Did Biology Emerge from Biotite in Micaceous Clay?

Mapping Intimacies ◽

10.20944/preprints202009.0409.v1 ◽

2020 ◽

Author(s):

H. Greenwood Hansma

Keyword(s):

Protein Synthesis ◽

Hydrogen Bonding ◽

Phase Separation ◽

Nucleic Acid ◽

Liquid Phase ◽

Crystal Lattice ◽

Living Cell ◽

Redox Reactions ◽

Energy Sources ◽

A Site

An origin of life between the sheets of micaceous clay is proposed to involve the following steps: 1) evolution of metabolic cycles and nucleic acid replication, in separate niches in biotite mica; 2) evolution of protein synthesis on ribosomes formed by liquid-in-liquid phase separation; 3) repeated encapsulation by membranes of molecules required for the metabolic cycles, replication, and protein synthesis; 4) interactions and fusion of the these membranes containing enclosed molecules; resulting eventually in 5) an occasional living cell, containing everything necessary for life. The spaces between mica sheets have many strengths as a site for life’s origins: mechanochemistry and wet-dry cycles as energy sources, an 0.5-nm anionic crystal lattice with potassium counterions (K+), hydrogen-bonding, enclosure, and more. Mica pieces in micaceous clay are large enough to support mechanochemistry from moving mica sheets. Biotite mica is an iron-rich mica capable of redox reactions, where the stages of life’s origins could have occurred, in micaceous clay.

Download Full-text

Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Polymers ◽

10.3390/polym13132074 ◽

2021 ◽

Vol 13 (13) ◽

pp. 2074

Author(s):

Sara Tabandeh ◽

Cristina Elisabeth Lemus ◽

Lorraine Leon

Keyword(s):

Hydrogen Bonding ◽

Phase Separation ◽

Liquid Phase ◽

Charge Density ◽

Secondary Structures ◽

Liquid Phase Separation ◽

Polyelectrolyte Complexes ◽

Π Interactions ◽

Liquid Liquid Phase Separation

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

Download Full-text

Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1

Nucleic Acids Research ◽

10.1093/nar/gkab080 ◽

2021 ◽

Author(s):

Fionna E Loughlin ◽

Danella L West ◽

Menachem J Gunzburg ◽

Saboora Waris ◽

Simon A Crawford ◽

...

Keyword(s):

Phase Separation ◽

Nucleic Acid ◽

Liquid Phase ◽

Binding Sites ◽

Rna Binding ◽

Liquid Phase Separation ◽

Stress Granule ◽

Granule Formation ◽

Self Association ◽

Liquid Liquid Phase Separation

Abstract TIA-1 is an RNA-binding protein that sequesters target RNA into stress granules under conditions of cellular stress. Promotion of stress granule formation by TIA-1 depends upon self-association of its prion-like domain that facilitates liquid-liquid phase separation and is thought to be enhanced via RNA binding. However, the mechanisms underlying the influence of RNA on TIA-1 self-association have not been previously demonstrated. Here we have investigated the self-associating properties of full-length TIA-1 in the presence of designed and native TIA-1 nucleic acid binding sites in vitro, monitoring phase separation, fibril formation and shape. We show that single stranded RNA and DNA induce liquid-liquid phase separation of TIA-1 in a multisite, sequence-specific manner and also efficiently promote formation of amyloid-like fibrils. Although RNA binding to a single site induces a small conformational change in TIA-1, this alone does not enhance phase separation of TIA-1. Tandem binding sites are required to enhance phase separation of TIA-1 and this is finely tuned by the protein:binding site stoichiometry rather than nucleic acid length. Native tandem TIA-1 binding sites within the 3′ UTR of p53 mRNA also efficiently enhance phase separation of TIA-1 and thus may potentially act as potent nucleation sites for stress granule assembly.

Download Full-text

Structure specific recognition of telomeric repeats containing RNA by the RGG-box of hnRNPA1

Nucleic Acids Research ◽

10.1093/nar/gkaa134 ◽

2020 ◽

Vol 48 (8) ◽

pp. 4492-4506 ◽

Cited By ~ 1

Author(s):

Meenakshi Ghosh ◽

Mahavir Singh

Keyword(s):

Phase Separation ◽

Nucleic Acid ◽

Liquid Phase ◽

Cell Interaction ◽

Protein Motifs ◽

G Quadruplex ◽

Separation Of Proteins ◽

Nucleic Acid Structures ◽

Dna Maintenance ◽

Liquid Liquid Phase Separation

Abstract The telomere repeats containing RNA (TERRA) is transcribed from the C-rich strand of telomere DNA and comprises of UUAGGG nucleotides repeats in humans. The TERRA RNA repeats can exist in single stranded, RNA-DNA hybrid and G-quadruplex forms in the cell. Interaction of TERRA RNA with hnRNPA1 has been proposed to play critical roles in maintenance of telomere DNA. hnRNPA1 contains an N-terminal UP1 domain followed by an RGG-box containing C-terminal region. RGG-motifs are emerging as key protein motifs that recognize the higher order nucleic acid structures as well as are known to promote liquid-liquid phase separation of proteins. In this study, we have shown that the RGG-box of hnRNPA1 specifically recognizes the TERRA RNA G-quadruplexes that have loops in their topology, whereas it does not interact with the single-stranded RNA. Our results show that the N-terminal UP1 domain in the presence of the RGG-box destabilizes the loop containing TERRA RNA G-quadruplex efficiently compared to the RNA G-quadruplex that lacks loops, suggesting that unfolding of G-quadruplex structures by UP1 is structure dependent. Furthermore, we have compared the telomere DNA and TERRA RNA G-quadruplex binding by the RGG-box of hnRNPA1 and discussed its implications in telomere DNA maintenance.

Download Full-text

CRISPR-based DNA and RNA detection with liquid-liquid phase separation

10.1101/471482 ◽

2018 ◽

Cited By ~ 3

Author(s):

Willem Kasper Spoelstra ◽

Jeroen M. Jacques ◽

Franklin L. Nobrega ◽

Anna C. Haagsma ◽

Marileen Dogterom ◽

...

Keyword(s):

Phase Separation ◽

Nucleic Acid ◽

Liquid Phase ◽

Clinical Diagnostics ◽

Liquid Phase Separation ◽

Molecular Diagnostic ◽

Target Sequence ◽

Dna And Rna ◽

Wide Range ◽

Liquid Liquid Phase Separation

AbstractThe ability to detect specific nucleic acid sequences allows for a wide range of applications including identification of pathogens, clinical diagnostics, and genotyping. CRISPR-Cas proteins Cas12a and Cas13a are RNA-guided endonucleases that bind and cleave specific DNA and RNA sequences, respectively. After recognition of a target sequence both enzymes activate a unique, indiscriminate nucleic acid cleavage activity, which has been exploited for detection of sequence specific nucleotides using labelled reporter molecules. We here present a label-free detection approach that uses a readout based on solution turbidity caused by liquid-liquid phase separation (LLPS). Turbidity arises from coacervates of positively charged polyelectrolytes with long poly(dT) or poly(U) oligonucleotides. In the presence of a target sequence, long oligonucleotides are progressively shortened, changing the solution from turbid to transparent. We explain how oligonucleotide cleavage resolves LLPS by using a mathematical model which we validate with poly(dT) phase separation experiments. The deployment of LLPS complements CRISPR-based molecular diagnostic applications and facilitates easy and low-cost nucleotide sequence detection.

Download Full-text

Starvation-induced proteasome assemblies in the nucleus link amino acid supply to apoptosis

Nature Communications ◽

10.1038/s41467-021-27306-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Maxime Uriarte ◽

Nadine Sen Nkwe ◽

Roch Tremblay ◽

Oumaima Ahmed ◽

Clémence Messmer ◽

...

Keyword(s):

Protein Synthesis ◽

Phase Separation ◽

Amino Acid ◽

Liquid Phase ◽

Mammalian Cells ◽

Proteasome Inhibition ◽

Eukaryotic Cells ◽

Amino Acid Deprivation ◽

Common Response ◽

Liquid Liquid Phase Separation

AbstractEukaryotic cells have evolved highly orchestrated protein catabolic machineries responsible for the timely and selective disposal of proteins and organelles, thereby ensuring amino acid recycling. However, how protein degradation is coordinated with amino acid supply and protein synthesis has remained largely elusive. Here we show that the mammalian proteasome undergoes liquid-liquid phase separation in the nucleus upon amino acid deprivation. We termed these proteasome condensates SIPAN (Starvation-Induced Proteasome Assemblies in the Nucleus) and show that these are a common response of mammalian cells to amino acid deprivation. SIPAN undergo fusion events, rapidly exchange proteasome particles with the surrounding milieu and quickly dissolve following amino acid replenishment. We further show that: (i) SIPAN contain K48-conjugated ubiquitin, (ii) proteasome inhibition accelerates SIPAN formation, (iii) deubiquitinase inhibition prevents SIPAN resolution and (iv) RAD23B proteasome shuttling factor is required for SIPAN formation. Finally, SIPAN formation is associated with decreased cell survival and p53-mediated apoptosis, which might contribute to tissue fitness in diverse pathophysiological conditions.

Download Full-text