Special Issue "Sub-cellular Proteomics"

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (31 March 2016)

Special Issue Editor

Guest Editor
Assoc. Prof. Nicolas L. Taylor

ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences & The Institute of Agriculture, The University of Western Australia, Crawley, WA 6009, Australia
Website | E-Mail
Interests: plant mitochondria; subcellular fractionation; protein; lipid and metabolite mass spectrometry; plant metabolism; abiotic stress; yield

Special Issue Information

Dear Colleagues,

Despite the increasing sensitivity of mass spectrometers released by instrument manufacturers, the challenge to identify all of the proteins in an organism remains unattained. Whilst typical whole organism studies do regularly characterize the top ~3000 most abundant proteins the remaining proteins are typically beyond the limited dynamic range of the current generation of mass spectrometers (typically ~103–104). To overcome this limitation and begin to identify these proteins, researchers have employed a number of strategies to reduce sample complexity and/or deplete high abundance proteins before undertaking proteomic analyses. Typically, these rely on combinations of tissue selection, subcellular fractionation and/or physiochemical separations of proteins. Whilst all of these approaches have merit, increasingly researchers are turning towards targeted enrichment of specific organellar or structure proteomes rather than selecting proteins based on parameters such as size, charge or chemical affinity. The major advantage of this approach is that the proteins that constitute these subcellular proteomes are likely to cooperate in a similar set of biochemical processes, because specific cellular functions are typically compartmentalized into discrete subcellular locations. Therefore, profiling these sets of functionally related proteins via proteomics approaches enables researchers to gather deeper information within a narrower set of biological pathways. This contrasts with data generated by whole-organism proteomics approaches, which typically gather shallow information across a wide range of biological processes. These subcellular proteomes provide insights into their function during disease or following various treatments and ultimately contribute to the wider understanding of the entire organism. This Special Issue aims to bring together the latest developments and approaches for the analysis of subcellular proteomes and to review our current understanding of subcellular proteomic analysis techniques.

Dr. Nicolas Taylor
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 550 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • Subcellular Proteomics
  • Organelle
  • Quantitative Proteomics
  • Mass Spectrometry
  • Subcellular fractionation

Published Papers (6 papers)

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Research

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Open AccessArticle Comparative “Golgi” Proteome Study of Lolium multiflorum and Populus trichocarpa
Received: 23 May 2016 / Revised: 8 July 2016 / Accepted: 8 July 2016 / Published: 20 July 2016
Cited by 1 | PDF Full-text (2974 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Golgi apparatus (GA) is a crucial organelle in the biosynthesis of non-cellulosic polysaccharides, glycoproteins and proteoglycans that are primarily destined for secretion to the cell surface (plasma membrane, cell wall and apoplast). Only a small proportion of the proteins involved in these
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The Golgi apparatus (GA) is a crucial organelle in the biosynthesis of non-cellulosic polysaccharides, glycoproteins and proteoglycans that are primarily destined for secretion to the cell surface (plasma membrane, cell wall and apoplast). Only a small proportion of the proteins involved in these processes have been identified in plants, with the majority of their functions still unknown. The availability of a GA proteome would greatly assist plant biochemists, cell and molecular biologists in determining the precise function of the cell wall-related proteins. There has been some progress towards defining the GA proteome in the model plant system Arabidopsis thaliana, yet in commercially important species, such as either the cereals or woody species there has been relatively less progress. In this study, we applied discontinuous sucrose gradient centrifugation to partially enrich GA from suspension cell cultures (SCCs) and combined this with stable isotope labelling (iTRAQ) to determine protein sub-cellular locations. Results from a representative grass species, Italian ryegrass (Lolium multiflorum) and a dicot species, black cottonwood (Populus trichocarpa) are compared. The results confirm that membrane fractionation approaches that provide effective GA-enriched fractions for proteomic analyses in Arabidopsis are much less effective in the species examined here and highlight the complexity of the GA, both within and between species. Full article
(This article belongs to the Special Issue Sub-cellular Proteomics)
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Open AccessArticle Understanding the Remodelling of Cell Walls during Brachypodium distachyon Grain Development through a Sub-Cellular Quantitative Proteomic Approach
Received: 28 April 2016 / Revised: 16 June 2016 / Accepted: 20 June 2016 / Published: 24 June 2016
Cited by 4 | PDF Full-text (2290 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Brachypodium distachyon is a suitable plant model for studying temperate cereal crops, such as wheat, barley or rice, and helpful in the study of the grain cell wall. Indeed, the most abundant hemicelluloses that are in the B. distachyon cell wall of grain
[...] Read more.
Brachypodium distachyon is a suitable plant model for studying temperate cereal crops, such as wheat, barley or rice, and helpful in the study of the grain cell wall. Indeed, the most abundant hemicelluloses that are in the B. distachyon cell wall of grain are (1-3)(1-4)-β-glucans and arabinoxylans, in a ratio similar to those of cereals such as barley or oat. Conversely, these cell walls contain few pectins and xyloglucans. Cell walls play an important role in grain physiology. The modifications of cell wall polysaccharides that occur during grain development and filling are key in the determination of the size and weight of the cereal grains. The mechanisms required for cell wall assembly and remodelling are poorly understood, especially in cereals. To provide a better understanding of these processes, we purified the cell wall at three developmental stages of the B. distachyon grain. The proteins were then extracted, and a quantitative and comparative LC-MS/MS analysis was performed to investigate the protein profile changes during grain development. Over 466 cell wall proteins (CWPs) were identified and classified according to their predicted functions. This work highlights the different proteome profiles that we could relate to the main phases of grain development and to the reorganization of cell wall polysaccharides that occurs during these different developmental stages. These results provide a good springboard to pursue functional validation to better understand the role of CWPs in the assembly and remodelling of the grain cell wall of cereals. Full article
(This article belongs to the Special Issue Sub-cellular Proteomics)
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Open AccessArticle Extracellular Matrix Proteome and Phosphoproteome of Potato Reveals Functionally Distinct and Diverse Canonical and Non-Canonical Proteoforms
Received: 27 March 2016 / Revised: 6 June 2016 / Accepted: 13 June 2016 / Published: 24 June 2016
Cited by 3 | PDF Full-text (1980 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The extracellular matrix (ECM) has a molecular machinery composed of diverse proteins and proteoforms that combine properties of tensile strength with extensibility exhibiting growth-regulatory functions and self- and non-self-recognition. The identification of ECM proteoforms is the prerequisite towards a comprehensive understanding of biological
[...] Read more.
The extracellular matrix (ECM) has a molecular machinery composed of diverse proteins and proteoforms that combine properties of tensile strength with extensibility exhibiting growth-regulatory functions and self- and non-self-recognition. The identification of ECM proteoforms is the prerequisite towards a comprehensive understanding of biological functions accomplished by the outermost layer of the cell. Regulatory mechanisms of protein functions rely on post-translational modifications, phosphorylation in particular, affecting enzymatic activity, interaction, localization and stability. To investigate the ECM proteoforms, we have isolated the cell wall proteome and phosphoproteome of a tuberous crop, potato (Solanum tuberosum). LC-MS/MS analysis led to the identification of 38 proteins and 35 phosphoproteins of known and unknown functions. The findings may provide a better understanding of biochemical machinery and the integrated protein and phosphoprotein network of ECM for future functional studies of different developmental pathways and guidance cues in mechanosensing and integrity signaling. Full article
(This article belongs to the Special Issue Sub-cellular Proteomics)
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Review

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Open AccessReview Extraction and Characterization of Extracellular Proteins and Their Post-Translational Modifications from Arabidopsis thaliana Suspension Cell Cultures and Seedlings: A Critical Review
Received: 4 July 2016 / Revised: 25 August 2016 / Accepted: 26 August 2016 / Published: 1 September 2016
Cited by 4 | PDF Full-text (1973 KB) | HTML Full-text | XML Full-text
Abstract
Proteins secreted by plant cells into the extracellular space, consisting of the cell wall, apoplastic fluid, and rhizosphere, play crucial roles during development, nutrient acquisition, and stress acclimation. However, isolating the full range of secreted proteins has proven difficult, and new strategies are
[...] Read more.
Proteins secreted by plant cells into the extracellular space, consisting of the cell wall, apoplastic fluid, and rhizosphere, play crucial roles during development, nutrient acquisition, and stress acclimation. However, isolating the full range of secreted proteins has proven difficult, and new strategies are constantly evolving to increase the number of proteins that can be detected and identified. In addition, the dynamic nature of the extracellular proteome presents the further challenge of identifying and characterizing the post-translational modifications (PTMs) of secreted proteins, particularly glycosylation and phosphorylation. Such PTMs are common and important regulatory modifications of proteins, playing a key role in many biological processes. This review explores the most recent methods in isolating and characterizing the plant extracellular proteome with a focus on the model plant Arabidopsis thaliana, highlighting the current challenges yet to be overcome. Moreover, the crucial role of protein PTMs in cell wall signalling, development, and plant responses to biotic and abiotic stress is discussed. Full article
(This article belongs to the Special Issue Sub-cellular Proteomics)
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Open AccessReview Protein Dynamics in the Plant Extracellular Space
Received: 28 May 2016 / Revised: 7 July 2016 / Accepted: 7 July 2016 / Published: 13 July 2016
Cited by 4 | PDF Full-text (2310 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The extracellular space (ECS or apoplast) is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF). The present review is focused on APF proteomics papers and intends to draw information
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The extracellular space (ECS or apoplast) is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF). The present review is focused on APF proteomics papers and intends to draw information on the metabolic processes occurring in the ECS under abiotic and biotic stresses, as well as under non-challenged conditions. The large majority of the proteins detected are involved in “cell wall organization and biogenesis”, “response to stimulus” and “protein metabolism”. It becomes apparent that some proteins are always detected, irrespective of the experimental conditions, although with different relative contribution. This fact suggests that non-challenged plants have intrinsic constitutive metabolic processes of stress/defense in the ECS. In addition to the multiple functions ascribed to the ECS proteins, should be considered the interactions established between themselves and with the plasma membrane and its components. These interactions are crucial in connecting exterior and interior of the cell, and even simple protein actions in the ECS can have profound effects on plant performance. The proteins of the ECS are permanently contributing to the high dynamic nature of this plant compartment, which seems fundamental to plant development and adaptation to the environmental conditions. Full article
(This article belongs to the Special Issue Sub-cellular Proteomics)
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Open AccessReview Mitochondrial Proteome Studies in Seeds during Germination
Received: 1 May 2016 / Revised: 9 June 2016 / Accepted: 16 June 2016 / Published: 21 June 2016
Cited by 4 | PDF Full-text (563 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is
[...] Read more.
Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination. Full article
(This article belongs to the Special Issue Sub-cellular Proteomics)
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