Journal of Data Mining in Genomics & Proteomics

Short Commentary on: Comparative Proteomics of Mesembryanthemum crystallinum Guard Cells and Mesophyll Cells in the Transition from C3 to CAM

Qijie Guan^1,2,3, Bowen Tan², Jingkui Tian^2,4* and Sixue Chen^{3,5* 1}National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
²College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China
³Department of Biology, University of Florida, Gainesville 32610, USA
⁴Key Lab for Biomedical Engineering of Ministry of Education, Zhejiang-Malaysia Joint Research Center for Traditional Medicine, Zhejiang University, Hangzhou 310027, China
⁵Genetics Institute, Genetics Institute, Plant Molecular and Cellular Program, University of Florida, Gainesville 32610, USA
^*Correspondence: Jingkui Tian, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, Email: Sixue Chen, Genetics Institute, Genetics Institute, Plant Molecular and Cellular Program, University of Florida, Gainesville 32610, USA, Email:

Received: 05-Jan-2021 Published: 26-Jan-2021, DOI: 10.35248/2153-0602.21.12.234

Description

Although isobaric chemical labeling proteomics approaches like TMT and iTRAQ have better performance in multiplexing, they are quite costly and require extra experimental steps such as in vitro N-hydroxysuccinimide chemical reaction. In this study, we applied a label-free quantitative proteomics method [1,2]. Guard cells respond to complex interplay of signals, and guard cell proteomics may reveal interesting protein changes underlying the responses [3]. Computational methods can be useful in normalizing label-free proteomics data and using relative quantification to determine proteins involved in the biological processes. Here we developed a method to select and cluster proteins that exhibit temporal inverse abundances during the ice plant photosynthetic transition from C3 to Crassulacean Acid Metabolism (CAM).

A workflow designed to analyze inverse protein abundance patterns (Figure 1) was applied to M. crystallinum guard cells and mesophyll cells during the C3 to CAM transition induced by salt stress [4]. First, the raw data were analyzed using Proteome Discoverer 2.3 and the peak area for each protein was used for quantification. To analyze the changes of diel protein abundance in the two cell-types during the transition, median normalization followed by z-score transformation was used as a normalization method. Secondly, proteins have Person Correlation Coefficient (PCC) score less than -0.8 were selected as inversely expressed proteins [5] in the analysis of temporal changes of proteins during the C3-CAM transition (control versus treatment) in guard cells and mesophyll cells. Out of a total of 1153 identified proteins, 165 and 151 proteins showed inversed protein change patterns in guard cells and mesophyll cells, respectively. Thirdly, clustering of k-means based on Euclidean distance for control group proteins, in which each time point acts as a dimension, was used as the clustering method. Lastly, each cluster was analyzed using Gene Ontology (GO) enrichment [6] so that the functional aspects of the changed proteins in each cell type could be analyzed.

Figure 1: Workflow for the analysis of inverse protein abundance patterns in M. crystallinumguard cells and mesophyll cells during the C3 to CAM transition.

According to our proteomic result, the light response proteins in guard cells showed inversed abundance patterns during the transition, while those in mesophyll cells did not. This result is consistent with the inversed stomata movement behavior in the CAM plants [7]. Based on the protein changing patterns and the transition taking place before day 7 of treatment [8], we focused on cluster 3 of guard cell proteins and cluster 4 of mesophyll cell proteins. Another interesting finding from the enriched GO functions in two clusters is that ATP binding proteins and zinc ion binding proteins in two cell-types had very similar abundance changing patterns. This result indicates that there are common processes in the guard cells and mesophyll cells during the C3 to CAM transition.

Limitations

Our results highlight that the mechanisms underlying the shift from C3 to CAM in the two cell-types in M. crystallinum are different. A stringent cutoff of PCC was used to filter the proteins with the inversed patterns. However, some other potentially useful information may be sifted out. In addition, functional testing using reverse genetics in ice plant is challenging. Developing a model system (e.g., Kalanchoe blossfeldiana in Crassulaceae [9,10] for functional analysis of the candidate proteins in the C3 to CAM transition is needed.

Acknowledgements

This work was supported by a University of Florida Faculty Retention Fund, the China Scholarship Council (201706320126, 201506610004), the National Science and Technology Major Project of China (2019ZX09301004), National Science Foundation of China (81872973).

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