Next Article in Journal
Two Distinct Conformations in Bet v 2 Determine Its Proteolytic Resistance to Cathepsin S
Next Article in Special Issue
Protein-Protein Interactions Prediction Using a Novel Local Conjoint Triad Descriptor of Amino Acid Sequences
Previous Article in Journal
Reactive Oxygen Species and NOX Enzymes Are Emerging as Key Players in Cutaneous Wound Repair
Previous Article in Special Issue
Protein Complexes Prediction Method Based on Core—Attachment Structure and Functional Annotations
Article Menu
Issue 10 (October) cover image

Export Article

Open AccessArticle
Int. J. Mol. Sci. 2017, 18(10), 2155; doi:10.3390/ijms18102155

Predicting Amyloidogenic Proteins in the Proteomes of Plants

1
Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 196608 Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia
2
Department of Genetics and Biotechnology, St. Petersburg State University, 199034 Universitetskaya nab., 7/9, St. Petersburg 199034, Russia
*
Author to whom correspondence should be addressed.
Received: 25 August 2017 / Revised: 12 October 2017 / Accepted: 13 October 2017 / Published: 16 October 2017
(This article belongs to the Special Issue Special Protein Molecules Computational Identification)
View Full-Text   |   Download PDF [5730 KB, uploaded 18 October 2017]   |  

Abstract

Amyloids are protein fibrils with characteristic spatial structure. Though amyloids were long perceived to be pathogens that cause dozens of incurable pathologies in humans and mammals, it is currently clear that amyloids also represent a functionally important form of protein structure implicated in a variety of biological processes in organisms ranging from archaea and bacteria to fungi and animals. Despite their social significance, plants remain the most poorly studied group of organisms in the field of amyloid biology. To date, amyloid properties have only been demonstrated in vitro or in heterologous systems for a small number of plant proteins. Here, for the first time, we performed a comprehensive analysis of the distribution of potentially amyloidogenic proteins in the proteomes of approximately 70 species of land plants using the Waltz and SARP (Sequence Analysis based on the Ranking of Probabilities) bioinformatic algorithms. We analyzed more than 2.9 million protein sequences and found that potentially amyloidogenic proteins are abundant in plant proteomes. We found that such proteins are overrepresented among membrane as well as DNA- and RNA-binding proteins of plants. Moreover, seed storage and defense proteins of most plant species are rich in amyloidogenic regions. Taken together, our data demonstrate the diversity of potentially amyloidogenic proteins in plant proteomes and suggest biological processes where formation of amyloids might be functionally important. View Full-Text
Keywords: amyloid; Waltz; SARP; plant; prion; seed storage protein; proteomics; compositionally biased region; amyloidogenic region amyloid; Waltz; SARP; plant; prion; seed storage protein; proteomics; compositionally biased region; amyloidogenic region
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Antonets, K.S.; Nizhnikov, A.A. Predicting Amyloidogenic Proteins in the Proteomes of Plants. Int. J. Mol. Sci. 2017, 18, 2155.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top