Non-coding RNAs’ partitioning in the evolution of photosynthetic organisms via energy transduction and redox signaling

Abstract

Ars longa, vita brevis —Hippocrates

Chloroplasts and mitochondria are genetically semi-autonomous organelles inside the plant cell. These constructions formed after endosymbiosis and keep evolving throughout the history of life. Experimental evidence is provided for active non-coding RNAs (ncRNAs) in these prokaryote-like structures, and a possible functional imprinting on cellular electrophysiology by those RNA entities is described. Furthermore, updated knowledge on RNA metabolism of organellar genomes uncovers novel inter-communication bridges with the nucleus. This class of RNA molecules is considered as a unique ontogeny which transforms their biological role as a genetic rheostat into a synchronous biochemical one that can affect the energetic charge and redox homeostasis inside cells. A hypothesis is proposed where such modulation by non-coding RNAs is integrated with genetic signals regulating gene transfer. The implications of this working hypothesis are discussed, with particular reference to ncRNAs involvement in the organellar and nuclear genomes evolution since their integrity is functionally coupled with redox signals in photosynthetic organisms.

Introduction

The functional identity of an RNA molecule ranges from its auto-catalytic ability to multiple levels of the (post)-transcriptional landscape such as splicing, editing and silencing. The so-called non-coding RNAs are evolutionarily conserved regulators from bacteria to higher eukaryotes, with a huge expansion in vertebrates¹ and a synchronous specialization on mRNA stability’ and consequent turnover’ affection, through high fidelity RNA-RNA interactions. Their functional maintenance is connected to a sum of unique biophysical properties, a critical prerequisite for their involvement in various developmental programs including mediation of stress physiology.²

Emerging data has given rise to a re-study of classical biological phenomena (e.g. buffering processes) by expanding the traditional role of known molecules to other levels of regulation based on their biochemical character.^3,4 Furthermore, interesting modes of action by old redox switches (i.e. hydrogen peroxide) have been discovered via sub-compartmental trafficking of the latter, through aquaporins^5,6 and other transmembrane diodes.

Here, an analogy is proposed between endogenous ncRNAs and redox signals, since their actions are equally rapid in plants. This is the first time this particular group of RNA molecules have been expressed as a biochemical entity and its biological role extended beyond the molecular regulation, in terms of redox signal mediation in cell physiology. Subsequently, the possible ncRNAs’ involvement in bioenergetic transductions that guide evolutionary events in photosynthetic cells is discussed.

New insights in the RNA world map

Sensing of aberrant transcripts inside the cell triggers the RNA silencing machinery toward production of ncRNAs. These easily diffused molecules, of 260–325 Å length are generated by ATP-fuelled reactions and they have unique biochemical features. There are several criteria for functional bona fide silencing ncRNAs identification: (i) small, 21–25 nt; (ii) initially double-stranded; (iii) 3′ 2-nt overhangs; and (iv) 5′ monophosphate and 3' hydroxyl termini.⁷

Very recently, a crosstalk between light intensity and RNA silencing has been identified in plants.⁸ It appears that a bioenergetic phenomenon is mediated, via photosynthetic regulation that can explain transient oscillations of endogenous ncRNAs throughout the year.⁹ Moreover, recent experimental data provide evidence that significant quantities of ncRNAs can alter the plant micro-environment, since the concentration of H⁺ ions around their nucleotide arm was found to be considerably higher in comparison to the remaining RNA species circulating in the plant cells tested. The electrostatic effect is integrated as a redox signal by the chloroplast and sensed by the plant's antioxidant machinery.¹⁰ Similar observations have been made in mammals, where siRNAs (short-interfering RNAs) over-dosage caused toxicity in the cell vigor.¹¹

Approximately 3.7% of the Arabidopsis thaliana genome contains loci encoding ncRNA sequences. NcRNAs are mainly located in the cytoplasm and the nucleus based on their biogenesis.¹² Given their mobility, they possibly can also act; in trans loci, on cognate genomic sequences.^13,14 Validation of plastid non-coding RNAs occurred¹⁵ and control of light-dependent operon-transcripts by antisense RNAs in chloroplast ancestors (i.e., cyanobacteria) has been noted.¹⁶ The latter is also shown in animals, via miRNAs’ (microRNAs) effect on mitochondrial metabolism.¹⁷

It is remarkable that chloroplast and mitochondrial RNA sequences constitute more than 50% of the total RNA inside the plant cell, with two-thirds of this percentage being chloroplastic.¹⁸ Recent studies have described gene transfer between nucleus and chloroplast¹⁹ and also aspects of non-coding RNA mediation in exchanges of genetic material.²⁰ Based on this growing body of evidence, a hypothesis for the contribution of ncRNAs in the inter-communication between nucleus and bioenergetic organelles is posed .

Redox-epigenetic inheritance via ncRNAs

Nucleic-acids circulating as signaling messengers have been previously reported inside the inter-, and intra-cellular plant space, through the phloem and via plasmodesmata.²¹ NcRNAs signal is mobile too and it can form genetic patterns in local and or/distant plant parts.²² Moreover, ncRNAs mediation is a very rapid type of response in comparison to DNA-DNA and nucleic acid-protein interactions.²³ Taking into consideration the experimental results described above, ncRNAs can contribute in the ATPases’ activity, through (sub-) compartmental electron to proton ratios alteration.

Additionally, redox poise and the ATP/ADP cellular ratio are crucial determinants of organellar genomes functionality, which indicates the probable evolutionary explanation^24,25 for hybrids of organellar and nucleic origin. These hybrids are redox-regulated components, which are differentially regulated even under short-term pH changes, upon changes in light intensity.²⁶ In conclusion, if de novo generation of functional ncRNAs is plausible within bioenergetic sub-compartments; i.e. chloroplasts and mitochondria,^27,28 we can speculate that these natural ncRNAs orchestrate the energetics of the extranuclear genomes, since such biogenic anions could act synergistically with protons in ATP synthesis.²⁹

In order to integrate all the above into a working model, light intensity might regulate photosynthetically the ncRNAs’ quantity (Fig. 1), providing the necessary energetic equivalents that are required for their production. Afterwards, the ncRNA populations can form locally mobile electrochemical sub-loci (Fig. 1) that affect a) ATPases’ activity and b) redox-responsive genes expression in the 3 genetic compartments of the plant cell (Fig. 1). As an additional consequence to the redox titration by ncRNAs' pool (Fig. 1), they can be regulators in RNA mediating-gene transfer processes between organellar and nucleic genomes (Fig. 1), contributing in gene evolution.

Figure 1.

Minimalistic sketch of the working hypothesis for a proposed evolutionary mechanism between ncRNAs and bioenergetics in plant biology: Novel (auto)-feeding loops of genetic regulation via endogenous ncRNAs circulation; due to the effective velocity that characterizes their kinetic properties, between different sub-cellular compartments, including chloroplast, mitochondrion, cytoplasm, and nucleus. Light may have a titrative effect on ncRNAs’ generation since energy (ATP) is required for their functionality maintenance. A redox coupling; through accumulation of electrons and protons (e⁻/H⁺) by those differentially charged RNA bridges, is mediated in the levels of regulation that are depicted in bullets.

Gene transfer is facilitated especially under environmental stress³⁰ that trigger ncRNAs production. So, the hypothesis can be expanded in cyanobacteria from extreme habitats with evolutionary significance, such as Antarctica³¹ and geothermal vents. The climatic periodicity in such micro-environments may engage catholic oscillations in the ncRNAs’ amount of archeal endosymbionts. This special organismal fitness might build cells that are highly conductive in ncRNA-redox signaling and thus increase the frequency of DNA gene transfer events between organellar and nucleic genomes. We envision these RNA molecules as evolutionary modulators; however, the probable ncRNAs redox-epigenetic signaling remains to be tested.

Concluding remarks

The class of non-coding silencing RNAs is elevated for discussion, in relation to bioenergetic pathways that drive chemiosmosis and redox signaling, under the endosymbiotic umbrella³² that guides cell evolution. The location of genetic information in cytoplasmic organelles permits regulation of its expression by the reduction-oxidation (“redox”) state of its gene products.³³ The endogenous ncRNAs as biochemical ontogenies in the literature can be re-evaluated and potentially re-partitioned on how the genetic autonomy of bioenergetic organelles and a complex network of redox signals are functionally synchronized in plants.

More specifically, this proposal considers those RNA molecules as redox-genetic modulars that can indirectly guide DNA-directed gene transfer,^34-36 potentially under stress conditions. Similar RNA-mediated phenomena aren't excluded based on old and recent reports.^37-40 RNA intermediates' partitioning in gene transfer induction are rare, possibly due to the fact that such mechanisms are activated under particular eco-evolutionary pressure.⁴¹ Hence, this minor contribution is biologically significant, taking into account the requirement for organellar genome regulation by redox balance.⁴² The development of sophisticated tools; a proper experimental design as well as selection of the suitable natural systems and model organisms is required for the functional elucidation of endosymbiotic gene transfer events.

New routes for ncRNAs evolution (i.e., gene duplication events)⁴³ per se can be discovered through probable ncRNAs mediating genetic transfer between the organellar genomes and the nuclear genome. Based on their universal character, ncRNAs could probably be applied as an indirect in vivo probing of the different sub-compartmental pH and redox potentials, since a detailed quantification is still missing in (plant) eukarya, due to the membrane barriers.

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

Christos Kotakis (BSc, MSc, PhD) would like to thank Brian Tokar (University of Vermont, USA) and Paula de Angelis (independent researcher, Adelaide, South Australia) for critical reading of the manuscript. Special respect is due to the advisors (Biology Department, University of Crete, GR) for encouraging free improvisation work as well as visionary discussions with all lab members and George C Papageorgiou. Figural architecture has been edited by Demetra Kotakis signature. The author declares that no conflict of interest exists regarding financial and competing issues, according to academia ethics.

Funding

The researcher's desk and funding were provided by the agricultural ‘Oikos’ K. Kotakis-D. Koutsodimos; organic farming in Citrus sp. orchards (BIO-211-511-10049/30 EU grant).