Special Issue: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA

Herbert, Alan; Karapetyan, Sergey; Poptsova, Maria; Vásquez, Karen M.; Vicens, Quentin; Vögeli, Beat

doi:10.3390/ijms22147686

Cited by 7 publications

(7 citation statements)

References 32 publications

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“…We call this U-to-Z tetraloop motif transition a shapeshifting process that is similar in spirit to the flipons described by A. Herbert. Flipons define a class of sequences capable of forming either left or right-handed helical structures [ 84 , 85 ].…”

Section: Resultsmentioning

confidence: 99%

Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey

Zirbel

Auffinger

2022

Molecules

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Z-DNA and Z-RNA have long appeared as oddities to nucleic acid scientists. However, their Z-step constituents are recurrently observed in all types of nucleic acid systems including ribosomes. Z-steps are NpN steps that are isostructural to Z-DNA CpG steps. Among their structural features, Z-steps are characterized by the presence of a lone pair…π contact that involves the stacking of the ribose O4′ atom of the first nucleotide with the 3′‑face of the second nucleotide. Recently, it has been documented that the CpG step of the ubiquitous r(UNCG) tetraloops is a Z-step. Accordingly, such r(UNCG) conformations were called Z-turns. It has also been recognized that an r(GAAA) tetraloop in appropriate conditions can shapeshift to an unusual Z-turn conformation embedding an ApA Z-step. In this report, we explore the multiplicity of RNA motifs based on Z-steps by using the WebFR3D tool to which we added functionalities to be able to retrieve motifs containing lone pair…π contacts. Many examples that underscore the diversity and universality of these motifs are provided as well as tutorial guidance on using WebFR3D. In addition, this study provides an extensive survey of crystallographic, cryo-EM, NMR, and molecular dynamics studies on r(UNCG) tetraloops with a critical view on how to conduct database searches and exploit their results.

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Section: Resultsmentioning

confidence: 99%

Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey

Zirbel

Auffinger

2022

Molecules

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“…We believe that additional studies might reveal the currently overlooked specifics of their structure and localization, leading to the additional sub-classification of TezRs. For example, considering the global functions that are regulated by TezRs, we expect that certain differences in their biological activity can be achieved based on the physical characteristics of TezRs, such as their length, formation of loops, or alternative confirmations and structures such as DNA-RNA hybrids or triplexes [159][160][161].…”

Section: Discussionmentioning

confidence: 99%

Novel Cell Receptor System of Eukaryotes Formed by Previously Unknown Nucleic Acid-Based Receptors

Tetz¹,

Tetz²

2022

Receptors

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Here, our data provide the first evidence for the existence of a previously unknown receptive system formed by novel DNA- and RNA-based receptors in eukaryotes. This system, named the TR-system, is capable of recognizing and generating a response to different environmental factors and has been shown to orchestrate major vital functions of fungi, mammalian cells, and plants. Recently, we discovered the existence of a similar regulatory system in prokaryotes. These DNA- and RNA-based receptors are localized outside of the membrane forming a type of a network around cells that responds to a variety of chemical, biological, and physical factors and enabled the TR-system to regulate major aspects of eukaryotic cell life as follows: growth, including reproduction and development of multicellular structures; sensitivity to temperature, geomagnetic field, UV, light, and hormones; interaction with viruses; gene expression, recognition and utilization of nutrients. The TR-system was also implicated in cell-memory formation and was determined to be responsible for its maintenance and the forgetting of preceding events. This system is the most distant receptive and regulatory system of the cell that regulates interactions with the outer environment and governs the functions of other receptor-mediated signaling pathways.

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“…Considering the various cell features that are regulated by TezRs, we hypothesize that their specific functions stem from their physical characteristics, such as length and presence of specific loops or nucleic acids conformations [ 140 , 141 ]. A better understanding of these properties could lead to further and more accurate sub-classification of TezRs.…”

Section: Discussionmentioning

confidence: 99%

Novel prokaryotic system employing previously unknown nucleic acids-based receptors

Tetz

2022

Microb Cell Fact

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The present study describes a previously unknown universal system that orchestrates the interaction of bacteria with the environment, named the Teazeled receptor system (TR-system). The identical system was recently discovered within eukaryotes. The system includes DNA- and RNA-based molecules named “TezRs”, that form receptor’s network located outside the membrane, as well as reverse transcriptases and integrases. TR-system takes part in the control of all major aspects of bacterial behavior, such as intra cellular communication, growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction, and DNA recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Importantly, the TR-system is responsible for the formation and maintenance of cell memory to preceding cellular events, as well the ability to “forget” preceding events. Transcriptome and biochemical analysis revealed that the loss of different TezRs instigates significant alterations in gene expression and proteins synthesis.

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Special Issue: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA

Cited by 7 publications

References 32 publications

Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey

Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey

Novel Cell Receptor System of Eukaryotes Formed by Previously Unknown Nucleic Acid-Based Receptors

Novel prokaryotic system employing previously unknown nucleic acids-based receptors

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