Seeing Is Believing: Opportunities, Challenges, and Solutions in Plant Cell Biology

The past few decades have witnessed dramatic leaps in our understanding of plant biology, especially in the areas of plant growth and development. This is largely due to the establishment of Arabidopsis as an experimental system for basic and translational research. The knowledge gained has far-reaching implications for understanding the fundamental molecular and genetic principles of biological processes and practical implications for various economically important crops. Tremendous advances in genetics, genomics, proteomics, and metabolomics technologies have also paved the way to an increased understanding of cellular networks. However, lagging behind is a clear view of dynamic activities at the cellular level during plant growth and development. Multicellular organisms depend on numerous intricate cellular processes, and thus the challenges for plant cell biology are similar to those of general cell biology: both require the development of dynamic, sensitive, and quantitative technologies to fully understand how cells work, communicate, and assemble into functional tissues. Plant cell biologists, however, are facing some unique challenges. Natasha Raikhel As multicellular organisms, plants possess many specialized cell types, each surrounded by cell walls and organized into functional tissues and organs. The cell walls act as defensive barriers and also provide many crucial biological benefits such as the ability to grow upright and maintain water. At the same time, cell wall barriers make it difficult to effectively apply the state-of-the-art, time- and space-resolved microscopy methods that have been used successfully in animal systems. The specific wavelength absorption properties of cell walls and chloroplasts (thermal damage), as well as the presence of many layers of nonhomogenous cells in plant organs, such as leaves and roots, limit the use of multiphoton technology, which is necessary for live-cell imaging in deep tissues. Cultured plant cell preparations display altered cell wall compositions and intrinsic properties compared with differentiated progenitor cells and may not recapitulate cellular behaviors in the intact organism. Thus, plant cell biologists need a microscope that addresses these specific, significant limitations. Such a “dream” microscope would incorporate multiple wavelength, such as uv visible and infrared, allowing visualization of many fluorescent probes simultaneously deep inside living plant tissues. In addition, collection of data at multiple spatial and temporal scales and sites would be of immense value to plant biologists at large. Such an instrument would allow scientists to make observations in real time at the subcellular level and at multiple sites of interest, even in tissues that are as complex as the root and the shoot, and thus bridge the gap between cell biology and development. Quantitative image analysis and computational informatic tools must be developed in parallel with instrument development to convert the visual data to meaningful measurements. Finally, to obtain the greatest benefit from these new technologies, plant biologists need to develop genetically encoded optical sensors to see where signaling pathways are activated and to quantify small molecules such as plant hormones or secondary metabolites. With these tools scientists could test hypotheses after genetically or chemically perturbing the system. This would permit the identification of genetic mutations and small molecules that affect cellular processes at the submicron level. Ideally, if automation could be effective enough, such an instrument would be able to handle moderate or high-throughput screening. Using data collected from various tissues and various environmental conditions, plant biologists would be able to create an extensive database of static and dynamic images for automated analysis of protein subcellular localization and to develop search engines based on both keywords and image recognition. A virtual plant cell with maps and videos for all subcellular structures and macromolecular complexes and their markers, as well as the locations and dynamics of all characterized plant proteins, could be created. This framework will allow us to see the big picture of known and unknown processes and how they fit together. It is needed for general comprehension of biological principles for education and for more specialized use by plant cell biologists as a toolkit. With these new technologies in hand, plant cell biologists can answer numerous outstanding questions including some of the following: How do underlying cellular processes control and modulate developmental signals and decisions? How are fundamental processes like oriented cell division, cell expansion, cell polarity and asymmetric cell division, and differentiation controlled? What is the role of vesicular trafficking in coordinating these multiple events in plant growth and development? How are plant cell walls synthesized and assembled? How do plant cells defend themselves from pathogen attack and environmental stress? What is the underlying molecular mechanism for the totipotency of plant somatic cells (the ability of somatic cells or differentiated cells to become an embryo)? What cytosolic, nonorganellar complexes—mega-enzyme complexes involved in biosynthetic processes, signaling scaffolds, and in organizing and coordinating other complex processes—have yet to be discovered? What are the roles of chromatin modification and nuclear architecture in development? Viewing the organism as a system based on cellular events, how do plant cells coordinate multiple levels of regulation, i.e., signaling, protein degradation, chromatin remodeling, transcription, and posttranscriptional regulation? How is growth and/or senescence within an organ coordinated? Finally, as a practical matter, what are the best ways to incorporate data from the subcellular to organ and then to organismal levels to gain a broader systems view of life?