A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

AbstractRiboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by recognizing a specific cellular effector. Although nearly 50 riboswitch classes are known, only a handful recognize multiple effectors. Here, we report the 2.60-Å resolution co-crystal structure of a class I type I preQ1-sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. Stacked effector recognition appears to be a hallmark of the largest subgroup of preQ1 riboswitches, including those from pathogens such as Neisseria gonorrhoeae. We postulate that binding to stacked effectors arose in the RNA World to closely position two substrates for RNA-mediated catalysis. These findings expand known effector recognition capabilities of riboswitches and have implications for antimicrobial development.

Download Full-text

The TWIST1-centered competing endogenous RNA network promotes proliferation, invasion, and migration of lung adenocarcinoma

Oncogenesis ◽

10.1038/s41389-019-0167-6 ◽

2019 ◽

Vol 8 (11) ◽

Cited By ~ 4

Author(s):

Wenjie Xia ◽

Qixing Mao ◽

Bing Chen ◽

Lin Wang ◽

Weidong Ma ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Migration And Invasion ◽

Circular Rnas ◽

Messenger Rnas ◽

Competing Endogenous Rna ◽

Invasion And Migration ◽

Non Coding Rnas ◽

And Migration

Abstract The proposed competing endogenous RNA (ceRNA) mechanism suggested that diverse RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs could communicate with each other by competing for binding to shared microRNAs. The ceRNA network (ceRNET) is involved in tumor progression and has become a hot research topic in recent years. To date, more attention has been paid to the role of non-coding RNAs in ceRNA crosstalk. However, coding transcripts are more abundant and powerful than non-coding RNAs and make up the majority of miRNA targets. In this study, we constructed a mRNA-mRNA related ceRNET of lung adenocarcinoma (LUAD) and identified the highlighted TWIST1-centered ceRNET, which recruits SLC12A5 and ZFHX4 as its ceRNAs. We found that TWIST1/SLC12A5/ZFHX4 are all upregulated in LUAD and are associated with poorer prognosis. SLC12A5 and ZFHX4 facilitated proliferation, migration, and invasion in vivo and in vitro, and their effects were reversed by miR-194–3p and miR-514a-3p, respectively. We further verified that SLC12A5 and ZFHX4 affected the function of TWIST1 by acting as ceRNAs. In summary, we constructed a mRNA-mRNA related ceRNET for LUAD and highlighted the well-known oncogene TWIST1. Then we verified that SLC12A5 and ZFHX4 exert their oncogenic function by regulating TWIST1 expression through a ceRNA mechanism.

Download Full-text

Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes

Nucleic Acids Research ◽

10.1093/nar/gkaa187 ◽

2020 ◽

Vol 48 (9) ◽

pp. 5054-5064 ◽

Cited By ~ 2

Author(s):

Amelia Cervera ◽

Marcos de la Peña

Keyword(s):

Rna World ◽

Hammerhead Ribozyme ◽

Circular Rnas ◽

Classical Type ◽

Type I ◽

Ltr Retrotransposons ◽

Animal Tissues ◽

Catalytic Rnas ◽

Human Genomes

Abstract Ribozymes are catalytic RNAs present in modern genomes but regarded as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of animals are contained within a novel family of non-autonomous non-LTR retrotransposons of the retrozyme class. These retroelements are expressed as abundant linear and circular RNAs of ∼170-400 nt in different animal tissues. Bioinformatic and in vitro analyses indicate an efficient self-cleavage of the HHRs harboured in most invertebrate retrozymes, whereas HHRs in retrozymes of vertebrates, such as the axolotl and other amphibians, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which opens the door for the development of new tools in the emerging field of study of circRNAs.

Download Full-text

EDTA treatment diminishes the antibacterial and anti-adherence effect of calcium hydroxide on Enterococcus faecalis: an in vitro study

Biofilms ◽

10.1017/s147905050800224x ◽

2008 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

S. George ◽

A. Kishen

Keyword(s):

Cell Surface ◽

Calcium Hydroxide ◽

Enterococcus Faecalis ◽

Type I Collagen ◽

Membrane Integrity ◽

Cell Surface Hydrophobicity ◽

Prior Exposure ◽

Type I ◽

Bacterial Cells

ABSTRACTThis study sought to understand the cell surface characteristics, viability and biofilm-forming potential ofEnterococcus faecaliscells sequentially exposed to EDTA and calcium hydroxide, as in endodontic treatment. Bacterial cells exposed to EDTA and calcium hydroxide were assayed for cell viability, membrane integrity, cell surface hydrophobicity and surface charge, while alteration in the surface topography ofE. faecaliscells was examined using atomic force microscopy (AFM). The bacterial adherence potential to type I collagen was also examined to assess the biofilm-forming capacity ofE. faecaliscells exposed to EDTA and calcium hydroxide. It was found that calcium hydroxide treatment reduced the viability ofE. faecalis. However, prior exposure to EDTA significantly reduced the antibacterial effect of calcium hydroxide (P< 0.05). Calcium hydroxide treatment resulted in impaired cell wall morphology, observed as increased surface roughness and pore formation under AFM. However, these topographical changes induced by calcium hydroxide were significantly reduced in EDTA pretreated cells (P< 0.05). Calcium hydroxide treatment caused reduction in hydrophobicity and adherence ofE. faecalisto type I collagen. These effects due to calcium hydroxide were also significantly altered in EDTA-pretreated cells (P< 0.001). The findings from this study showed that the antibacterial and anti-adherence effect of calcium hydroxide was diminished by prior exposure ofE. faecaliscells to EDTA.

Download Full-text

Small circRNAs with self-cleaving ribozymes are frequently expressed in metazoan transcriptomes

10.1101/721605 ◽

2019 ◽

Author(s):

Amelia Cervera ◽

Marcos De la Pena

Keyword(s):

Rna World ◽

Hammerhead Ribozyme ◽

Circular Rnas ◽

Classical Type ◽

Type I ◽

Ltr Retrotransposons ◽

Animal Tissues ◽

Catalytic Rnas ◽

Human Genomes

Ribozymes are catalytic RNAs present in modern genomes but considered as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of diverse animals are contained within a novel family of non-autonomous non-LTR retrotransposons. These retroelements are expressed as abundant linear and circular RNAs of ~170-400 nt in different animal tissues. In vitro analyses confirm an efficient self-cleavage of the HHRs harboured in invertebrate retrozymes, whereas those in retrozymes of vertebrates, such as the axolotl, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, in eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which will allow the development of biotechnological tools in the emerging field of circRNAs.

Download Full-text

Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA

10.1101/2021.08.14.456336 ◽

2021 ◽

Author(s):

Xi Mou ◽

Shiau Wei Liew ◽

Chun Kit Kwok

Keyword(s):

High Specificity ◽

Messenger Rnas ◽

Functional Roles ◽

Cellular Processes ◽

Multiple Strategies ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Nuclear Cell

RNA G-quadruplexes (rG4s) have functional roles in many cellular processes in diverse organisms. While a number of rG4 examples have been reported in coding messenger RNAs (mRNA), so far only limited works have studied rG4s in non-coding RNAs (ncRNAs), especially in long non-coding RNAs (lncRNAs) that are of emerging interest and significance in biology. Herein, we report that MALAT1 lncRNA contains conserved rG4 motifs, forming thermostable rG4 structures with parallel topology. We also show that rG4s in MALAT1 lncRNA can interact with NONO protein with high specificity and affinity in vitro and in nuclear cell lysate, and we provide in vivo data to support that NONO protein recognizes MALAT1 lncRNA via rG4 motifs. Notably, we demonstrate that rG4s in MALAT1 lncRNA can be targeted by rG4-specific small molecule, peptide, and L-aptamer, leading to the dissociation of MALAT1 rG4-NONO protein interaction. Altogether, this study uncovers new and important rG4s in MALAT1 lncRNAs, reveals their specific interactions with NONO protein, offers multiple strategies for targeting MALAT1 and its RNA-protein complex via its rG4 structure, and illustrates the prevalence and significance of rG4s in ncRNAs.

Download Full-text

The rapamycin sensitivity of human T-cell leukaemia virus type I-induced T-cell proliferation is mediated independently of the polypyrimidine motifs in the 5′ long terminal repeat

Journal of General Virology ◽

10.1099/0022-1317-82-2-435 ◽

2001 ◽

Vol 82 (2) ◽

pp. 435-439 ◽

Cited By ~ 2

Author(s):

Nicola J. Rose ◽

Andrew M. L. Lever

Keyword(s):

T Cell ◽

Long Terminal Repeat ◽

Virus Type ◽

Terminal Repeat ◽

Cell Leukaemia ◽

Type I ◽

Messenger Rnas ◽

Leukaemia Virus ◽

Human T Cell

The immunosuppressant rapamycin can regulate the translation of a subset of messenger RNAs, a phenotype which has been linked to the presence of a polypyrimidine motif [C(N)4–14] downstream of the mRNA cap structure. T-cell clones naturally infected with transcriptionally active human T-cell leukaemia virus, type I (HTLV-I) undergo autologous proliferation; this phenotype is inhibited by rapamycin but not FK506, which reverses the rapamycin effect. Within the R region of the HTLV-I 5′ long terminal repeat (LTR) there are seven polypyrimidine motifs. We sought to determine if these were involved in the sensitivity of proliferation to the presence of rapamycin. Here we illustrate the generation of an in vitro model of this rapamycin-sensitivity and the analysis of LTR mutants which were created to determine the importance of the polypyrimidine motifs. Reporter gene assays suggest the effect is independent of the polypyrimidine motifs in the virus leader sequence.

Download Full-text

Collagen fibrillogenesis in vitro: interaction of types I and V collagen

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100142670 ◽

1986 ◽

Vol 44 ◽

pp. 210-211

Author(s):

Arthur J. Wasserman ◽

Kathy C. Kloos ◽

David E. Birk

Keyword(s):

Type I Collagen ◽

Corneal Stroma ◽

Minor Component ◽

Homogeneous Distribution ◽

Type I ◽

Type V Collagen ◽

Fibril Morphology ◽

Type V ◽

In Vitro Interaction

Type I collagen is the predominant collagen in the cornea with type V collagen being a quantitatively minor component. However, the content of type V collagen (10-20%) in the cornea is high when compared to other tissues containing predominantly type I collagen. The corneal stroma has a homogeneous distribution of these two collagens, however, immunochemical localization of type V collagen requires the disruption of type I collagen structure. This indicates that these collagens may be arranged as heterpolymeric fibrils. This arrangement may be responsible for the control of fibril diameter necessary for corneal transparency. The purpose of this work is to study the in vitro assembly of collagen type V and to determine whether the interactions of these collagens influence fibril morphology.

Download Full-text

Plasminogen Activation in Diabetes Mellitus: Normalization of Blood Sugar Levels Improves Impaired Enzyme Kinetics In Vitro

Thrombosis and Haemostasis ◽

10.1055/s-0038-1657861 ◽

1985 ◽

Vol 54 (02) ◽

pp. 413-414 ◽

Cited By ~ 10

Author(s):

Margarethe Geiger ◽

Bernd R Binder

Keyword(s):

Plasminogen Activator ◽

Blood Sugar ◽

Metabolic Disorders ◽

Normal Values ◽

Diabetic Patients ◽

Type I ◽

Plasminogen Activation ◽

Lag Period ◽

Sugar Levels

SummaryWe have demonstrated previously that fibrin enhanced plasmin formation by the vascular plasminogen activator was significantly impaired, when components isolated from the plasma of three uncontrolled diabetic patients (type I) were used to study plasminogen activation in vitro. In the present study it can be demonstrated that functional properties of the vascular plasminogen activators as well as of the plasminogens from the same three diabetic patients are significantly improved after normalization of blood sugar levels and improvement of HbAlc values. Most pronounced the Km of diabetic vascular plasminogen activator in the presence of fibrin returned to normal values, and for diabetic plasminogen the prolonged lag period until maximal plasmin formation occurred was shortened to almost control values. From these data we conclude that the observed abnormalities of in vitro fibrinolysis are not primarily associated with the diabetic disease, but might be secondary to metabolic disorders caused by diabetes.

Download Full-text