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Robledo M, García-Tomsig NI, Matia-González AM, García-Rodríguez FM, Jiménez-Zurdo JI. Synthetase of the methyl donor S-adenosylmethionine from nitrogen-fixing α-rhizobia can bind functionally diverse RNA species. RNA Biol 2021; 18:1111-1123. [PMID: 33043803 PMCID: PMC8244774 DOI: 10.1080/15476286.2020.1829365] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Function of bacterial small non-coding RNAs (sRNAs) and overall RNA metabolism is largely shaped by a vast diversity of RNA-protein interactions. However, in non-model bacteria with defined non-coding transcriptomes the sRNA interactome remains almost unexplored. We used affinity chromatography to capture proteins associated in vivo with MS2-tagged trans-sRNAs that regulate nutrient uptake (AbcR2 and NfeR1) and cell cycle (EcpR1) mRNAs by antisense-based translational inhibition in the nitrogen-fixing α-rhizobia Sinorhizobium meliloti. The three proteomes were rather distinct, with that of EcpR1 particularly enriched in cell cycle-related enzymes, whilst sharing several transcription/translation-related proteins recurrently identified associated with sRNAs. Strikingly, MetK, the synthetase of the major methyl donor S-adenosylmethionine, was reliably recovered as a binding partner of the three sRNAs, which reciprocally co-immunoprecipitated with a FLAG-tagged MetK variant. Induced (over)expression of the trans-sRNAs and MetK depletion did not influence canonical riboregulatory traits, `for example, protein titration or sRNA stability, respectively. An in vitro filter assay confirmed binding of AbcR2, NfeR1 and EcpR1 to MetK and further revealed interaction of the protein with other non-coding and coding transcripts but not with the 5S rRNA. These findings uncover a broad specificity for RNA binding as an unprecedented feature of this housekeeping prokaryotic enzyme.
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MESH Headings
- Gene Expression Regulation, Bacterial
- Methionine Adenosyltransferase/genetics
- Methionine Adenosyltransferase/metabolism
- Nitrogen Fixation/physiology
- Plant Root Nodulation/physiology
- Plants/microbiology
- Protein Binding
- Protein Interaction Mapping
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- S-Adenosylmethionine/metabolism
- Sinorhizobium meliloti/enzymology
- Sinorhizobium meliloti/genetics
- Symbiosis/physiology
- Transcriptome
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Affiliation(s)
- Marta Robledo
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Natalia I. García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Ana M. Matia-González
- Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Fernando M. García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - José I. Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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2
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Lakshmanan V, Sujith TN, Bansal D, Shivaprasad PV, Palakodeti D, Krishna S. Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs). RNA 2021; 27:477-495. [PMID: 33446492 PMCID: PMC7962491 DOI: 10.1261/rna.077701.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological processes such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration, suggesting a possible role for these small RNAs in the regulation of regeneration. In order to characterize planarian tRFs, we first annotated 457 tRNAs in S. mediterranea combining two tRNA prediction algorithms. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians-the shorter tRF-5s and itRFs, and the abundantly expressed 5'-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5'-tsRNA in planaria interact with all three SMEDWI proteins and an involvement of AGO1 in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalog of posttranscriptional regulatory systems in planaria, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.
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MESH Headings
- Algorithms
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Base Pairing
- Base Sequence
- Gene Expression Regulation
- Helminth Proteins/genetics
- Helminth Proteins/metabolism
- Molecular Sequence Annotation
- Nucleic Acid Conformation
- Planarians/genetics
- Planarians/metabolism
- RNA, Helminth/chemistry
- RNA, Helminth/classification
- RNA, Helminth/genetics
- RNA, Helminth/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/classification
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Regeneration/genetics
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Affiliation(s)
- Vairavan Lakshmanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
| | - T N Sujith
- National Centre for Biological Sciences (NCBS), 560065 Bangalore, India
| | - Dhiru Bansal
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | | | - Dasaradhi Palakodeti
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | - Srikar Krishna
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
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3
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Johnson NR, dePamphilis CW, Axtell MJ. Compensatory sequence variation between trans-species small RNAs and their target sites. eLife 2019; 8:e49750. [PMID: 31845648 PMCID: PMC6917502 DOI: 10.7554/elife.49750] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/25/2019] [Indexed: 01/04/2023] Open
Abstract
Trans-species small regulatory RNAs (sRNAs) are delivered to host plants from diverse pathogens and parasites and can target host mRNAs. How trans-species sRNAs can be effective on diverse hosts has been unclear. Multiple species of the parasitic plant Cuscuta produce trans-species sRNAs that collectively target many host mRNAs. Confirmed target sites are nearly always in highly conserved, protein-coding regions of host mRNAs. Cuscuta trans-species sRNAs can be grouped into superfamilies that have variation in a three-nucleotide period. These variants compensate for synonymous-site variation in host mRNAs. By targeting host mRNAs at highly conserved protein-coding sites, and simultaneously expressing multiple variants to cover synonymous-site variation, Cuscuta trans-species sRNAs may be able to successfully target multiple homologous mRNAs from diverse hosts.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis/parasitology
- Base Sequence
- Codon
- Computational Biology
- Conserved Sequence
- Cuscuta/genetics
- Cuscuta/growth & development
- Cuscuta/metabolism
- Gene Expression Regulation, Plant
- Genetic Variation
- Genome, Plant
- Host-Parasite Interactions
- Open Reading Frames
- Plant Proteins/genetics
- Plant Proteins/metabolism
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- Sequence Alignment
- Nicotiana/genetics
- Nicotiana/growth & development
- Nicotiana/parasitology
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Affiliation(s)
- Nathan R Johnson
- Intercollege PhD Program in Plant Biology, Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkUnited States
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkUnited States
| | - Claude W dePamphilis
- Intercollege PhD Program in Plant Biology, Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkUnited States
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkUnited States
| | - Michael J Axtell
- Intercollege PhD Program in Plant Biology, Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkUnited States
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkUnited States
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4
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Pagès A, Dotu I, Pallarès-Albanell J, Martí E, Guigó R, Eyras E. The discovery potential of RNA processing profiles. Nucleic Acids Res 2018; 46:e15. [PMID: 29155959 PMCID: PMC5814818 DOI: 10.1093/nar/gkx1115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure. We developed SeRPeNT, a new computational method that exploits reproducibility across replicates and uses dynamic time-warping and density-based clustering algorithms to identify, characterize and compare sncRNAs by harnessing the power of read profiles. We applied SeRPeNT to: (i) generate an extended human annotation with 671 new sncRNAs from known classes and 131 from new potential classes, (ii) show pervasive differential processing of sncRNAs between cell compartments and (iii) predict new molecules with miRNA-like behaviour from snoRNA, tRNA and long non-coding RNA precursors, potentially dependent on the miRNA biogenesis pathway. Furthermore, we validated experimentally four predicted novel non-coding RNAs: a miRNA, a snoRNA-derived miRNA, a processed tRNA and a new uncharacterized sncRNA. SeRPeNT facilitates fast and accurate discovery and characterization of sncRNAs at an unprecedented scale. SeRPeNT code is available under the MIT license at https://github.com/comprna/SeRPeNT.
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Affiliation(s)
- Amadís Pagès
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Ivan Dotu
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- IMIM—Hospital del Mar Medical Research Institute, E08003 Barcelona, Spain
| | - Joan Pallarès-Albanell
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Eulàlia Martí
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Roderic Guigó
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Eduardo Eyras
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), E08010 Barcelona, Spain
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5
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Miller DFB, Yan PX, Fang F, Buechlein A, Ford JB, Tang H, Huang TH, Burow ME, Liu Y, Rusch DB, Nephew KP. Stranded Whole Transcriptome RNA-Seq for All RNA Types. Curr Protoc Hum Genet 2015; 84:11.14.1-11.14.23. [PMID: 25599667 PMCID: PMC4337225 DOI: 10.1002/0471142905.hg1114s84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA), and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libraries for multiplexing on the Illumina platform are generated with this approach but it can be applied to other platforms with a few modifications.
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MESH Headings
- DNA, Complementary/analysis
- DNA, Complementary/genetics
- Gene Library
- High-Throughput Nucleotide Sequencing/instrumentation
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Polymerase Chain Reaction/methods
- RNA/analysis
- RNA/genetics
- RNA, Long Noncoding/analysis
- RNA, Long Noncoding/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Mitochondrial
- RNA, Small Untranslated/analysis
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Transfer/analysis
- RNA, Transfer/genetics
- Reverse Transcription
- Transcriptome
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Affiliation(s)
- David F B Miller
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Pearlly X Yan
- Department of Internal Medicine, OSUCCC-Illumina Core, Columbus, Ohio
| | - Fang Fang
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Aaron Buechlein
- Indiana University Center for Genomics and Bioinformatics, Bloomington, Indiana
| | - James B Ford
- Indiana University Center for Genomics and Bioinformatics, Bloomington, Indiana
| | - Haixu Tang
- Indiana University Center for Genomics and Bioinformatics, Bloomington, Indiana
| | - Tim H Huang
- Department of Molecular Medicine, University of Texan Health Science Center, San Antonio, Texas
| | - Matthew E Burow
- Department of Medicine, Tulane University, New Orleans, Louisiana
| | - Yunlong Liu
- Indiana University School of Medicine, Center for Computation Biology and Bioinformatics, Indianapolis, Indiana
| | - Douglas B Rusch
- Indiana University Center for Genomics and Bioinformatics, Bloomington, Indiana
| | - Kenneth P Nephew
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
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6
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Abstract
The majority of the genomic DNA sequence in mammalian and other higher organisms can be transcribed into abundant functional RNA transcripts, especially regulatory non-coding RNAs (ncRNAs) that are expressed in a developmentally and species-specific regulated manner. Here, we review various regulatory non-coding RNAs, including regulatory small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs), and summarize two and eight kinds of distinct modes of action for sncRNAs and lncRNAs respectively, by which functional ncRNAs mediate the regulation of intracellular events.
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Affiliation(s)
- Biao Huang
- Research Center of Basic Medical Science; Department of Immunology, Basic Medical College; Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironments and Diseases of Educational Ministry of China, Tianjin Medical University, Tianjin, 300070, China
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7
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Yan Y, Su S, Meng X, Ji X, Qu Y, Liu Z, Wang X, Cui Y, Deng Z, Zhou D, Jiang W, Yang R, Han Y. Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection. PLoS One 2013; 8:e74495. [PMID: 24040259 PMCID: PMC3770706 DOI: 10.1371/journal.pone.0074495] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 08/02/2013] [Indexed: 12/21/2022] Open
Abstract
Background Small non-coding RNAs (sRNAs) facilitate host-microbe interactions. They have a central function in the post-transcriptional regulation during pathogenic lifestyles. Hfq, an RNA-binding protein that many sRNAs act in conjunction with, is required for Y. pestis pathogenesis. However, information on how Yersinia pestis modulates the expression of sRNAs during infection is largely unknown. Methodology and Principal Findings We used RNA-seq technology to identify the sRNA candidates expressed from Y. pestis grown invitro and in the infected lungs of mice. A total of 104 sRNAs were found, including 26 previously annotated sRNAs, by searching against the Rfam database with 78 novel sRNA candidates. Approximately 89% (93/104) of these sRNAs from Y. pestis are shared with its ancestor Y. pseudotuberculosis. Ninety-seven percent of these sRNAs (101/104) are shared among more than 80 sequenced genomes of 135 Y. pestis strains. These 78 novel sRNAs include 62 intergenic and 16 antisense sRNAs. Fourteen sRNAs were selected for verification by independent Northern blot analysis. Results showed that nine selected sRNA transcripts were Hfq-dependent. Interestingly, three novel sRNAs were identified as new members of the transcription factor CRP regulon. Semi-quantitative analysis revealed that Y. pestis from the infected lungs induced the expressions of six sRNAs including RyhB1, RyhB2, CyaR/RyeE, 6S RNA, RybB and sR039 and repressed the expressions of four sRNAs, including CsrB, CsrC, 4.5S RNA and sR027. Conclusions and Significance This study is the first attempt to subject RNA from Y. pestis-infected samples to direct high-throughput sequencing. Many novel sRNAs were identified and the expression patterns of relevant sRNAs in Y. pestis during invitro growth and invivo infection were revealed. The annotated sRNAs accounted for the most abundant sRNAs either expressed in bacteria grown invitro or differentially expressed in the infected lungs. These findings suggested these sRNAs may have important functions in Y. pestis physiology or pathogenesis.
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Affiliation(s)
- Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shanchun Su
- Microbiology Laboratory, Sichuan Agricultural University, Yaan, Sichuan province, China
| | - Xiangrong Meng
- Clinical Laboratory, Huzhong Hispital, Guangzhou, Guangdong province, China
| | - Xiaolan Ji
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yi Qu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zizhong Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoyi Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhongliang Deng
- Department of Sanitary Inspection, School of Public Health, University of South China, Hengyang, Hunan province, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wencan Jiang
- Microbiology Laboratory, Sichuan Agricultural University, Yaan, Sichuan province, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (YH); (RY)
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (YH); (RY)
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8
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Su AAH, Tripp V, Randau L. RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri. Nucleic Acids Res 2013; 41:6250-8. [PMID: 23620296 PMCID: PMC3695527 DOI: 10.1093/nar/gkt317] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/03/2013] [Accepted: 04/05/2013] [Indexed: 11/29/2022] Open
Abstract
The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution.
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MESH Headings
- Euryarchaeota/genetics
- Euryarchaeota/metabolism
- High-Throughput Nucleotide Sequencing
- Hot Temperature
- Inverted Repeat Sequences
- RNA Editing
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/classification
- RNA, Archaeal/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Sequence Analysis, RNA
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Affiliation(s)
- Andreas A. H. Su
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
| | - Vanessa Tripp
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
| | - Lennart Randau
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
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9
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Abstract
Regulatory small RNAs, which range in size from 20 to 24 nucleotides, are ubiquitous components of endogenous plant transcriptomes, as well as common responses to exogenous viral infections and introduced double-stranded RNA (dsRNA). Endogenous small RNAs derive from the processing of helical RNA precursors and can be categorized into several groups based on differences in biogenesis and function. A major distinction can be observed between small RNAs derived from single-stranded precursors with a hairpin structure [referred to here as hairpin RNAs (hpRNAs)] and those derived from dsRNA precursors [small interfering RNAs (siRNAs)]. hpRNAs in plants can be divided into two secondary groups: microRNAs and those that are not microRNAs. The currently known siRNAs fall mostly into one of three secondary groups: heterochromatic siRNAs, secondary siRNAs, and natural antisense transcript siRNAs. Tertiary subdivisions can be identified within many of the secondary classifications as well. Comparisons between the different classes of plant small RNAs help to illuminate key goals for future research.
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Affiliation(s)
- Michael J Axtell
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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10
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Langenberger D, Bermudez-Santana CI, Stadler PF, Hoffmann S. Identification and classification of small RNAs in transcriptome sequence data. Pac Symp Biocomput 2010:80-7. [PMID: 19908360 DOI: 10.1142/9789814295291_0010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Current methods for high throughput sequencing (HTS) for the first time offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. In many species, small non-coding RNAs with specific secondary structures constitute a significant part of the transcriptome. Some of these RNA classes, in particular microRNAs and snoRNAs, undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome specific patterns of short reads can be observed. These read patterns seem to reflect the processing and thus are specific for the RNA transcripts of which they are derived from. We explore here the potential of short read sequence data in the classification and identification of non-coding RNAs.
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Affiliation(s)
- D Langenberger
- University Leipzig, Interdisciplinary Center for Bioinformatics, Haertelstrasse 16-18, D-04107 Leipzig, Germany
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