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  1. AU="Koch, Karen E"
  2. AU="Kelly, Allicia P"
  3. AU=Kakinuma Takashi
  4. AU="Nachira, Lorenza"
  5. AU="Wei, Xiang"
  6. AU="Daniell, Esther"
  7. AU="Chou, Chau-Wen"
  8. AU=Kaur Supreet
  9. AU="Yun, Joho"
  10. AU="Tran, Bao G"
  11. AU="Ou Li"
  12. AU="Ting Chen" AU="Ting Chen"
  13. AU="Wilson, Jaymi"
  14. AU="Vane, Christopher H"
  15. AU="Mabbott, Donald"
  16. AU="Martín-Trejo, Jorge Alfonso"
  17. AU=Rieder Hans L

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  1. Artikel ; Online: Independent evolution of transposase and TIRs facilitated by recombination between

    Hunter, Charles T / McCarty, Donald R / Koch, Karen E

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Band 120, Heft 31, Seite(n) e2305298120

    Abstract: Nearly all eukaryotes carry DNA transposons of the Robertson' ... ...

    Abstract Nearly all eukaryotes carry DNA transposons of the Robertson's
    Mesh-Begriff(e) Zea mays/genetics ; Transposases/genetics ; DNA Transposable Elements/genetics ; Terminal Repeat Sequences/genetics ; Recombination, Genetic
    Chemische Substanzen Transposases (EC 2.7.7.-) ; DNA Transposable Elements
    Sprache Englisch
    Erscheinungsdatum 2023-07-25
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2305298120
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Independent evolution of transposase and TIRs facilitated by recombination between transposons from divergent clades in maize

    Hunter, Charles T. / McCarty, Donald R. / Koch, Karen E.

    Proceedings of the National Academy of Sciences. 2023 July 25, v. 120, no. 31 p.e2305298120-

    2023  

    Abstract: Nearly all eukaryotes carry DNA transposons of the Robertson’s () 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. ...

    Abstract Nearly all eukaryotes carry DNA transposons of the Robertson’s () 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 transposase genes and TIRs. To address the extent of this relationship and its impact, we compared separate phylogenies of TIRs and gene sequences from elements in the maize genome. Five major clades were identified. As expected, most 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, anal
    Schlagwörter DNA ; coevolution ; corn ; eukaryotic cells ; genes ; genetic instability ; genetic variation ; phylogeny ; transposases ; transposons
    Sprache Englisch
    Erscheinungsverlauf 2023-0725
    Erscheinungsort Proceedings of the National Academy of Sciences
    Dokumenttyp Artikel ; Online
    Anmerkung Resource is Open Access
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2305298120
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  3. Artikel: Tomato fruit quality is more strongly affected by scion type and planting season than by rootstock type.

    Gong, Tian / Brecht, Jeffrey K / Hutton, Samuel F / Koch, Karen E / Zhao, Xin

    Frontiers in plant science

    2022  Band 13, Seite(n) 948556

    Abstract: Previous studies of tomato rootstock effects on fruit quality have yielded mixed results, and few attempts have been made to systematically examine the association between rootstock characteristics and tomato fruit quality. In this study, grape tomato (' ... ...

    Abstract Previous studies of tomato rootstock effects on fruit quality have yielded mixed results, and few attempts have been made to systematically examine the association between rootstock characteristics and tomato fruit quality. In this study, grape tomato ('BHN 1022') and beefsteak tomato ('Skyway') were grafted onto four rootstocks ['Estamino' (vigorous and "generative"), 'DR0141TX' (vigorous and "vegetative"), 'RST-04-106-T' (uncharacterized), and 'SHIELD RZ F1 (61-802)' (mid-vigor, uncharacterized)] and compared to non-grafted scion controls for two growing seasons (Spring and Fall in Florida) in organically managed high tunnels. In both seasons and for both scions, the two vigorous rootstocks, regardless of their designation as "vegetative" ('DR0141TX') or "generative" ('Estamino'), exhibited negative impacts on dry matter content, soluble solids content (SSC), SSC/titratable acidity (TA), lycopene, and ascorbic acid contents. Similar effects on fruit dry matter content and SSC were also observed with the 'RST-04-106-T' rootstock, although little to no change was seen with grafting onto 'SHIELD RZ F1 (61-802)'. Further studies are needed to elucidate the impact of rootstock vigor on tomato volatile profiles and consumer sensory acceptability in order to better determine whether any of the documented effects are of practical importance. On the other hand, the evident effects of scion cultivar and planting season on fruit quality were observed in most of the measurements. The scion by rootstock interaction affected fruit length, firmness, pH, and total phenolic content, while the planting season by rootstock interaction impacted fruit firmness, pH, total antioxidant capacity, and ascorbic acid and lycopene contents. The multivariate separation pattern of planting season, scion, and rootstock treatments as revealed by the canonical discriminant analysis further indicated that the influence of scion cultivar and planting season on tomato fruit quality could be much more pronounced than the rootstock effects. The fruit color (
    Sprache Englisch
    Erscheinungsdatum 2022-12-15
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2022.948556
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Transposon Mutagenesis and Analysis of Mutants in UniformMu Maize (Zea mays).

    Liu, Peng / McCarty, Donald R / Koch, Karen E

    Current protocols in plant biology

    2019  Band 1, Heft 3, Seite(n) 451–465

    Abstract: A wealth of maize mutants is now available with known sites of transposon insertions in over 45% of maize genes. Materials can be obtained free of charge from the UniformMu public resource through MaizeGDB.org or directly from the Maize Genetics COOP ... ...

    Abstract A wealth of maize mutants is now available with known sites of transposon insertions in over 45% of maize genes. Materials can be obtained free of charge from the UniformMu public resource through MaizeGDB.org or directly from the Maize Genetics COOP Stock Center. Specific mutants can be sought online based on gene-sequences of interest. A key feature of the UniformMu resource is the uniformity of wild-type controls, which facilitates characterization of mutant phenotypes. Methods developed for construction (transposon mutagenesis), analysis and utilization of the resource are described here. These include the high-throughput Mu-seq genotyping protocol that enables both forward and reverse approaches for linking genotypes-to-phenotypes. © 2016 by John Wiley & Sons, Inc.
    Sprache Englisch
    Erscheinungsdatum 2019-11-14
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2379-8068
    ISSN (online) 2379-8068
    DOI 10.1002/cppb.20029
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Regulation of invertase: a 'suite' of transcriptional and post-transcriptional mechanisms.

    Huang, Li-Fen / Bocock, Philip N / Davis, John M / Koch, Karen E

    Functional plant biology : FPB

    2020  Band 34, Heft 6, Seite(n) 499–507

    Abstract: Recent evidence indicates that several mechanisms can alter invertase activity and, thus, affect sucrose metabolism and resource allocation in plants. One of these mechanisms is the compartmentalisation of at least some vacuolar invertases in precursor ... ...

    Abstract Recent evidence indicates that several mechanisms can alter invertase activity and, thus, affect sucrose metabolism and resource allocation in plants. One of these mechanisms is the compartmentalisation of at least some vacuolar invertases in precursor protease vesicles (PPV), where their retention could control timing of delivery to vacuoles and hence activity. PPV are small, ER-derived bodies that sequester a subset of vacuolar-bound proteins (such as invertases and protease precursors) releasing them to acid vacuoles in response to developmental or environmental signals. Another newly-identified effector of invertases is wall-associated kinase 2 (WAK2), which can regulate a specific vacuolar invertase in Arabidopsis (AtvacINV1) and alter root growth when osmolyte supplies are limiting. WAKs are ideally positioned to sense changes in the interface between the cell wall and plasma membrane (such as turgor), because the N-terminus of each WAK extends into the cell wall matrix (where a pectin association is hypothesised) and the C-terminus has a cytoplasmic serine/threonine kinase domain (signalling). Still other avenues of invertase control are provided by a diverse group of kinases and phosphatases, consistent with input from multiple sensing systems for sugars, pathogens, ABA and other hormones. Mechanisms of regulation may also vary for the contrasting sugar responses of different acid invertase transcripts. Some degree of hexokinase involvement and distinctive kinetics have been observed for the sugar-repressed invertases, but not for the more common, sugar-induced forms examined thus far. An additional means of regulation for invertase gene expression lies in the multiple DST (Down STream) elements of the 3' untranslated region for the most rapidly repressed invertases. Similar sequences were initially identified in small auxin-up RNAs (SAUR) where they mediate rapid mRNA turnover. Finally, the invertase inhibitors, cell wall- and vacuolar inhibitors of fructosidase (CIF and VIF, respectively) are indistinguishable by sequence alone from pectin methylesterase inhibitors (PMEI); however, recent evidence suggests binding specificity may be determined by flexibility of a short, N-terminal region. These recently characterised processes increase the suite of regulatory mechanisms by which invertase - and, thus, sucrose metabolism and resource partitioning - can be altered in plants.
    Sprache Englisch
    Erscheinungsdatum 2020-07-21
    Erscheinungsland Australia
    Dokumenttyp Journal Article
    ZDB-ID 2071582-1
    ISSN 1445-4416 ; 1445-4408
    ISSN (online) 1445-4416
    ISSN 1445-4408
    DOI 10.1071/FP06227
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: Genetic Perturbation of the Starch Biosynthesis in Maize Endosperm Reveals Sugar-Responsive Gene Networks.

    Finegan, Christina / Boehlein, Susan K / Leach, Kristen A / Madrid, Gabriela / Hannah, L Curtis / Koch, Karen E / Tracy, William F / Resende, Marcio F R

    Frontiers in plant science

    2022  Band 12, Seite(n) 800326

    Abstract: In maize, starch mutants have facilitated characterization of key genes involved in endosperm starch biosynthesis such ... ...

    Abstract In maize, starch mutants have facilitated characterization of key genes involved in endosperm starch biosynthesis such as
    Sprache Englisch
    Erscheinungsdatum 2022-02-08
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2021.800326
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  7. Artikel ; Online: A time and a place for sugar in your ears.

    Guan, Jiahn-Chou / Koch, Karen E

    Nature biotechnology

    2015  Band 33, Heft 8, Seite(n) 827–828

    Mesh-Begriff(e) Biotechnology ; Droughts ; Genetic Engineering ; Plants, Genetically Modified/chemistry ; Plants, Genetically Modified/genetics ; Plants, Genetically Modified/metabolism ; Plants, Genetically Modified/physiology ; Stress, Physiological ; Trehalose/metabolism ; Zea mays/chemistry ; Zea mays/genetics ; Zea mays/metabolism ; Zea mays/physiology
    Chemische Substanzen Trehalose (B8WCK70T7I)
    Sprache Englisch
    Erscheinungsdatum 2015-08
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/nbt.3315
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2167: Hefte anzeigen Standort:
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  8. Artikel ; Online: Causes and consequences of endogenous hypoxia on growth and metabolism of developing maize kernels.

    Langer, Matthias / Hilo, Alexander / Guan, Jiahn-Chou / Koch, Karen E / Xiao, Hui / Verboven, Pieter / Gündel, Andre / Wagner, Steffen / Ortleb, Stefan / Radchuk, Volodymyr / Mayer, Simon / Nicolai, Bart / Borisjuk, Ljudmilla / Rolletschek, Hardy

    Plant physiology

    2023  Band 192, Heft 2, Seite(n) 1268–1288

    Abstract: Maize (Zea mays) kernels are the largest cereal grains, and their endosperm is severely oxygen deficient during grain fill. The causes, dynamics, and mechanisms of acclimation to hypoxia are minimally understood. Here, we demonstrate that hypoxia ... ...

    Abstract Maize (Zea mays) kernels are the largest cereal grains, and their endosperm is severely oxygen deficient during grain fill. The causes, dynamics, and mechanisms of acclimation to hypoxia are minimally understood. Here, we demonstrate that hypoxia develops in the small, growing endosperm, but not the nucellus, and becomes the standard state, regardless of diverse structural and genetic perturbations in modern maize (B73, popcorn, sweet corn), mutants (sweet4c, glossy6, waxy), and non-domesticated wild relatives (teosintes and Tripsacum species). We also uncovered an interconnected void space at the chalazal pericarp, providing superior oxygen supply to the placental tissues and basal endosperm transfer layer. Modeling indicated a very high diffusion resistance inside the endosperm, which, together with internal oxygen consumption, could generate steep oxygen gradients at the endosperm surface. Manipulation of oxygen supply induced reciprocal shifts in gene expression implicated in controlling mitochondrial functions (23.6 kDa Heat-Shock Protein, Voltage-Dependent Anion Channel 2) and multiple signaling pathways (core hypoxia genes, cyclic nucleotide metabolism, ethylene synthesis). Metabolite profiling revealed oxygen-dependent shifts in mitochondrial pathways, ascorbate metabolism, starch synthesis, and auxin degradation. Long-term elevated oxygen supply enhanced the rate of kernel development. Altogether, evidence here supports a mechanistic framework for the establishment of and acclimation to hypoxia in the maize endosperm.
    Mesh-Begriff(e) Pregnancy ; Female ; Humans ; Zea mays/metabolism ; Starch/metabolism ; Placenta/metabolism ; Endosperm/metabolism ; Oxygen/metabolism ; Hypoxia/metabolism
    Chemische Substanzen Starch (9005-25-8) ; Oxygen (S88TT14065)
    Sprache Englisch
    Erscheinungsdatum 2023-01-24
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208914-2
    ISSN 1532-2548 ; 0032-0889
    ISSN (online) 1532-2548
    ISSN 0032-0889
    DOI 10.1093/plphys/kiad038
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  9. Artikel ; Online: Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture.

    Guan, Jiahn-Chou / Li, Changsheng / Flint-Garcia, Sherry / Suzuki, Masaharu / Wu, Shan / Saunders, Jonathan W / Dong, Lemeng / Bouwmeester, Harro J / McCarty, Donald R / Koch, Karen E

    The Plant cell

    2022  Band 35, Heft 3, Seite(n) 1013–1037

    Abstract: The maize (Zea mays) ear represents one of the most striking domestication phenotypes in any crop species, with the cob conferring an exceptional yield advantage over the ancestral form of teosinte. Remodeling of the grain-bearing surface required ... ...

    Abstract The maize (Zea mays) ear represents one of the most striking domestication phenotypes in any crop species, with the cob conferring an exceptional yield advantage over the ancestral form of teosinte. Remodeling of the grain-bearing surface required profound developmental changes. However, the underlying mechanisms remain unclear and can only be partly attributed to the known domestication gene Teosinte glume architecture 1 (Tga1). Here we show that a more complete conversion involves strigolactones (SLs), and that these are prominent players not only in the Tga1 phenotype but also other domestication features of the ear and kernel. Genetic combinations of a teosinte tga1 allele with three SL-related mutants progressively enhanced ancestral morphologies. The SL mutants, in addition to modulating the tga1 phenotype, also reshaped kernel-bearing pedicels and cupules in a teosinte-like manner. Genetic and molecular evidence are consistent with SL regulation of TGA1, including direct interaction of TGA1 with components of the SL-signaling system shown here to mediate TGA1 availability by sequestration. Roles of the SL network extend to enhancing maize seed size and, importantly, coordinating increased kernel growth with remodeling of protective maternal tissues. Collectively, our data show that SLs have central roles in releasing kernels from restrictive maternal encasement and coordinating other factors that increase kernel size, physical support, and their exposure on the grain-bearing surface.
    Mesh-Begriff(e) Domestication ; Zea mays/genetics ; Lactones ; Edible Grain/genetics ; Phenotype
    Chemische Substanzen GR24 strigolactone ; Lactones
    Sprache Englisch
    Erscheinungsdatum 2022-12-27
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 623171-8
    ISSN 1532-298X ; 1040-4651
    ISSN (online) 1532-298X
    ISSN 1040-4651
    DOI 10.1093/plcell/koac370
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  10. Artikel ; Online: Sugar modulation of anaerobic-response networks in maize root tips.

    Sanclemente, Maria-Angelica / Ma, Fangfang / Liu, Peng / Della Porta, Adriana / Singh, Jugpreet / Wu, Shan / Colquhoun, Thomas / Johnson, Timothy / Guan, Jiahn-Chou / Koch, Karen E

    Plant physiology

    2021  Band 185, Heft 2, Seite(n) 295–317

    Abstract: Sugar supply is a key component of hypoxia tolerance and acclimation in plants. However, a striking gap remains in our understanding of mechanisms governing sugar impacts on low-oxygen responses. Here, we used a maize (Zea mays) root-tip system for ... ...

    Abstract Sugar supply is a key component of hypoxia tolerance and acclimation in plants. However, a striking gap remains in our understanding of mechanisms governing sugar impacts on low-oxygen responses. Here, we used a maize (Zea mays) root-tip system for precise control of sugar and oxygen levels. We compared responses to oxygen (21 and 0.2%) in the presence of abundant versus limited glucose supplies (2.0 and 0.2%). Low-oxygen reconfigured the transcriptome with glucose deprivation enhancing the speed and magnitude of gene induction for core anaerobic proteins (ANPs). Sugar supply also altered profiles of hypoxia-responsive genes carrying G4 motifs (sources of regulatory quadruplex structures), revealing a fast, sugar-independent class followed more slowly by feast-or-famine-regulated G4 genes. Metabolite analysis showed that endogenous sugar levels were maintained by exogenous glucose under aerobic conditions and demonstrated a prominent capacity for sucrose re-synthesis that was undetectable under hypoxia. Glucose abundance had distinctive impacts on co-expression networks associated with ANPs, altering network partners and aiding persistence of interacting networks under prolonged hypoxia. Among the ANP networks, two highly interconnected clusters of genes formed around Pyruvate decarboxylase 3 and Glyceraldehyde-3-phosphate dehydrogenase 4. Genes in these clusters shared a small set of cis-regulatory elements, two of which typified glucose induction. Collective results demonstrate specific, previously unrecognized roles of sugars in low-oxygen responses, extending from accelerated onset of initial adaptive phases by starvation stress to maintenance and modulation of co-expression relationships by carbohydrate availability.
    Mesh-Begriff(e) Anaerobiosis ; Glucose/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Oxygen/metabolism ; Plant Proteins/genetics ; Plant Roots/genetics ; Plant Roots/metabolism ; Pyruvate Decarboxylase/genetics ; Stress, Physiological ; Sugars/metabolism ; Transcriptome ; Zea mays/genetics ; Zea mays/metabolism
    Chemische Substanzen Plant Proteins ; Sugars ; Glyceraldehyde-3-Phosphate Dehydrogenases (EC 1.2.1.-) ; Pyruvate Decarboxylase (EC 4.1.1.1) ; Glucose (IY9XDZ35W2) ; Oxygen (S88TT14065)
    Sprache Englisch
    Erscheinungsdatum 2021-03-15
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 208914-2
    ISSN 1532-2548 ; 0032-0889
    ISSN (online) 1532-2548
    ISSN 0032-0889
    DOI 10.1093/plphys/kiaa029
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