects that included epithelial cell sloughing, necrosis, inflammation and hyperplasia. Owing to the death of ICKO mice, we adjusted the dose of tamoxifen to a dose of 100 µl in sunflower oil at 10 mg/ml per mouse (aged more than 8 weeks old) every 4 days. And we could induce atypical hyperplasia and adenoma in the intestine. Immunofluorescent staining indicated that the intestinal epithelial structure was destroyed. Electron microscopy experimental analysis indicated that the intercellular gap along the basolateral membrane of Cldn7 inducible conditional knockout mice in the intestine was increased and that contact between the cells and matrix was loosened. CONCLUSIONS We generated a model of intestinal Cldn7 inducible conditional knockout mice. Intestinal Cldn7 deletion induced by tamoxifen initiated inflammation and hyperplasia in mice.
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A Novel Inhibitor of the LolCDE ABC Transporter Essential for Lipoprotein Trafficking in Gram-Negative Bacteria. Antimicrob Agents Chemother 2018; 62:AAC.02151-17. [PMID: 29339384 DOI: 10.1128/aac.02151-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/06/2018] [Indexed: 12/14/2022] Open
Abstract
The outer membrane is an essential structural component of Gram-negative bacteria that is composed of lipoproteins, lipopolysaccharides, phospholipids, and integral β-barrel membrane proteins. A dedicated machinery, called the Lol system, ensures proper trafficking of lipoproteins from the inner to the outer membrane. The LolCDE ABC transporter is the inner membrane component, which is essential for bacterial viability. Here, we report a novel pyrrolopyrimidinedione compound, G0507, which was identified in a phenotypic screen for inhibitors of Escherichia coli growth followed by selection of compounds that induced the extracytoplasmic σE stress response. Mutations in lolC, lolD, and lolE conferred resistance to G0507, suggesting LolCDE as its molecular target. Treatment of E. coli cells with G0507 resulted in accumulation of fully processed Lpp, an outer membrane lipoprotein, in the inner membrane. Using purified protein complexes, we found that G0507 binds to LolCDE and stimulates its ATPase activity. G0507 still binds to LolCDE harboring a Q258K substitution in LolC (LolCQ258K), which confers high-level resistance to G0507 in vivo but no longer stimulates ATPase activity. Our work demonstrates that G0507 has significant promise as a chemical probe to dissect lipoprotein trafficking in Gram-negative bacteria.
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Abstract
The apparent mislocalization or excretion of cytoplasmic proteins is a commonly observed phenomenon in both bacteria and eukaryotes. However, reports on the mechanistic basis and the cellular function of this so-called “nonclassical protein secretion” are limited. Here we report that protein overexpression in recombinant cells and antibiotic-induced translation stress in wild-type Escherichia coli cells both lead to excretion of cytoplasmic protein (ECP). Condition-specific metabolomic and proteomic analyses, combined with genetic knockouts, indicate a role for both the large mechanosensitive channel (MscL) and the alternative ribosome rescue factor A (ArfA) in ECP. Collectively, the findings indicate that MscL-dependent protein excretion is positively regulated in response to both osmotic stress and arfA-mediated translational stress. Protein translocation is an essential feature of cellular organisms. Bacteria, like all single-cell organisms, interact with their environment by translocation of proteins across their cell membranes via dedicated secretion pathways. Proteins destined for secretion are directed toward the secretion pathways by the presence of specific signal peptides. This study demonstrates that under conditions of both osmotic stress and translation stress, E. coli cells undergo an excretion phenomenon whereby signal peptide-less proteins are translocated across both the inner and outer cell membranes into the extracellular environment. Confirming the presence of alternative translocation/excretion pathways and understanding their function and regulation are thus important for fundamental microbiology and biotechnology.
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Local Corticotropin-Releasing Factor Signaling in the Hypothalamic Paraventricular Nucleus. J Neurosci 2018; 38:1874-1890. [PMID: 29352046 DOI: 10.1523/jneurosci.1492-17.2017] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 01/28/2023] Open
Abstract
Corticotropin-releasing factor (CRF) neurons in the hypothalamic paraventricular nucleus (PVN) initiate hypothalamic-pituitary-adrenal axis activity through the release of CRF into the portal system as part of a coordinated neuroendocrine, autonomic, and behavioral response to stress. The recent discovery of neurons expressing CRF receptor type 1 (CRFR1), the primary receptor for CRF, adjacent to CRF neurons within the PVN, suggests that CRF also signals within the hypothalamus to coordinate aspects of the stress response. Here, we characterize the electrophysiological and molecular properties of PVN-CRFR1 neurons and interrogate their monosynaptic connectivity using rabies virus-based tracing and optogenetic circuit mapping in male and female mice. We provide evidence that CRF neurons in the PVN form synapses on neighboring CRFR1 neurons and activate them by releasing CRF. CRFR1 neurons receive the majority of monosynaptic input from within the hypothalamus, mainly from the PVN itself. Locally, CRFR1 neurons make GABAergic synapses on parvocellular and magnocellular cells within the PVN. CRFR1 neurons resident in the PVN also make long-range glutamatergic synapses in autonomic nuclei such as the nucleus of the solitary tract. Selective ablation of PVN-CRFR1 neurons in male mice elevates corticosterone release during a stress response and slows the decrease in circulating corticosterone levels after the cessation of stress. Our experiments provide evidence for a novel intra-PVN neural circuit that is activated by local CRF release and coordinates autonomic and endocrine function during stress responses.SIGNIFICANCE STATEMENT The hypothalamic paraventricular nucleus (PVN) coordinates concomitant changes in autonomic and neuroendocrine function to organize the response to stress. This manuscript maps intra-PVN circuitry that signals via CRF, delineates CRF receptor type 1 neuron synaptic targets both within the PVN and at distal targets, and establishes the role of this microcircuit in regulating hypothalamic-pituitary-adrenal axis activity.
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Armbruster CE, Forsyth-DeOrnellas V, Johnson AO, Smith SN, Zhao L, Wu W, Mobley HLT. Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements. PLoS Pathog 2017; 13:e1006434. [PMID: 28614382 PMCID: PMC5484520 DOI: 10.1371/journal.ppat.1006434] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/26/2017] [Accepted: 05/25/2017] [Indexed: 12/31/2022] Open
Abstract
The Gram-negative bacterium Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs), which are often polymicrobial. Numerous prior studies have uncovered virulence factors for P. mirabilis pathogenicity in a murine model of ascending UTI, but little is known concerning pathogenesis during CAUTI or polymicrobial infection. In this study, we utilized five pools of 10,000 transposon mutants each and transposon insertion-site sequencing (Tn-Seq) to identify the full arsenal of P. mirabilis HI4320 fitness factors for single-species versus polymicrobial CAUTI with Providencia stuartii BE2467. 436 genes in the input pools lacked transposon insertions and were therefore concluded to be essential for P. mirabilis growth in rich medium. 629 genes were identified as P. mirabilis fitness factors during single-species CAUTI. Tn-Seq from coinfection with P. stuartii revealed 217/629 (35%) of the same genes as identified by single-species Tn-Seq, and 1353 additional factors that specifically contribute to colonization during coinfection. Mutants were constructed in eight genes of interest to validate the initial screen: 7/8 (88%) mutants exhibited the expected phenotypes for single-species CAUTI, and 3/3 (100%) validated the expected phenotypes for polymicrobial CAUTI. This approach provided validation of numerous previously described P. mirabilis fitness determinants from an ascending model of UTI, the discovery of novel fitness determinants specifically for CAUTI, and a stringent assessment of how polymicrobial infection influences fitness requirements. For instance, we describe a requirement for branched-chain amino acid biosynthesis by P. mirabilis during coinfection due to high-affinity import of leucine by P. stuartii. Further investigation of genes and pathways that provide a competitive advantage during both single-species and polymicrobial CAUTI will likely provide robust targets for therapeutic intervention to reduce P. mirabilis CAUTI incidence and severity. Proteus mirabilis is a common cause of single-species and polymicrobial catheter-associated urinary tract infections (CAUTIs). Prior studies have uncovered P. mirabilis virulence factors for single-species ascending UTI, but little is known concerning pathogenesis during CAUTI or polymicrobial infection. Using transposon insertion-site sequencing (Tn-Seq), we performed a global assessment of P. mirabilis fitness factors for CAUTI while simultaneously determining how coinfection with another CAUTI pathogen, Providencia stuartii, alters P. mirabilis fitness requirements. This approach provides six important contributions to the field: 1) the first global estimation of P. mirabilis genes essential for growth, 2) validation of a role for known P. mirabilis fitness factors during CAUTI, 3) identification of novel fitness factors, 4) identification of core fitness factors for both single-species and polymicrobial CAUTI, 5) identification of single-species fitness factors that are complemented during polymicrobial infection, and 6) identification of factors that only provide a competitive advantage during polymicrobial infection. We further demonstrate that the CAUTI model can be used to examine the interplay between fitness requirements of both species during coinfection. Investigation of fitness requirements for other pathogens during single-species and polymicrobial CAUTI will elucidate complex interactions that contribute to disease severity and uncover conserved targets for therapeutic intervention.
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Affiliation(s)
- Chelsie E. Armbruster
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
- * E-mail: (CEA); (HLTM)
| | - Valerie Forsyth-DeOrnellas
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Alexandra O. Johnson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sara N. Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lili Zhao
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Weisheng Wu
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (CEA); (HLTM)
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Chen A, Li J, Song L, Ji C, Böing M, Chen J, Brand-Saberi B. GGNBP2 is necessary for testis morphology and sperm development. Sci Rep 2017; 7:2998. [PMID: 28592902 PMCID: PMC5462834 DOI: 10.1038/s41598-017-03193-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
Gametogenetin Binding Protein 2 (GGNBP2) was identified as a tumor suppressor and verified as such by several studies. GGNBP2 has also been reported to be essential for pregnancy maintenance via regulation of trophoblast stem cells. Gametogenetin (GGN) is a testicular germ cell-specific gene expressed in adult testes. As a potential GGN1-interacting protein, the role of GGNBP2 in spermatogenesis has not yet been clarified. We generated heterozygous GGNBP2 knockout mice and bred them by intercrossing. We found that among the offspring, homozygous GGNBP2 knockout (KO) mice were present in severely reduced numbers. The GGNBP2 KO pups developed normally, but the male siblings showed dramatically reduced fertility. In these male homozygous GGNBP2 KO mice, the only pathological finding was abnormal morphology of the testes and absence of spermatozoa. In addition, increased apoptosis was observed in the testes of GGNBP2 KO mice. SOX9 staining revealed that SOX9-positive Sertoli cells were absent in the seminiferous tubules. In homozygous mice, proliferating cell nuclear antigen (PCNA)-positive cells were localized in the lumen of the convoluted seminiferous tubules. These results suggest that GGNBP2 plays a key role in spermatogenesis by affecting the morphology and function of SOX9-positive Sertoli cells.
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Affiliation(s)
- Anqi Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China.,Department of Anatomy and Molecular Embryology, Ruhr-University Bochum, Bochum, Germany
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Lesheng Song
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Marion Böing
- Department of Anatomy and Molecular Embryology, Ruhr-University Bochum, Bochum, Germany
| | - Jinzhong Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China.
| | - Beate Brand-Saberi
- Department of Anatomy and Molecular Embryology, Ruhr-University Bochum, Bochum, Germany.
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The Autographa californica Multiple Nucleopolyhedrovirus ac83 Gene Contains a cis-Acting Element That Is Essential for Nucleocapsid Assembly. J Virol 2017; 91:JVI.02110-16. [PMID: 28031366 DOI: 10.1128/jvi.02110-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023] Open
Abstract
Baculoviridae is a family of insect-specific viruses that have a circular double-stranded DNA genome packaged within a rod-shaped capsid. The mechanism of baculovirus nucleocapsid assembly remains unclear. Previous studies have shown that deletion of the ac83 gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) blocks viral nucleocapsid assembly. Interestingly, the ac83-encoded protein Ac83 is not a component of the nucleocapsid, implying a particular role for ac83 in nucleocapsid assembly that may be independent of its protein product. To examine this possibility, Ac83 synthesis was disrupted by insertion of a chloramphenicol resistance gene into its coding sequence or by deleting its promoter and translation start codon. Both mutants produced progeny viruses normally, indicating that the Ac83 protein is not required for nucleocapsid assembly. Subsequently, complementation assays showed that the production of progeny viruses required the presence of ac83 in the AcMNPV genome instead of its presence in trans Therefore, we reasoned that ac83 is involved in nucleocapsid assembly via an internal cis-acting element, which we named the nucleocapsid assembly-essential element (NAE). The NAE was identified to lie within nucleotides 1651 to 1850 of ac83 and had 8 conserved A/T-rich regions. Sequences homologous to the NAE were found only in alphabaculoviruses and have a conserved positional relationship with another essential cis-acting element that was recently identified. The identification of the NAE may help to connect the data of viral cis-acting elements and related proteins in the baculovirus nucleocapsid assembly, which is important for elucidating DNA-protein interaction events during this process.IMPORTANCE Virus nucleocapsid assembly usually requires specific cis-acting elements in the viral genome for various processes, such as the selection of the viral genome from the cellular nucleic acids, the cleavage of concatemeric viral genome replication intermediates, and the encapsidation of the viral genome into procapsids. In linear DNA viruses, such elements generally locate at the ends of the viral genome; however, most of these elements remain unidentified in circular DNA viruses (including baculovirus) due to their circular genomic conformation. Here, we identified a nucleocapsid assembly-essential element in the AcMNPV (the archetype of baculovirus) genome. This finding provides an important reference for studies of nucleocapsid assembly-related elements in baculoviruses and other circular DNA viruses. Moreover, as most of the previous studies of baculovirus nucleocapsid assembly have been focused on viral proteins, our study provides a novel entry point to investigate this mechanism via cis-acting elements in the viral genome.
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Li XT, Sou C, Jun S. Protocol for Construction of a Tunable CRISPR Interference (tCRISPRi) Strain for Escherichia coli. Bio Protoc 2017; 7:e2574. [PMID: 29082292 DOI: 10.21769/bioprotoc.2574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present a protocol for construction of tunable CRISPR interference (tCRISPRi) strains for Escherichia coli. The tCRISPRi system alleviates most of the known problems of plasmid-based expression methods, and can be immediately used to construct libraries of sgRNAs that can complement the Keio collection by targeting both essential and nonessential genes. Most importantly from a practical perspective, construction of tCRISPRi to target a new gene requires only one-step oligo recombineering. Additional advantages of tCRISPRi over other existing CRISPRi methods include: (1) tCRISPRi shows significantly less than 10% leaky repression; (2) tCRISPRi uses a tunable arabinose operon promoter and modifications in transporter genes to allow a wide dynamic range with graded control by arabinose inducer; (3) tCRISPRi is plasmid free and the entire system is integrated into the chromosome; (4) tCRISPRi strains show desirable physiological properties.
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Affiliation(s)
- Xin-Tian Li
- UC San Diego, Department of Physics and Section of Molecular Biology, Division of Biology, La Jolla, CA, USA
| | - Cindy Sou
- UC San Diego, Department of Physics and Section of Molecular Biology, Division of Biology, La Jolla, CA, USA
| | - Suckjoon Jun
- UC San Diego, Department of Physics and Section of Molecular Biology, Division of Biology, La Jolla, CA, USA
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Kumagai K, Takanashi M, Ohno SI, Kuroda M, Sudo K. An improved Red/ET recombineering system and mouse ES cells culture conditions for the generation of targeted mutant mice. Exp Anim 2016; 66:125-136. [PMID: 27890869 PMCID: PMC5411299 DOI: 10.1538/expanim.16-0075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Targeted mutant mice generated on a C57BL/6 background are powerful tools for analysis of
the biological functions of genes, and gene targeting technologies using mouse embryonic
stem (ES) cells have been used to generate such mice. Recently, a bacterial artificial
chromosome (BAC) recombineering system was established for the construction of targeting
vectors. However, gene retrieval from BACs for the generation of gene targeting vectors
using this system remains difficult. Even when construction of a gene targeting vector is
successful, the efficiency of production of targeted mutant mice from ES cells derived
from C57BL/6 mice are poor. Therefore, in this study, we first improved the strategy for
the retrieval of genes from BACs and their transfer into a DT-A plasmid, for the
generation of gene targeting vectors using the BAC recombineering system. Then, we
attempted to generate targeted mutant mice from ES cell lines derived from C57BL/6 mice,
by culturing in serum-free medium. In conclusion, we established an improved strategy for
the efficient generation of targeted mutant mice on a C57BL/6 background, which are useful
for the in vivo analysis of gene functions and regulation.
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Affiliation(s)
- Katsuyoshi Kumagai
- Pre-Clinical Research Center, University-related Facilities, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | | | | | - Masahiko Kuroda
- Department of Pathology, Tokyo Medical University, Tokyo, Japan
| | - Katsuko Sudo
- Pre-Clinical Research Center, University-related Facilities, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
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Powder KE, Albertson RC. Cichlid fishes as a model to understand normal and clinical craniofacial variation. Dev Biol 2016; 415:338-346. [PMID: 26719128 PMCID: PMC4914429 DOI: 10.1016/j.ydbio.2015.12.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 01/26/2023]
Abstract
We have made great strides towards understanding the etiology of craniofacial disorders, especially for 'simple' Mendelian traits. However, the facial skeleton is a complex trait, and the full spectrum of genetic, developmental, and environmental factors that contribute to its final geometry remain unresolved. Forward genetic screens are constrained with respect to complex traits due to the types of genes and alleles commonly identified, developmental pleiotropy, and limited information about the impact of environmental interactions. Here, we discuss how studies in an evolutionary model - African cichlid fishes - can complement traditional approaches to understand the genetic and developmental origins of complex shape. Cichlids exhibit an unparalleled range of natural craniofacial morphologies that model normal human variation, and in certain instances mimic human facial dysmorphologies. Moreover, the evolutionary history and genomic architecture of cichlids make them an ideal system to identify the genetic basis of these phenotypes via quantitative trait loci (QTL) mapping and population genomics. Given the molecular conservation of developmental genes and pathways, insights from cichlids are applicable to human facial variation and disease. We review recent work in this system, which has identified lbh as a novel regulator of neural crest cell migration, determined the Wnt and Hedgehog pathways mediate species-specific bone morphologies, and examined how plastic responses to diet modulate adult facial shapes. These studies have not only revealed new roles for existing pathways in craniofacial development, but have identified new genes and mechanisms involved in shaping the craniofacial skeleton. In all, we suggest that combining work in traditional laboratory and evolutionary models offers significant potential to provide a more complete and comprehensive picture of the myriad factors that are involved in the development of complex traits.
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Affiliation(s)
- Kara E Powder
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
| | - R Craig Albertson
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
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Hayes S, Wang W, Rajamanickam K, Chu A, Banerjee A, Hayes C. Lambda gpP-DnaB Helicase Sequestration and gpP-RpoB Associated Effects: On Screens for Auxotrophs, Selection for Rif(R), Toxicity, Mutagenicity, Plasmid Curing. Viruses 2016; 8:E172. [PMID: 27338450 PMCID: PMC4926192 DOI: 10.3390/v8060172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/25/2016] [Accepted: 06/09/2016] [Indexed: 12/03/2022] Open
Abstract
The bacteriophage lambda replication initiation protein P exhibits a toxic effect on its Escherichia coli (E. coli) host, likely due to the formation of a dead-end P-DnaB complex, sequestering the replicative DnaB helicase from further activity. Intracellular expression of P triggers SOS-independent cellular filamentation and rapidly cures resident ColE1 plasmids. The toxicity of P is suppressed by alleles of P or dnaB. We asked whether P buildup within a cell can influence E. coli replication fidelity. The influence of P expression from a defective prophage, or when cloned and expressed from a plasmid was examined by screening for auxotrophic mutants, or by selection for rifampicin resistant (Rif(R)) cells acquiring mutations within the rpoB gene encoding the β-subunit of RNA polymerase (RNAP), nine of which proved unique. Using fluctuation assays, we show that the intracellular expression of P evokes a mutator effect. Most of the Rif(R) mutants remained P(S) and localized to the Rif binding pocket in RNAP, but a subset acquired a P(R) phenotype, lost sensitivity to ColE1 plasmid curing, and localized outside of the pocket. One P(R) mutation was identical to rpo*Q148P, which alleviates the UV-sensitivity of ruv strains defective in the migration and resolution of Holliday junctions and destabilizes stalled RNAP elongation complexes. The results suggest that P-DnaB sequestration is mutagenic and supports an earlier observation that P can interact with RNAP.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Wen Wang
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Karthic Rajamanickam
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Audrey Chu
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Anirban Banerjee
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Connie Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
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Shinnakasu R, Inoue T, Kometani K, Moriyama S, Adachi Y, Nakayama M, Takahashi Y, Fukuyama H, Okada T, Kurosaki T. Regulated selection of germinal-center cells into the memory B cell compartment. Nat Immunol 2016; 17:861-9. [DOI: 10.1038/ni.3460] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 04/07/2016] [Indexed: 12/11/2022]
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Li TY, Wang XN, Li WJ, Gao H, Ding L. Generation of an inducible Claudin-7 conditional knockout mouse line. Shijie Huaren Xiaohua Zazhi 2015; 23:5017-5023. [DOI: 10.11569/wcjd.v23.i31.5017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To create an inducible Claudin-7 conditional knockout (ICKO) mouse line using the Cre/LoxP system and analyze the phenotype after inducing knockout in the intestine.
METHODS: Claudin-7 conditional knockout targeted vector was constructed and then transfected into embryonic stem (ES) cells by electroporation. The targeted ES cells were screened by positive-negative selection, and identified by PCR and Southern blot. The screened targeted ES cells were microinjected into the blastula of C57BL/6N mice. Chimerical mice were generated after transplanting the blastula into the host mice, and then the Claudin-7-floxed mice were generated by crossing between the chimerical mice and C57BL/6N mice. Claudin-7 ICKO mice could be obtained by crossing between Pvillin-CreERT2 transgenic mice and Claudin-7-floxed mice. A further phenotype analysis was made by HE staining.
RESULTS: We obtained Claudin-7-floxed mice and Cldn7fl/flVillin-CreERT2 homozygous mice successfully. The deletion of Claudin-7 gene expression in mouse intestinal epithelial cells was successfully induced by tamoxifen. After tamoxifen induction, the mice developed dehydration, the degree of living activity decreased, and death occurred.
CONCLUSION: We have successfully created an inducible Claudin-7 conditional knockout mouse line and induced the gene deletion in the intestine using tamoxifen, which may be used as a model of intestinal inflammation.
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