Studies on the Role of Methylated Bases in the Biological Activity of Soluble Ribonucleic Acid

Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

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Differential Role of Threonine and Tyrosine Phosphorylation in the Activation and Activity of the Yeast MAPK Slt2

International Journal of Molecular Sciences ◽

10.3390/ijms22031110 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1110

Author(s):

Gema González-Rubio ◽

Ángela Sellers-Moya ◽

Humberto Martín ◽

María Molina

Keyword(s):

Cell Wall ◽

Biological Activity ◽

Biological Significance ◽

Mitogen Activated Protein Kinase ◽

Activation Loop ◽

High Increase ◽

Dual Specificity ◽

Mitogen Activated Protein ◽

Full Activation

The Mitogen-Activated Protein Kinase (MAPK) Slt2 is central to signaling through the yeast Cell Wall Integrity (CWI) pathway. MAPKs are regulated by phosphorylation at both the threonine and tyrosine of the conserved TXY motif within the activation loop (T190/Y192 in Slt2). Since phosphorylation at both sites results in the full activation of MAPKs, signaling through MAPK pathways is monitored with antibodies that detect dually phosphorylated forms. However, most of these antibodies also recognize monophosphorylated species, whose relative abundance and functionality are diverse. By using different phosphospecific antibodies and phosphate-affinity (Phos-tag) analysis on distinct Slt2 mutants, we determined that Y192- and T190-monophosphorylated species coexist with biphosphorylated Slt2, although most of the Slt2 pool remains unphosphorylated following stress. Among the monophosphorylated forms, only T190 exhibited biological activity. Upon stimulation, Slt2 is first phosphorylated at Y192, mainly by the MAPKK Mkk1, and this phosphorylation is important for the subsequent T190 phosphorylation. Similarly, dephosphorylation of Slt2 by the Dual Specificity Phosphatase (DSP) Msg5 is ordered, with dephosphorylation of T190 depending on previous Y192 dephosphorylation. Whereas Y192 phosphorylation enhances the Slt2 catalytic activity, T190 is essential for this activity. The conserved T195 residue is also critical for Slt2 functionality. Mutations that abolish the activity of Slt2 result in a high increase in inactive Y192-monophosphorylated Slt2. The coexistence of different Slt2 phosphoforms with diverse biological significance highlights the importance of the precise detection of the Slt2 phosphorylation status.

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Role of conformational heterogeneity in ligand recognition by viral RNA molecules

Physical Chemistry Chemical Physics ◽

10.1039/d1cp00679g ◽

2021 ◽

Author(s):

Lev Levintov ◽

Harish Vashisth

Keyword(s):

Conformational Changes ◽

Ribonucleic Acid ◽

Viral Rna ◽

Ligand Recognition ◽

Conformational Heterogeneity ◽

Rna Molecules ◽

Environmental Stimuli

Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response to various environmental stimuli including temperature, pH, and ligands. In particular, viral RNA molecules are a key example...

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Role of Sulfhydryl Residues of Escherichia coli Ribonucleic Acid Polymerase in Template Recognition and Specific Initiation

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)42485-x ◽

1974 ◽

Vol 249 (13) ◽

pp. 4079-4085

Author(s):

Lynwood R. Yarbrough ◽

Cheng-Wen Wu

Keyword(s):

Escherichia Coli ◽

Ribonucleic Acid

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Prebiotic studies on the interaction of zirconia nanoparticles and ribose nucleotides and their role in chemical evolution

International Journal of Astrobiology ◽

10.1017/s1473550421000033 ◽

2021 ◽

Vol 20 (2) ◽

pp. 142-149

Author(s):

Avnish Kumar Arora ◽

Pankaj Kumar

Keyword(s):

Electron Microscopy ◽

Metal Oxide ◽

Metal Oxides ◽

Chemical Evolution ◽

Ribonucleic Acid ◽

Zirconium Oxide ◽

Origins Of Life ◽

Neutral Ph ◽

Interaction Studies

AbstractStudies on the interaction of biomolecules with inorganic compounds, mainly mineral surfaces, are of great concern in identifying their role in chemical evolution and origins of life. Metal oxides are the major constituents of earth and earth-like planets. Hence, studies on the interaction of biomolecules with these minerals are the point of concern for the study of the emergence of life on different planets. Zirconium oxide is one of the metal oxides present in earth's crust as it is a part of several types of rocks found in sandy areas such as beaches and riverbeds, e.g. pebbles of baddeleyite. Different metal oxides have been studied for their role in chemical evolution but no studies have been reported about the role of zirconium oxide in chemical evolution and origins of life. Therefore, studies were carried out on the interaction of ribonucleic acid constituents, 5′-CMP (cytidine monophosphate), 5′-UMP (uridine monophosphate), 5′-GMP (guanosine monophosphate) and 5′-AMP (adenosine monophosphate), with zirconium oxide. Synthesized zirconium oxide particles were characterized by using vibrating sample magnetometer, X-Ray Diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy. Zirconia particles were in the nanometre range, from 14 to 27 nm. The interaction of zirconium oxide with ribonucleic acid constituents was performed in the concentration range of 5 × 10−5–300 × 10−5 M. Interaction studies were carried out in three mediums; acidic (pH 4.0), neutral (pH 7.0) and basic (pH 9.0). At neutral pH, maximum interaction was observed. The interaction of zirconium oxide with 5′-UMP was 49.45% and with 5′-CMP 67.98%, while with others it was in between. Interaction studies were Langmurian in nature. Xm and KL values were calculated. Infrared spectral studies of ribonucleotides, metal oxide and ribonucleotide–metal oxide adducts were carried out to find out the interactive sites. It was observed that the nitrogen base and phosphate moiety of ribonucleotides interact with the positive charge surface of metal oxide. SEM was also carried out to study the adsorption. The results of the present study favour the important role of zirconium oxide in concentrating the organic molecules from their dilute aqueous solutions in primeval seas.

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