About

Anna Stepanova is a Professor of Plant and Microbial Biology at North Carolina State University, serving on the GGA Executive Committee. Her research focuses on understanding how plants adapt to their environment through hormonal regulation, particularly the roles of auxin and ethylene in phenotypic plasticity and root growth. Her work has uncovered previously unknown ethylene-mediated regulation of auxin biosynthesis and explores the mechanisms of ethylene signal transduction, hormone pathway crosstalk, and translational regulation of hormone responses. She employs a combination of classical and molecular genetics, cell biology, genomics, and synthetic biology techniques in Arabidopsis and tomato to decipher the molecular mechanisms underlying plant adaptation and phenotypic plasticity. Her research aims to elucidate how plants integrate developmental programs with environmental signals to produce appropriate responses, utilizing advanced biotechnological tools such as CRISPR-based synthetic genetic devices to manipulate hormone expression with precision. Her contributions include developing innovative approaches to study gene-specific translation regulation, which has the potential to transform understanding of gene expression control in plants and beyond.

Research topics

• Computer Science
• Political Science
• Sociology
• Biology
• Ecology
• Biochemistry
• Data Mining
• Botany
• Artificial Intelligence
• Engineering
• Environmental resource management
• Algorithm
• Mathematics
• Data science
• Cell biology
• Environmental science
• Public relations
• Statistics
• Engineering ethics

Selected publications

• Translational control in plants: from basic mechanisms to environmental and developmental responses

  The Plant Journal · 2026-01-01 · 1 citations

  articleOpen access

  Protein synthesis is an essential process for all living organisms and is tightly regulated to ensure the proper production of proteins needed for growth, development, and stress responses. As sessile organisms, plants have evolved distinct mechanisms to regulate translation, allowing them to adapt to their environment. In this review, we highlight the general translation process, discuss the translational machinery in plants, and examine cis-regulatory elements that influence translation. Additionally, we explore recent studies on how plants regulate translation in response to environmental and developmental cues.

  PublisherOA PDFDOI

• Non-invasive imaging of defence responses in plants

  Nature Communications · 2026-03-13

  articleOpen access

  Jasmonic and salicylic acids are key hormones involved in plant responses to pests and pathogens. Existing fluorescence-based approaches to imaging plant defence hormones are constrained by the need for external illumination and by autofluorescence of plant tissues, while luminescence-based ones require exogenous substrates. Here, we use jasmonate- and salicylate-responsive promoters to engineer autoluminescent plants that report hormone signalling activity with up to a 53-fold contrast. Using consumer-grade cameras, we image reporter Arabidopsis thaliana and Nicotiana benthamiana plants throughout normal development and in response to pest and pathogen attacks, visualising local and systemic responses. Because the luminescence is self-sustained, these reporters enable non-invasive, substrate-free imaging of defence signalling over extended time courses without specialised equipment.

  PublisherDOI

• Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate

  Science · 2026-02-12 · 1 citations

  articleOpen access

  Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In Arabidopsis , the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SUPPRESSOR-OF-ACAULIS51 (SAC51) and SAC51-LIKEs (SACLs), which inhibit heterodimerization of the xylem development proteins LONESOME-HIGHWAY (LHW) and TARGET-OF-MONOPTEROS5. Here, we report a methyltransferase, OVERACHIEVER, that methylates the peptidyl transferase center of the 25 S ribosomal RNA (rRNA). Residue m 3 U2952 promotes functional tSpm binding to a specific site connecting the P-site transfer RNA (tRNA) with rRNA residues in the peptidyl transferase center. This interaction enhances the translation of SACLs but inhibits that of LHW. Our study uncovers the dependency between a conserved rRNA base methylation and a polyamine in orchestrating cell fate decisions, highlighting a role for the ribosome chemical landscape in translational regulation.

  PublisherDOI

• Synthetic promoter design in plants: integration of computational and experimental approaches

  Frontiers in Plant Science · 2026-02-13

  articleOpen accessSenior author

  Understanding how to engineer transcriptional regulation in plants is key to advancing both fundamental knowledge and practical applications in plant biology. Native gene promoters, while widely used, are constrained by evolutionary pressures that limit their modularity, tunability, and predictability across genetic backgrounds and species. Synthetic promoters, artificial DNA sequences composed of defined cis-regulatory elements (CREs) for recruitment of gene-specific transcription factors (TFs) and general transcriptional machinery, provide a powerful alternative for achieving fine-tuned transcriptional control. This review examines the design and application of synthetic promoters in plants, emphasizing current strategies, ongoing challenges, and avenues for innovation. We cover the structure of plant promoter architecture, including the contributions of core, proximal, and distal regions, and highlight how promoter grammar (i.e., motif identity, motif distance from transcription start site, spacing between motifs, helical phase of TF binding, motif orientation, and combinatorial interactions between motifs) impacts transcriptional activity. We outline how synthetic promoters are designed and validated via high-throughput reporter assays. Applications of synthetic promoters are discussed across functional genomics studies, biosensor creation, logic gate-based genetic circuits, and practical crop engineering, with examples covering constitutively expressing, hormone-responsive, pathogen-inducible, and abiotic stress-responsive promoter designs. We discuss traditional and emerging computational frameworks that enable CRE identification, novel synthetic promoter generation, and prediction of promoter sequence activity in silico to inform the rational design of promoters with predictable performance and spatiotemporal expression. We emphasize the importance of integrating experimental studies and computational approaches through iterative Design-Build-Test-Learn (DBTL) cycles to standardize and optimize frameworks for synthetic promoter development. By combining insights from plant promoter studies with advances in both plant-specific and non-plant synthetic promoter generation and computational modeling, researchers can expand synthetic promoter libraries to enable complex man-driven transcriptional regulation across various plant systems.

  PublisherOA PDFDOI

• Arabidopsis lines with modified ascorbate concentrations reveal a link between ascorbate and auxin biosynthesis

  PLANT PHYSIOLOGY · 2025-12-19

  articleOpen access

  Ascorbate is the most abundant water-soluble antioxidant in plants and an essential molecule for normal plant development. Although present in all green plants, ascorbate concentrations vary among plant species and tissues. While ascorbate accumulation is a trait of nutritional, and therefore, agronomical interest, the impact of different concentrations on cellular homeostasis remains elusive. To shed light on this question, we compared Arabidopsis (Arabidopsis thaliana) lines with very low (vtc2 mutant, 20% of wild-type (WT) levels), low (vtc4 mutant, 65% of WT levels), and high (vtc2/OE-VTC2, 165% of WT levels) ascorbate concentration in 4-wk-old rosette leaves. An 80% reduction of ascorbate increased the expression of genes implicated in defense against pathogens but repressed genes associated with abiotic stress responses. Unexpectedly, lines with increased (165% of WT) and decreased (65% of WT) ascorbate levels shared 85% of induced transcription factors and the gene ontology terms associated with their transcriptional programs. We identified TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1), a gene encoding the enzyme that catalyzes the first step of auxin biosynthesis, among the group of genes whose expression was positively correlated with ascorbate content. Using a combination of genetic and pharmacological approaches in fluorescent and histochemical reporter lines for auxin biosynthesis and signaling activity, we revealed that TAA1- and TAA1 RELATED 2 (TAR2)-mediated auxin biosynthesis is necessary for plants to cope with increased ascorbate concentration in a light-dependent manner, revealing a layer of complexity in the regulatory landscape of redox homeostasis.

  PublisherDOI

• DASH: A versatile and high-capacity gene stacking system for plant synthetic biology

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-06

  preprint

  Abstract DNA assembly systems based on the Golden Gate method are popular in synthetic biology but have several limitations: small insert size, incompatibility with other cloning platforms, DNA domestication requirement, generation of fusion scars, and lack of post-assembly modification. To address these obstacles, we present the DASH assembly toolset, which combines features of Golden Gate-based cloning, recombineering, and site-specific recombinase systems. We developed (1) a set of donor vectors based on the GoldenBraid platform, (2) an acceptor vector derived from the plant transformation-competent artificial chromosome (TAC) vector, pYLTAC17, and (3) a re-engineered recombineering-ready E. coli strain, CZ105, based on SW105. The initial assembly steps are carried out using the donor vectors following standard GoldenBraid assembly procedures. Importantly, existing parts and transcriptional units created using compatible Golden Gate-based systems can be transferred to the DASH donor vectors using standard single-tube restriction/ligation reactions. The cargo DNA from a DASH donor vector is then efficiently transferred in vivo in E. coli into the acceptor vector by the sequential action of a rhamnose-inducible phage-derived PhiC31 integrase and arabinose-inducible yeast-derived Flippase (FLP) recombinase using CZ105. Furthermore, recombineering-based post-assembly modification, including the removal of undesirable scars, is greatly simplified. To demonstrate the utility of the DASH system, a 116 kb DNA construct harboring a 97 kb cargo consisting of 35 transcriptional units was generated. One of the CDSs in the final assembly was replaced through recombineering, and the in planta functionality of the entire construct was tested in both transient and stable transformants.

  PublisherDOI

• <i>EBSn,</i> a robust synthetic reporter for monitoring ethylene responses in plants

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-28 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Ethylene is a gaseous plant hormone that controls a wide array of physiologically relevant processes, including plant responses to biotic and abiotic stress, and induces ripening in climacteric fruits. To monitor ethylene in plants, analytical methods, phenotypic assays, gene expression analysis, and transcriptional or translational reporters are typically employed. In the model plant Arabidopsis, two ethylene-sensitive synthetic transcriptional reporters have been described, 5xEBS:GUS and 10x2EBS-S10:GUS . These reporters harbor a different type, arrangement, and number of homotypic cis -elements in their promoters and thus may recruit the ethylene master regulator EIN3 in the context of alternative transcriptional complexes. Accordingly, the patterns of GUS activity in these transgenic lines differ and neither of them encompasses all plant tissues even in the presence of saturating levels of exogenous ethylene. Herein, we set out to develop and test a more sensitive version of the ethylene-inducible promoter that we refer to as EBSnew (abbreviated as EBSn ). EBSn leverages a tandem of ten non-identical, natural copies of a novel, dual, everted, 11bp-long EIN3-binding site, 2EBS(−1) . We show that in Arabidopsis, EBSn outperforms its predecessors in terms of its ethylene sensitivity, having the capacity to monitor endogenous levels of ethylene and displaying more ubiquitous expression in response to the exogenous hormone. We demonstrate that the EBSn promoter is also functional in tomato, opening new avenues to manipulating ethylene-regulated processes, such as ripening and senescence, in crops.

  PublisherOA PDFDOI

• Arabidopsis lines with modified ascorbate concentrations reveal a link between ascorbate and auxin biosynthesis

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-16

  preprintOpen access

  Abstract Ascorbate is the most abundant water-soluble antioxidant in plants, and it is an essential molecule for normal plant development. It is present in all green plants, with very different concentrations in different plant species. While ascorbate accumulation is a trait of nutritional, and therefore, agronomical interest, the impact of different concentrations over cellular homeostasis remains elusive. In order to shed light over this question, we leveraged Arabidopsis lines with very low ascorbate ( vtc2 mutant with 20% of WT ascorbate levels), and low ascorbate concentration ( vtc4 mutant with 65% of WT levels), and we generated a line that accumulates 165% of WT levels ( vtc2/OE-VTC2 ). An 80% reduction of ascorbate increased the expression of genes implicated in defense against pathogens, but repressed genes associated with abiotic stress responses. Unexpectedly, lines with increased (165% of WT) and decreased (65% of WT) ascorbate levels shared 85% of induced transcription factors and the GO terms associated with their transcriptional programs. Among the group of genes whose expression is positively correlated with ascorbate content, we identified TAA1/WEI8 , a gene encoding a tryptophan aminotransferase that catalyzes the first step of auxin biosynthesis. Using a combination of genetic and pharmacological approaches in fluorescent and histochemical reporter lines for auxin biosynthesis and signaling activity, we revealed that TAA1- and TAA1-RELATED2 (TAR2)-mediated auxin biosynthesis is necessary for plants to cope with increased ascorbate concentration in a light-dependent manner, revealing a new layer of complexity in the regulatory landscape of redox homeostasis.

  PublisherOA PDFDOI

• Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes

  Nature Biotechnology · 2025-09-04 · 3 citations

  articleOpen access

  Base editors create precise genomic edits by directing nucleobase deamination or removal without inducing double-stranded DNA breaks. However, a vast chemical space of other DNA modifications remains to be explored for genome editing. Here we harness the bacterial antiphage toxin DarT2 to append ADP-ribosyl moieties to DNA, unlocking distinct editing outcomes in bacteria versus eukaryotes. Fusing an attenuated DarT2 to a Cas9 nickase, we program site-specific ADP-ribosylation of thymines within a target DNA sequence. In tested bacteria, targeting drives homologous recombination, offering flexible and scar-free genome editing without base replacement or counterselection. In tested yeast, plant and human cells, targeting drives substitution of the modified thymine to adenine or a mixture of adenine and cytosine with limited insertions or deletions, offering edits inaccessible to current base editors. Altogether, our approach, called append editing, leverages the addition of chemical moieties to DNA to expand current modalities for precision gene editing.

  PublisherOA PDFDOI

• Plant cell biology: subcellular dynamics and mechanisms of plant cell organization and adaptation

  Journal of Experimental Botany · 2025-11-09

  editorialSenior author

  Plant cells were one of the first cell types to be imaged by biologists seeking to understand the organizational properties of organisms and to develop new approaches for probing the inner workings of life. Since then, a myriad of new technologies have further enhanced our ability to define and understand the cell biology of plants. Plant cells display a diversity of highly organized and complex forms that are shaped dynamically by developmental programming and external factors. The beauty and wonder of the plant subcellular world continue to fascinate researchers and inspire new questions and technological innovation. This Special Issue aims to highlight recent advances in understanding the structural organization of plant cells, the function of subcellular organelles, and their dynamic relationship with each other and in response to endogenous and exogenous inputs. Additionally, this Special Issue features a sample of new technologies that are enabling cell biologists to probe plant cells with unparalleled precision, resolution, and scale. From these reviews, several themes emerge, as elaborated below.

  PublisherDOI

Recent grants

• CAREER: Tailoring hormone responses in plants via synthetic signal integration devices

  NSF · $1.3M · 2018–2026

• PAPM-EAGER: Single-locus multi-hormone reporters for comprehensive plant phenotyping: a synthetic-biology approach.

  NSF · $300k · 2016–2020

Frequent coauthors

• José M. Alonso

  North Carolina State University

  83 shared

• Joseph R. Ecker

  Salk Institute for Biological Studies

  42 shared

• Roberto Solano

  Centro Nacional de Biotecnología

  17 shared

• Ellen Wisman

  Max Planck Institute for Plant Breeding Research

  16 shared

• Frederick M. Ausubel

  Massachusetts General Hospital

  16 shared

• Simone Ferrari

  Sapienza University of Rome

  16 shared

• Javier Brumós

  Universitat Politècnica de València

  14 shared

• Jeonga Yun

  11 shared

Labs

• Plant and Microbial BiologyPI

Education

• PhD, Biology

  University of Pennsylvania

  2001

• BS, Biology

  University of Nevada Reno

  1995

• BS/MS, Biology

  N. I. Lobachevsky State University of Nizhny Novgorod

  1995

Awards & honors

• CAREER: Tailoring hormone responses in plants via synthetic…
• EAGER: TRTech-PGR: New Methods to Study Gene-specific Transl…
• Identification of Translational Hormone-Response Gene Networ…