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Journal articles on the topic 'Riboregulator'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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1

Rostain, William, Shensi Shen, Teresa Cordero, Guillermo Rodrigo, and Alfonso Jaramillo. "Engineering a Circular Riboregulator in Escherichia coli." BioDesign Research 2020 (September 14, 2020): 1–9. http://dx.doi.org/10.34133/2020/1916789.

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RNAs of different shapes and sizes, natural or synthetic, can regulate gene expression in prokaryotes and eukaryotes. Circular RNAs have recently appeared to be more widespread than previously thought, but their role in prokaryotes remains elusive. Here, by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme, we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli. We showed that the resulting riboregulator can trans-activate gene expression by interacting with a cis-repressed messenger RNA. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker, and we modeled this novel posttranscriptional mechanism. This first reported example of a circular RNA regulating gene expression in E. coli adds to an increasing repertoire of RNA synthetic biology parts, and it highlights that topological molecules can play a role in the case of prokaryotic regulation.

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2

Nechooshtan, Gal, Maya Elgrably-Weiss, Abigail Sheaffer, Eric Westhof, and Shoshy Altuvia. "A pH-responsive riboregulator." Genes & Development 23, no. 22 (November 15, 2009): 2650–62. http://dx.doi.org/10.1101/gad.552209.

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3

Narita, Atsushi, Kazumasa Ogawa, Shinsuke Sando, and Yasuhiro Aoyama. "Highly sensitive genotyping using artificial riboregulator system." Nucleic Acids Symposium Series 49, no. 1 (September 1, 2005): 271–72. http://dx.doi.org/10.1093/nass/49.1.271.

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4

WANG, YANHONG, KELVIN J. A. DAVIES, J. ANDRES MELENDEZ, and DANA R. CRAWFORD. "Characterization of adapt33, a Stress-Inducible Riboregulator." Gene Expression 11, no. 2 (January 1, 2003): 85–94. http://dx.doi.org/10.3727/000000003108748982.

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5

Krishnamurthy, Malathy, Scott P. Hennelly, Taraka Dale, Shawn R. Starkenburg, Ricardo Martí-Arbona, David T. Fox, Scott N. Twary, Karissa Y. Sanbonmatsu, and Clifford J. Unkefer. "Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression." ACS Synthetic Biology 4, no. 12 (July 27, 2015): 1326–34. http://dx.doi.org/10.1021/acssynbio.5b00041.

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6

Ueno, Kinuko, Kaori Tsukakoshi, and Kazunori Ikebukuro. "Riboregulator elements as tools to engineer gene expression in cyanobacteria." Applied Microbiology and Biotechnology 102, no. 18 (July 13, 2018): 7717–23. http://dx.doi.org/10.1007/s00253-018-9221-0.

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7

Turbant, Florian, Pengzhi Wu, Frank Wien, and Véronique Arluison. "The Amyloid Region of Hfq Riboregulator Promotes DsrA:rpoS RNAs Annealing." Biology 10, no. 9 (September 12, 2021): 900. http://dx.doi.org/10.3390/biology10090900.

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Hfq is a bacterial RNA chaperone which promotes the pairing of small noncoding RNAs to target mRNAs, allowing post-transcriptional regulation. This RNA annealing activity has been attributed for years to the N-terminal region of the protein that forms a toroidal structure with a typical Sm-fold. Nevertheless, many Hfqs, including that of Escherichia coli, have a C-terminal region with unclear functions. Here we use a biophysical approach, Synchrotron Radiation Circular Dichroism (SRCD), to probe the interaction of the E. coli Hfq C-terminal amyloid region with RNA and its effect on RNA annealing. This C-terminal region of Hfq, which has been described to be dispensable for sRNA:mRNA annealing, has an unexpected and significant effect on this activity. The functional consequences of this novel property of the amyloid region of Hfq in relation to physiological stress are discussed.

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8

M. Cech, Grzegorz, and Agnieszka Szalewska-Pałasz. "THE HFQ PROTEIN - A NOVEL VIEW ON THE WELL-KNOWN RIBOREGULATOR." Postępy Mikrobiologii - Advancements of Microbiology 57, no. 1 (2019): 12–21. http://dx.doi.org/10.21307/pm-2018.57.1.012.

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9

Willkomm, Dagmar K., and Roland K. Hartmann. "6S RNA – an ancient regulator of bacterial RNA polymerase rediscovered." Biological Chemistry 386, no. 12 (December 1, 2005): 1273–77. http://dx.doi.org/10.1515/bc.2005.144.

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AbstractThe bacterial riboregulator 6S RNA was one of the first non-coding RNAs to be discovered in the late 1960s, but its cellular role remained enigmatic until the year 2000. 6S RNA, only recognized to be ubiquitous among bacteria in 2005, binds to RNA polymerase in a σ factor-dependent manner to repress transcription from a subgroup of promoters. The common feature of a double-stranded rod with a central bulge has led to the proposal that 6S RNA may mimic an open promoter complex.

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10

Janssen, R. A., and J. W. Mier. "Tropomyosin-2 cDNA lacking the 3' untranslated region riboregulator induces growth inhibition of v-Ki-ras-transformed fibroblasts." Molecular Biology of the Cell 8, no. 5 (May 1997): 897–908. http://dx.doi.org/10.1091/mbc.8.5.897.

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The levels of high molecular weight isoforms of tropomyosin (TM) are markedly reduced in ras-transformed cells. Previous studies have demonstrated that the forced expression of tropomyosin-1 (TM-1) induces reversion of the transformed phenotype of ras-transformed fibroblasts. The effects of the related isoform TM-2 on transformation are less clear. To assess the effects of forced expression of the TM-2 protein on ras-induced tumorigenicity, we introduced a TM-2 cDNA lacking the 3' untranslated region riboregulator into ras-transformed NIH 3T3 fibroblasts. TM-2 expression resulted in a flatter cell morphology and restoration of stress fibers. TM-2 expression also significantly reduced growth rates in low serum, soft agar, and nude mice. The reduced growth rates were associated with a prolongation of G0-G1. To identify the mechanism of TM-2-induced growth inhibition, we analyzed the effects of TM-2 reexpression of ERK and c-jun N-terminal kinase (JNK) activities. Levels of ERK phosphorylation and activity in TM-2-transfected tumor cells were comparable to those in mock-transfected tumor cells. JNK activity was only modestly increased in ras-transformed cells relative to untransformed NIH 3T3 cells and only slightly reduced as result of forced TM-2 expression. We conclude that the partially restored expression of the TM-2 protein induces growth inhibition of ras-transformed NIH 3T3 cells without influencing ERK or JNK activities. Furthermore, the 3' untranslated region riboregulator of the alpha-tropomyosin gene is not needed for the inhibition of ras-induced growth.

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11

Tsang, W. P., and T. T. Kwok. "Riboregulator H19 induction of MDR1-associated drug resistance in human hepatocellular carcinoma cells." Oncogene 26, no. 33 (February 5, 2007): 4877–81. http://dx.doi.org/10.1038/sj.onc.1210266.

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12

Horos, Rastislav, Magdalena Büscher, Rozemarijn Kleinendorst, Anne-Marie Alleaume, Abul K. Tarafder, Thomas Schwarzl, Dmytro Dziuba, et al. "The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy." Cell 176, no. 5 (February 2019): 1054–67. http://dx.doi.org/10.1016/j.cell.2019.01.030.

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13

Bohn, Chantal, Candice Rigoulay, Svetlana Chabelskaya, Cynthia M. Sharma, Antonin Marchais, Patricia Skorski, Elise Borezée-Durant, et al. "Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism." Nucleic Acids Research 38, no. 19 (May 28, 2010): 6620–36. http://dx.doi.org/10.1093/nar/gkq462.

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14

Wang, Jing, Haoyuan Wang, Le Yang, Liping Lv, Zhe Zhang, Bin Ren, Lichun Dong, and Ning Li. "A novel riboregulator switch system of gene expression for enhanced microbial production of succinic acid." Journal of Industrial Microbiology & Biotechnology 45, no. 4 (February 5, 2018): 253–69. http://dx.doi.org/10.1007/s10295-018-2019-3.

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15

Durand, Sylvain, Adam Callan-Sidat, Josie McKeown, Stephen Li, Gergana Kostova, Juan R. Hernandez-Fernaud, Mohammad Tauqeer Alam, et al. "Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis." Nucleic Acids Research 49, no. 11 (June 7, 2021): 6399–419. http://dx.doi.org/10.1093/nar/gkab444.

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Abstract sRNAs are a taxonomically-restricted but transcriptomically-abundant class of post-transcriptional regulators. While of major importance for adaption to the environment, we currently lack global-scale methodology enabling target identification, especially in species without known RNA hub proteins (e.g. Hfq). Using psoralen RNA cross-linking and Illumina-sequencing we identify RNA–RNA interacting pairs in vivo in Bacillus subtilis, resolving previously well-described interactants. Although sRNA–sRNA pairings are rare (compared with sRNA–mRNA), we identify a robust example involving the conserved sRNA RoxS and an unstudied sRNA RosA (Regulator of sRNA A). We show RosA to be the first confirmed RNA sponge described in a Gram-positive bacterium. RosA interacts with at least two sRNAs, RoxS and FsrA. The RosA/RoxS interaction not only affects the levels of RoxS but also its processing and regulatory activity. We also found that the transcription of RosA is repressed by CcpA, the key regulator of carbon-metabolism in B. subtilis. Since RoxS is already known to be transcriptionally controlled by malate via the transcriptional repressor Rex, its post-transcriptional regulation by CcpA via RosA places RoxS in a key position to control central metabolism in response to varying carbon sources.

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16

Srivastava, Richa, Anantha-Barathi Muthukrishnan, and Guhan Jayaraman. "Design and Construction of a Synthetic Riboregulator-Based Platform for Metabolic Shunting of Pathways in Lactococcus lactis." Proceedings of the Singapore National Academy of Science 13, no. 01 (December 2019): 17–26. http://dx.doi.org/10.1142/s2591722619400027.

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Microbial cell factories are subjected to rewiring of basic metabolism to enhance the carbon flux towards the desired product pathway. Conventionally, this metabolic engineering approach often involves over-expression of pathway genes and knocking out genes in the competing pathways. However, these approaches result in severe metabolic burden and eventual poor performance of the cells. Particularly, where biomass formation and product synthesis depend on common precursors, permanent changes like knocking out genes will only result in poor titer. Hence, temporary decoupling of biomass formation and product synthesis is considered to be a potential alternative. In this study, we designed synthetic riboregulators, which are RNA-based genetic switches, to shunt metabolic pathways in Lactococcus lactis bacteria, a GRAS organism employed as a cell factory for many biocompounds. The riboregulators are then subjected to evaluation by tagging the cis-repressive sequence (crRNA) to mCherry, a fluorescent reporter and regulated by the constitutive promoter, [Formula: see text]. The trans-activating RNA (taRNA) that interacts with the crRNA is placed under the control of another inducible promoter, [Formula: see text]. First, we observed that when there is no induction of taRNA, there is negligible fluorescence of mCherry indicating the successful repression of translation by the cis-sequence as expected. This has been further verified by comparing this expression level with the expression level of [Formula: see text]-mCherry without the cis-sequence, using fluorometer. Results from this analysis suggest that there is [Formula: see text]% repression by the designed crRNA sequence. Next, we induced the cells with 2[Formula: see text]ng/mL of nisin in the mid-log phase. Upon induction, there is a maximum of three fold increase in the fluorescence levels when compared to the uninduced cells, suggesting that the trans-activation takes place inside the live cells. However, further studies are necessary to optimize the cis-trans ratio to achieve better dynamic range for expression modulation and time window for operating metabolic shunting of competing pathways successfully in L. lactis.

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17

Lebars, Isabelle, D. Martinez-Zapien, A. Durand, J. Coutant, B. Kieffer, and Anne-Catherine Dock-Bregeon. "HEXIM1 targets a repeated GAUC motif in the riboregulator of transcription 7SK and promotes base pair rearrangements." Nucleic Acids Research 38, no. 21 (July 31, 2010): 7749–63. http://dx.doi.org/10.1093/nar/gkq660.

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18

Valverde, Claudio, Magnus Lindell, E. Gerhart H. Wagner, and Dieter Haas. "A Repeated GGA Motif Is Critical for the Activity and Stability of the Riboregulator RsmY ofPseudomonas fluorescens." Journal of Biological Chemistry 279, no. 24 (March 18, 2004): 25066–74. http://dx.doi.org/10.1074/jbc.m401870200.

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19

Papenfort, Kai, Verena Pfeiffer, Sacha Lucchini, Avinash Sonawane, Jay C. D. Hinton, and Jörg Vogel. "Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis." Molecular Microbiology 68, no. 4 (May 2008): 890–906. http://dx.doi.org/10.1111/j.1365-2958.2008.06189.x.

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20

Shen, Ruizhong, and W. Allen Miller. "Subgenomic RNA as a riboregulator: negative regulation of RNA replication by Barley yellow dwarf virus subgenomic RNA 2." Virology 327, no. 2 (October 2004): 196–205. http://dx.doi.org/10.1016/j.virol.2004.06.025.

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21

Augagneur, Yoann, Alyssa N. King, Noëlla Germain‐Amiot, Mohamed Sassi, John W. Fitzgerald, Gyan S. Sahukhal, Mohamed O. Elasri, Brice Felden, and Shaun R. Brinsmade. "Analysis of the CodY RNome reveals RsaD as a stress‐responsive riboregulator of overflow metabolism in Staphylococcus aureus." Molecular Microbiology 113, no. 2 (December 16, 2019): 309–25. http://dx.doi.org/10.1111/mmi.14418.

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22

Aoki, Kazuma, Akira Harashima, Miho Sano, Takahide Yokoi, Shuji Nakamura, Masayoshi Kibata, and Tetsuro Hirose. "A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines." BMC Molecular Biology 11, no. 1 (2010): 99. http://dx.doi.org/10.1186/1471-2199-11-99.

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23

Ueno, Kinuko, Yuta Sakai, Chika Shono, Ippei Sakamoto, Kaori Tsukakoshi, Yukako Hihara, Koji Sode, and Kazunori Ikebukuro. "Applying a riboregulator as a new chromosomal gene regulation tool for higher glycogen production in Synechocystis sp. PCC 6803." Applied Microbiology and Biotechnology 101, no. 23-24 (October 16, 2017): 8465–74. http://dx.doi.org/10.1007/s00253-017-8570-4.

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24

Sando, Shinsuke, Atsushi Narita, Kenji Abe, and Yasuhiro Aoyama. "Doubly Catalytic Sensing of HIV-1-Related CCR5 Sequence in Prokaryotic Cell-Free Translation System using Riboregulator-Controlled Luciferase Activity." Journal of the American Chemical Society 127, no. 15 (April 2005): 5300–5301. http://dx.doi.org/10.1021/ja0507057.

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25

Rodrigo, Guillermo, Thomas E. Landrain, and Alfonso Jaramillo. "De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells." Proceedings of the National Academy of Sciences 109, no. 38 (September 4, 2012): 15271–76. http://dx.doi.org/10.1073/pnas.1203831109.

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A grand challenge in synthetic biology is to use our current knowledge of RNA science to perform the automatic engineering of completely synthetic sequences encoding functional RNAs in living cells. We report here a fully automated design methodology and experimental validation of synthetic RNA interaction circuits working in a cellular environment. The computational algorithm, based on a physicochemical model, produces novel RNA sequences by exploring the space of possible sequences compatible with predefined structures. We tested our methodology in Escherichia coli by designing several positive riboregulators with diverse structures and interaction models, suggesting that only the energy of formation and the activation energy (free energy barrier to overcome for initiating the hybridization reaction) are sufficient criteria to engineer RNA interaction and regulation in bacteria. The designed sequences exhibit nonsignificant similarity to any known noncoding RNA sequence. Our riboregulatory devices work independently and in combination with transcription regulation to create complex logic circuits. Our results demonstrate that a computational methodology based on first-principles can be used to engineer interacting RNAs with allosteric behavior in living cells.

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26

Laporte, P., F. Merchan, B. B. Amor, S. Wirth, and M. Crespi. "Riboregulators in plant development." Biochemical Society Transactions 35, no. 6 (November 23, 2007): 1638–42. http://dx.doi.org/10.1042/bst0351638.

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npcRNA (non-protein-coding RNAs) are an emerging class of regulators, so-called riboregulators, and include a large diversity of small RNAs [miRNAs (microRNAs)/siRNAs (small interfering RNAs)] that are involved in various developmental processes in plants and animals. In addition, several other npcRNAs encompassing various transcript sizes (up to several kilobases) have been identified using different genomic approaches. Much less is known about the mechanism of action of these other classes of riboregulators also present in the cell. The organogenesis of nitrogen-fixing nodules in legume plants is initiated in specific root cortical cells that express the npcRNA MtENOD40 (Medicago truncatula early nodulin 40). We have identified a novel RBP (RNA-binding protein), MtRBP1 (M. truncatula RBP 1), which interacts with the MtENOD40 RNA, and is exported into the cytoplasm during legume nodule development in the region expressing MtENOD40. A direct involvement of the MtENOD40 RNA in the relocalization of this RBP into cytoplasmic granules could be demonstrated, revealing a new RNA function in the cell. To extend these results, we searched for npcRNAs in the model plant Arabidopsis thaliana whose genome is completely known. We have identified 86 novel npcRNAs from which 27 corresponded to antisense RNAs of known coding regions. Using a dedicated ‘macroarray’ containing these npcRNAs and a collection of RBPs, we characterized their regulation in different tissues and plants subjected to environmental stresses. Most of the npcRNAs showed high variations in gene expression in contrast with the RBP genes. Recent large-scale analysis of the sRNA component of the transcriptome revealed an enormous diversity of siRNAs/miRNAs in the Arabidopsis genome. Bioinformatic analysis revealed that 34 large npcRNAs are precursors of siRNAs/miRNAs. npcRNAs, which are a sensitive component of the transcriptome, may reveal novel riboregulatory mechanisms involved in post-transcriptional control of differentiation or environmental responses.

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27

Robinson, Kirsten E., Jillian Orans, Alexander R. Kovach, Todd M. Link, and Richard G. Brennan. "Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching." Nucleic Acids Research 42, no. 4 (November 27, 2013): 2736–49. http://dx.doi.org/10.1093/nar/gkt1171.

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Abstract Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A15 and U6 RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)3A, (AU)3A and (AC)3A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)3G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)3G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)n distal face-binding motif should be redefined as an (A-A-N)n binding motif. TFQ data also demonstrated that the 5′-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus.

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28

Shen, Ruizhong, Aurélie M. Rakotondrafara, and W. Allen Miller. "trans Regulation of Cap-Independent Translation by a Viral Subgenomic RNA." Journal of Virology 80, no. 20 (October 15, 2006): 10045–54. http://dx.doi.org/10.1128/jvi.00991-06.

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ABSTRACT Many positive-strand RNA viruses generate 3′-coterminal subgenomic mRNAs to allow translation of 5′-distal open reading frames. It is unclear how viral genomic and subgenomic mRNAs compete with each other for the cellular translation machinery. Translation of the uncapped Barley yellow dwarf virus genomic RNA (gRNA) and subgenomic RNA1 (sgRNA1) is driven by the powerful cap-independent translation element (BTE) in their 3′ untranslated regions (UTRs). The BTE forms a kissing stem-loop interaction with the 5′ UTR to mediate translation initiation at the 5′ end. Here, using reporter mRNAs that mimic gRNA and sgRNA1, we show that the abundant sgRNA2 inhibits translation of gRNA, but not sgRNA1, in vitro and in vivo. This trans inhibition requires the functional BTE in the 5′ UTR of sgRNA2, but no translation of sgRNA2 itself is detectable. The efficiency of translation of the viral mRNAs in the presence of sgRNA2 is determined by proximity to the mRNA 5′ end of the stem-loop that kisses the 3′ BTE. Thus, the gRNA and sgRNA1 have “tuned” their expression efficiencies via the site in the 5′ UTR to which the 3′ BTE base pairs. We conclude that sgRNA2 is a riboregulator that switches off translation of replication genes from gRNA while permitting translation of structural genes from sgRNA1. These results reveal (i) a new level of control of subgenomic-RNA gene expression, (ii) a new role for a viral subgenomic RNA, and (iii) a new mechanism for RNA-mediated regulation of translation.

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29

Gildehaus, Nina, Thomas Neußer, Reinhild Wurm, and Rolf Wagner. "Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts." Nucleic Acids Research 35, no. 6 (March 1, 2007): 1885–96. http://dx.doi.org/10.1093/nar/gkm085.

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30

Rusk, Nicole. "De novo–designed riboregulators." Nature Methods 11, no. 12 (November 25, 2014): 1192. http://dx.doi.org/10.1038/nmeth.3197.

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31

Micura, Ronald. "Programmable Ligand-Controlled Riboregulators." Angewandte Chemie International Edition 45, no. 1 (January 2006): 30–31. http://dx.doi.org/10.1002/anie.200502700.

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32

Fantappiè, Laura, Matteo M. E. Metruccio, Kate L. Seib, Francesca Oriente, Elena Cartocci, Francesca Ferlicca, Marzia M. Giuliani, Vincenzo Scarlato, and Isabel Delany. "The RNA Chaperone Hfq Is Involved in Stress Response and Virulence in Neisseria meningitidis and Is a Pleiotropic Regulator of Protein Expression." Infection and Immunity 77, no. 5 (February 17, 2009): 1842–53. http://dx.doi.org/10.1128/iai.01216-08.

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ABSTRACT The well-conserved protein Hfq has emerged as the key modulator of riboregulation in bacteria. This protein is thought to function as an RNA chaperone and to facilitate base pairing between small regulatory RNA (sRNA) and mRNA targets, and many sRNAs are dependent on the Hfq protein for their regulatory functions. To address the possible role of Hfq in riboregulated circuits in Neisseria meningitidis, we generated an Hfq mutant of the MC58 strain, and the knockout mutant has pleiotropic phenotypes; it has a general growth phenotype in vitro in culture media, and it is sensitive to a wide range of stresses, including those that it may encounter in the host. Furthermore, the expression profile of a vast number of proteins is clearly altered in the mutant, and we have identified 27 proteins by proteomics. All of the phenotypes tested to date are also restored by complementation of Hfq expression in the mutant strain. Importantly, in ex vivo and in vivo models of infection the Hfq mutant is attenuated. These data indicate that Hfq plays a key role in stress response and virulence, and we propose a major role for Hfq in regulation of gene expression. Moreover, this study suggests that in meningococcus there is a large Hfq-mediated sRNA network which so far is largely unexplored.

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33

Micura, Ronald. "Programmierbare Ligand-kontrollierte Riboregulatoren." Angewandte Chemie 118, no. 1 (January 2006): 32–34. http://dx.doi.org/10.1002/ange.200502700.

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34

Erdmann, V. A. "The non-coding RNAs as riboregulators." Nucleic Acids Research 29, no. 1 (January 1, 2001): 189–93. http://dx.doi.org/10.1093/nar/29.1.189.

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35

Karolina, Dwi Setyowati, E. M. Wintour, John Bertram, and Kandiah Jeyaseelan. "Riboregulators in kidney development and function." Biochimie 92, no. 3 (March 2010): 217–25. http://dx.doi.org/10.1016/j.biochi.2009.12.008.

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36

Büscher, Magdalena, Rastislav Horos, and Matthias W. Hentze. "‘High vault-age’: non-coding RNA control of autophagy." Open Biology 10, no. 2 (February 2020): 190307. http://dx.doi.org/10.1098/rsob.190307.

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RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the protein's function. We refer to this process as ‘riboregulation'. Here, we discuss this newly uncovered vault RNA function against the background of three decades of vault RNA research. We highlight the vtRNA1-1-p62 interaction as an example of riboregulation of a key cellular process.

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37

Minuesa, Gerard, Cristina Alsina, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, and Ivan Dotu. "MoiRNAiFold: a novel tool for complex in silico RNA design." Nucleic Acids Research 49, no. 9 (May 6, 2021): 4934–43. http://dx.doi.org/10.1093/nar/gkab331.

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Abstract Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/).

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Sakamoto, Ippei, Koichi Abe, Sumiya Kawai, Kaori Tsukakoshi, Yuta Sakai, Koji Sode, and Kazunori Ikebukuro. "Improving the induction fold of riboregulators for cyanobacteria." RNA Biology 15, no. 3 (February 1, 2018): 353–58. http://dx.doi.org/10.1080/15476286.2017.1422470.

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Bayer, Travis S., and Christina D. Smolke. "Programmable ligand-controlled riboregulators of eukaryotic gene expression." Nature Biotechnology 23, no. 3 (February 20, 2005): 337–43. http://dx.doi.org/10.1038/nbt1069.

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40

Becker, Anke, Aaron Overlöper, Jan-Philip Schlüter, Jan Reinkensmeier, Marta Robledo, Robert Giegerich, Franz Narberhaus, and Elena Evguenieva-Hackenberg. "Riboregulation in plant-associated α-proteobacteria." RNA Biology 11, no. 5 (May 2014): 550–62. http://dx.doi.org/10.4161/rna.29625.

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Robledo, Marta, Natalia I. García-Tomsig, and José I. Jiménez-Zurdo. "Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria." Microorganisms 8, no. 3 (March 10, 2020): 384. http://dx.doi.org/10.3390/microorganisms8030384.

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Abstract:

Small non-coding RNAs (sRNAs) are ubiquitous components of bacterial adaptive regulatory networks underlying stress responses and chronic intracellular infection of eukaryotic hosts. Thus, sRNA-mediated regulation of gene expression is expected to play a major role in the establishment of mutualistic root nodule endosymbiosis between nitrogen-fixing rhizobia and legume plants. However, knowledge about this level of genetic regulation in this group of plant-interacting bacteria is still rather scarce. Here, we review insights into the rhizobial non-coding transcriptome and sRNA-mediated post-transcriptional regulation of symbiotic relevant traits such as nutrient uptake, cell cycle, quorum sensing, or nodule development. We provide details about the transcriptional control and protein-assisted activity mechanisms of the functionally characterized sRNAs involved in these processes. Finally, we discuss the forthcoming research on riboregulation in legume symbionts.

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42

Ellis, Michael J., and David B. Haniford. "Riboregulation of bacterial and archaeal transposition." Wiley Interdisciplinary Reviews: RNA 7, no. 3 (February 4, 2016): 382–98. http://dx.doi.org/10.1002/wrna.1341.

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Cayrol, Bastien, Emilie Fortas, Claire Martret, Grzegorz Cech, Anna Kloska, Stephane Caulet, Marion Barbet, et al. "Riboregulation of the bacterial actin-homolog MreB by DsrA small noncoding RNA." Integrative Biology 7, no. 1 (2015): 128–41. http://dx.doi.org/10.1039/c4ib00102h.

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Hess, Wolfgang R., Bork A. Berghoff, Annegret Wilde, Claudia Steglich, and Gabriele Klug. "Riboregulators and the role of Hfq in photosynthetic bacteria." RNA Biology 11, no. 5 (February 10, 2014): 413–26. http://dx.doi.org/10.4161/rna.28035.

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Goss, Dixie J., and Elizabeth C. Theil. "Iron Responsive mRNAs: A Family of Fe2+Sensitive Riboregulators." Accounts of Chemical Research 44, no. 12 (December 20, 2011): 1320–28. http://dx.doi.org/10.1021/ar2001149.

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Isaacs, Farren J., Daniel J. Dwyer, Chunming Ding, Dmitri D. Pervouchine, Charles R. Cantor, and James J. Collins. "Engineered riboregulators enable post-transcriptional control of gene expression." Nature Biotechnology 22, no. 7 (June 20, 2004): 841–47. http://dx.doi.org/10.1038/nbt986.

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Callura, J. M., D. J. Dwyer, F. J. Isaacs, C. R. Cantor, and J. J. Collins. "Tracking, tuning, and terminating microbial physiology using synthetic riboregulators." Proceedings of the National Academy of Sciences 107, no. 36 (August 16, 2010): 15898–903. http://dx.doi.org/10.1073/pnas.1009747107.

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Hong, Fan, Duo Ma, Kaiyue Wu, Lida A. Mina, Rebecca C. Luiten, Yan Liu, Hao Yan, and Alexander A. Green. "Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators." Cell 180, no. 5 (March 2020): 1018–32. http://dx.doi.org/10.1016/j.cell.2020.02.011.

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Hong, Fan, Duo Ma, Kaiyue Wu, Lida A. Mina, Rebecca C. Luiten, Yan Liu, Hao Yan, and Alexander A. Green. "Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators." Cell 183, no. 3 (October 2020): 835–36. http://dx.doi.org/10.1016/j.cell.2020.10.020.

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Rodrigo, G., and A. Jaramillo. "RiboMaker: computational design of conformation-based riboregulation." Bioinformatics 30, no. 17 (May 14, 2014): 2508–10. http://dx.doi.org/10.1093/bioinformatics/btu335.

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