About

Sally Assmann is the Waller Professor of Biology at Penn State University. Her research focuses on the molecular biology of plant G-proteins and kinases, phytohormone regulation of signal transduction, and RNA processing. She investigates second messenger regulation of ion channels in plant cells, contributing to the understanding of plant signal transduction mechanisms. Her work has provided insights into plant decision-making processes, energy management, and stress responses, with implications for crop improvement and agricultural resilience.

Research topics

• Biology
• Cell biology
• Biochemistry
• Biophysics
• Computer Science
• Chemistry
• Ecology
• Biological system
• Genetics

Selected publications

• Phosphovariants of the canonical heterotrimeric Gα protein, GPA1, differentially affect G protein activity and Arabidopsis development

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-12

  articleOpen accessSenior authorCorresponding

  Abstract Heterotrimeric G protein signaling downstream of receptor-like kinases (RLKs) is an emerging and important signal transduction mechanism in plants. However, little is known about the effects of phosphorylation events on the function of the canonical Gα subunit, GPA1. That several known phosphosites reside within important nucleotide co-factor binding sites suggests a role of phosphorylation in modulating the GTP/GDP binding and hydrolysis cycle of GPA1. To mimic and assess the effects of GPA1 phosphorylation, we created ten different phosphovariants of GPA1 and then comprehensively measured in vitro biochemical activity, in vivo protein-protein interactions, and developmental phenotypes of phosphomutant-complemented Arabidopsis gpa1 null mutants. Our assays confirmed both that phosphovariants of S49 and S52 in the G1 nucleotide binding motif impair GTP and GDP binding, and that the gpa1 morphological phenotypes of reduced etiolated hypocotyl elongation, rounded leaves, and short round flowers are not dependent on the nucleotide status of GPA1. Phosphomimetic mutations at S49, S52, T53, and T164 each exhibited a distinct pattern in complementing gpa1 phenotypes, indicating that GPA1 employs multiple signaling states based on phosphorylation status. The multi-state hypothesis provides a key insight into the mechanism by which a limited repertoire of plant heterotrimeric G protein subunits can transduce a wide variety of signals with exquisite specificity.

  PublisherDOI

• Ca and pH as integrating signals in transport control

  Blackwell eBooks · 2026-02-10

  book-chapter

  Plant transporters are often placed in the context of the functional machinery that maintains the plant. For example, K+ channels are essential for regulating membrane potential and for K+ nutrition, and sucrose transporters are part of the symplastic photosynthate highway. However, it is becoming increasingly clear that, in addition to these ‘maintenance ’ functions, transporters are essential elements of environmental sensing, response and developmental control within the plant body. Our understanding of these regulatory roles has advanced considerably in the last 5 years with the advent of genomic tools that are allowing us to define these transport activities at the molecular level. In this chapter, we will explore the themes of how transporters are involved in developmental processes and control and how environmental signals are processed through transport phenomena.

  PublisherDOI

• Apoplastic metabolomics reveals sugars as mesophyll messengers regulating guard cell ion transport under red light

  Nature Plants · 2025-08-25 · 12 citations

  articleOpen accessSenior author

  Guard cell pairs in the leaf epidermis enclose stomata, microscopic pores mediating CO2 uptake and water loss. Historical data suggest that signals from interior mesophyll tissue may modulate guard-cell regulation of stomatal apertures, but the molecular identity of any metabolite-based signals has remained elusive. We discovered that extracellular (apoplastic) fluid from Arabidopsis thaliana and Vicia faba enhances red-light-induced stomatal opening. Our extensive metabolomics analyses identified 448 apoplastic metabolites; among these, both sugars (photosynthetic products) and maleic acid increased under red light and caused enhanced stomatal opening. Immunohistochemical assays demonstrated sucrose upregulation of H+-ATPase phosphorylation, indicating increased ATPase activity. Patch clamp assays revealed that sucrose inhibits slow anion currents, thus opposing anion efflux. These impacts occurred at sucrose concentrations matching those present endogenously under red light. These regulatory influences promote guard-cell solute import and retention, which drive stomatal opening. Our research thus addresses the decades-long question concerning the existence, identity and mechanistic impact of mesophyll messengers that coordinate photosynthesis with stomatal response. Guard cells define microscopic stomatal pores for CO2 uptake and water loss. Characterization of the extracellular metabolome revealed sugars as ‘mesophyll messengers’ from the leaf interior that enhance stomatal opening via regulation of the guard-cell H+-ATPase and anion channels.

  PublisherOA PDFDOI

• Influence of expression and purification protocols on Gα biochemical activity: kinetics of plant and mammalian G protein cycles

  Frontiers in Molecular Biosciences · 2025-04-07 · 1 citations

  articleOpen accessSenior author

  Heterotrimeric G proteins, composed of Gα, Gβ, and Gγ subunits, are a class of signal transduction complexes with broad roles in human health and agriculturally relevant plant physiological and developmental traits. In the classic paradigm, guanine nucleotide binding to the Gα subunit regulates the activation status of the complex. We sought to develop improved methods for heterologous expression and rapid purification of Gα subunits, initially targeting GPA1, the sole canonical Gα subunit of the model plant species, Arabidopsis thaliana. Compared to conventional methods, our expression methodology and rapid StrepII-tag mediated purification facilitates substantially higher yield, and isolation of protein with increased GTP binding and hydrolysis activities. Human GNAI1 purified using our approach displayed the expected binding and hydrolysis activities, indicating our protocol is applicable to mammalian Gα subunits, potentially including those for which purification of enzymatically active protein has been historically problematic. We subsequently utilized domain swaps of GPA1 and human GNAO1 to demonstrate that the inherent instability of GPA1 is a function of the interaction between the Ras and helical domains. Additionally, we found that GPA1-GNAO1 domain swaps partially uncouple the instability from the rapid nucleotide binding kinetics displayed by GPA1. In summary, our work provides insights into methods to optimally study heterotrimeric G proteins, and reveals roles of the helical domain in Gα kinetics and stability.

  PublisherDOI

• Translational insights into abiotic interactions: From Arabidopsis to crop plants

  The Plant Cell · 2025-06-21 · 8 citations

  reviewOpen access

  Understanding crop plants responses to abiotic stress is increasingly important in this changing climate. We asked experts how discoveries in Arabidopsis thaliana have translated into advancements in abiotic crop stress resilience. The theme is that core regulatory networks identified in Arabidopsis are conserved in crops, but the molecular regulation varies among species. For cold tolerance, the regulatory framework is conserved, but MAP Kinase signaling promotes degradation of the INDUCER OF DREB1 EXPRESSION transcription factor in Arabidopsis but inhibits it in rice. For hypoxia, manipulation of the oxygen sensing Arg/N-degron pathway discovered in Arabidopsis has improved waterlogging and flood tolerance in barley, maize, wheat, and soybean. For light signaling, overexpression of PHYTOCHROME B reduces shade avoidance, improving yield under dense planting in potato, soybean, and maize. In rice, understanding of nitrogen responsiveness, uptake, and transport in Arabidopsis has inspired engineering of the NRT1 nitrate transceptor to increase yield. Arabidopsis research has provided leads for genetic manipulations that may improve drought resilience in crop species. Growing plants in space generates a complex array of stresses, and Arabidopsis experiments in the space station prepare for future development of robust crops as integral components of the life support systems. For environmental regulation of flowering time, the role of the GIGANTEA - CONTANS - FLOWERING LOCUS T module elucidated in Arabidopsis is largely conserved in crop plants, although additional regulators modify short-day responsiveness in rice, soybean, chrysanthemum, and potato.

  PublisherOA PDFDOI

• VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction

  NAR Genomics and Bioinformatics · 2025-03-29

  articleOpen accessSenior author

  Single nucleotide polymorphisms (SNPs) can alter RNA structure by changing the proportions of existing conformations or leading to new conformations in the structural ensemble. Such structure-changing SNPs, or riboSNitches, have been associated with diseases in humans and climate adaptation in plants. While several computational tools are available for predicting whether an SNP is a riboSNitch, these tools were generally developed to analyze individual RNAs and are not optimized for genome-wide analyses. To fill this gap, we developed VariantFoldRNA, a flexible, containerized, and automated pipeline for genome-wide prediction of riboSNitches. Our pipeline automatically installs all dependencies, can be run locally or on high-performance clusters, and is modular, enabling the user to customize the analysis for the research question of interest. VariantFoldRNA can predict riboSNitches genome-wide at user-specified temperatures and splicing conditions, opening the door to novel analyses. The pipeline is an open-source command-line tool that is freely available at https://github.com/The-Bevilacqua-Lab/variantfoldrna.

  PublisherDOI

• Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research

  Nucleic Acids Research · 2025-12-03 · 4 citations

  articleOpen access

  Gramene (gramene.org) is a comprehensive reference database for comparative plant genomics and pathway analysis, integrating functional annotations, evidence-based curated pathways and their projections, and multi-omics datasets. Since our last report, Gramene has added crop-specific pan-genome portals for maize, sorghum, rice, and grapevine. These pan-genome portals host population-scale datasets and multiple assembled genomes per species, all anchored by shared reference genomes. Importantly, these portals now adopt standardized rsIDs for genetic variants, advancing FAIR data principles and enabling cross-database interoperability. The main site is now Gramene Plants, emphasizing its broad genome coverage. Release 69 features 233 reference genomes, curated pathways for 139 species, expression data from 1026 studies across 27 species, and genetic variation data mapped to 27 genomes from 19 species. Key updates to the integrated search functionality include embedded expression viewers from the Bio-Analytic Resource for Plant Biology and EMBL-EBI Expression Atlas, a literature-curated catalog of gene functions, and a new Germplasm tab linking accessions with loss-of-function alleles to seed repositories. These advances reinforce Gramene as a comprehensive platform for exploring plant genomic diversity, gene function, and evolutionary conservation across the Green Tree of Life and within key agricultural species.

  PublisherOA PDFDOI

• Is GCR1 the GPR157 of plants?

  PLANT PHYSIOLOGY · 2025-02-01 · 4 citations

  articleOpen accessSenior author
  PublisherDOI

• Oryza CLIMtools: A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

  Plant Communications · 2024-01-11 · 16 citations

  articleOpen accessSenior authorCorresponding

  Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To address this issue, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that enable the user to (1) explore the local environments of traditional rice varieties (landraces) in South-East Asia and (2) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We demonstrate the value of these resources by identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior quantitative trait locus analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits, including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

  PublisherDOI

• Manipulating rice canonical Gα and extra-large G protein subunits for improved agronomic traits

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-19 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Rice productivity is fundamentally linked to its architecture, governed by signaling networks including those based on heterotrimeric G proteins. In this study, we investigated the individual gene impacts and genetic interactions of the canonical Gα gene ( RGA1 ), and the non-canonical extra-large Gα genes ( OsXLG1, OsXLG3a, OsXLG3b, OsXLG4 ) in controlling plant architecture. We generated OsXLG mutants using CRISPR/Cpf1 gene editing in Nipponbare (WT) and d1 , a Nipponbare null mutant of RGA1 . We then phenotyped 25 different genotypes in the greenhouse for 19 different agronomic traits. In wild type (WT), mutations in RGA1 , OsXLG3a , OsXLG3b , or OsXLG4 , as well as any combination of Gα genes, resulted in a shorter stature, a desirable trait. Mutations in OsXLG1 and OsXLG4 increased the number of spikelets and grains per panicle, showcasing advantageous traits that led to higher yield. Mutations in OsXLG3a , OsXLG3b , any combination of OsXLGs , or any OsXLG combined with the d1 mutation, reduced seed production and yield. Flag leaf width was the only trait influenced solely by RGA1. RGA1 transcript abundance in the osxlg mutants was positively correlated with height, culm length, panicle exsertion, and harvest index, implicating OsXLG regulation of RGA1 expression as an underlying mechanism. Overall, increased RGA1 expression is correlated with more favorable reproductive traits but less favorable vegetative traits. Our study reveals the complex interaction of RGA1 and OsXLGs within the signaling networks that shape rice architecture, from vegetative to post-harvest stages. Our results suggest modulation of RGA1, OsXLG1, OsXLG3a, or OsXLG4 expression as strategies to enhance yield.

  PublisherOA PDFDOI

Recent grants

• Regulation of heterotrimeric G protein signaling by subunit phosphorylation

  NIH · $1.2M · 2018–2023

• COLLABORATIVE RESEARCH: Metabolomic Characterization of Red Light and CO2 Signaling in Guard Cells and Mesophyll Cells

  NSF · $723k · 2012–2018

• Systems Biology of Plant Heterotrimeric G-protein Signaling in Overlapping Pathways Regulating Stomatal Closure

  NSF · $900k · 2017–2023

• Collaborative Research: Redox Regulation of Protein Kinase Functions in Guard Cell Signaling

  NSF · $325k · 2014–2018

• Roles of the Arabidopsis AKIP RNA-Binding-Proteins in Guard Cell Function

  NSF · $680k · 2004–2010

Frequent coauthors

• Philip C. Bevilacqua

  42 shared

• Sona Pandey

  Donald Danforth Plant Science Center

  23 shared

• Alan M. Jones

  University of Illinois Urbana-Champaign

  20 shared

• David Chakravorty

  Pennsylvania State University

  18 shared

• Ángel Ferrero‐Serrano

  Pennsylvania State University

  15 shared

• José Ramón Botella

  University of Queensland

  15 shared

• Yin Tang

  Second Affiliated Hospital of Zhejiang University

  14 shared

• Réka Albert

  14 shared

Labs

• Assmann LabPI

Awards & honors

• Plant biologist awarded the Masatoshi Nei Innovation Prize i…