Environmental Transformations and Interactions
Uncovering the Spatial Gene Expression of Major Cell Types from the Stems of Sorghum
Generation of the first comprehensive gene expression atlas of major types of cells from the stems of the sorghum plant sets up the ability for engineering sorghum to increase its bioenergy potential.
A fluorescence probe indicates the spatial expression location of the homeodomain gene KNAT1 as yellow sparkles on a thin slice of part of a sorghum bicolor shoot apex attached with several nascent leaves. Tissue anatomical structure is viewed by nuclei stained in blue. (Image courtesy of Brandon James | HudsonAlpha Institute for Biotechnology)
The Science
Sorghum is a well-known sustainable resource for the production of biofuels and bioproducts. The plant’s stem, however, is an overlooked type of plant tissue with great engineering potential for the production of these products. Stems accumulate high levels of sucrose that could be used to create bioethanol and useful biopolymers, but more information is needed about the expression and regulation of the genes in the major types of cells in stems. A multi-institutional team of researchers used laser capture microdissection combined with transcriptome analysis to examine five cell types from the stems of sorghum to increase understanding of the genetics and regulatory pathways of these types of cells. The team examined gene expression profiles across different types of cells and the regulatory networks that control them. Their research revealed gene expression patterns, how cell wall accumulation is regulated in different parts of the plant, as well as what controls cell-type-specific gene expression across the stem.
The Impact
The team successfully generated the first comprehensive gene expression atlas of the sorghum stem, which revealed cell-type-specific expression patterns, pathways, and underlying regulatory networks. This was achieved using innovative approaches developed by researchers at the Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy Office of Science user facility, which overcame inherent challenges associated with the properties of mature sorghum stems. This new high-throughput gene expression dataset can be used to generate new hypotheses and explore many scientific questions related to the genetic and biochemical pathways of stems from various types of grasses. For example, researchers identified promoter elements that can be used to directly produce genes of novel bioproducts in a cell-type-specific manner. The team also developed an Rshiny website to enable convenient data exploration and mining for the scientific community.
Summary
Sorghum stems have great engineering potential for bioproduct production. However, mature sorghum stems have rigid cell walls that make it challenging to apply commonly used single cell techniques, which are needed to obtain detailed cellular information for targeted engineering. To overcome this challenge, in collaboration with EMSL researchers, a multi-institutional team developed a protocol to isolate cell types for deep sequencing analysis. Using cryosectioning followed by laser capture microdissection, the team isolated five cell types across the sorghum stem for deep sequencing with NextSeq 500/550. The high-quality, cell-type-specific transcriptome profiles were analyzed using the Tau index in combination with the Wilcoxon test to identify genes uniquely expressed in only one cell type. The analysis revealed expression patterns that distinguished vascular versus nonvascular cells. Secondary cell wall accumulation appeared to be differently regulated in the sclerenchyma (supporting tissues) compared to the epidermis (outermost layer of cells covering the stem). Additionally, the team found that different transcription factor families appear to control the cell-type-specific expression of genes across the stem.
Contacts
Amy Marshall-Colon, University of Illinois Urbana-Champaign, amymc@illinois.edu
Kankshita Swaminathan, HudsonAlpha Institute for Biotechnology, kswaminathan@hudsonalpha.org
William Chrisler, Pacific Northwest National Laboratory, william.chrisler@pnnl.gov
Funding
This work was funded by the DOE Center for Advanced Bioenergy and Bioproducts Innovation and the DOE Great Lakes Bioenergy Research Center. A portion of this research was performed on a Large-Scale Research award from EMSL, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program.
Publication
J. Fu, et al. "Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems." The Plant Journal 118, 1668–1688 (2024) [DOI: 10.1111/tpj.16690]