About

Heike Sederoff is a William Neal Reynolds Distinguished Professor and University Faculty Scholar at North Carolina State University in the Department of Plant and Microbial Biology. Her research focuses on metabolic engineering to improve the sustainability of agricultural crop production, addressing challenges such as increasing food and feed demand under changing climate conditions. Her work aims to understand the molecular mechanisms behind plant responses to nutrient limitations of nitrogen, phosphate, and water, and to engineer pathways that enhance photosynthetic CO2 fixation, reduce energy and carbon losses, and improve nutrient use efficiency. Sederoff's research includes engineering oil seed crops like Camelina sativa to increase yield and stress tolerance, as well as re-establishing symbiotic relationships between plants and fungi to optimize nutrient acquisition. She investigates plant-microbe interactions, particularly the role of arbuscular mycorrhizal symbiosis, and works on comparative genome analysis to reintroduce symbiosis genes into crops that have lost this ability. Her work is supported by grants such as the InRoot project, which explores plant-microbe interactions at the root-soil interface, and the NRT-INFEWS project, which addresses biotechnology's role in food, energy, and water systems. Sederoff also teaches courses in applied bioinformatics, plant physiology, and agricultural biotechnology, contributing to education in plant biology and metabolic engineering.

Research topics

• Environmental science
• Biology
• Agronomy
• Ecology
• Computer Science
• Biochemistry
• Chemistry
• Physics
• Engineering
• Agricultural engineering
• Economics
• Cell biology
• Optics
• Environmental engineering
• Biotechnology
• Organic chemistry
• Philosophy
• Electrical engineering

Selected publications

• Balancing crop production and energy harvesting in organic solar-powered greenhouses

  UNC Libraries · 2026-02-25

  articleOpen access
  PublisherDOI

• Circular RNAs in Lotus japonicus Responses to Nutrient Supply and Mesorhizobium Symbiosis

  Plant Cell & Environment · 2026-03-23

  articleOpen accessSenior authorCorresponding

  Symbiotic interactions between legumes and rhizobia enable nitrogen fixation under low nutrient conditions. The establishment and function of symbiotic interactions require coordinated changes in gene expression in both the host and the microbe. Circular RNAs (circRNAs) are endogenous gene-specific molecules that can regulate transcription and translation in response to biotic and abiotic stress through various mechanisms. Our objective was to identify circRNAs specifically generated in response to nutrient supply and rhizobial symbiosis. We sequenced nodulated and non-inoculated roots from Lotus japonicus and identified a total of 11,923 putative circRNAs originating from 5,290 nuclear-encoded transcripts in Lotus roots under low or high nutrient supply and nodulated roots. Of those, 58 circRNAs were specific and present in most nodulated root samples. We identified circRNAs for more than half of the known symbiosis-associated genes, including SymRK, CCamK, and Cyclops, and showed that several of those genes also generated circRNAs in Phaseolus vulgaris nodules. We validated select circRNAs potentially involved in regulating symbiosis and predicted miRNA recognition elements (MREs) created only by the backsplice junctions of circRNAs. These putative backsplice-generated MREs could represent an additional mechanism by which circRNAs may modulate the abundance and translation of mRNAs in competing endogenous RNA-regulatory networks.

  PublisherDOI

• Qu-1: a transformation-and regeneration-amenable doubled haploid cell line with a reference genome sequence for genetic and functional studies in <i>Populus</i>

  Forestry Research · 2025-01-01

  articleOpen access

  Plant suspension homogeneous cells are invaluable materials for investigating molecular mechanisms underlying various biological processes. In this study, we established and characterized a doubled haploid cell line from <italic>Populus</italic> <italic>simonii</italic> × <italic>P.</italic> <italic>nigra</italic>, designated as Qu-1. This cell line exhibited high viability and dispersibility under suspension culture conditions and retained the ability to regenerate into whole plants. <italic>K</italic>-mer analysis confirmed the homozygous genome of Qu-1, and a chromosome-level genome assembly was subsequently achieved by using PacBio sequencing. Additionally, we established an efficient transient transformation protocol using PEG-mediated protoplasts and a stable <italic>Agrobacterium</italic>-mediated transformation system for Qu-1. To explore the mutagenesis potential of this cell line, we treated the cell line with ethyl methanesulfonate (EMS) and performed genome resequencing to identify mutation sites. Overall, Qu-1 represents the first poplar cell line with a homozygous genome and is as a powerful tool for molecular biology research in woody plants.

  PublisherDOI

• In vitro demonstration and in planta characterization of a condensed, reverse TCA (crTCA) cycle

  Frontiers in Plant Science · 2025-06-09

  articleOpen accessSenior authorCorresponding

  Introduction Plants employ the Calvin-Benson cycle (CBC) to fix atmospheric CO 2 for the production of biomass. The flux of carbon through the CBC is limited by the activity and selectivity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO). Alternative CO 2 fixation pathways that do not use RuBisCO to fix CO 2 have evolved in some anaerobic, autotrophic microorganisms. Methods Rather than modifying existing routes of carbon metabolism in plants, we have developed a synthetic carbon fixation cycle that does not exist in nature but is inspired by metabolisms of bacterial autotrophs. In this work, we build and characterize a condensed, reverse tricarboxylic acid (crTCA) cycle in vitro and in planta . Results We demonstrate that a simple, synthetic cycle can be used to fix carbon in vitro under aerobic and mesophilic conditions and that these enzymes retain activity whenexpressed transiently in planta . We then evaluate stable transgenic lines of Camelina sativa that have both phenotypic and physiologic changes. Transgenic C. sativa are shorter than controls with increased rates of photosynthetic CO 2 assimilation and changes in photorespiratory metabolism. Discussion This first iteration of a build-test-learn phase of the crTCA cycle provides promising evidence that this pathway can be used to increase photosynthetic capacity in plants.

  PublisherOA PDFDOI

• Circular RNAs in Lotus japonicus Responses to Nutrient Supply and Symbiotic Interactions

  2025-09-03

  preprintOpen accessSenior author

  Symbiotic relationships, such as those formed between legumes and rhizobia or arbuscular mycorrhizal (AM) fungi, function by enhancing the nutrient uptake into the plant. The establishment and coordination of the symbiotic interactions requires changes in gene expression in the host and microbe. Circular RNAs (circRNAs) can function through sponging of microRNAs (miRNAs), resulting in changes in transcript abundances. We identified 15,252 unique nuclear circRNAs in Lotus japonicus under different nutrient conditions and symbiotic interactions with rhizobia or AMF. Our results revealed treatment-specific circRNAs and circRNAs originating from key genes in the Common Symbiosis Pathway, suggesting their potential role in the establishment of these symbioses. We validated select circRNAs potentially involved in the regulation of symbiosis and predicted miRNA recognition elements (MREs) that were only created by the backsplice junction of circRNAs. Backsplice-generated MREs represent an additional mechanism through which circRNAs may modulate abundances and translation of mRNAs. Our sequencing approach using random hexamer primers also enabled us to simultaneously characterize the transcriptome of the symbionts and host.

  PublisherOA PDFDOI

• Advances in lignocellulosic feedstocks for bioenergy and bioproducts

  Nature Communications · 2025-02-01 · 160 citations

  reviewOpen access

  Lignocellulose, an abundant renewable resource, presents a promising alternative for sustainable energy and industrial applications. However, large-scale adoption of lignocellulosic feedstocks faces considerable obstacles, including scalability, bioprocessing efficiency, and resilience to climate change. This Review examines current efforts and future opportunities for leveraging lignocellulosic feedstocks in bio-based energy and products, with a focus on enhancing conversion efficiency and scalability. It also explores emerging biotechnologies such as CRISPR-based genome editing informed by machine learning, aimed at improving feedstock traits and reducing the environmental impact of fossil fuel dependence. Lignocellulose is a promising feedstock to produce bioenergy and biomaterials. Here, the authors review current efforts, including genome editing informed by machine learning, for lignocellulosic feedstock-based bioenergy and biomaterials production and provide outlook for improving feedstock traits.

  PublisherOA PDFDOI

• Circular RNAs in Lotus japonicus Responses to Nutrient Supply and Symbiotic Interactions

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-01

  preprintOpen accessSenior authorCorresponding

  Abstract Symbiotic relationships, such as those formed between legumes and rhizobia or arbuscular mycorrhizal (AM) fungi, function by enhancing the nutrient uptake into the plant. The establishment and coordination of the symbiotic interactions requires changes in gene expression in the host and microbe. Circular RNAs (circRNAs) can function through sponging of microRNAs (miRNAs), resulting in changes in transcript abundances. We identified 15,252 unique nuclear circRNAs in Lotus japonicus under different nutrient conditions and symbiotic interactions with rhizobia or AMF. Our results revealed treatment-specific circRNAs and circRNAs originating from key genes in the Common Symbiosis Pathway, suggesting their potential role in the establishment of these symbioses. We validated select circRNAs potentially involved in the regulation of symbiosis and predicted miRNA recognition elements (MREs) that were only created by the backsplice junction of circRNAs. Backsplice-generated MREs represent an additional mechanism through which circRNAs may modulate abundances and translation of mRNAs. Our sequencing approach using random hexamer primers also enabled us to simultaneously characterize the transcriptome of the symbionts and host.

  PublisherOA PDFDOI

• IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

  Plant Molecular Biology · 2024-02-18 · 4 citations

  articleOpen accessSenior author

  Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

  PublisherOA PDFDOI

• Camelina CircRNA Landscape: Implications for Gene Regulation and Fatty Acid Metabolism

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-07-03

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3’ and 5’ ends, the backsplice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from its cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in regulation of their cognate RNAs by increasing transcription rates, RNA stability and alternative splicing. We have identified circRNAs from Camelina sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3,447 circRNAs from 2,763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlates with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts. Core ideas First discovery of 3,447 genic and 307 intergenic unique putative circRNAs from Camelina sativa . We identified circRNAs that were regulated in response to seedling de-etiolation. Most circRNAs originate from only one homeolog of the three subgenomes in this allohexaploid Camelina. Alternative splicing of exon skipping and intron retention positively correlate with circRNA occurrence. Validation of KASII circRNAs as an example of lipid metabolism pathways potentially regulated by circRNA.

  PublisherOA PDFDOI

• Long‐ and short‐read sequencing methods discover distinct circular RNA pools in <i>Lotus japonicus</i>

  The Plant Genome · 2024-01-20 · 11 citations

  articleOpen accessSenior authorCorresponding

  Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5' site to an upstream 3' end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.

  PublisherOA PDFDOI

Frequent coauthors

• Ronald R. Sederoff

  12 shared

• Brianne Edwards

  North Carolina State University

  12 shared

• Bode A. Olukolu

  11 shared

• Harald Ade

  11 shared

• Aaron T. Asare

  University of Cape Coast

  10 shared

• Samuel Acheampong

  Instituto Gulbenkian de Ciência

  10 shared

• Vincent L. Chiang

  Northeast Forestry University

  10 shared

• G. Craig Yencho

  North Carolina State University

  10 shared

Labs

• Heike Sederoff LabPI

Education

• Ph.D., Plant Biology

  University of California, Berkeley

  1993

• M.S., Plant Biology

  University of California, Berkeley

  1988

• B.S., Botany

  University of California, Davis

  1985

Awards & honors

• William Neal Reynolds Distinguished Professor