Abstract
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.
Highlights
The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but being found in non-plant species
Results from Clustering LEA Protein Probability Profiles Recalling that the aim of unsupervised machine learning is to cluster the input data so that related objects are associated, while dissimilar objects are in different clusters, a POPP vector was created for each LEA protein sequence, including the three members of the Uncharacterised set
Bearing in mind that POPPs are not constrained to be in any particular cluster, and that the clusters can appear in any number of families and superfamilies, there is a remarkable level of agreement between the membership of the superfamilies versus the Groups derived from the literature and those observed in the supervised learning experiments discussed above
Summary
The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but 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. The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins whose precise function is unknown. While considerable evidence suggests that LEA proteins are involved in desiccation resistance, a variety of mechanisms for achieving this end (page number not for citation purposes). The somewhat more recent survey by Close [13] of Group 2 LEA proteins includes a discussion of predicted secondary structure for this Group
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