About

Jose Alonso is the William Neal Reynolds Distinguished Professor at North Carolina State University. His contact email is jmalonso@ncsu.edu and his phone number is 919-515-5729. The provided page text does not include specific details about his research focus, background, or key contributions.

Research topics

• Biology
• Botany
• Biochemistry
• Cell biology
• Artificial Intelligence
• Ecology
• Computer Science
• Data Mining
• Genetics
• Algorithm
• Statistics
• Mathematics

Selected publications

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

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

  articleOpen accessSenior author

  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

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

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

  preprintOpen access

  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

• The <i>CYP71A</i> , <i>NIT</i> , <i>AMI,</i> and <i>IAMH</i> gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in Arabidopsis

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

  preprintOpen access

  Abstract Indole-3-acetic acid (IAA) is a crucial auxin governing plant development and environmental responses. While the indole-3-pyruvic acid (IPyA) pathway is the predominant IAA biosynthesis route, other pathways, like the indole-3-acetaldoxime (IAOx) pathway, have been proposed. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g., sur1, sur2, ugt74b1 ) and the auxin-like responses triggered by exogenous application of its proposed intermediates: IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite supporting evidence for individual steps, conclusive physiological relevance of the IAOx pathway remains unproven. Using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway does not result in prominent auxin-deficient phenotypes, nor are these genes required for high-auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. While exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo , they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet uncharacterized auxin biosynthetic route, likely involving IAOx as an intermediate, for the production of IAA in the sur2 mutant. Future identification of the metabolic steps and the corresponding genes in this new pathway may uncover the previously unknown way of synthesizing IAA in plants.

  PublisherOA PDFDOI

• <i>EBSn</i> , a Robust Synthetic Reporter for Monitoring Ethylene Responses in Plants

  Plant Biotechnology Journal · 2025-09-21 · 4 citations

  articleOpen accessCorresponding

  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 harbour 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 10 non-identical, natural copies of a novel, dual, everted, 11 bp-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

• 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

• 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

• Beyond a few bases: methods for large <scp>DNA</scp> insertion and gene targeting in plants

  The Plant Journal · 2025-03-01 · 8 citations

  reviewOpen access

  Genome editing technologies like CRISPR/Cas have greatly accelerated the pace of both fundamental research and translational applications in agriculture. However, many plant biologists are functionally limited to creating small, targeted DNA changes or large, random DNA insertions. The ability to efficiently generate large, yet precise, DNA changes will massively accelerate crop breeding cycles, enabling researchers to more efficiently engineer crops amidst a rapidly changing agricultural landscape. This review provides an overview of existing technologies that allow plant biologists to integrate large DNA sequences within a plant host and some associated technical bottlenecks. Additionally, this review explores a selection of emerging techniques in other host systems to inspire tool development in plants.

  PublisherOA PDFDOI

• The <i>CYP71A</i> , <i>NIT</i> , <i>AMI</i> , and <i>IAMH</i> gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in <i>Arabidopsis</i>

  The Plant Cell · 2025-10-15 · 4 citations

  articleOpen access

  The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g. sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.

  PublisherDOI

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

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

  preprintSenior author

  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

• <scp>DASH</scp> : a versatile and high‐capacity gene stacking system for plant synthetic biology

  Plant Biotechnology Journal · 2025-06-10

  reviewOpen accessSenior authorCorresponding

  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 kilobase (kb) DNA construct harbouring a 97 kb cargo consisting of 35 transcriptional units was generated. One of the coding DNA sequences (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.

  PublisherOA PDFDOI

Recent grants

• Molecular Genetics of Ethylene-Auxin Interactions in Arabidopsis

  NSF · $427k · 2005–2009

• Arabidopsis 2010: The Arabidopsis Localizome

  NSF · $250k · 2008–2011

• Molecular Genetics of Ethylene-auxin Interactions in Arabidopsis

  NSF · $734k · 2009–2013

• Identification of Translational Hormone-Response Gene Networks and cis-Regulatory Elements

  NSF · $3.2M · 2015–2025

• EAGER: TRTech-PGR: New methods to study gene-specific translation regulation

  NSF · $300k · 2023–2026

Frequent coauthors

• Joseph R. Ecker

  Salk Institute for Biological Studies

  231 shared

• Anna N. Stepanova

  North Carolina State University

  83 shared

• Huaming Chen

  75 shared

• Ryan C. O’Neil

  La Trobe University

  64 shared

• Hongyu Chen

  64 shared

• Mathew G. Lewsey

  Australian Research Council

  64 shared

• Mingtang Xie

  University of Southern California

  64 shared

• Ling Huang

  Beijing University of Technology

  64 shared

Labs

• Jose Alonso LabPI

Awards & honors

• Fellow of the American Association for the Advancement of Sc…
• Elected to the National Academy of Sciences (2026)