Aleksandra V. Suhorukova

Mitogen-activated protein kinases (MPKs) are involved in the cold response of plants; however, in tomatoes, their regulation has been studied only at the mRNA level. In this study, a comparative analysis of the transcriptional and translational regulation of the MAPK cascade in tomato (Solanum lycopersicum) under cold stress and hardening was conducted using polysomic profiling with parallel sequencing of total and polysomic RNA fractions. For representatives of all four groups (A–D), as well as the upstream kinases SlMAPKKK, we calculated mRNA differential expression and translational efficiency. Most cascade components were regulated predominantly at the translational level and mRNA levels remained stable. Groups C and D were profiled for the first time under cold conditions, and candidate translational cold regulators were identified.

One of the unresolved questions in stress-response biology is how plants coordinate expression levels between the response and adaptation. In this work, we proposed a two-level analysis that examines both transcriptional and translational profiles of Solanum lycopersicum under conditions of short-term cold stress, hardening, and their combination. By combining polysome profiling and total transcriptome analysis, we revealed that expression under cold stress is not a simple linear process but a structurally distinct system with two coordinated regulation centres. Hardening triggers a strong transcriptional program focused on biogenesis, light signalling, and structural adaptations. In contrast, acute stress prompts selective translation of metabolic and defence proteins without prior transcriptional increase. Modular analysis (WGCNA) showed little overlap between transcriptional and translational networks, indicating functional differences between regulation levels. This work demonstrates that the cold response involves a strategic reallocation of resources between transcription and translation based on the type of signal. It bridges basic biology and applied breeding, providing targets promising for improving plant stress tolerance and advancing bioengineering of adaptive agriculture.

One of the unresolved questions in stress-response biology remains the mechanism of coordination of expression levels in plants between the slow preparation phase and the rapid reactive response to stress exposure. In this work, we proposed a two-level analysis covering simultaneously transcriptional and translational profiles of Solanum lycopersicum under short-term cold stress, hardening and their combination. By combining polysome profiling and total transcriptome analysis, we revealed that expression under cold stress is not a linear chain but a structurally separated system with two coordinated centres of regulation. Hardening activates a robust transcriptional programme with a focus on biogenesis, light signalling and structural adaptations. In contrast, acute stress initiates selective translation of metabolic and defence proteins without prior enhancement of transcription. Modular analysis (WGCNA) showed low overlap between transcriptional and translational networks, indicating functional divergence between levels of regulation. In this work, we demonstrate that the cold response is a strategic reallocation of resources between expression levels depending on the type of signal. The work forms a bridge between basic biology and applied breeding, offering targets promising for targeted improvement of plant stress tolerance and further bioengineering of adaptive agrocultures.

Evolution generates a vast repertoire of solutions enabling organisms to adapt to diverse environmental challenges. In plants, these solutions primarily manifest as reactive responses involving anatomical reconfigurations, biochemical adjustments, and physiological adaptations. Efficient responses require precise coordination across multiple cellular processes and reaction cascades. A critical evolutionary objective is to minimize the collateral effects associated with activating complex regulatory networks. To this end, nature evolves independent regulatory modules that decouple key stages of genetic information processing. This modularity underpins the diversity of regulatory mechanisms and patterns observed in cells. Here, we present an investigation of how tomato (Solanum lycopersicum L.) plants respond to low-temperature stress. By analyzing gene expression profiles at the transcriptional and translational levels, we aim to elucidate the coordination and decoupling of these processes during stress responses.

The complexities of translational strategies make this stage of implementing genetic information one of the most challenging to comprehend and, simultaneously, perhaps the most engaging. It is evident that this diverse range of strategies results not only from a long evolutionary history, but is also of paramount importance for refining gene expression and metabolic modulation. This notion is particularly accurate for organisms that predominantly exhibit biochemical and physiological reactions with a lack of behavioural ones. Plants are a group of organisms that exhibit such features. Addressing unfavourable environmental conditions plays a pivotal role in plant physiology. This is particularly evident with the changing conditions of global warming and the irrevocable loss or depletion of natural ecosystems. In conceptual terms, the plant response to abiotic stress comprises a set of elaborate and intricate strategies. This is influenced by a range of abiotic factors that cause stressful conditions, and molecular genetic mechanisms that fine-tune metabolic pathways allowing the plant organism to overcome non-standard and non-optimal conditions. This review aims to focus on the current state of the art in the field of translational regulation in plants under abiotic stress conditions. Different regulatory elements and patterns are being assessed chronologically. We deem it important to focus on significant high-performance techniques for studying the genetic information dynamics during the translation phase.

The intricacies of translational strategies make this stage of the implementation of genetic information one of the most difficult to understand and, at the same time, perhaps the most interesting. It also becomes clear that all this variety of strategies is not just a consequence of a long evolutionary history but is of paramount importance for fine-tuning gene expression and metabolic modulation. This is especially true for those organisms that demonstrate predominantly biochemical and physiological reactions with a lack of behavioural ones. Plants are just such a group of organisms. Overcoming unfavourable environmental conditions occupies a key place in plant physiology. This is especially true with the changing conditions of global warming and the irretrievable loss or depletion of natural ecosystems. Conceptually, the response of plants to abiotic stress is a set of complex and intricate strategies. This is dictated both by a variety of abiotic factors that provoke stressful conditions and by a variety of molecular genetic mechanisms that make it possible to fine-tune the metabolic pathways through which the plant organism overcomes non-standard and non-optimal conditions. In the presented review, we tried to focus on the state-of-the-art in the field of translational regulation in plants under abiotic stress conditions. Various regulatory elements and patterns are considered in relative chronological order. We also considered it necessary to pay attention to key high-performance methods for studying the dynamics of genetic information at the stage of translation.

Stress is one of the important factors affecting the growth and development of plants. In recent years, a large body of data on transcriptional changes in response to stress in plants has been obtained. Despite the fact that the important role of the regulation of translation in response to stress has been proven in plants, knowledge in this area remains extremely scarce. In this review, we focused on mRNA translation in the cytoplasm of higher plants. Most of the current research on the effects of translation has been done in yeast and mammalian systems. Translation factors and mechanisms are mostly conserved among eukaryotes; however, some differences are known to exist among plants. A comprehensive understanding of the complex apparatus of translation and its regulation in plants is required. In this work, we have tried to update modern ideas about the regulation of translation under conditions of abiotic stress.

A broad and amazingly intricate network of mechanisms underlying the decoding of a plant genome into the proteome forces the researcher to design new strategies to enhance both the accumulation of recombinant proteins and their purification from plants and to improve the available relevant strategies. In this paper, we propose new approaches to optimize a codon composition of target genes (case study of interferon-αA) and to search for regulatory sequences (case study of 5′UTR), and we demonstrated their effectiveness in increasing the synthesis of recombinant proteins in plant systems. In addition, we convincingly show that the approach utilizing stabilization of the protein product according to the N-end rule or a new protein-stabilizing partner (thermostable lichenase) is sufficiently effective and results in a significant increase in the protein yield manufactured in a plant system. Moreover, it is validly demonstrated that thermostable lichenase as a protein-stabilizing partner not only has no negative effect on the target protein activity (interferon-αA) integrated in its sequence, but rather enhances the accumulation of the target protein product in plant cells. In addition, the retention of lichenase enzyme activity and interferon biological activity after the incubation of plant protein lysates at 65 °C and precipitation of nontarget proteins with ethanol is applicable to a rapid and inexpensive purification of fusion proteins, thereby confirming the utility of thermostable lichenase as a protein-stabilizing partner for plant systems.

Background: For the needs of modern biotechnology, a quantitative approach to the control of regulatory elements at all stages of gene expression has long become indispensable. Such a control regime is impossible without a quantitative analysis of the role of each regulatory element or pattern used. Therefore, it seems important to modify and develop the accuracy, reproducibility, and availability of methods for quantifying the contribution of each regulatory code to the implementation of genetic information. Results: A new vector system for transient expression in plants is described; this system is intended for quantitative analysis of the contribution of regulatory elements to transcription and translation efficiencies. The proposed vector comprises two expression cassettes carrying reporter genes (of the Clostridium thermocellum thermostable lichenase and E. coliβ-glucuronidase) under the control of different promoters. Herewith we also propose a new method for quantification of the effect of tested regulatory elements on expression, which relies on assessment of the enzyme activities of reporter proteins taking into account the transcription of their genes. Conclusions: In our view, this approach makes it possible to precisely determine the amounts of reporter proteins and their transcripts at all stages of expression. The efficiency of the proposed system has been validated by the analysis of the roles of known translation enhancers at the stages of transcription and translation.