Comparative Proteomic Analysis of Cotton Fiber Development and Protein Extraction Method Comparison in Late Stage Fibers

A cell fractionation and quantitative proteomics pipeline to enable functional analyses of cotton fiber development

Cotton fibers are aerial trichoblasts that employ a highly polarized diffuse growth mechanism to emerge from the developing ovule epidermis. After executing a complicated morphogenetic program, the cells reach lengths over 2 cm and serve as the foundation of a multi-billion-dollar textile industry. Important traits such as fiber diameter, length, and strength are defined by the growth patterns and cell wall properties of individual cells. At present, the ability to engineer fiber traits is limited by our lack of understanding regarding the primary controls governing the rate, duration, and patterns of cell growth. To gain insights into the compartmentalized functions of proteins in cotton fiber cells, we developed a label-free liquid chromatography mass spectrometry method for systems-level analyses of fiber proteome. Purified fibers from a single locule were used to fractionate the fiber proteome into apoplast (APOT), membrane-associated (p200), and crude cytosolic (s200) fractions. Subsequently, proteins were identified, and their localizations and potential functions were analyzed using combinations of size exclusion chromatography, statistical and bioinformatic analyses. This method had good coverage of the p200 and APOT fractions, the latter of which was dominated by proteins associated with particulate membrane-enclosed compartments. The apoplastic proteome was diverse, the proteins were not degraded, and some displayed distinct multimerization states compared to their cytosolic pool. This quantitative proteomic pipeline can be used to improve coverage and functional analyses of the cotton fiber proteome as a function of developmental time or differing genotypes.

Comparing and integrating TMT-SPS-MS3 and label-free quantitative approaches for proteomics scrutiny in recalcitrant Mango (Mangifera indica L.) peel tissue during postharvest period

Despite substantial advances in the use of proteomic technologies, their widespread application in fruit tissues of non-model and recalcitrant species remains limited. This hampers the understanding of critical molecular events during the postharvest period of fleshy tropical fruits. Therefore, we evaluated label-free quantitation (LFQ) and TMT-SPS-MS3 (TMT) approaches to analyse changes in the protein profile of mango peels during postharvest period. We compared two extraction methods (phenol and chloroform/methanol) and two peptide fractionation schemes (SCX and HPRP). We accurately identified 3065 proteins, of which, 1492 were differentially accumulated over at 6 days after harvesting (DAH). Both LFQ and TMT approaches share 210 differential proteins including cell wall proteins associated with fruit softening, as well as aroma and flavour-related proteins, which were increased during postharvest period. The phenolic protein extraction and the high-pH reverse-phase peptide fractionation was the most effective pipeline for relative quantification. Nevertheless, the information provided by the other tested strategies was significantly complementary. Besides, LFQ spectra allowed us to track down intact N-glycopeptides corroborating N-glycosylations on the surface of a desiccation-related protein. This work represents the largest proteomic comparison of mango peels during postharvest period made so far, shedding light on the molecular foundation of edible fruit during ripening.

Mitochondrial proteomic analysis reveals that proteins relate to oxidoreductase activity play a central role in pollen fertility in cotton

Cotton (Gossypium hirsutum L.) is an important economic crop. Cytoplasm male sterility (CMS) has been used to develop hybrid system and to produce hybrid seeds in cotton, but the molecular mechanism of CMS remains unclear. Mitochondria are semi-autonomous organelles, which play an important role in the reproduction of flowering plants. Male sterility has been proved associated with mitochondrial dysfunction in plants. In present study, a new strategy of proteomic sequencing data-independent acquisition (DIA) was used to analysis protein abundance across CMS lines 2074A (cytoplasm of Gossypium harknessii, D_2-2) and 2074S (cytoplasm of G. hirsutum, AD₁), and their maintainer 2074B. Comparing with transcriptome results showed that there is little consistence between proteome and transcriptome. A total of 2095 protein species were identified in three materials, and 186 and 161 differentially proteins were detected in the comparisons of 2074A vs 2074B, and 2074S vs 2074B, respectively. Among them, 49 and 50 proteins were specific existed in anther, and mainly participated in oxidoreductase activity, carbohydrate metabolism, fatty acid metabolism, cell aging, wax or cutin deposition and signal transduction. Gh_A07G0770 and Gh_D05G1908 were specific up-regulated in sterility lines, and the other genes Gh_D08G1196, Gh_D12G1971, Gh_A11G1250, Gh_D08G0388 were down-regulated, which presented similar expression tendency verified by qRT-PCR, transcriptome and proteome results. These six genes related to lipid synthesis, response to oxidative stress and cell aging, suggested them being involved in CMS occurrence. Using virus-induced gene silencing (VIGS) system, sterility obtained demonstrated the silencing Gh_A11G1250 in maintainer 2074B led to partial anthers abortion. Gh_A11G1250 encoded a mitochondrial localization of peroxisomal-like protein, participated in response to reactive oxygen species (ROS). Twenty-two proteins interacting with Gh_A11G1250 mainly related to chlorophyll biosynthetic process, photoperiodism and flowering, which showed different expression pattern between the male sterile line 2074A and maintainer 2074B. This novel research based on mitochondrial proteomics comparison confirmed that DAPs related to oxidative stress are critical to pollen abortion. BIOLOGICAL SIGNIFICANCE: Cytoplasm male sterility (CMS) system is utilized widely for hybrid production in cotton. However, the genetic and molecular mechanisms of CMS still need to be further elucidated. Up till now, fewer comprehensive comparisons of the mitochondrial proteomes from cotton CMS line and maintainer line have been reported. In this study, we performed a novel comparison of mitochondrial protein profiles in two CMS lines and their common maintainer line. Based on our results, we found a potential protein related to oxidative stress led to the anthers abortion. These results accumulate data to interpret the molecular mechanisms of CMS in cotton.

Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development

BACKGROUND

Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development.

RESULTS

In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development.

CONCLUSION

The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality.

Plant Systems Biology at the Single-Cell Level

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.

Comparative proteomic analyses of Asian cotton ovules with attached fibers in the early stages of fiber elongation process

BACKGROUND

Plenty of proteomic studies were performed to characterize the allotetraploid upland cotton fiber elongation process, whereas little is known about the elongating diploid cotton fiber proteome.

METHODS

In this study, we used a two-dimensional electrophoresis-based comparative proteomic approach to profile dynamic proteomes of diploid Asian cotton ovules with attached fibers in the early stages of fiber elongation process. One-way ANOVA and Student-Newman-Keuls test were used to find the differentially displayed protein (DDP) spots.

RESULTS

A total of 55 protein spots were found having different abundance ranging from 1 to 9 days post-anthesis (DPA) in a two-day interval. These 55 DDP spots were all successfully identified using high-resolution mass spectrometric analyses. Gene ontology analyses revealed that proteoforms involved in energy/carbohydrate metabolism, redox homeostasis, and protein metabolism are the most abundant. In addition, orthologues of the 13 DDP spots were also found in differential proteome of allotetraploid elongating cotton fibers, suggesting their possible essential roles in fiber elongation process.

CONCLUSIONS

Our results not only revealed the dynamic proteome change of diploid Asian cotton fiber and ovule during early stages of fiber elongation process but also provided valuable resource for future studies on the molecular mechanism how the polyploidization improves the trait of fiber length.