Dataset Information

Pleiotropic roles of late embryogenesis abundant proteins of Deinococcus radiodurans against oxidation and desiccation.

ABSTRACT: Deinococcus radiodurans, an important extremophile, possesses extraordinary stress tolerance ability against lethal and mutagenic effects of DNA-damaging agents, such as γ-rays, ultraviolet, oxidation, and desiccation. How global regulators of this bacterium function in response to oxidation and desiccation has been an intense topic as elucidating such mechanisms may help to facilitate some beneficial applications in agriculture or medicine. Particularly, a variety of functional proteins have been characterized for D. radiodurans' behaviors under abiotic stresses. Interestingly, a group of Late Embryogenesis Abundant proteins (LEAs) in D. radiodurans have been characterized both biochemically and physiologically, which are shown indispensable for stabilizing crucial metabolic enzymes in a chaperone-like manner and thereby maintaining the metal ion homeostasis under oxidation and desiccation. The rapid progress in understanding deinococcal LEA proteins has substantially extended their functions in both plants and animals. Herein, we discuss the latest studies of radiodurans LEA proteins ranging from the classification to structures to functions. Importantly, the harnessing of these proteins may have unlimited potential for biotechnology, engineering and disease treatments.

SUBMITTER: Liu Y

PROVIDER: S-EPMC8213827 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Pleiotropic roles of late embryogenesis abundant proteins of <i>Deinococcus radiodurans</i> against oxidation and desiccation.

Liu Yingying Y Zhang Chen C Wang Zhihan Z Lin Min M Wang Jin J Wu Min M

Computational and structural biotechnology journal 20210604

<i>Deinococcus radiodurans,</i> an important extremophile, possesses extraordinary stress tolerance ability against lethal and mutagenic effects of DNA-damaging agents, such as γ-rays, ultraviolet, oxidation, and desiccation. How global regulators of this bacterium function in response to oxidation and desiccation has been an intense topic as elucidating such mechanisms may help to facilitate some beneficial applications in agriculture or medicine. Particularly, a variety of functional proteins ...[more]

PMID: 34188783

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Project description:BackgroundThe late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties.ResultsPrevious research has suggested that glycine is characteristic of LEA proteins, but it is only highly over-represented in Groups 1 and 2, while alanine, thought characteristic of Group 2, is over-represented in Group 3, 4 and 6 but under-represented in Groups 1 and 2. However, for LEA Groups 1 2 and 3 it is shown that glutamine is very significantly over-represented, while cysteine, phenylalanine, isoleucine, leucine and tryptophan are significantly under-represented. There is also evidence that the Group 4 LEA proteins are more appropriately redistributed to Group 2 and Group 3. Similarly, Group 5 is better found among the Group 3 LEA proteins.ConclusionsThere is evidence that Group 2 and Group 3 LEA proteins, though distinct, might be related. This relationship is also evident in the overlapping sets of keywords for the two Groups, emphasising alpha-helical structure and, at a larger scale, filaments, all of which fits well with experimental evidence that proteins from both Groups are natively unstructured, but become structured under stress conditions. The keywords support localisation of LEA proteins both in the nucleus and associated with the cytoskeleton, and a mode of action similar to chaperones, perhaps the cold shock chaperones, via a role in DNA-binding. In general, non-globular and low-complexity proteins, such as the LEA proteins, pose particular challenges in determining their functions and modes of action. Rather than masking off and ignoring low-complexity domains, novel tools and tool combinations are needed which are capable of analysing such proteins in their entirety.

Project description:BackgroundLEA (late embryogenesis abundant) proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown.ResultsWe present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE) and/or low temperature response (LTRE) elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded.ConclusionThe analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for future efforts to elucidate the functional role of these enigmatic proteins.

Dataset Information

Pleiotropic roles of late embryogenesis abundant proteins of Deinococcus radiodurans against oxidation and desiccation.

Publications

Pleiotropic roles of late embryogenesis abundant proteins of <i>Deinococcus radiodurans</i> against oxidation and desiccation.

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