Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

Li, Nan; Hennelly, Scott P.; Stubben, Chris J.; Micheva-Viteva, Sofiya; Hu, Bin; Shou, Yulin; Vuyisich, Momchilo; Tung, Chang -Shung; Chain, Patrick S.; Sanbonmatsu, Karissa Y.; Hong-Geller, Elizabeth; Roop, Roy Martin

doi:10.1371/journal.pone.0168915

Title: Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

Journal Article · Wed Dec 28 00:00:00 EST 2016 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0168915· OSTI ID:1351188

Li, Nan ^[1];

^[1]; Stubben, Chris J. ^[2];

^[1]; Hu, Bin ^[3]; Shou, Yulin ^[1]; Vuyisich, Momchilo ^[4];

^[1];

^[1]; Hong-Geller, Elizabeth ^[1]; Roop, Roy Martin ^[5]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Univ. of Utah, Salt Lake City, UT (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
SRA International, Atlanta, GA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Viome Inc., Los Alamos, NM (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
East Carolina Univ. Brody School of Medicine, Greenville, NC (United States)

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis. In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. We found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Lastly, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1351188

Report Number(s):: LA-UR-16-20099

Journal Information:: PLoS ONE, Vol. 11, Issue 12; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 8 works

Citation information provided by
Web of Science

References (45)

Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis Achtman, M.; Zurth, K.; Morelli, G. Proceedings of the National Academy of Sciences, Vol. 96, Issue 24 https://doi.org/10.1073/pnas.96.24.14043	journal	November 1999
Yersinia type III secretion Cornelis, Guy R. Journal of Cell Biology, Vol. 158, Issue 3 https://doi.org/10.1083/jcb.200205077	journal	August 2002
The role of RNAs in the regulation of virulence-gene expression Romby, Pascale; Vandenesch, François; Wagner, E. Gerhart H. Current Opinion in Microbiology, Vol. 9, Issue 2 https://doi.org/10.1016/j.mib.2006.02.005	journal	April 2006
Small noncoding RNAs controlling pathogenesis Toledo-Arana, Alejandro; Repoila, Francis; Cossart, Pascale Current Opinion in Microbiology, Vol. 10, Issue 2 https://doi.org/10.1016/j.mib.2007.03.004	journal	April 2007
Regulatory RNAs in Bacteria Waters, Lauren S.; Storz, Gisela Cell, Vol. 136, Issue 4 https://doi.org/10.1016/j.cell.2009.01.043	journal	February 2009
Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions Stubben, Chris J.; Micheva-Viteva, Sofiya N.; Shou, Yulin BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-385	journal	January 2014
The Attachment Site of Streptomycin to the 30S Ribosomal Subunit Biswas, D. K.; Gorini, L. Proceedings of the National Academy of Sciences, Vol. 69, Issue 8 https://doi.org/10.1073/pnas.69.8.2141	journal	August 1972
Effects of Tetracycline and Spectinomycin on the Tertiary Structure of Ribosomal RNA in the Escherichia coli 30 S Ribosomal Subunit Noah, James W.; Dolan, Michael A.; Babin, Patricia Journal of Biological Chemistry, Vol. 274, Issue 23 https://doi.org/10.1074/jbc.274.23.16576	journal	June 1999
Identification and characterization of small RNAs in Yersinia pestis Beauregard, Arthur; Smith, Eric; Petrone, Brianna RNA Biology, Vol. 10, Issue 3 https://doi.org/10.4161/rna.23590	journal	March 2013
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
Rfam: Wikipedia, clans and the "decimal" release Gardner, P. P.; Daub, J.; Tate, J. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1129	journal	November 2010
Determination of sRNA Expressions by RNA-seq in Yersinia pestis Grown In Vitro and during Infection Yan, Yanfeng; Su, Shanchun; Meng, Xiangrong PLoS ONE, Vol. 8, Issue 9 https://doi.org/10.1371/journal.pone.0074495	journal	September 2013
Computational analysis of bacterial RNA-Seq data McClure, Ryan; Balasubramanian, Divya; Sun, Yan Nucleic Acids Research, Vol. 41, Issue 14 https://doi.org/10.1093/nar/gkt444	journal	May 2013
High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs Livny, Jonathan; Teonadi, Hidayat; Livny, Miron PLoS ONE, Vol. 3, Issue 9 https://doi.org/10.1371/journal.pone.0003197	journal	September 2008
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake Kingsford, Carleton L.; Ayanbule, Kunmi; Salzberg, Steven L. Genome Biology, Vol. 8, Issue 2 https://doi.org/10.1186/gb-2007-8-2-r22	journal	January 2007
Differential expression analysis for sequence count data Anders, Simon; Huber, Wolfgang Genome Biology, Vol. 11, Issue 10 https://doi.org/10.1186/gb-2010-11-10-r106	journal	October 2010
Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq Kawamoto, Hiroshi; Koide, Yukari; Morita, Teppei Molecular Microbiology, Vol. 61, Issue 4 https://doi.org/10.1111/j.1365-2958.2006.05288.x	journal	August 2006
A Fast-Acting Reagent for Accurate Analysis of RNA Secondary and Tertiary Structure by SHAPE Chemistry Mortimer, Stefanie A.; Weeks, Kevin M. Journal of the American Chemical Society, Vol. 129, Issue 14 https://doi.org/10.1021/ja0704028	journal	April 2007
All-atom homology model of the Escherichia coli 30S ribosomal subunit Tung, Chang-Shung; Joseph, Simpson; Sanbonmatsu, Kevin Y. Nature Structural Biology, Vol. 9, Issue 10 https://doi.org/10.1038/nsb841	journal	September 2002
Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence Koo, J. T.; Alleyne, T. M.; Schiano, C. A. Proceedings of the National Academy of Sciences, Vol. 108, Issue 37 https://doi.org/10.1073/pnas.1101655108	journal	August 2011
c-KIT signaling is targeted by pathogenic Yersinia to suppress the host immune response Micheva-Viteva, Sofiya N.; Shou, Yulin; Nowak-Lovato, Kristy L. BMC Microbiology, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2180-13-249	journal	January 2013
YERSINIA OUTER PROTEINS: Role in Modulation of Host Cell Signaling Responses and Pathogenesis Viboud, Gloria I.; Bliska, James B. Annual Review of Microbiology, Vol. 59, Issue 1 https://doi.org/10.1146/annurev.micro.59.030804.121320	journal	October 2005
The role of Hfq in bacterial pathogens Chao, Yanjie; Vogel, Jörg Current Opinion in Microbiology, Vol. 13, Issue 1 https://doi.org/10.1016/j.mib.2010.01.001	journal	February 2010
QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis Karabiber, F.; McGinnis, J. L.; Favorov, O. V. RNA, Vol. 19, Issue 1 https://doi.org/10.1261/rna.036327.112	journal	November 2012
HmsB enhances biofilm formation in Yersinia pestis Fang, Nan; Qu, Shi; Yang, Huiying Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00685	journal	December 2014
The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch Hennelly, Scott P.; Novikova, Irina V.; Sanbonmatsu, Karissa Y. Nucleic Acids Research, Vol. 41, Issue 3 https://doi.org/10.1093/nar/gks978	journal	December 2012
Identifying and characterizing Hfq–RNA interactions Faner, M. A.; Feig, A. L. Methods, Vol. 63, Issue 2 https://doi.org/10.1016/j.ymeth.2013.04.023	journal	September 2013
Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs Novikova, Irina V.; Hennelly, Scott P.; Tung, Chang-Shung Journal of Molecular Biology, Vol. 425, Issue 19 https://doi.org/10.1016/j.jmb.2013.02.030	journal	October 2013
Interaction of antibiotics with functional sites in 16S ribosomal RNA Moazed, Danesh; Noller, Harry F. Nature, Vol. 327, Issue 6121 https://doi.org/10.1038/327389a0	journal	June 1987
Neomycin Inhibition of the Hammerhead Ribozyme Involves Ionic Interactions Clouet-d'Orval, Beatrice; Stage, Tracy K.; Uhlenbeck, Olke C. Biochemistry, Vol. 34, Issue 35 https://doi.org/10.1021/bi00035a025	journal	September 1995
Aminoglycoside antibiotics bind to the influenza A virus RNA promoter Kim, Henna; Lee, Mi-Kyung; Ko, Junsang Molecular BioSystems, Vol. 8, Issue 11 https://doi.org/10.1039/c2mb25333j	journal	January 2012
Inhibitors of Protein−RNA Complexation That Target the RNA: Specific Recognition of Human Immunodeficiency Virus Type 1 TAR RNA by Small Organic Molecules Mei, Houng-Yau; Cui, Mei; Heldsinger, Andrea Biochemistry, Vol. 37, Issue 40 https://doi.org/10.1021/bi981308u	journal	October 1998
Aminoglycoside Antibiotics Are Able To Specifically Bind the 5‘-Untranslated Region of Thymidylate Synthase Messenger RNA ^† Tok, Jeffrey B. -H.; Cho, Junhyeong; Rando, Robert R. Biochemistry, Vol. 38, Issue 1 https://doi.org/10.1021/bi9819428	journal	January 1999
Involvement of the Post-Transcriptional Regulator Hfq in Yersinia pestis Virulence Geng, Jing; Song, Yajun; Yang, Lei PLoS ONE, Vol. 4, Issue 7 https://doi.org/10.1371/journal.pone.0006213	journal	July 2009
Hfq binding changes the structure of Escherichia coli small noncoding RNAs OxyS and RprA, which are involved in the riboregulation of rpoS Henderson, C. A.; Vincent, H. A.; Casamento, A. RNA, Vol. 19, Issue 8 https://doi.org/10.1261/rna.034595.112	journal	June 2013
The low-resolution solution structure of Vibrio cholerae Hfq in complex with Qrr1 sRNA Vincent, Helen A.; Henderson, Charlotte A.; Stone, Carlanne M. Nucleic Acids Research, Vol. 40, Issue 17 https://doi.org/10.1093/nar/gks582	journal	June 2012
Structural flexibility of RNA as molecular basis for Hfq chaperone function de Almeida Ribeiro, Euripedes; Beich-Frandsen, Mads; Konarev, Petr V. Nucleic Acids Research, Vol. 40, Issue 16 https://doi.org/10.1093/nar/gks510	journal	June 2012
Small molecules that selectively block RNA binding of HIV-1 rev protein inhibit rev function and viral production Zapp, Maria L.; Stern, Seth; Green, Michael R. Cell, Vol. 74, Issue 6 https://doi.org/10.1016/0092-8674(93)90720-b	journal	September 1993
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli Argaman, Liron; Hershberg, Ruth; Vogel, Jörg Current Biology, Vol. 11, Issue 12 https://doi.org/10.1016/s0960-9822(01)00270-6	journal	June 2001
Counting Small RNA in Pathogenic Bacteria Shepherd, Douglas P.; Li, Nan; Micheva-Viteva, Sofiya N. Analytical Chemistry, Vol. 85, Issue 10 https://doi.org/10.1021/ac303792p	journal	April 2013
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W. Nature Genetics, Vol. 53, Issue 3 https://doi.org/10.1038/s41588-021-00778-2	journal	March 2021
Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis Freyria, Nastasia J.; Kuo, Alan; Chovatia, Mansi Communications Biology, Vol. 5, Issue 1 https://doi.org/10.1038/s42003-022-03461-2	journal	May 2022
Impact of Host Membrane Pore Formation by the Yersinia pseudotuberculosis Type III Secretion System on the Macrophage Innate Immune Response Kwuan, Laura; Adams, Walter; Auerbuch, Victoria Infection and Immunity, Vol. 81, Issue 3 https://doi.org/10.1128/iai.01014-12	journal	January 2013
Structural Organization and Functional Properties of Miniature DNA Insertion Sequences in Yersiniae De Gregorio, Eliana; Silvestro, Giustina; Venditti, Rossella Journal of Bacteriology, Vol. 188, Issue 22 https://doi.org/10.1128/jb.00942-06	journal	September 2006
Genome-Wide Analysis of Small RNAs Expressed by Yersinia pestis Identifies a Regulator of the Yop-Ysc Type III Secretion System Schiano, C. A.; Koo, J. T.; Schipma, M. J. Journal of Bacteriology, Vol. 196, Issue 9 https://doi.org/10.1128/jb.01456-13	journal	February 2014

Cited By (4)

PKC-η-MARCKS Signaling Promotes Intracellular Survival of Unopsonized Burkholderia thailandensis Micheva-Viteva, Sofiya N.; Shou, Yulin; Ganguly, Kumkum Frontiers in Cellular and Infection Microbiology, Vol. 7 https://doi.org/10.3389/fcimb.2017.00231	journal	June 2017
Enteropathogens: Tuning Their Gene Expression for Hassle-Free Survival Chatterjee, Ritika; Shreenivas, Meghanashree M.; Sunil, Rohith Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03303	journal	January 2019
Discovering RNA-Based Regulatory Systems for Yersinia Virulence Knittel, Vanessa; Vollmer, Ines; Volk, Marcel Frontiers in Cellular and Infection Microbiology, Vol. 8 https://doi.org/10.3389/fcimb.2018.00378	journal	October 2018
RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions Diallo, Idrissa; Provost, Patrick International Journal of Molecular Sciences, Vol. 21, Issue 5 https://doi.org/10.3390/ijms21051627	journal	February 2020

Similar Records

Glutathionylation of Yersinia pestis LcrV and Its Effects on Plague Pathogenesis

Journal Article · Tue May 16 00:00:00 EDT 2017 · mBio (Online) · OSTI ID:1351188

Mitchell, Anthony; Tam, Christina; Elli, Derek; +6 more

Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis

Journal Article · Mon Sep 26 00:00:00 EDT 2011 · PLoS ONE · OSTI ID:1351188

Torres, Rodrigo; Swift, Robert V.; Chim, Nicholas; +8 more

Investigation of Yersinia pestis laboratory adaptation through a combined genomics and proteomics approach

Journal Article · Tue Nov 24 00:00:00 EST 2015 · PLoS ONE · OSTI ID:1351188

Leiser, Owen P.; Merkley, Eric D.; Clowers, Brian H.; +8 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
biological science
Yersinia pestis
RNA folding
RNA structure
bacterial pathogens
RNA sequencing
intracellular pathogens
Yersinia
Yersinia pseudotuberculosis

Title: Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

Citation Formats

References (45)

Cited By (4)

Similar Records

Related Subjects