Polyadenylate-containing RNA in dormant and germinating Botryodiplodia theobromae pycnidiospores

1979 ◽  
Vol 25 (3) ◽  
pp. 375-379 ◽  
Author(s):  
James L. Van Etten ◽  
Carroll D. Rawn
Keyword(s):  
Germ Tube ◽  
De Novo ◽  
Segment Length ◽  
Botryodiplodia Theobromae ◽  
Rna Molecules ◽  
Polyuridylic Acid ◽  
Tube Emergence ◽  
Dormant Spore ◽  
Average Size

Hybridization of [3H]polyuridylic acid to RNA isolated from Botryodiplodia theobromae pycnidiospores yielded an estimate of about 6.25 × 105 polyadenylate-containing RNA (poly A(+) RNA) molecules per dormant spore. The number increased about fourfold by the time of germ tube emergence at 3 h. The average size of this presumed mRNA was about 4.1 × 105 daltons (1275 nucleotides), with an average polyadenylate segment length of 26 nucleotides. Neither of these values changed significantly during germination. The earliest detectable (first 30 min of germination) de novo synthesized mRNA's were rapidly incorporated into polyribosomes. This newly synthesized, presumably functional, mRNA was composed of both poly A(+) RNA and polyadenylate-lacking RNA. The average sizesof the two polyribosomal mRNA subpopulations and the total poly A(+) RNA population were identical.

scholarly journals Induction of Promoter DNA Methylation Upon High-Pressure Spraying of Double-Stranded RNA in Plants

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 789
Author(s):  
Athanasios Dalakouras ◽  
Ioannis Ganopoulos
Keyword(s):  
High Pressure ◽  
De Novo ◽  
Epigenetic Changes ◽  
Double Stranded Rna ◽  
Rna Molecules ◽  
Promoter Sequences ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
First Time ◽  
De Novo Methylation

Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic changes was never addressed. Here, we report for the first time that high-pressure spraying of dsRNAs can trigger de novo methylation of promoter sequences in plants.

scholarly journals Comparative Genetic Analysis of Yersinia pestis Strains Isolated on the Ukok Plateau and other Territories of the Altai Mountains

2021 ◽  
pp. 59-69
Author(s):  
G. A. Eroshenko ◽  
A. N. Balykova ◽  
Ya. M. Krasnov ◽  
E. A. Naryshkina ◽  
E. N. Rozhdestvensky ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
De Novo ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
Likelihood Method ◽  
High Mountain ◽  
Altai Mountains ◽  
Natural Foci ◽  
Ukok Plateau ◽  
Average Size

The aim of the study was molecular-genetic identification and analysis of the phylogenetic relationship of Yersinia pestis strains isolated on the Ukok Plateau in 2020, in order to establish the current boundaries of the natural mega focus of plague in the Altai Mountains in Russia and Mongolia.Materials and methods. 37 strains of Y. pestis of the main subspecies isolated in the Tuva mountain and Gorno-Altai high-mountain plague foci and adjacent territories of Mongolia in 1971–2020 were studied. The whole genome sequencing of the strains was performed using the Ion S5 XL System (Thermo Fischer Scientific). Ion Torrent Suite software package 5.12 and Newbler gsAssembler 2.6 were used to process the data and assemble de novo the sequences of raw reads. The average size of the collected genome was 4.55 million base pairs. Core SNPs were detected by aligning the contigs of Y. pestis strains on the CO92 genome using the Snippy 4.6 program, then 28 SNP homoplasies were removed. The resulting set of SNPs contained only the core region of the genome (955 SNPs). The dendrogram was constructed using the Maximum Likelihood method applying the PhyML 3.1 program.Results and discussion. The current population structure of Y. pestis of the main subspecies, antique biovar, phylogenetic line 4.ANT, endemic to the foci of the Altai Mountains in Russia and Mongolia has been determined. The presence of 4.ANT-21 clone, which became widespread in the territory of these natural foci of plague at the begining of the XXI century, was revealed. It is shown that three strains isolated on the Ukok Plateau in 2020 belong to clone 4.ANT-21. According to phylogenetic analysis, evidence of 4.ANT circulation on the Ukok Plateau before 2018 was obtained. The lesson that has been learned is that it is necessary to study the territories of Mongolia, Kazakhstan and China bordering the Ukok Plateau in order to establish the current boundaries of the 4.ANT mega focus. 

scholarly journals Using de novo transcriptome assembly and analysis to study RNAi in Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Satnam Singh ◽  
Mridula Gupta ◽  
Suneet Pandher ◽  
Gurmeet Kaur ◽  
Neha Goel ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Instar Nymph ◽  
Future Research ◽  
Rnai Machinery ◽  
Phenacoccus Solenopsis ◽  
Atpase Subunit ◽  
Molecular Sequence ◽  
Rnai Efficiency ◽  
Average Size

Abstract Phenacoccus solenopsis is one of the major polyphagous crop pests in India. Inadequate genomic or transcriptomic resources have limited the molecular studies in this insect despite its huge economic importance. The existing molecular sequence resources of this insect were supplemented through RNA sequencing, de novo transcriptome assembly and analysis, which generated 12, 925 CDS from 23,643 contigs with an average size of 1077.5 bp per CDS and 85.1% positive BLAST hits with NCBI Non redundant (nr) database. Twenty three genes involved in RNAi machinery identified through BLASTx search against NCBI nr database suggested the existence of robust RNAi in mealybug. RNAi in P. solenopsis was demonstrated through knockdown of IAP (Inhibitor of Apoptosis), AQP (Aquaporin), CAL (Calcitonin), VATPase (V-type proton ATPase subunit F 1), bursicon, chitin synthase, SNF7 and α-amylase by injecting sequence specific dsRNA of respective genes in adult female. Additionally, feeding RNAi has been demonstrated in 2nd instar nymph through dsRNA uptake in plant. The knockdown of core RNAi machinery genes such as Dicer, Argonaute and Staufen significantly hampered RNAi efficiency in this insect. However, downregulation of dsRNases improved RNAi efficiency. Sequential studies for understanding RNAi in P. solenopsis using transcriptome sequences have also been reported. The present study provides a base for future research on developing RNAi as strategy for management of this pest.

Flunarizine affects F-actin pattern in Mucor rouxii germlings

1994 ◽  
Vol 40 (9) ◽  
pp. 730-735 ◽  
Author(s):  
Jiří Hašek ◽  
Eva Streiblová
Keyword(s):  
Plasma Membrane ◽  
Germ Tube ◽  
Tip Growth ◽  
Apical Growth ◽  
Mucor Rouxii ◽  
Yeast Form ◽  
Tube Emergence

The effect of the Ca2+ antagonist flunarizine on Mucor rouxii germlings was analyzed. In sporangiospores cultivated in aerobiosis, the drug blocked germ tube emergence, but enlarged spheres continued to grow isodiametrically. The formation of broad protuberances and irregular buds was observed. Calcofluor staining indicated aberrations on the surface of the flunarizine-treated cells. This was not a simple switch to the yeast form, since labelling with rhodarmine-tagged phalloidin revealed various ring-shaped structures of F-actin, indicating furrowing of the plasma membrane. Flunarizine apparently did not interfere with nuclear divisions or with the integrity of microtubules. In young germlings, flunarizine treatment induced cessation of tip growth and promoted septation associated with the rearrangement of F-actin. Apical growth was reestablished after either the drug was removed or an excess of Ca2+ ions was added to the medium. The results suggest that tip-related arrangement of F-actin requires flunarizine-sensitive Ca2+ entry.Key words: Mucor rouxii, F-actin, Ca2+ antagonist, flunarizine, germination.

Carbon dioxide induces endotrophic germ tube formation in Candida albicans

1990 ◽  
Vol 36 (4) ◽  
pp. 249-253 ◽  
Author(s):  
Ruth C. Mock ◽  
Jordan H. Pollack ◽  
Tadayo Hashimoto
Keyword(s):  
Carbon Dioxide ◽  
Candida Albicans ◽  
Sodium Bicarbonate ◽  
Key Words ◽  
Germ Tube ◽  
Tube Formation ◽  
Chemical Inducers ◽  
Tube Emergence ◽  
Ph Range ◽  
Germ Tubes

Candida albicans formed germ tubes when exposed to air containing 5 to 15% carbon dioxide (CO2). The CO2-mediated germ tube formation occurred optimally at 37 °C in a pH range of 5.5 to 6.5. No germ tubes were produced at 25 °C, even when the optimal concentration of CO2 (10%) was present in the environment. The requirement of CO2 for germ tube formation could be partially substituted by sodium bicarbonate but not by N2. Carbon dioxide was required to be present throughout the entire course of germ tube emergence suggesting that its role is not limited to an initial triggering of morphogenic change. We suggest that carbon dioxide may be a common effector responsible for the germ tube promoting activity of certain chemical inducers for C. albicans. Key words: Candida albican germ tubes, CO2-induced germ tube formation, endotrophic germ tube formation.

Pattern of protein degradation during germination of Streptomyces antibioticus spores

1983 ◽  
Vol 29 (6) ◽  
pp. 637-643 ◽  
Author(s):  
J. A. Guijarro ◽  
J. E. Suarez ◽  
J. A. Salas ◽  
C. Hardisson
Keyword(s):  
Protein Degradation ◽  
Protease Activity ◽  
Germ Tube ◽  
Synthetic Medium ◽  
Distilled Water ◽  
Streptomyces Antibioticus ◽  
Constant Rate ◽  
Degradation Pattern ◽  
Tube Emergence ◽  
Inhibition Studies

The pattern of protein degradation during germination of Streptomyces antibioticus spores was studied by the pulse and chase technique. Two different protein fractions were found. First, a fraction of the proteins synthesized during the darkening process (20–30%) was quickly degraded in the 30 min following the labelling period. This rapid protein degradation was partially inhibited by protease inhibitors: p-chloromercuribenzoic acid, phenylmethylsulphonylfluoride, and o-phenanthroline. Second, the remaining 70–80% and the entire protein population formed during spore swelling and germ tube emergence were degraded with a lower and constant rate (3.3–6.0%/h). A stable mRNA fraction of the dormant spores was translated upon incubation of the spores in a minimal synthetic medium (MSM) or in distilled water. However, the degradation of these proteins did not occur unless the spores were then incubated in the MSM. A strong correlation between the degradation pattern of these proteins and that of those quickly degraded at the beginning of germination was observed. Protease activity in cell-free extracts of dormant spores was detected. Inhibition studies suggest the presence of serine, thiol, and metalloproteases. The protease activity, using casein as substrate, remained constant during the darkening process and started to increase progressively from the beginning of spore swelling.

Viroid-induced DNA methylation in plants

2013 ◽  
Vol 4 (6) ◽  
pp. 557-565 ◽  
Author(s):  
Athanasios Dalakouras ◽  
Elena Dadami ◽  
Michael Wassenegger
Keyword(s):  
Dna Methylation ◽  
Small Rnas ◽  
Rna Silencing ◽  
De Novo ◽  
Rna Degradation ◽  
Double Stranded Rna ◽  
Methyl Group ◽  
Rna Molecules ◽  
Cumulative Data

AbstractIn eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). RdDM was first discovered in viroid-infected plants. Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. Here, we provide an overview of the cumulative data on the field of viroid-induced RdDM and discuss three possible scenarios concerning the mechanistic details of its establishment.

scholarly journals FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds

2019 ◽  
Author(s):  
Andrew M. Watkins ◽  
Rhiju Das
Keyword(s):  
Experimental Data ◽  
De Novo ◽  
Accurate Prediction ◽  
Human Intervention ◽  
Fragment Assembly ◽  
3D Structures ◽  
Rna Molecules ◽  
Fragment Libraries ◽  
Large Model

SummaryMethods to predict RNA 3D structures from sequence are needed to understand the exploding number of RNA molecules being discovered across biology. As assessed during community-wide RNA-Puzzles trials, Rosetta’s Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) enables accurate prediction of complex folds, but it remains unclear how much human intervention and experimental guidance is needed to achieve this performance. Here, we present FARFAR2, a protocol integrating recent innovations with updated RNA fragment libraries and helix modeling. In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARFAR2 recovers structures that are more accurate than the original models submitted by our group and other participants during the RNA-Puzzles trials. In five prospective tests, pre-registered FARFAR2 models for riboswitches and adenovirus VA-I achieved 3–8 Å RMSD accuracies. Finally, we present a server and three large model archives (FARFAR2-Classics, FARFAR2-Motifs, and FARFAR2-Puzzles) to guide future applications and advances.

scholarly journals Revealing the host antiviral protein ZAP-S as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

2021 ◽  
Author(s):  
Matthias Michael Zimmer ◽  
Anuja Nitin Kibe ◽  
Ulfert Rand ◽  
Lukas Pekarek ◽  
Luca Cicin-Sain ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Specific Inhibitor ◽  
Antiviral Protein ◽  
Ribosomal Frameshifting ◽  
Reading Frame ◽  
Rna Molecules ◽  
Cellular Factors ◽  
Infected Cells

Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses including SARS-CoV-2, which allows production of essential structural and replicative enzymes from an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshifting RNA molecules and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the host proteome and the SARS-CoV-2 frameshift element. Here, we reveal that zinc-finger antiviral protein (ZAP-S) is a direct and specific regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and ribosomes and interferes with the folding of the frameshift RNA. Together these data illuminate ZAP-S as de novo host-encoded specific inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.

ANGEL2 is a member of the CCR4 family of deadenylases with 2′,3′-cyclic phosphatase activity

Science ◽  
2020 ◽  
Vol 369 (6503) ◽  
pp. 524-530
Author(s):  
Paola H. Pinto ◽  
Alena Kroupova ◽  
Alexander Schleiffer ◽  
Karl Mechtler ◽  
Martin Jinek ◽  
...  
Keyword(s):  
Messenger Rna ◽  
De Novo ◽  
Mrna Splicing ◽  
Rna Molecules ◽  
Unfolded Protein ◽  
Rna Pathways ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Cyclic Phosphates ◽  
Hydrolysis Of

RNA molecules are frequently modified with a terminal 2′,3′-cyclic phosphate group as a result of endonuclease cleavage, exonuclease trimming, or de novo synthesis. During pre-transfer RNA (tRNA) and unconventional messenger RNA (mRNA) splicing, 2′,3′-cyclic phosphates are substrates of the tRNA ligase complex, and their removal is critical for recycling of tRNAs upon ribosome stalling. We identified the predicted deadenylase angel homolog 2 (ANGEL2) as a human phosphatase that converts 2′,3′-cyclic phosphates into 2′,3′-OH nucleotides. We analyzed ANGEL2’s substrate preference, structure, and reaction mechanism. Perturbing ANGEL2 expression affected the efficiency of pre-tRNA processing, X-box–binding protein 1 (XBP1) mRNA splicing during the unfolded protein response, and tRNA nucleotidyltransferase 1 (TRNT1)–mediated CCA addition onto tRNAs. Our results indicate that ANGEL2 is involved in RNA pathways that rely on the ligation or hydrolysis of 2′,3′-cyclic phosphates.

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