ROS as Top down and Bottom up Messengers
In chapters 4.1-4.3 we have found a broad series of ROS signaling that might comprise both bottom up or top down signaling (see Figure 71). Indeed some of the effects described were formerly believed as unknown top down signaling procedures, however, as we will point out in the following, bottom up and top down might occur concomitantly and it is not easy to comprise only one direction in a complicated communicating network.
Figure 71. Hypothetical scheme of pathways of selected photosynthetic redox signal transduction in plants initiated at the thylakoid membrane. For the sake of simplicity, other cell organells (nucleus, mitochondrion, peroxisome) are symbolized by colored ovals. Interrupted arrows designate hypothetic pathways of signal transduction. The question marks designate unknown components of signal transduction pathways. Solid lines designate signal transduction pathways with some experimental confirmation. Dotted lines designate experimentally established signal transduction pathways in chloroplast ETC and in the stroma. The abbreviations RS, MAPK and TF denote redox-sensitive protein(s), MAP-kinase and transcription factor(s), respectively according to (Schmitt et al., 2014a). Image reproduced with permission.
To reconcile some examples we might first look at the mechanism of EF-G oxidation which stops the translation of RNA and therefore the overall protein novosynthesis in cyanobacteria under severe ROS stress (see chapter 4.1). As the primary oxidation of a single complex, the EF-G compartment of ribosomes, the activity of ribosomes is stopped. The activity of the ribosomes in gene translation is stopped and the level of certain proteins will decrease according to their average lifetime. The scheme is rather simple and is sometimes understood as a typical bottom up communication as from the presence of ROS molecules in the microenvironment the expression level of proteins changes and therefore finally the whole organism is transformed. On the other hand the original trigger for the EF-G oxidation might be intense sunlight and concomitant ROS that disactivate the protein production machinery. In such way the change of the microenvironment follows a macroscopic command from top down. If the plant could make the voluntary decision to expose itself to intense sunlight or to bring its organism into a situation of ROS overproduction most people would agree that we have a top down communication of the whole organism towards its molecular composition. It is comparable with a decision to exchange single elements to enforce a variation on the microscale and therefore enforcing the whole structure to behave differently.
A more complicated example is the activation of histidine kinases, as Hik33; this is a typical reaction to enhanced membrane rigidity as a consequence of a higher ROS levels. Here the macroscopic change of a structure induces the change of a single molecule configuration (see chap. 4.3). We acknowledge that transmission of stress signals operates in large cell cultures and tissues, and Hik33 is understood to be a multisensory protein in Synechocystis. As the molecular answer to membrane rigidity instead of direct oxidation of molecular cysteines the reaction scheme appears generalized to “membrane tension” instead of ROS defining the multisensory character of Hik33. Any change of the membrane fluidity, which might be ROS, salt, cold stress or age activates Hik33 and the typical property of a larger structure to react to stress in a common way (changing fluidity of the membrane). The ROS signals are transduced by rather macroscopic structures like membranes that regulate single molecules like Hik signaling directly to the molecular fundament of each cell, the genome. It seems as we have a generalized top down communication where the membrane reacts to an external trigger and induces a change on the moleculare level. However finally the activation of genes is bottom up again. In fact a top down strategy seems more likely be able to induce a bottom up change while a bottom up change will change if induced by a macroscopic signal. So top down and bottom up strategies somewhat go hand in hand and ROS signaling covers a large hierarchy from top down and bottom up mechanisms involving the genome, the proteome, cell tissues and the whole organism.
Other examples arise as structural modifications give rise to detachment of weakly bound enzymes from the cell wall, as shown for the isoforms of peroxidases (Minibayeva and Gordon, 2003). On the other side again, ROS modulate the activity of antioxidant enzymes, e.g. in case of catalase and ascorbate peroxidases (Shao et al., 2008). Likewise, also the redox state of cell components acting as antioxidants or being involved in signaling (glutathione system, ascorbate system, plastoquinone pool, thioredoxin, etc.).
Bottom up ROS can oxidize EF-G (see chapter 4.1) and translation of genes is stopped. Top down the ROS level determines the change of macroscopic structures and therefore the activity of histidine kinases. However that is only a single aspect as the existence of ROS signalling itself might be understood as a top down phenomenon.
In higher animals ROS level change due to voluntary activation of ROS. Animals that carry a free will might just make the decision to raise their ROS level. The body can be activated and activity, active movement, i.e. “sport” conducted as a consequence of the free will, can raise the ROS level severely and therefore activate changes on the molecular level down to gene expression in both ways, by direct oxidation and by transmitted activation of structural changes that initiate the activity changes of multisensory proteins.
But should we therefore always understand top down as a consequence of free will? It seems more likely that a pattern interaction in hierarchical systems contributes to phenomena of both qualities: top down and bottom up signaling. Indeed all these interaction schemes follow a long evolutionary adaption process that adds up to a higher reproduction probability under given constraints. So in both directions, bottom up as well as top down, we find the most important regulatory control in acclimation of organisms to different stress factors - the modulation of gene expression (Apel and Hirt, 2004; Laloi et al., 2007). As mentioned above, this response can sometimes comprise up to one third of the entire genome.
Redox-sensitive enzymes serve as a molecular “switch” by undergoing reversible oxidation and reduction reactions in response to redox changes within the cells. ROS can oxidize the redox-sensitive enzymes directly or indirectly under the participation of low-molecular redox-sensitive molecules like glutathione or thioredoxin, from which the latter interacts with ferredoxin (Foyer and Noctor, 2005; Shao et al., 2008). In this way, the whole cell metabolism can be tuned. On the other hand, redox- sensitive signaling proteins function in combination with other components of signaling pathways, including MAPKs, phosphatases, transcription factors, etc. (Foyer and Noctor, 2005; Shao et al., 2008, Pfannschmidt et al., 2009). Redox regulators available in the apoplast have been suggested to be among the key ROS sources during stress (Minibayeva et al., 1998, 2009; Minibayeva and Gordon, 2003). It has to be mentioned that the molecular mechanisms that transfer ROS by dedicated oxidation of covalent bonds producing chemical oxidation products are maybe just a minor example of the general regulation that occurs from the overall redox state of the cell. Fundamental concepts may also arise from physical principles like the membrane potential or the decoupling or coupling of photosynthetic subunits by electrostatic interaction, which has been suggested to be the driving mechanism for the coupling state of cyanobacterial light-harvesting complexes and the cell membrane in A. marina (see Schmitt et al., 2006; 2007) or in artificial systems consisting of cyanobacterial antenna complexes and semiconductor quantum dots (Schmitt et al., 2010; 2011; Schmitt, 2011).
If we look to the activation of ROS as messenger or defense molecules we find another situation where two directions of a reaction pattern are conducted depending on the general circumstances in which the system is found. As mentioned above ROS is generated in response to different types of stress acting as signal molecules, but via generation of second messengers (e.g. oxidation products of Cars and lipids, vide supra), also pathways operating in the opposite direction are established in plants. This does not only account for producing ROS as defensive molecules but it also accounts for the active production of ROS as messenger molecules.
Therefore we have again something that might be understood as being top down and bottom up regarding the point of view from where we look at it. Active production of ROS as single molecules initiated by external stimuli or by free will is top down as it deactivates single cells (for example biotic pathogens) as a reaction to an externally introduced cell damage or even as a consequence of free will and a decision of the whole organism (if it carries consciousness, like animals and humans and is able to conduct “decisions”). Bottom up the signal molecules oxidize MAPKs and therefore directly influence gene expression.
In the following we will try to establish this kind of understanding of top down and bottom up networking in another, more generalized point of view.
Light is the most important signal in regulating a vast majority of processes in living organisms, as reflected by numerous light sensors and biological clocks. But light has to be understood as both, a top down messenger (as it is conducted from the solar radiation field onto the earth surface) and additionally as a bottom up messenger (as it induces conformational changes on the molecular level that conduct molecular reaction schemes changing finally the basic chemical composition in cells).
Light is at first the unique Gibbs free energy source for the existence of living matter though the process of photosynthesis. Light should generally be understood as the most basic prerequisite of life as it carries a reduced entropy as compared to the thermal equilibrium of the planet. When light is transferred to a planetary surface and reemitted as heat radiation and in such way carrying away the most entropic radiation, the black body radiation, from the planetary surface, it can take up entropy and therefore allow for the growth of complex structures and locally less entropic systems.
On the other hand, light at high intensities also leads to stress giving rise to the deleterious process of photoinhibition in photosynthetic organisms (Adir et al., 2003; Allakhverdiev and Murata, 2004; Nishiyama et al., 2006; Murata et al., 2007; Vass and Aro, 2008; Li et al., 2009; Goh et al., 2012; Allahverdiyeva and Aro, 2012). Imbalances in the redox state of components of the electron transfer chain (ETC) lead to dangerous ROS production. Therefore, suitable sensors are required to permit efficient adaptation to illumination conditions which vary in time (diurnal, seasonal rhythm) and space (e.g. plants in different altitudes of a tropical rain forest or bacteria in different water depth and living environment).