Two Autographa californica nucleopolyhedrovirus (AcMNPV) encoded miRNAs, AcMNPV-miR-1 and -miR-3, have been reported in 2013 and 2019. Here, we present an integrated investigation of AcMNPV-encoded miRNAs. Six candidate miRNAs were predicted through small RNA deep sequencing and bioinformatics, of which, five validated by experiments. Three miRNAs perfectly matched the coding sequence of viral genes. The other two are located in coding sequences of viral genes. Targets in both virus and host were predicted and subsequently tested using dual-luciferase reporter assay. The validated targets were found mainly in AcMNPV, except for the targets of AcMNPV-miR-4, which are all host genes. Based on reporter assays, the five miRNAs predominantly function by down-regulating their targets, though individual target is slightly up-regulated. The transcription start sites of these miRNAs were analyzed. Our results suggest that AcMNPV-encoded miRNAs function as fine modulators of the interactions between host and virus by regulating viral and/or host genes. Author summaryVirus-encoded miRNAs have been widely reported as modulators participating in almost all biological processes. However, among Baculoviridae, which consists of a large family of dsDNA viruses that infect numerous beneficial insects and agricultural pests, only several have been reported encoding miRNAs. To clarify the roles of AcMNPV-encoded miRNAs in host-pathogen interactions, we employed RNA deep sequencing and series of experimental approaches identifying AcMNPV-encoded miRNAs, followed by target validation and function deduction. Among them, AcMNPV-miR-1 and AcMNPV-miR-3 have been reported in 2013 and 2019, respectively. This study reveals the sites of these miRNAs in the genome, both in coding sequences and complements, suggesting diverse functions. These miRNAs target genes in the virus itself and in the host, largely by suppressing expression, with some enhancing it. The transcription initiations of the miRNAs were analyzed. Our results provide some insight into the finely regulated process of baculovirus infection. baculovirus molecular biology, was also reported encoding miRNAs, AcMNPV-miR-1 and AcMNPV-miR-3 in 2013 [8, 12] by us, respectively.AcMNPV-miR-1 can down-regulate viral gene ac94, reducing the production of infectious budded virions (BVs) and accelerating the formation of occlusion-derived virions (ODVs) [8]. In 2016, we further reported two more target genes (ac95 and ac18) of AcMNPV-miR-1, and depicted the function pathway of this miRNA [13]. As for AcMNPV-miR-3, it mainly down-regulates viral gene ac101, meanwhile, it also regulates other five viral genes [12]. All these findings indicate that baculovirus-encoded miRNAs play roles in multiple aspects of virus infection.Here, we provide an integrated characterization of these miRNAs which AcMNPV encoded. The investigation for AcMNPV-encoded miRNAs and their functions began with sequencing four small RNA samples collected from Sf9 cells infected with AcMNPV at three different time intervals...
20Metatranscriptomic sequencing has recently been applied to study how pathogens and probiotics 21 affect human gastrointestinal (GI) tract microbiota, which provides new insights into their 22 mechanisms of action. In this study, metatranscriptomic sequencing was applied to deduce the in 23 vivo expression patterns of an ingested Lactobacillus casei strain, which was compared with its in 24 vitro growth transcriptomes. Extraction of the strain-specific reads revealed that transcripts from 25 the ingested L. casei were increased, while those from the resident L. paracasei strains remained 26unchanged. Mapping of all metatranscriptomic reads and transcriptomic reads to L. casei genome 27 showed that gene expression in vitro and in vivo differed dramatically. About 39% (1163) mRNAs 28 and 45% (93) sRNAs of L. casei well-expressed were repressed after ingested into human gut. 29Expression of ABC transporter genes and amino acid metabolism genes was induced at day-14 of 30 ingestion; and genes for sugar and SCFA metabolisms were activated at day-28 of ingestion. 31Moreover, expression of sRNAs specific to the in vitro log phase was more likely to be activated 32 in human gut. Expression of rli28c sRNA with peaked expression during the in vitro stationary 33 phase was also activated in human gut; this sRNA repressed L. casei growth and lactic acid 34 production in vitro. These findings implicate that the ingested L. casei might have to successfully 35 change its transcription patterns to survive in human gut, and the time-dependent activation 36 patterns indicate a highly dynamic cross-talk between the probiotic and human gut including its 37 microbe community. 38 39 Keywords: Metagenomic, metatranscriptomic, probiotic, Lactobacillus, transcriptional regulation, 40 gut microbiota 41 42 Dynamic transcription of probiotic mRNAs and sRNAs in human gut 3 Importance 43 Probiotic bacteria are important in food industry and as model microorganisms in understanding 44 bacterial gene regulation. Although probiotic functions and mechanisms in human gastrointestinal 45 tract are linked to the unique probiotic gene expression, it remains elusive how transcription of 46probiotic bacteria is dynamically regulated after being ingested. Previous study of probiotic gene 47 expression in human fecal samples has been restricted due to its low abundance and the presence 48 of of closely related species. In this study, we took the advantage of the good depth of 49 metatranscriptomic sequencing reads and developed a strain-specific read analysis method to 50 discriminate the transcription of the probiotic Lactobacillus casei and those of its resident relatives. 51This approach and additional bioinformatics analysis allowed the first study of the dynamic 52 transcriptome profiles of probiotic L casei in vivo. The novel findings indicate a highly regulated 53 repression and dynamic activation of probiotic genome in human GI tract. 54 55 56
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.