About

Karen E. Koch is a Professor in the Department of Horticultural Sciences at the University of Florida, Institute of Food and Agricultural Sciences. Her research focuses on the physiology and genetics of sugar metabolism, sensing, and partitioning in plants. She teaches graduate courses such as Environmental Physiology of Plants and Plant Biochemistry - Central Metabolism, and mentors a diverse group of students and research personnel including high school interns, undergraduates, PhD students, postdoctoral associates, and associate research professors. Dr. Koch has a distinguished career in plant biology, with educational backgrounds in biology from the University of Wisconsin and botany with a focus on plant physiology from the University of Iowa. She has been a faculty member at the University of Florida since 1981, contributing significantly to research, teaching, and community service. Her honors include the Charles Reid Barnes Life Membership Award from the American Society of Plant Biologists, fellowship in the American Association for the Advancement of Science, and recognition as a Fellow of the American Society of Plant Biologists. She has also received the Howard Hughes Medical Institute Distinguished Mentor Award. Dr. Koch has served on numerous national panels and committees related to plant biology and genetics, and has made substantial contributions to the scientific community through her research, mentorship, and service.

Research topics

• Biology
• Genetics
• Biochemistry
• Botany
• Endocrinology
• Evolutionary biology
• Agronomy

Selected publications

• Schelling, Hegel, and the Philosophy of Nature : From Matter to Spirit by Benjamin Berger (review)

  Journal of the history of philosophy · 2026-01-01

  article1st authorCorresponding
  PublisherDOI

• Over-expression of XA21 binding protein 3 enhances rice survival under water-deficit stress

  Plant Science · 2025-02-28 · 1 citations

  article
  PublisherDOI

• Functional genomics and structural insights into maize aldo-keto reductase-4 family: Stress metabolism and substrate specificity in embryos

  Journal of Biological Chemistry · 2025-06-20

  articleOpen accessSenior author

  Aldo-keto reductases (AKRs) are ubiquitous in nature and are able to reduce a wide range of substrates, from simple sugars to potentially toxic aldehydes. In plants, AKRs are involved in key metabolic processes including reactive aldehyde detoxification. This study aimed to (i) delineate a maize gene family encoding aldo keto reductase-4s (AKR4s) (ii) help bridge sequence-to-function gaps among them, and (iii) focus on a family member implicated in embryo specific stress metabolism. We employed a genome-wide analysis approach to identify maize genes encoding AKR4s, defining and annotating a 15-member gene family that clustered into three subgroups. Expression profiling, validated through wet lab experiments, revealed distinct functional roles: (i) AKR4C Zm-1 functions in aldehyde detoxification during stress, (ii) AKR4C Zm-2 includes stress-responsive AKRs with diverse substrate affinities, and (iii) AKR4A/B Zm-3 contributes to specialized metabolites like phytosiderophores for iron transport. To investigate the impact of sequence variation on function, we characterized ZmAKR4C13, a representative of AKR4C Zm-1. Its mRNA and protein were predominantly localized in embryos, suggesting a specialized role. Recombinant ZmAKR4C13 efficiently reduced methylglyoxal and small aldehydes but showed poor activity toward aldoses larger than four carbons. Crystallographic analysis identified a size constraint at the active site, attributed to the bulkier LEU residue at position 294. Collectively, our results emphasize how subtle modifications in active-site architecture influence AKR substrate specificity. They also demonstrate a potential role of maize ZmAKR4C13 in detoxifying methylglyoxal and other small metabolites that could contribute to stress signaling in embryos.

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• The UniformMu National Public Resource: Transposon <i>-</i> Induced Mutant Seeds for Functional Genomics Studies in Maize

  Cold Spring Harbor Protocols · 2025-11-13

  preprint1st authorCorresponding

  Geneticists frequently use loss-of-function (knockout) mutations to reveal the effects of a gene's dysfunction at the organismal level, observed as the mutant phenotype. This strategy is facilitated by creation of large, searchable collections of knockout mutants in an organism of interest. Paramount among such resources in maize is the UniformMu National Resource, a large collection of genetic stocks carrying mutations generated by insertions of Robertson's Mutator ( Mu ) transposons. The name UniformMu refers to the phenotypic uniformity of the W22 inbred genetic background in which Mu insertion mutants were created. This community resource continues its pivotal role in providing seeds containing beneficial knockout and knockdown mutations in targeted genes, which can be used to elucidate gene function. The resource offers an invaluable complement to other functional genomics approaches aimed at bridging the gap between genome sequences and plant performance in the field. Several key features are central to the success of the UniformMu National Public Resource. First, mapped insertions are linked to seed stocks that are readily available through the Maize Genetics and Genomics Database (MaizeGDB) and the Maize Genetics Cooperation Stock Center. Second, a uniform inbred background facilitates analysis of mutant phenotypes, by providing uniform wild-type controls. Third, mutant alleles are reliably heritable and consistently recovered in stated lines. Finally, lines are stable, with no continuing transposition of Mu insertions. The collective effort of the maize community allows UniformMu to provide readily accessible knockout and knockdown mutant seeds, as well as, ultimately, highly sought evidence for gene function in planta.

  PublisherDOI

• Functional Genomic Analysis of Transposon Insertion Mutant Maize Plants from the UniformMu National Public Resource

  Cold Spring Harbor Protocols · 2025-11-13

  preprintSenior author

  The UniformMu National Public Resource is a widely used, functional genomics tool for maize, constructed by backcross introgression of active Robertson's Mutator ( Mu ) transposons into the W22 inbred line, creating a large, searchable collection of lines that together carry transposon insertions in thousands of maize genes. This resource provides (1) a ready supply of freely available mutant seed stocks, each linked to mapped gene sequences; (2) uniform controls in an inbred background, for precision analysis of mutant phenotypes; (3) a reliable source of heritable mutants that are consistently recovered in stated lines; and (4) stable mutant lines with no Mu activity. This low-cost resource provides a consummate experimental system for linking gene sequences with their function in a species that has long served humanity, not only as a preeminent genetic model, but also as one of the world's most productive grain crops. Here, we describe how to perform an initial, online search of insertions in the UniformMu population, request seeds, generate segregating families, PCR-genotype seedlings for Mu insertions of interest, and associate genotypes with phenotypes. Resulting analyses provide definitive, in planta evidence for genotype–phenotype relationships that either support or refute hypotheses regarding gene function.

  PublisherDOI

• Rhomboid-mediated cleavage of the immune receptor XA21 protects grain set and male fertility in rice

  Proceedings of the National Academy of Sciences · 2025-05-30 · 5 citations

  articleOpen access

  To maintain growth and to successfully reproduce, organisms must protect key functions in specific tissues, particularly when countering pathogen invasion using internal defensive proteins that may disrupt their own developmental processes. The rice immune receptor XA21 confers race-specific resistance against Xanthomonas oryzae pv. oryzae , which causes the deadly disease bacterial leaf blight. Here, we demonstrate that XA21 is cleaved by the rhomboid-like protease OsRBL3b, likely within its transmembrane domain. OsRBL3b mRNA transcripts are preferentially expressed in rice spikelets. Rice plants expressing Xa21 but lacking a functional OsRBL3b displayed impaired anther dehiscence and pollen viability, resulting in male sterility and yield reduction with high levels of XA21 protein present in spikelets during anthesis. In leaves, osrbl3b mutants expressing XA21 had normal levels of this resistance protein and disease immunity. This balance between reproduction and disease resistance through the specific expression of a rhomboid protease may be key to limiting the detrimental effects of an active immune response and may be useful in future for genetic improvement of crops.

  PublisherOA PDFDOI

• A sucrose ferulate cycle linchpin for feruloylation of arabinoxylans in plant commelinids

  Nature Plants · 2024-09-04 · 9 citations

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  PublisherDOI

• Strigolactones are involved in enhancing iron uptake in maize

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-02 · 1 citations

  preprintOpen access

  Abstract Strigolactones are plant hormones with roles in a wide range of signaling and developmental processes. A yellow-striped maize mutant, ( inter v einal y ellow ) ivy , was determined to have low iron in tissues under normal growth conditions. The gene underlying the ivy mutation was mapped and identified as ZmCCD8 , a key enzyme in the biosynthesis of strigolactones. Under iron-replete conditions, comparison of the transcriptomes of wild-type plants and maize ccd8 mutants revealed suppression of several iron-regulated genes in ccd8 . These genes are normally up-regulated during iron deficiency and include the key iron-regulated transcription factor IRO2 as well as genes involved in the biosynthesis of iron chelators and transporters. External supply of synthetic strigolactone to ivy mutants alleviated chlorosis and returned iron-regulated gene expression to wild-type levels. In iron limited conditions, iron-regulated gene expression in ccd8 mutants responded normally, indicating that strigolactones are not required for response to externally imposed iron deficiency. However, they are required for basal expression of iron-regulated genes when adequate iron is available, highlighting a distinction between iron homeostasis during normal growth, and the iron deficiency response triggered by the lack of external available iron. The connection between strigolactones and iron homeostasis is not limited to maize, as Arabidopsis ccd8 mutants also show strong chlorosis when grown on medium with moderate levels of iron. This previously unappreciated role may have implications for the use of strigolactones in agricultural contexts.

  PublisherOA PDFDOI

• Strigolactone roles in maize tolerance to low nitrogen involve shifts in acquisition and partitioning of protein, sulfur, and iron

  Plant and Soil · 2024-02-22 · 5 citations

  articleOpen accessCorresponding

  Abstract Background and Aims Nitrogen (N) is an essential macronutrient that can limit plant development and crop yield through widespread physiological and molecular impacts. In maize, N-starvation enhances biosynthesis and exudation of strigolactones (SLs) in a process reversible by nitrate addition and consequent repression of genes for SL biosynthesis. Methods In the present study, a maize mutant deficient in SL biosynthesis ( zmccd8 ) allowed an in-depth analysis of SL contributions under low N. Both hydroponic and field conditions were used to better characterize the response of the mutant to N availability. Results The severity of responses to N-limitation by the SL-deficient zmccd8 mutant extended from growth parameters to content of iron, sulfur, protein, and photosynthetic pigments, as well as pronounced impacts on expression of key genes, which could be crucial molecular target for the SL-mediated acclimatation to N shortage. Conclusions Our results demonstrate that SLs are critical for physiological acclimation to N deficiency by maize and identify central players in this action. Further contributions by iron and sulfur are implicated in the complex pathway underlying SL modulation of responses to N-deprivation, thus widening our knowledge on SL functioning and providing new hints on their potential use in agriculture.

  PublisherOA PDFDOI

• Independent evolution of transposase and TIRs facilitated by recombination between <i>Mutator</i> transposons from divergent clades in maize

  Proceedings of the National Academy of Sciences · 2023-07-25 · 3 citations

  articleOpen accessSenior author

  Nearly all eukaryotes carry DNA transposons of the Robertson’s Mutator ( Mu ) superfamily, a widespread source of genome instability and genetic variation. Despite their pervasive impact on host genomes, much remains unknown about the evolution of these transposons. Transposase recognition of terminal inverted repeats (TIRs) is thought to drive and constrain coevolution of MuDR transposase genes and TIRs. To address the extent of this relationship and its impact, we compared separate phylogenies of TIRs and MuDR gene sequences from Mu elements in the maize genome. Five major clades were identified. As expected, most Mu elements were bound by highly similar TIRs from the same clade (homomorphic type). However, a subset of elements contained dissimilar TIRs derived from divergent clades. These “heteromorphs” typically occurred in multiple copies indicating active transposition in the genome. In addition, analysis of internal sequences showed that exchanges between elements having divergent TIRs produced new mudra and mudrb gene combinations. In several instances, TIR homomorphs had been regenerated within a heteromorph clade with retention of distinctive internal MuDR sequence combinations. Results reveal that recombination between divergent clades facilitates independent evolution of transposase ( mudra ), transposase-binding targets (TIRs), and capacity for insertion ( mudrb ) of active Mu elements. This mechanism would be enhanced by the preference of Mu insertions for recombination-rich regions near the 5′ ends of genes. We suggest that cycles of recombination give rise to alternating homo- and heteromorph forms that enhance the diversity on which selection for Mu fitness can operate.

  PublisherOA PDFDOI

Recent grants

• EAGER: An Unexplored Avenue of Striga Resistance in Maize

  NSF · $360k · 2015–2019

Frequent coauthors

• J. Remohi

  192 shared

• John Martin

  128 shared

• Joop S.E. Laven

  Erasmus University Rotterdam

  128 shared

• Ken McElreavey

  Institut Pasteur

  120 shared

• C. Rubio

  Copenhagen University Hospital

  72 shared

• J. Giles

  The Open University

  64 shared

• P. H. Vogt

  Drexel University

  64 shared

• J. McGrath

  64 shared

Labs

• Koch LabPI

Awards & honors

• Charles Reid Barnes Life Membership Award, American Society…
• Fellow of the American Association for the Advancement of Sc…
• Elected Member-at-Large for AAAS National Section on Agricul…
• Fellow of the American Society of Plant Biologists (2012-pre…
• Howard Hughes Medical Institute (HHMI) Distinguished Mentor…