The control of translation in the course of gene expression regulation plays a crucial role in plants’ cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein products in eukaryotic cells, including plants, requires thorough investigation of the regulatory mechanisms of translation. A wide and amazingly complex network of mechanisms decoding the plant genome into proteome challenges researchers to design new methods for genome-wide analysis of translational control, develop computational algorithms detecting regulatory mRNA contexts, and to establish rules underlying differential translation. The aims of this review are to (i) describe the experimental approaches for investigation of differential translation in plants on a genome-wide scale; (ii) summarize the current data on computational algorithms for detection of specific structure–function features and key determinants in plant mRNAs and their correlation with translation efficiency; (iii) highlight the methods for experimental verification of existed and theoretically predicted features within plant mRNAs important for their differential translation; and finally (iv) to discuss the perspectives of discovering the specific structural features of plant mRNA that mediate differential translation control by the combination of computational and experimental approaches.

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.

Emergence of sn-1,2-diacylglycerol-3-acyltransferases (DGATs)—the key enzymes of triacylglycerol (TAG) biosynthesis—may be regarded as an important aromorphosis in the evolution of the organic world in general and that of plants in particular. In fact, the newly originated ability to store carbon, energy, water, and “building blocks” in a form of hydrophobic compounds enabled increasing the “capacity” of storage compounds in the cells and to simultaneously reduce volumes of storage organs. DGATs are present in almost any organisms from myxomycetes, mosses, fungi, and algae to mammals, including humans. Although these enzymes are so widespread in a world of live matter, it is difficult to follow principles of their organization, evolution, and functioning because an organism may possess several DGATs belonging to different types, differently localized in the cell, and employing different substrates or competing for one substrate. They are relatives owing to only one common function—the transfer of a fatty acid residue from acyl-CoA to sn-1,2-diacyl-glycerol yielding a TAG molecule. In some cases, DGATs can acylate sterols, higher fatty alcohols, and other substrates bringing about the same product. Intense investigations of these enzymes have been continuing for the last 50 years and they present more questions than answers so far. However, clear comprehension of the traits of organization and function of DGATs opens up fantastic prospects in biotechnology and genetic engineering of functional lipids for food and pharmaceutical industries, and agriculture. This review attempts to summarize the recent data on structural and functional peculiarities of DGATs, effects of endogenous and exogenous factors on the expression levels of their genes, and the adaptive roles of these genes in the evolution of living organisms.

Background: Since the beginning of the use of reporter proteins for expression analysis, a variety of approaches have been developed and proposed; both qualitative and quantitative. The lack of simple methods for direct observation of gene expression in living organisms makes it necessary to continue to propose new methods. In this work, we consider a method for the quantitative analysis of the expression of thermostable lichenase from Clostridium thermocellum used as a sensitive reporter protein. Results: In this study, we report the design a high throughput fluorometric method for quantification of thermostable lichenase C. thermocellum using Congo red and further experimental verification of its relevance and efficiency in assessment of the functional role of regulatory sequences in the plant cell. Conclusions: The specific interaction between the dye Congo red and $$\beta$$β -d-glucans formed the background for designing a high-throughput fluorometric assay for quantification of C. thermocellum thermostable lichenase as a reporter protein for plants. This assay (i) makes it possible to precisely measure the amount of reporter protein in a plant sample; (ii) has shown a high sensitivity for quantification of thermostable lichenase; (iii) is more time- and cost-efficient as compared with the Somogyi–Nelson assay; and (iv) is to the least degree dependent on the presence of the tested buffer components as compared with the Somogyi–Nelson assay.

Clostridium thermocellum lichenase (endo-β-1,3;1,4-glucan-D-glycosyl hydrolase, EC 3.2.1.73 (P29716)) has been tested for the insertion of two model fluorescent proteins (EGFP and TagRFP) into two regions of this enzyme. Functional folding of the resulting proteins was confirmed by retention of lichenase activity and EGFP and TagRFP fluorescence. These results convincingly demonstrate that (i) the two experimentally selected lichenase loop regions may serve as the areas for domain insertion without disturbing enzyme folding in vivo; (ii) lichenase permits not only single but also tandem insertions of large protein domains. High specific activity, outstanding thermostability, and efficient in vitro refolding of thermostable lichenase make it an attractive new host protein for the insertional fusion of domains in the engineering of multifunctional proteins.

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.