Removal of high‐abundance proteins for nuclear subproteome studies in rice (<b><i>Oryza sativa</i></b>) endosperm

Li, Guosheng; Nallamilli, Babi Ramesh Reddy; Tan, Feng; Peng, Zhaohua

doi:10.1002/elps.200700412

Cited by 44 publications

(69 citation statements)

References 46 publications

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“…To determine how many Pack-MULEs are translated, we collected peptide sequences that represent 3230 rice proteins from recent proteomic analyses in rice (Koller et al, 2002;Chitteti and Peng, 2007;Lee et al, 2007;Tan et al, 2007;Li et al, 2008). The 3230 proteins represent 6% of all of the annotated genes (56,278 genes) based on information from release 5 of rice pseudomolecules from the J. Craig Venter Institute (The Institute for Genome Research [TIGR]).…”

Section: Translation Of Pack-mulesmentioning

confidence: 99%

“…Peptide sequences or accession numbers representing 3230 proteins were downloaded from the relevant references (Koller et al, 2002;Chitteti and Peng, 2007;Lee et al, 2007;Tan et al, 2007;Li et al, 2008) used as queries to search (TBLASTN; Altschul et al, 1990) against all Pack-MULE sequences. Peptide sequences that generated perfect hits with Pack-MULE sequences were then used to search the rice genomic database.…”

Section: Expression Analysismentioning

confidence: 99%

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The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

et al. 2009

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Gene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.

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Section: Translation Of Pack-mulesmentioning

confidence: 99%

Section: Expression Analysismentioning

confidence: 99%

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

et al. 2009

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“…The main problem is the presence of some high-abundance proteins, which are limiting the detection of low-abundance proteins (Peck, 2005). In leaves, Rubisco accumulates up to 40% of total leaf protein (Stitt et al, 2010), and in the seed endosperm, storage proteins are present in massive amounts (Li et al, 2008). But even less extreme examples, like many housekeeping proteins, are present in sufficient amounts to hinder the analysis of lowabundance proteins.…”

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Looking Deep Inside: Detection of Low-Abundance Proteins in Leaf Extracts of Arabidopsis and Phloem Exudates of Pumpkin

et al. 2012

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The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic analysis. In the human field, combinatorial hexapeptide ligand libraries (CPLL; such as ProteoMiner) have been used for reduction of the dynamic range of protein concentrations; however, this technique is not established in plant research. In this work, we present the application of CPLL to Arabidopsis (Arabidopsis thaliana) leaf proteins. One-and two-dimensional gel electrophoresis showed a decrease in high-abundance proteins and an enrichment of less abundant proteins in CPLL-treated samples. After optimization of the CPLL protocol, mass spectrometric analyses of leaf extracts led to the identification of 1,192 proteins in control samples and an additional 512 proteins after the application of CPLL. Upon leaf infection with virulent Pseudomonas syringae DC3000, CPLL beads were also used for investigating the bacterial infectome. In total, 312 bacterial proteins could be identified in infected Arabidopsis leaves. Furthermore, phloem exudates of pumpkin (Cucurbita maxima) were analyzed. CPLL prefractionation caused depletion of the major phloem proteins 1 and 2 and improved phloem proteomics, because 67 of 320 identified proteins were detectable only after CPLL treatment. In sum, our results demonstrate that CPLL beads are a time-and cost-effective tool for reducing major proteins, which often interfere with downstream analyses. The concomitant enrichment of less abundant proteins may facilitate a deeper insight into the plant proteome.

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“…Nonetheless the plant nuclear proteome is still in its infancy particularly with respect to stress tolerance (15,20). In rice, most proteomics studies to date have primarily focused on developing proteome maps and constructing databases of expressed proteins for various organs, tissues, and subcellular components (16,18,24,25), whereas there is far less information available on stress-induced temporal changes.…”

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confidence: 99%

Dehydration-responsive Nuclear Proteome of Rice (Oryza sativa L.) Illustrates Protein Network, Novel Regulators of Cellular Adaptation, and Evolutionary Perspective

Choudhary

Basu

Datta

et al. 2009

Molecular & Cellular Proteomics

134

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Water deficit or dehydration is the most crucial environmental constraint on plant growth and development and crop productivity. It has been postulated that plants respond and adapt to dehydration by altering their cellular metabolism and by activating various defense machineries. The nucleus, the regulatory hub of the eukaryotic cell, is a dynamic system and a repository of various macromolecules that serve as modulators of cell signaling dictating the cell fate decision. To better understand the molecular mechanisms of dehydration-responsive adaptation in plants, we developed a comprehensive nuclear proteome of rice. The proteome was determined using a sequential method of organellar enrichment followed by two-dimensional electrophoresis-based protein identification by LC-ESI-MS/MS. We initially screened several commercial rice varieties and parental lines and established their relative dehydration tolerance. The differential display of nuclear proteins in the tolerant variety under study revealed 150 spots that showed changes in their intensities by more than 2.5-fold. The proteomics analysis led to the identification of 109 differentially regulated proteins presumably involved in a variety of functions, including transcriptional regulation and chromatin remodeling, signaling and gene regulation, cell defense and rescue, and protein degradation. The dehydration-responsive nuclear proteome revealed a coordinated response involving both regulatory and functional proteins, impinging upon the molecular mechanism of dehydration adaptation. Furthermore a comparison between the dehydrationresponsive nuclear proteome of rice and that of a legume, the chickpea, showed an evolutionary divergence in dehydration response comprising a few conserved proteins, whereas most of the proteins may be involved in cropspecific adaptation. These results might help in understanding the spectrum of nuclear proteins and the biological processes they control under dehydration as well as having implications for strategies to improve dehydration tolerance in plants. Molecular

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Removal of high‐abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endosperm

Cited by 44 publications

References 46 publications

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

Looking Deep Inside: Detection of Low-Abundance Proteins in Leaf Extracts of Arabidopsis and Phloem Exudates of Pumpkin

Dehydration-responsive Nuclear Proteome of Rice (Oryza sativa L.) Illustrates Protein Network, Novel Regulators of Cellular Adaptation, and Evolutionary Perspective

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