The molecular mass and isoelectric point of plant proteomes

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Abstract

Background

Cell contain diverse array of proteins with different molecular weight and isoelectric point (pI). The molecular weight and pI of protein play important role in determining the molecular biochemical function. Therefore, it was important to understand the detail regarding the molecular weight and pI of the plant proteins.

Results

A proteome-wide analysis of plant proteomes from 145 species revealed a pI range of 1.99 (epsin) to 13.96 (hypothetical protein). The spectrum of molecular mass of the plant proteins varied from 0.54 to 2236.8 kDa. A putative Type-I polyketide synthase (22244 amino acids) in Volvox carteri was found to be the largest protein in the plant kingdom. However, Type-I polyketide synthase was not found in higher plant species. Titin (806.46 kDa) and misin/midasin (730.02 kDa) were the largest proteins identified in higher plant species. The pI and molecular weight of the plant proteins showed a trimodal distribution. An acidic pI (56.44% of proteins) was found to be predominant over a basic pI (43.34% of proteins) and the abundance of acidic pI proteins was higher in unicellular algae species relative to multicellular higher plants. In contrast, the seaweed, Porphyra umbilicalis, possesses a higher proportion of basic pI proteins (70.09%). Plant proteomes were also found to contain selenocysteine (Sec), amino acid that was found only in lower eukaryotic aquatic plant lineage. Amino acid composition analysis showed Leu was high and Trp was low abundant amino acids in the plant proteome. Additionally, the plant proteomes also possess ambiguous amino acids Xaa (unknown), Asx (asparagine or aspartic acid), Glx (glutamine or glutamic acid), and Xle (leucine or isoleucine) as well.

Conclusion

The diverse molecular weight and isoelectric point range of plant proteome will be helpful to understand their biochemical and functional aspects. The presence of selenocysteine proteins in lower eukaryotic organism is of interest and their expression in higher plant system can help us to understand their functional role.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5983-8) contains supplementary material, which is available to authorized users.

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Most cited references 63

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New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants.

Vered Tzin, Gad Galili (2010)

The aromatic amino acids phenylalanine, tyrosine, and tryptophan in plants are not only essential components of protein synthesis, but also serve as precursors for a wide range of secondary metabolites that are important for plant growth as well as for human nutrition and health. The aromatic amino acids are synthesized via the shikimate pathway followed by the branched aromatic amino acids biosynthesis pathway, with chorismate serving as a major intermediate branch point metabolite. Yet, the regulation and coordination of synthesis of these amino acids are still far from being understood. Recent studies on these pathways identified a number of alternative cross-regulated biosynthesis routes with unique evolutionary origins. Although the major route of Phe and Tyr biosynthesis in plants occurs via the intermediate metabolite arogenate, recent studies suggest that plants can also synthesize phenylalanine via the intermediate metabolite phenylpyruvate (PPY), similarly to many microorganisms. Recent studies also identified a number of transcription factors regulating the expression of genes encoding enzymes of the shikimate and aromatic amino acids pathways as well as of multiple secondary metabolites derived from them in Arabidopsis and in other plant species.

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The origin and establishment of the plastid in algae and plants.

Jonathon Weber, Adrian Reyes-Prieto, Debashish Bhattacharya (2006)

The establishment of the photosynthetic organelle (plastid) in eukaryotes and the diversification of algae and plants were landmark evolutionary events because these taxa form the base of the food chain for many ecosystems on our planet. The plastid originated via a putative single, ancient primary endosymbiosis in which a heterotrophic protist engulfed and retained a cyanobacterium in its cytoplasm. Once successfully established, this plastid spread into other protist lineages through eukaryote-eukaryote (secondary and tertiary) endosymbioses. This process of serial cell capture and enslavement explains the diversity of photosynthetic eukaryotes. Recent genomic and phylogenomic approaches have significantly clarified plastid genome evolution, the movement of endosymbiont genes to the "host" nuclear genome (endosymbiotic gene transfer), and plastid spread throughout the eukaryotic tree of life. Here we review these aspects of plastid evolution with a focus on understanding early events in plastid endosymbiosis.

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Is Open Access

IPC – Isoelectric Point Calculator

Lukasz P. Kozlowski (2016)

Background Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, pI estimation can be helpful during protein crystallization trials. Results Here, I present the Isoelectric Point Calculator (IPC), a web service and a standalone program for the accurate estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including two new computationally optimized pKa sets. According to the presented benchmarks, the newly developed IPC pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Moreover, the prediction of pI using the IPC pKa’s leads to fewer outliers, i.e., predictions affected by errors greater than a given threshold. Conclusions The IPC service is freely available at http://isoelectric.ovh.org Peptide and protein datasets used in the study and the precalculated pI for the PDB and some of the most frequently used proteomes are available for large-scale analysis and future development. Reviewers This article was reviewed by Frank Eisenhaber and Zoltán Gáspári Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0159-9) contains supplementary material, which is available to authorized users.

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Author and article information

Contributors

Tapan Kumar Mohanta: nostoc.tapan@gmail.com , tapan.mohanta@unizwa.edu.om

Abdullatif Khan: abdullatif@unizwa.edu.om

Abeer Hashem: habeer@ksu.edu.sa

Elsayed Fathi Abd_Allah: eabdallah@ksu.edu.sa

Ahmed Al-Harrasi: aharrasi@unizwa.edu.om

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 5 August 2019

Publication date PMC-release: 5 August 2019

Publication date Collection: 2019

Volume: 20

Electronic Location Identifier: 631

Affiliations

[1 ]GRID grid.444752.4, Natural and Medical Science Research Centre, , University of Nizwa, ; 616 Nizwa, Oman

[2 ]ISNI 0000 0004 1773 5396, GRID grid.56302.32, Botany and Microbiology Department, , King Saud University, ; Riyadh, 11451 Saudi Arabia

[3 ]ISNI 0000 0004 1773 5396, GRID grid.56302.32, Plant Production Department, , King Saud University, ; Riyadh, 11451 Saudi Arabia

Article

Publisher ID: 5983

DOI: 10.1186/s12864-019-5983-8

PMC ID: 6681478

PubMed ID: 31382875

SO-VID: a4a44a42-a10d-42ce-95ef-0fae902f6d0c

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 2 May 2019

Date accepted : 17 July 2019

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: proteome,amino acids,isoelectric point,molecular weight,selenocysteine,pyrrolysine

Data availability:

ScienceOpen disciplines: Genetics

Keywords: proteome, amino acids, isoelectric point, molecular weight, selenocysteine, pyrrolysine

The molecular mass and isoelectric point of plant proteomes

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Abstract

Background

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Electronic supplementary material

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Genes & Diseases

Most cited references 63

New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants.

The origin and establishment of the plastid in algae and plants.

IPC – Isoelectric Point Calculator

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