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      Integration of RNAi and RNA-seq Reveals the Immune Responses of Epinephelus coioides to sigX Gene of Pseudomonas plecoglossicida

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          Abstract

          Pseudomonas plecoglossicida is an important pathogen for aquaculture and causes high mortality in various marine fishes. Expression of sigX was found significantly up-regulated at 18°C than at 28°C, which was verified by quantitative real-time PCR (qRT-PCR). RNAi significantly reduced the content of sigX mRNA of P. plecoglossicida, whether in in vitro or in the spleen at all sampling time points. Compared with the wild-type strain, the infection of sigX-RNAi strain resulted in the onset time delay, and 20% reduction in mortality of Epinephelus coioides, as well as alleviates in the symptoms of E. coioides spleen. Compared with wild-type strain, the gene silence of sigX in P. plecoglossicida resulted in a significant change in transcriptome of infected E. coioides. The result of gene ontology and KEGG analysis on E. coioides showed that genes of serine-type endopeptidase and chemokine signaling pathway, coagulation and complement system, and intestinal immune network for IgA production pathway were mostly affected by sigX of P. plecoglossicida. Meanwhile, the immune genes were associated with different number of miRNA and lncRNA, and some miRNAs were associated with more than one gene at the same time. The results indicated that sigX was a virulent gene of P. plecoglossicida. The up-regulation of the immune pathways made E. coioides more likely to kill sigX-RNAi strain than the wild-type strain of P. plecoglossicida, while the immune genes were regulated by miRNA and lncRNA by a complex mode.

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          Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.

          Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.
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            Mice lacking neutrophil elastase reveal impaired host defense against gram negative bacterial sepsis.

            Neutrophil elastase (NE) is a potent serine proteinase whose expression is limited to a narrow window during myeloid development. In neutrophils, NE is stored in azurophil granules along with other serine proteinases (cathepsin G, proteinase 3 and azurocidin) at concentrations exceeding 5 mM. As a result of its capacity to efficiently degrade extracellular matrix, NE has been implicated in a variety of destructive diseases. Indeed, while much interest has focused on the pathologic effects of this enzyme, little is known regarding its normal physiologic function(s). Because previous in vitro data have shown that NE exhibits antibacterial activity, we investigated the role of NE in host defense against bacteria. Generating strains of mice deficient in NE (NE-/-) by targeted mutagenesis, we show that NE-/- mice are more susceptible than their normal littermates to sepsis and death following intraperitoneal infection with Gram negative (Klebsiella pneumoniae and Escherichia coli) but not Gram positive (Staphylococcus aureus) bacteria. Our data indicate that neutrophils migrate normally to sites of infection in the absence of NE, but that NE is required for maximal intracellular killing of Gram negative bacteria by neutrophils.
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              mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa.

              Broad host-range mini-Tn7 vectors facilitate integration of single-copy genes into bacterial chromosomes at a neutral, naturally evolved site. Here we present a protocol for employing the mini-Tn7 system in bacteria with single attTn7 sites, using the example Pseudomonas aeruginosa. The procedure involves, first, cloning of the genes of interest into an appropriate mini-Tn7 vector; second, co-transfer of the recombinant mini-Tn7 vector and a helper plasmid encoding the Tn7 site-specific transposition pathway into P. aeruginosa by either transformation or conjugation, followed by selection of insertion-containing strains; third, PCR verification of mini-Tn7 insertions; and last, optional Flp-mediated excision of the antibiotic-resistance selection marker present on the chromosomally integrated mini-Tn7 element. From start to verification of the insertion events, the procedure takes as little as 4 d and is very efficient, yielding several thousand transformants per microgram of input DNA or conjugation mixture. In contrast to existing chromosome integration systems, which are mostly based on species-specific phage or more-or-less randomly integrating transposons, the mini-Tn7 system is characterized by its ready adaptability to various bacterial hosts, its site specificity and its efficiency. Vectors have been developed for gene complementation, construction of gene fusions, regulated gene expression and reporter gene tagging.
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                Author and article information

                Contributors
                Journal
                Front Immunol
                Front Immunol
                Front. Immunol.
                Frontiers in Immunology
                Frontiers Media S.A.
                1664-3224
                16 July 2018
                2018
                : 9
                : 1624
                Affiliations
                [1] 1Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University , Xiamen, China
                [2] 2State Key Laboratory of Large Yellow Croaker Breeding , Ningde, China
                Author notes

                Edited by: Gerardo R. Vasta, University of Maryland, Baltimore, United States

                Reviewed by: Hai-peng Liu, Xiamen University, China; Hao-Ching Wang, Taipei Medical University, Taiwan

                *Correspondence: Qingpi Yan, yanqp@ 123456jmu.edu.cn

                Specialty section: This article was submitted to Comparative Immunology, a section of the journal Frontiers in Immunology

                Article
                10.3389/fimmu.2018.01624
                6054955
                30061893
                19f88db7-2cee-4ecd-8b95-3e3e69f52fcf
                Copyright © 2018 Sun, Luo, Zhao, Huang, Qin, Su and Yan.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 25 April 2018
                : 02 July 2018
                Page count
                Figures: 5, Tables: 0, Equations: 0, References: 40, Pages: 11, Words: 6169
                Categories
                Immunology
                Original Research

                Immunology
                immune response,epinephelus coioides,pseudomonas plecoglossicida,sigx,rnai,rna-seq,mirna,lncrna
                Immunology
                immune response, epinephelus coioides, pseudomonas plecoglossicida, sigx, rnai, rna-seq, mirna, lncrna

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