scholarly journals Opposing Effects of Polyadenylation on the Stability of Edited and Unedited Mitochondrial RNAs in Trypanosoma brucei

2005 ◽  
Vol 25 (5) ◽  
pp. 1634-1644 ◽  
Author(s):  
Chia-Ying Kao ◽  
Laurie K. Read
Keyword(s):  
Trypanosoma Brucei ◽  
Rna Stability ◽  
Protein S ◽  
Rna Degradation ◽  
Nucleotide Composition ◽  
Rna Turnover ◽  
Degradation Reactions ◽  
The Stability ◽  
Opposing Effects

ABSTRACT Mitochondrial RNAs in Trypanosoma brucei undergo posttranscriptional RNA editing and polyadenylation. We previously showed that polyadenylation stimulates turnover of unedited RNAs. Here, we investigated the role of polyadenylation in decay of edited RPS12 RNA. In in vitro turnover assays, nonadenylated fully edited RNA degrades significantly faster than its unedited counterpart. Rapid turnover of nonadenylated RNA is facilitated by editing at just six editing sites. Surprisingly, in direct contrast to unedited RNA, turnover of fully edited RNA is dramatically slowed by addition of a poly(A)20 tail. The same minimal edited sequence that stimulates decay of nonadenylated RNA is sufficient to switch the poly(A) tail from a destabilizing to a stabilizing element. Both nucleotide composition and length of the 3′ extension are important for stabilization of edited RNA. Titration of poly(A) into RNA degradation reactions has no effect on turnover of polyadenylated edited RNA. These results suggest the presence of a protective protein(s) that simultaneously recognizes the poly(A) tail and small edited element and which blocks the action of a 3′-5′ exonuclease. This study provides the first evidence for opposing effects of polyadenylation on RNA stability within a single organelle and suggests a novel and unique regulation of RNA turnover in this system.

scholarly journals Differential regulation of two distinct families of glucose transporter genes in Trypanosoma brucei.

1993 ◽  
Vol 13 (2) ◽  
pp. 1146-1154 ◽  
Author(s):  
F Bringaud ◽  
T Baltz
Keyword(s):  
Trypanosoma Brucei ◽  
Xenopus Oocytes ◽  
Glucose Transporter ◽  
Protein S ◽  
Life Cycle Stage ◽  
Good Target ◽  
Hexose Transporters ◽  
Moderate Sensitivity ◽  
Mrna Analysis

A tandemly arranged multigene family encoding putative hexose transporters in Trypanosoma brucei has been characterized. It is composed of two 80% homologous groups of genes called THT1 (six copies) and THT2 (five copies). When Xenopus oocytes are microinjected with in vitro-transcribed RNA from a THT1 gene, they express a glucose transporter with properties similar to those of the trypanosome bloodstream-form protein(s). This THT1-encoded transport system for glucose differs from the human erythrocyte-type glucose transporter by its moderate sensitivity to cytochalasin B and its capacity to transport D-fructose. These properties suggest that the trypanosomal transporter may be a good target for antitrypanosomal drugs. mRNA analysis revealed that expression of these genes was life cycle stage dependent. Bloodstream forms express 40-fold more THT1 than THT2. In contrast, procyclic trypanosomes express no detectable THT1 but demonstrate glucose-dependent expression of THT2.

Protein synthesis is required for rapid degradation of tubulin mRNA and other deflagellation-induced RNAs in Chlamydomonas reinhardi

1986 ◽  
Vol 6 (1) ◽  
pp. 54-61
Author(s):  
E J Baker ◽  
L R Keller ◽  
J A Schloss ◽  
J L Rosenbaum
Keyword(s):  
Protein Synthesis ◽  
Transcriptional Control ◽  
Protein S ◽  
Protein Synthesis Inhibitors ◽  
Control Factors ◽  
Flagellar Proteins ◽  
The Stability ◽  
And Control

After flagellar detachment in Chlamydomonas reinhardi, there is a rapid synthesis and accumulation of mRNAs for tubulin and other flagellar proteins. Maximum levels of these mRNAs (flagellar RNAs) are reached within 1 h after deflagellation, after which they are rapidly degraded to their predeflagellation levels. The degradation of alpha- and beta-tubulin RNAs was shown to be due to the shortening of their half-lives after accumulation (Baker et al., J. Cell Biol. 99:2074-2081, 1984). Deflagellation in the presence of protein synthesis inhibitors results in the accumulation of tubulin and other flagellar mRNAs by kinetics similar to those of controls. However, unlike controls, in which the accumulated mRNAs are rapidly degraded, these mRNAs are stabilized in cycloheximide. The stabilization by cycloheximide is specific for the flagellar mRNAs accumulated after deflagellation, since there is no change in the levels of flagellar mRNAs in nondeflagellated (uninduced) cells in the presence of cycloheximide. The kinetics of flagellar mRNA synthesis after deflagellation are shown to be the same in cycloheximide-treated and control cells by in vivo labeling and in vitro nuclear runoff experiments. These results show that protein synthesis is not required for the induced synthesis of flagellar mRNAs, and that all necessary transcriptional control factors are present in the cell before deflagellation, but that protein synthesis is required for the accelerated degradation of the accumulated flagellar mRNAs. Since cycloheximide prevents the induced synthesis and accumulation of flagellar proteins, it is possible that the product(s) of protein synthesis required for the accelerated decay of these mRNAs is a flagellar protein(s). The possibility that one or more flagellar proteins autoregulate the stability of the flagellar mRNAs is discussed.

scholarly journals UTP-Dependent and -Independent Pathways of mRNA Turnover in Trypanosoma brucei Mitochondria

2000 ◽  
Vol 20 (7) ◽  
pp. 2308-2316 ◽  
Author(s):  
Kevin T. Militello ◽  
Laurie K. Read
Keyword(s):  
Steady State ◽  
Trypanosoma Brucei ◽  
Mitochondrial Gene ◽  
Rna Stability ◽  
Degradation Pathway ◽  
Mitochondrial Rna ◽  
In Organello ◽  
Steady State Levels ◽  
The Stability ◽  
Mrna Polyadenylation

ABSTRACT Although primary transcripts are polycistronic in the mitochondria of Trypanosoma brucei, steady-state levels of mature, monocistronic RNAs change throughout the parasitic life cycle. This indicates that steady-state RNA abundance is controlled by posttranscriptional mechanisms involving differential RNA stability. In this study, in organello pulse-chase labeling experiments were used to analyze the stability of different T. brucei mitochondrial RNA populations. In this system, total RNA and rRNA are stable for many hours. In contrast, mRNAs can be degraded by two biochemically distinct turnover pathways. The first pathway results in the rapid degradation of mRNA (half-life [t 1/2] of 11 to 18 min) and is dependent upon the presence of an mRNA poly(A) tail. Remarkably, this pathway also requires the addition of UTP and therefore is termed UTP dependent. The second pathway results in slow turnover of mitochondrial mRNA (t 1/2 of ∼3 h) and is not dependent upon the presence of an mRNA poly(A) tail or the addition of exogenous UTP. In summary, these results demonstrate the presence of a novel, UTP-dependent degradation pathway for T. bruceimitochondrial mRNAs and reveal an unprecedented role for both UTP and mRNA polyadenylation in T. brucei mitochondrial gene expression.

scholarly journals Protein synthesis is required for rapid degradation of tubulin mRNA and other deflagellation-induced RNAs in Chlamydomonas reinhardi.

1986 ◽  
Vol 6 (1) ◽  
pp. 54-61 ◽  
Author(s):  
E J Baker ◽  
L R Keller ◽  
J A Schloss ◽  
J L Rosenbaum
Keyword(s):  
Protein Synthesis ◽  
Transcriptional Control ◽  
Protein S ◽  
Protein Synthesis Inhibitors ◽  
Control Factors ◽  
Flagellar Proteins ◽  
The Stability ◽  
And Control

After flagellar detachment in Chlamydomonas reinhardi, there is a rapid synthesis and accumulation of mRNAs for tubulin and other flagellar proteins. Maximum levels of these mRNAs (flagellar RNAs) are reached within 1 h after deflagellation, after which they are rapidly degraded to their predeflagellation levels. The degradation of alpha- and beta-tubulin RNAs was shown to be due to the shortening of their half-lives after accumulation (Baker et al., J. Cell Biol. 99:2074-2081, 1984). Deflagellation in the presence of protein synthesis inhibitors results in the accumulation of tubulin and other flagellar mRNAs by kinetics similar to those of controls. However, unlike controls, in which the accumulated mRNAs are rapidly degraded, these mRNAs are stabilized in cycloheximide. The stabilization by cycloheximide is specific for the flagellar mRNAs accumulated after deflagellation, since there is no change in the levels of flagellar mRNAs in nondeflagellated (uninduced) cells in the presence of cycloheximide. The kinetics of flagellar mRNA synthesis after deflagellation are shown to be the same in cycloheximide-treated and control cells by in vivo labeling and in vitro nuclear runoff experiments. These results show that protein synthesis is not required for the induced synthesis of flagellar mRNAs, and that all necessary transcriptional control factors are present in the cell before deflagellation, but that protein synthesis is required for the accelerated degradation of the accumulated flagellar mRNAs. Since cycloheximide prevents the induced synthesis and accumulation of flagellar proteins, it is possible that the product(s) of protein synthesis required for the accelerated decay of these mRNAs is a flagellar protein(s). The possibility that one or more flagellar proteins autoregulate the stability of the flagellar mRNAs is discussed.

scholarly journals Comprehensive Pan-Cancer Analysis of the Prognostic and Immunological Roles of the METTL3/lncRNA-SNHG1/miRNA-140-3p/UBE2C Axis

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiulin Jiang ◽  
Yixiao Yuan ◽  
Lin Tang ◽  
Juan Wang ◽  
Qianqian Liu ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Immune Cell ◽  
Critical Role ◽  
Clinical Importance ◽  
Prognostic Indicator ◽  
Rna Degradation ◽  
Regulation Mechanism ◽  
The Stability ◽  
Pan Cancer

Growing evidence has demonstrated that UBE2C plays a critical role in cancer progression, but there is no study focusing on the prognosis, upstream regulation mechanism, and immunological roles of UBE2C across diverse tumor types. In this study, we found that UBE2C was elevated in this human pan-cancer analysis, and high expression of UBE2C was correlated with poor prognosis. In addition, UBE2C expression was markedly associated with tumor mutation burden (TMB), microsatellite instability (MSI), immune cell infiltration, and diverse drug sensitivities. Finally, we showed that the METTL3/SNHG1/miRNA-140-3p axis could potentially regulate UBE2C expression. N(6)-Methyladenosine (m6A) modifications improved the stability of methylated SNHG1 transcripts by decreasing the rate of RNA degradation, which lead to upregulation of SNHG1 in non-small cell lung cancer (NSCLC). In vitro functional experiments showed that SNHG1, as a competing endogenous RNA, sponges miR-140-3p to increase UBE2C expression in NSCLC cell lines. Our study elucidates the clinical importance and regulatory mechanism of the METTL3/SNHG1/miRNA-140-3p/UBE2C axis in NSCLC and provides a prognostic indicator, as well as a promising therapeutic target for patients with NSCLC.

scholarly journals Principles of mRNA control by human PUM proteins elucidated from multi-modal experiments and integrative data analysis

2020 ◽  
Author(s):  
Michael B. Wolfe ◽  
Trista L. Schagat ◽  
Michelle T. Paulsen ◽  
Brian Magnuson ◽  
Mats Ljungman ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Rna Stability ◽  
Decay Rates ◽  
Metabolic Labeling ◽  
Rna Turnover ◽  
Regulate Gene Expression ◽  
Recognition Element ◽  
Rna Targets ◽  
Functional Regulation

AbstractThe human PUF-family proteins, PUM1 and PUM2, post-transcriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3’ UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a ‘rulebook’ of key contextual features that differentiate functional vs. non-functional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.

Differential regulation of two distinct families of glucose transporter genes in Trypanosoma brucei

1993 ◽  
Vol 13 (2) ◽  
pp. 1146-1154
Author(s):  
F Bringaud ◽  
T Baltz
Keyword(s):  
Trypanosoma Brucei ◽  
Xenopus Oocytes ◽  
Glucose Transporter ◽  
Protein S ◽  
Life Cycle Stage ◽  
Good Target ◽  
Hexose Transporters ◽  
Moderate Sensitivity ◽  
Mrna Analysis

A tandemly arranged multigene family encoding putative hexose transporters in Trypanosoma brucei has been characterized. It is composed of two 80% homologous groups of genes called THT1 (six copies) and THT2 (five copies). When Xenopus oocytes are microinjected with in vitro-transcribed RNA from a THT1 gene, they express a glucose transporter with properties similar to those of the trypanosome bloodstream-form protein(s). This THT1-encoded transport system for glucose differs from the human erythrocyte-type glucose transporter by its moderate sensitivity to cytochalasin B and its capacity to transport D-fructose. These properties suggest that the trypanosomal transporter may be a good target for antitrypanosomal drugs. mRNA analysis revealed that expression of these genes was life cycle stage dependent. Bloodstream forms express 40-fold more THT1 than THT2. In contrast, procyclic trypanosomes express no detectable THT1 but demonstrate glucose-dependent expression of THT2.

scholarly journals RNase/Anti-RNase Activities of the Bacterial parD Toxin-Antitoxin System

2005 ◽  
Vol 187 (9) ◽  
pp. 3151-3157 ◽  
Author(s):  
Ana J. Muñoz-Gómez ◽  
Marc Lemonnier ◽  
Sandra Santos-Sierra ◽  
Alfredo Berzal-Herranz ◽  
Ramón Díaz-Orejas
Keyword(s):  
Protein Synthesis ◽  
Dna Replication ◽  
Rna Degradation ◽  
Double Stranded Rna ◽  
Cellular Processes ◽  
Inhibition Of Protein Synthesis ◽  
Reticulocyte Lysates ◽  
The Stability ◽  
Cole1 Replication

ABSTRACT The bacterial parD toxin-antitoxin system of plasmid R1 encodes two proteins, the Kid toxin and its cognate antitoxin, Kis. Kid cleaves RNA and inhibits protein synthesis and cell growth in Escherichia coli. Here, we show that Kid promotes RNA degradation and inhibition of protein synthesis in rabbit reticulocyte lysates. These new activities of the Kid toxin were counteracted by the Kis antitoxin and were not displayed by the KidR85W variant, which is nontoxic in E. coli. Moreover, while Kid cleaved single- and double-stranded RNA with a preference for UAA or UAC triplets, KidR85W maintained this sequence preference but hardly cleaved double-stranded RNA. Kid was formerly shown to inhibit DNA replication of the ColE1 plasmid. Here we provide in vitro evidence that Kid cleaves the ColE1 RNA II primer, which is required for the initiation of ColE1 replication. In contrast, KidR85W did not affect the stability of RNA II, nor did it inhibit the in vitro replication of ColE1. Thus, the endoribonuclease and the cytotoxic and DNA replication-inhibitory activities of Kid seem tightly correlated. We propose that the spectrum of action of this toxin extends beyond the sole inhibition of protein synthesis to control a broad range of RNA-regulated cellular processes.

scholarly journals The Vc2 cyclic di-GMP dependent riboswitch ofVibrio choleraeregulates expression of an upstream small RNA by controlling RNA stability

2019 ◽  
Author(s):  
Benjamin R. Pursley ◽  
Christopher M. Waters
Keyword(s):  
Gene Regulation ◽  
Vibrio Cholerae ◽  
Small Rnas ◽  
Molecular Mechanisms ◽  
Rna Stability ◽  
Second Messenger ◽  
Rna Degradation ◽  
Transcriptional Termination ◽  
The Stability ◽  
Messenger Molecule

SUMMARYCyclic di-GMP (c-di-GMP) is a bacterial second messenger molecule that is important in the biology ofVibrio cholerae, but the molecular mechanisms by which this molecule regulates downstream phenotypes have not been fully characterized. We have previously shown that the Vc2 c-di-GMP-binding riboswitch, encoded upstream of the genetfoY, functions as an off-switch in response to c-di-GMP. However, the mechanism by which c-di-GMP controls expression oftfoYhas not been fully elucidated. During our studies of this mechanism, we determined that c-di-GMP binding to Vc2 also controls the abundance and stability of upstream non-coding small RNAs (sRNA) with 3’-ends located immediately downstream of the Vc2 riboswitch. Our results suggest these sRNAs are not generated by transcriptional termination but rather by preventing degradation of the upstream untranslated RNA when c-di-GMP is bound to Vc2.IMPORTANCERiboswitches are typically RNA elements located in the 5’ untranslated region of mRNAs. They are highly structured and specifically recognize and respond to a given chemical cue to alter transcription termination or the translation initiation. In this work, we report a novel mechanism of riboswitch mediated gene regulation inVibrio choleraewhereby a 3’ riboswitch, named Vc2, controls the stability of upstream untranslated RNA upon binding to its cognate ligand, the second messenger cyclic di-GMP, leading to the accumulation of previously undescribed sRNAs. We further demonstrate that binding of the ligand to the riboswitch prevents RNA degradation. As binding of riboswitches to their ligands often produces compactly structure RNA, we hypothesize this mechanism of gene regulation could be widespread.

scholarly journals The poly(A) tail inhibits the assembly of a 3'-to-5' exonuclease in an in vitro RNA stability system.

1997 ◽  
Vol 17 (1) ◽  
pp. 398-406 ◽  
Author(s):  
L P Ford ◽  
P S Bagga ◽  
J Wilusz
Keyword(s):  
Mrna Stability ◽  
Binding Proteins ◽  
Rna Stability ◽  
Rna Degradation ◽  
Exonuclease Activity ◽  
Stem Loop ◽  
In Vitro System ◽  
Loop Element

We have developed an in vitro system which faithfully reproduces several aspects of general mRNA stability. Poly(A)- RNAs were rapidly and efficiently degraded in this system with no detectable intermediates by a highly processive 3'-to-5' exonuclease activity. The addition of a poly(A) tail of at least 30 bases, or a 3' histone stem-loop element, specifically stabilized these transcripts. Stabilization by poly(A) required the interaction of proteins with the poly(A) tail but did not apparently require a 3' OH or interaction with the 5' cap structure. Finally, movement of the poly(A) tract internal to the 3' end caused a loss of its ability to stabilize transcripts incubated in the system but did not affect its ability to interact with poly(A) binding proteins. The requirement for the poly(A) tail to be proximal to the 3' end indicates that it mediates RNA stability by blocking the assembly, but not the action, of an exonuclease involved in RNA degradation in vitro.

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