Comparative Analyses of Extracellular Matrix Proteome: An Under-Explored Area in Plant Research

Narula, Kanika; Elagamey, Eman; Datta, Asis; Chakraborty, Niranjan; Chakraborty, Subhra

doi:10.5772/37502

Cited by 4 publications

(4 citation statements)

References 73 publications

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“…The field of proteomics is evolving from cataloguing the proteins under static conditions to comparative analyses (Narula et al, 2012). Defining proteins that change in abundance, form, location or other activities may indicate the presence and functional significance of a protein.…”

Section: What Have We Learnt?mentioning

confidence: 99%

Comparative analyses of nuclear proteome: extending its function

Narula¹,

Datta²,

Chakraborty³

et al. 2013

Front. Plant Sci.

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Organeller proteomics is an emerging technology that is critical in determining the cellular signal transduction pathways. Nucleus, the regulatory hub of the eukaryotic cell is a dynamic system and a repository of various macromolecules that serve as modulators of such signaling that dictate cell fate decisions. Nuclear proteins (NPs) are predicted to comprise about 10–20% of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. Indeed, NPs constitute a highly organized but complex network that plays diverse roles during development and physiological processes. In plants, relatively little is known about the nature of the molecular components and mechanisms involved in coordinating NP synthesis, their action and function. Proteomic study hold promise to understand the molecular basis of nuclear function using an unbiased comparative and differential approach. We identified a few hundred proteins that include classical and non-canonical nuclear components presumably associated with variety of cellular functions impinging on the complexity of nuclear proteome. Here, we review the nuclear proteome based on our own findings, available literature, and databases focusing on detailed comparative analysis of NPs and their functions in order to understand how plant nucleus works. The review also shed light on the current status of plant nuclear proteome and discusses the future prospect.

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Section: What Have We Learnt?mentioning

confidence: 99%

Comparative analyses of nuclear proteome: extending its function

Narula¹,

Datta²,

Chakraborty³

et al. 2013

Front. Plant Sci.

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“…Of these, 489 are involved in dehydration, while 20 proteins were identified under cold stress. − Organellar proteomics is essential for both a complete understanding of organelle function and the detection of dynamic changes that may occur during various responses. Applications of this methodology to isolate nucleus, extracellular matrix (ECM), and secretory systems have produced insights into the identity and possible function of these organelles (as reviewed in refs − ). These studies identified 91 proteins from total elements of the cell, whereas 388 proteins were identified from the ECM, 479 from the nucleus, and 91 from the membrane.…”

Section: Agricultural Problems and The Current Status Of Crop Proteomicsmentioning

confidence: 99%

“…Organ level proteomics [200][201][202] ). These studies identified 91 proteins from total element of the cell, whereas 388 proteins were identified from the ECM, 479 proteins were identified from the nucleus and 91 proteins were identified from the membrane.…”

Section: The Current Status Of Proteomics In Chickpeamentioning

confidence: 99%

Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives

et al. 2015

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ABSTRACT:In the rapidly growing economies of Asia and Oceania, food security has become a primary concern. With the rising population, growing more food at affordable prices is becoming even more important. In addition, the predicted climate change will lead to drastic changes in global surface temperature and changes in rainfall patterns that in turn would pose a serious threat to plant vegetation worldwide.As a result, understanding how plants will survive in a changing climate will be increasingly important. Such challenges require integrated approaches to increase agricultural production and cope with environmental threats. Proteomics can play a role in unravel the underlying mechanisms for food production to address the growing demand for food. In this review, the current status of food crop proteomics is discussed, especially in regards to the Asia and Oceania regions. Furthermore, the future perspective in relation to proteomic techniques for the important food crops is highlighted.

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“…ECM proteins comprise less than 10% of cell wall dry weight [2] and represent a comprehensive catalog of the cell wall proteins that spread throughout the extracellular milieu and range from highly mobile with no apparent interaction, to covalently-bound proteins. ECM protein populations of many plant organs and tissues have been reported [3,4,5,6,7] together with detailed methodologies to optimize extraction [8,9,10]. In fact, different ECM proteins, particularly phosphoprotein epitopes, are not evenly distributed (or accessible) within the cell wall, nor are these epitopes distributed uniformly across two adjacent walls [11].…”

Section: Introductionmentioning

confidence: 99%

Extracellular Matrix Proteome and Phosphoproteome of Potato Reveals Functionally Distinct and Diverse Canonical and Non-Canonical Proteoforms

et al. 2016

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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.

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Comparative Analyses of Extracellular Matrix Proteome: An Under-Explored Area in Plant Research

Cited by 4 publications

References 73 publications

Comparative analyses of nuclear proteome: extending its function

Comparative analyses of nuclear proteome: extending its function

Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives

Extracellular Matrix Proteome and Phosphoproteome of Potato Reveals Functionally Distinct and Diverse Canonical and Non-Canonical Proteoforms

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