Co-expression and regulation of photorespiratory genes in Arabidopsis thaliana: A bioinformatic approach

Peterhänsel, 2010, Photorespiration, Arabidopsis Book, 8, e0130, 10.1199/tab.0130 Decker, 1955, A rapid, postillumination deceleration of respiration in green leaves, Plant Physiol., 30, 82, 10.1104/pp.30.1.82 Decker, 1959, Some effects of temperature and carbon dioxide concentration on photosynthesis of Mimulus, Plant Physiol., 34, 103, 10.1104/pp.34.2.103 Tregunna, 1961, Evolution of carbon dioxide by tobacco leaves during the dark period following illumination with the light of different intensities, Can. J. Bot., 39, 1045, 10.1139/b61-091 Tregunna, 1964, Further evidence on the effects of light on respiration during photosynthesis, Can. J. Bot., 42, 989, 10.1139/b64-090 Turner, 1962, Oxygen as a factor in photosynthesis, Biol. Rev. Camb. Philos. Soc., 37, 130, 10.1111/j.1469-185X.1962.tb01607.x Somerville, 1979, A phosphoglycolate phosphatase-deficient mutant of Arabidopsis, Nature, 280, 833, 10.1038/280833a0 Somerville, 1982, Genetic modification of photorespiration, Trends Biochem. Sci., 7, 171, 10.1016/0968-0004(82)90130-X Somerville, 1980, Photorespiration mutants of Arabidopsis thaliana deficient in serine-glyoxylate aminotransferase activity, Proc. Natl. Acad. Sci. U. S. A., 77, 2684, 10.1073/pnas.77.5.2684 Somerville, 1981, Photorespiration-deficient mutants of Arabidopsis thaliana lacking mitochondrial serine transhydroxymethylase activity, Plant Physiol., 67, 666, 10.1104/pp.67.4.666 Somerville, 1982, Mutants of the cruciferous plant Arabidopsis thaliana lacking glycine decarboxylase activity, Biochem. J., 202, 373, 10.1042/bj2020373 Somerville, 1983, An Arabidopsis thaliana mutant defective in chloroplast dicarboxylate transport, Proc. Natl. Acad. Sci. U. S. A., 80, 1290, 10.1073/pnas.80.5.1290 Schwarte, 2007, Identification of the photorespiratory 2-phosphoglycolate phosphatase, PGLP1, in Arabidopsis, Plant Physiol., 144, 1580, 10.1104/pp.107.099192 Dellero, 2016, Decreased glycolate oxidase activity leads to altered carbon allocation and leaf senescence after a transfer from high CO2 to ambient air in Arabidopsis thaliana, J. Exp. Bot., 67, 3149, 10.1093/jxb/erw054 Murray, 1989, Metabolism of hydroxypyruvate in a mutant of barley lacking NADH-dependent hydroxypyruvate reductase, an important photorespiratory enzyme activity, Plant Physiol., 91, 395, 10.1104/pp.91.1.395 Givan, 1992, The enzymic reduction of glyoxylate and hydroxypyruvate in leaves of higher plants, Plant Physiol., 100, 552, 10.1104/pp.100.2.552 Timm, 2008, A cytosolic pathway for the conversion of hydroxypyruvate to glycerate during photorespiration in Arabidopsis, Plant Cell, 20, 2848, 10.1105/tpc.108.062265 Cousins, 2011, Peroxisomal hydroxypyruvate reductase is not essential for photorespiration in Arabidopsis but its absence causes an increase in the stoichiometry of photorespiratory CO2 release, Photosynth. Res., 108, 91, 10.1007/s11120-011-9651-3 Igarashi, 2003, Identification of photorespiratory glutamate: glyoxylate aminotransferase (GGAT) gene in Arabidopsis, Plant J., 33, 975, 10.1046/j.1365-313X.2003.01688.x Dellero, 2015, Arabidopsis thaliana ggt1 photorespiratory mutants maintain leaf carbon/nitrogen balance by reducing RuBisCO content and plant growth, Plant J., 83, 1005, 10.1111/tpj.12945 Murray, 1987, Photorespiratory N donors, aminotransferase specificity and photosynthesis in a mutant of barley deficient in serine: glyoxylate aminotransferase activity, Planta, 172, 106, 10.1007/BF00403035 McHale, 1989, Photorespiratory toxicity in autotrophic cell cultures of a mutant of Nicotiana sylvestris lacking serine: glyoxylate aminotransferase activity, Planta, 179, 67, 10.1007/BF00395772 Modde, 2017, High serine:glyoxylate aminotransferase activity lowers leaf daytime serine levels, inducing the phosphoserine pathway in Arabidopsis, J. Exp. Bot., 68, 643 Igamberdiev, 2001, The role of photorespiration in redox and energy balance of photosynthetic plant cells: a study with a barley mutant deficient in glycine decarboxylase, Physiol. Plant., 111, 427, 10.1034/j.1399-3054.2001.1110402.x Bykova, 2005, Interaction between photorespiration and respiration in transgenic potato plants with antisense reduction in glycine decarboxylase, Planta, 222, 130, 10.1007/s00425-005-1505-9 Engel, 2007, Deletion of glycine decarboxylase in Arabidopsis is lethal under non-photorespiratory conditions, Plant Physiol., 144, 1328, 10.1104/pp.107.099317 Beckmann, 1997, Planta, 202, 379, 10.1007/s004250050140 Kuhn, 2013, D-2-hydroxyglutarate metabolism is linked to photorespiration in the shm1-1 mutant, Plant Biol., 15, 776, 10.1111/plb.12020 Brestic, 2014, Reduced glutamine synthetase activity plays a role in control of photosynthetic responses to high light in barley leaves, Plant Physiol. Biochem., 81, 74, 10.1016/j.plaphy.2014.01.002 Foyer, 2009, Photorespiratory metabolism: genes, mutants, energetics, and redox signaling, Annu. Rev. Plant Biol., 60, 455, 10.1146/annurev.arplant.043008.091948 Taniguchi, 2002, Identifying and characterizing plastidic 2-oxoglutarate/malate and dicarboxylate transporters in Arabidopsis thaliana, Plant Cell Physiol., 43, 706, 10.1093/pcp/pcf109 Hoffmann, 2013, From endoplasmic reticulum to mitochondria: absence of the Arabidopsis ATP antiporter endoplasmic reticulum adenylate transporter 1 perturbs photorespiration, Plant Cell, 25, 2647, 10.1105/tpc.113.113605 Eisenhut, 2013, Arabidopsis A BOUT DE SOUFFLE is a putative mitochondrial transporter involved in photorespiratory metabolism and is required for meristem growth at ambient CO2 levels, Plant J., 73, 836, 10.1111/tpj.12082 Pick, 2013, PLGG1, a plastidic glycolate glycerate transporter, is required for photorespiration and defines a unique class of metabolite transporters, Proc. Natl. Acad. Sci. U. S. A., 110, 3185, 10.1073/pnas.1215142110 Vauclare, 1998, The gene encoding T protein of the glycine decarboxylase complex involved in the mitochondrial step of the photorespiratory pathway in plants exhibits features of light-induced genes, Plant Mol. Biol., 37, 309, 10.1023/A:1005954200042 Engelmann, 2008, The gene for the P-subunit of glycine decarboxylase from the C4 species Flaveria trinervia: analysis of transcriptional control in transgenic Flaveria bidentis (C4) and Arabidopsis (C3), Plant Physiol., 146, 1773, 10.1104/pp.107.114462 Hu, 2010, Functional comparison of catalase genes in the elimination of photorespiratory H2O2 using promoter- and 3'-untranslated region exchange experiments in the Arabidopsis cat2 photorespiratory mutant, Plant Cell Environ., 33, 1656, 10.1111/j.1365-3040.2010.02171.x Adwy, 2015, A simple mechanism for the establishment of C2-specific gene expression in Brassicaceae, Plant J., 84, 1231, 10.1111/tpj.13084 Laxa, 2016, The 5’UTR intron of Arabidopsis GGT1 aminotransferase enhances promoter activity by recruiting RNA polymerase II, Plant Physiol., 172, 313, 10.1104/pp.16.00881 Laxa, 2017, Regulatory cis-elements are located in accessible promoter regions of the CAT2 promoter and affect activating histone modifications in Arabidopsis thaliana, Plant Mol. Biol., 93, 49, 10.1007/s11103-016-0546-8 Timm, 2013, Serine acts as a metabolic signal for the transcriptional control of photorespiration-related genes in Arabidopsis, Plant Physiol., 162, 379, 10.1104/pp.113.215970 Goodstein, 2012, Phytozome: a comparative platform for green plant genomics, Nucl. Acids Res., 40, D1178, 10.1093/nar/gkr944 Jefferson, 1987, GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants, EMBO J., 6, 3901, 10.1002/j.1460-2075.1987.tb02730.x Lee, 2015, AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species, Nucl. Acids Res., 43, D996, 10.1093/nar/gku1053 Obayashi, 2007, ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis, Nucl. Acids Res., 35, D863, 10.1093/nar/gkl783 Van Bel, 2017, Exploring plant co-expression and gene-gene interactions with CORNET 3.0, Methods Mol. Biol., 1533, 201, 10.1007/978-1-4939-6658-5_11 Wei, 2006, Transcriptional coordination of the metabolic network in Arabidopsis, Plant Physiol., 142, 762, 10.1104/pp.106.080358 Steinhauser, 2004, C.S.B. DB: a comprehensive systems-biology database, Bioinformatics, 20, 3647, 10.1093/bioinformatics/bth398 Warde-Farley, 2010, The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function, Nucl. Acids Res., 38, W214, 10.1093/nar/gkq537 Mutwil, 2011, PlaNet: combined sequence and expression comparisons across plant networks derived from seven species, Plant Cell, 23, 895, 10.1105/tpc.111.083667 O’Connor, 2005, Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences, Bioinformatics, 21, 4411, 10.1093/bioinformatics/bti714 Usadel, 2005, Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses, Plant Physiol., 138, 1195, 10.1104/pp.105.060459 Chang, 2013, Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis, eLife, 2, e00675, 10.7554/eLife.00675 Rose, 2008, Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression, Plant Cell, 20, 543, 10.1105/tpc.107.057190 Schläpfer, 2017, Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants, Plant Physiol., 173, 2041, 10.1104/pp.16.01942 Liebthal, 2016, Redox-dependent conformational dynamics of decameric 2-cysteine peroxiredoxin and its interaction with cyclophilin 20-3, Plant Cell Physiol., 57, 1415 Usadel, 2009, Co-expression tools for plant biology: opportunities for hypothesis generation and caveats, Plant Cell Environ., 32, 1633, 10.1111/j.1365-3040.2009.02040.x Bloom, 2015, Photorespiration and nitrate assimilation: a major intersection between plant carbon and nitrogen, Photosynth. Res., 123, 117, 10.1007/s11120-014-0056-y Rachmilevitch, 2004, Nitrate assimilation in plant shoots depends on photorespiration, Proc. Natl. Acad. Sci. U. S. A., 101, 11506, 10.1073/pnas.0404388101 Pérez-Delgado, 2015, Reassimilation of photorespiratory ammonium in Lotus japonicus plants deficient in plastidic glutamine synthetase, PLoS One, 10, e0130438, 10.1371/journal.pone.0130438 Queval, 2007, Plant J., 52, 640, 10.1111/j.1365-313X.2007.03263.x Anjum, 2016, Catalase and ascorbate peroxidase-representative H2O2-detoxifying heme enzymes in plants, Environ. Sci. Pollut. Res., 23, 19002, 10.1007/s11356-016-7309-6 Beevers, 1979, Microbodies in higher plants, Annu. Rev. Plant Physiol., 30, 159, 10.1146/annurev.pp.30.060179.001111 Timm, 2015, Mitochondrial dihydrolipoyl dehydrogenase activity shapes photosynthesis and photorespiration of Arabidopsis thaliana, Plant Cell, 27, 1968, 10.1105/tpc.15.00105 Timm, 2018, T-protein is present in large excess over the other proteins of the glycine cleavage system in leaves of Arabidopsis, Planta, 247, 41, 10.1007/s00425-017-2767-8 Douce, 2001, The glycine decarboxylase system: a fascinating complex, Trends Plant Sci., 6, 167, 10.1016/S1360-1385(01)01892-1 Weber, 2002, Interaction of cytosolic and plastidic nitrogen metabolism in plants, J. Exp. Bot., 53, 865, 10.1093/jexbot/53.370.865 Pracharoenwattana, 2007, Arabidopsis peroxisomal malate dehydrogenase functions in b-oxidation but not in the glyoxylate cycle, Plant J., 50, 381, 10.1111/j.1365-313X.2007.03055.x Zybailov, 2008, Sorting signals, N-terminal modifications and abundance of the chloroplast proteome, PLoS One, 3, e1994, 10.1371/journal.pone.0001994 Qi, 2012, Arabidopsis CSP41 proteins form multimeric complexes that bind and stabilize distinct plastid transcripts, J. Exp. Bot., 63, 1251, 10.1093/jxb/err347 Leister, 2014, Complex(iti)es of the ubiquitous RNA-binding CSP41 proteins, Front. Plant Sci., 5, 255, 10.3389/fpls.2014.00255 Fettke, 2011, Identification of a novel heteroglycan-interacting protein, HIP1.3, from Arabidopsis thaliana, J. Plant Physiol., 168, 1415, 10.1016/j.jplph.2010.09.008 Beligni, 2008, Arabidopsis thaliana mutants reveal a role for CSP41a and CSP41b, two ribosome-associated endonucleases, in chloroplast ribosomal RNA metabolism, Plant Mol. Biol., 67, 389, 10.1007/s11103-008-9328-2 Bollenbach, 2009, The RNA-binding proteins CSP41a and CSP41b may regulate transcription and translation of chloroplast-encoded RNAs in Arabidopsis, Plant Mol. Biol., 69, 541, 10.1007/s11103-008-9436-z Mei, 2017, Newly identified CSP41b gene localized in chloroplasts affects leaf color in rice, Plant Sci., 256, 39, 10.1016/j.plantsci.2016.12.005 Baek, 2016, A role for Arabidopsis miR399f in salt, drought, and ABA signaling, Mol. Cells, 39, 111, 10.14348/molcells.2016.2188 Harrison, 1998, Reduced sedoheptulose-1,7-bisphosphatase levels in transgenic tobacco lead to decreased photosynthetic capacity and altered carbohydrate accumulation, Planta, 204, 27, 10.1007/s004250050226 Raines, 2000, Investigating the role of the thiol-regulated enzyme sedoheptulose-1, 7-bisphosphatase in the control of photosynthesis, Physiol. Plant., 110, 303, 10.1034/j.1399-3054.2000.1100303.x Feng, 2007, Overexpression of sedoheptulose-1,7-bisphosphatase enhances photosynthesis and growth under salt stress in transgenic rice plants, Funct. Plant Biol., 34, 822, 10.1071/FP07074 Feng, 2007, Overexpression of SBPase enhances photosynthesis against high temperature stress in transgenic rice plants, Plant Cell Rep., 26, 1635, 10.1007/s00299-006-0299-y Ding, 2016, Changes in SBPase activity influence photosynthetic capacity, growth, and tolerance to chilling stress in transgenic tomato plants, Sci. Rep., 6, 32741, 10.1038/srep32741 Liu, 2012, Carbonylation and loss-of-function analyses of SBPase reveal its metabolic interface role in oxidative stress, carbon assimilation, and multiple aspects of growth and development in Arabidopsis, Mol. Plant, 5, 1082, 10.1093/mp/sss012 Uematsu, 2012, Increased fructose 1,6-bisphosphate aldolase in plastids enhances growth and photosynthesis of tobacco plants, J. Exp. Bot., 63, 3001, 10.1093/jxb/ers004 Kangasjärvi, 2012, Photosynthesis, photorespiration, and light signalling in defence responses, J. Exp. Bot., 63, 1619, 10.1093/jxb/err402 Xu, 2009, Inducible antisense suppression of glycolate oxidase reveals its strong regulation over photosynthesis in rice, J. Exp. Bot., 60, 1799, 10.1093/jxb/erp056 Timm, 2012, Glycine decarboxylase controls photosynthesis and plant growth, FEBS Lett., 586, 3692, 10.1016/j.febslet.2012.08.027 Lu, 2014, Suppression of glycolate oxidase causes glyoxylate accumulation that inhibits photosynthesis through deactivating Rubisco in rice, Physiol. Plant., 150, 463, 10.1111/ppl.12104 Dellero, 2015, Arabidopsis thaliana ggt1 photorespiratory mutants maintain leaf carbon/nitrogen balance by reducing RuBisCO content and plant growth, Plant J., 83, 1005, 10.1111/tpj.12945 Lin, 2016, Targeted knockdown of GDCH in rice leads to a photorespiratory-deficient phenotype useful as a building block for C4 rice, Plant Cell Physiol., 57, 919, 10.1093/pcp/pcw033 Flügel, 2017, The photorespiratory metabolite 2-phosphoglycolate regulates photosynthesis and starch accumulation in Arabidopsis, Plant Cell, 29, 2537, 10.1105/tpc.17.00256 Rojas, 2012, Glycolate oxidase modulates reactive oxygen species-mediated signal transduction during nonhost resistance in Nicotiana benthamiana and Arabidopsis, Plant Cell, 24, 336, 10.1105/tpc.111.093245 Gilbert, 2013, Characterization of the LOV1-mediated, victorin-induced, cell-death response with virus-induced gene silencing, Mol. Plant Microbe Interact., 26, 903, 10.1094/MPMI-01-13-0014-R Palmieri, 2010, Regulation of plant glycine decarboxylase by S-nitrosylation and glutathionylation, Plant Physiol., 152, 1514, 10.1104/pp.109.152579 Zaffagnini, 2007, The thioredoxin-independent isoform of chloroplastic glyceraldehyde-3-phosphate dehydrogenase is selectively regulated by glutathionylation, FEBS J., 274, 212, 10.1111/j.1742-4658.2006.05577.x Mhamdi, 2010, Catalase function in plants: a focus on Arabidopsis mutants as stress-mimic models, J. Exp. Bot., 61, 4197, 10.1093/jxb/erq282 Smale, 2001, Core promoters: active contributors to combinatorial gene regulation, Genes Dev., 15, 2503, 10.1101/gad.937701 Thomas, 2006, The general transcription machinery and general cofactors, Crit. Rev. Biochem. Mol. Biol., 41, 105, 10.1080/10409230600648736 Lee, 2000, Transcription of eukaryotic protein-coding genes, Annu. Rev. Genet., 34, 77, 10.1146/annurev.genet.34.1.77 Corden, 1980, Promoter sequences of eukaryotic protein-coding genes, Science, 209, 1406, 10.1126/science.6251548 Smale, 1989, The "initiator" as a transcription control element, Cell., 57, 103, 10.1016/0092-8674(89)90176-1 Kiran, 2006, The TATA-box sequence in the basal promoter contributes to determining light-dependent gene expression in plants, Plant Physiol., 142, 364, 10.1104/pp.106.084319 Stracke, 2001, The R2R3-MYB gene family in Arabidopsis thaliana, Curr. Opin. Plant Biol., 4, 447, 10.1016/S1369-5266(00)00199-0 Kranz, 1998, Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana, Plant J., 16, 263, 10.1046/j.1365-313x.1998.00278.x Ambawat, 2013, MYB transcription factor genes as regulators for plant responses: an overview, Physiol. Mol. Biol. Plants, 19, 307, 10.1007/s12298-013-0179-1 Roy, 2016, Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome, Plant Signal. Behav., 11, e1117723, 10.1080/15592324.2015.1117723 Jin, 2000, Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis, EMBO J., 19, 6150, 10.1093/emboj/19.22.6150 Russell, 1967, The cinnamic acid 4-hydroxylase of pea seedlings, Arch. Biochem. Biophys., 122, 256, 10.1016/0003-9861(67)90150-6 Russell, 1971, The metabolism of aromatic compounds in higer plants. X. Properties of the cinnamic acid 4-hydroxylase of pea seedlings and some aspects of its metabolic and developmental control, J. Biol. Chem., 246, 3870, 10.1016/S0021-9258(18)62115-5 Niu, 2010, Coordinated regulation of anthocyanin biosynthesis in Chinese bayberry (Myrica rubra) fruit by a R2R3 MYB transcription factor, Planta, 231, 887, 10.1007/s00425-009-1095-z Du, 2012, The R2R3-MYB transcription factor gene family in maize, PLoS One, 7, e37463, 10.1371/journal.pone.0037463 Feldbrugge, 1997, PcMYB1 novel plant protein containing a DNA-binding domain with one Myb repeat, interacts in vivo with a light-regulatory promoter unit, Plant J., 11, 1079, 10.1046/j.1365-313X.1997.11051079.x Chen, 2005, Cloning and characterization of a drought inducible MYB gene from Boea crassifolia, Plant Sci., 168, 493, 10.1016/j.plantsci.2004.09.013 Wang, 2014, Overexpression of a R2R3 MYB gene MdSIMYB1 increases tolerance to multiple stresses in transgenic tobacco and apples, Physiol. Plant., 150, 76, 10.1111/ppl.12069 Sørhagen, 2013, The emerging role of photorespiration and non-photorespiratory peroxisomal metabolism in pathogen defence, Plant Biol., 15, 723, 10.1111/j.1438-8677.2012.00723.x Schenke, 2011, Crosstalk between abiotic ultraviolet-B stress and biotic (flg22) stress signalling in Arabidopsis prevents flavonol accumulation in favor of pathogen defence compound production, Plant Cell Environ., 34, 1849, 10.1111/j.1365-3040.2011.02381.x Jenkins, 2009, Signal transduction in responses to UV-B radiation, Annu. Rev. Plant Biol., 60, 407, 10.1146/annurev.arplant.59.032607.092953 Logemann, 2002, Crosstalk among stress responses in plants: pathogen defense overrides UV protection through an inversely regulated ACE/ACE type of light-responsive gene promoter unit, Proc. Natl. Acad. Sci. U. S. A., 99, 2428, 10.1073/pnas.042692199 Stracke, 2007, Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling, Plant J., 50, 660, 10.1111/j.1365-313X.2007.03078.x Ülker, 2004, WRKY transcription factors: from DNA binding towards biological function, Curr. Opin. Plant Biol., 7, 491, 10.1016/j.pbi.2004.07.012 Gendra, 2007, A sequence motif in the simian virus 40 (SV40) early core promoter affects alternative splicing of transcribed mRNA, J. Biol. Chem., 282, 11648, 10.1074/jbc.M611126200 Srivastava, 2018, UTR-dependent control of gene expression in plants, Trends Plant Sci., 23, 248, 10.1016/j.tplants.2017.11.003 Hornyik, 2010, Alternative polyadenylation of antisense RNAs and flowering time control, Biochem. Soc. Trans., 38, 1077, 10.1042/BST0381077 Macknight, 2002, Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA, Plant Cell, 14, 877, 10.1105/tpc.010456 Tang, 2003, Binding site selection for the plant MADS domain protein AGL15: an in vitro and in vivo study, J. Biol. Chem., 278, 28154, 10.1074/jbc.M212976200 Heck, 1995, AGL15, a MADS domain protein expressed in developing embryos, Plant Cell, 7, 1271, 10.1105/tpc.7.8.1271 Hayashi, 2000, Functional transformation of plant peroxisomes, Cell Biochem. Biophys., 32, 295, 10.1385/CBB:32:1-3:295 Titus, 1985, Investigation of the glyoxysome-peroxisome transition in germinating cucumber cotyledons using double-label immunoelectron microscopy, J. Cell Biol., 101, 1288, 10.1083/jcb.101.4.1288 Nishimura, 1986, Immunocytochemical analysis shows that glyoxysomes are directly transformed to leaf peroxisomes during greening of pumpkin cotyledons, Plant Physiol., 81, 313, 10.1104/pp.81.1.313 Nishimura, 1993, Leaf peroxisomes are directly transformed to glyoxysomes during senescence of pumpkin cotyledons, Protoplasma, 175, 131, 10.1007/BF01385011 Ogawa, 2003, Gibberellin biosynthesis and response during Arabidopsis seed germination, Plant Cell, 15, 1591, 10.1105/tpc.011650 Koornneef, 1980, Induction and analysis of gibberellin sensitive mutants in Arabidopsis thaliana (L.) Heynh, Theor. Appl. Genet., 58, 257, 10.1007/BF00265176 Jeong, 2006, Distinct roles of the first introns on the expression of Arabidopsis profilin gene family members, Plant Physiol., 140, 196, 10.1104/pp.105.071316 Meagher, 1999, The evolution of new structures: clues from plant cytoskeletal genes, Trends Genet., 15, 278, 10.1016/S0168-9525(99)01759-X Vitale, 2003, Multiple conserved 5′ elements are required for high-level pollen expression of the Arabidopsis reproductive actin ACT1, Plant Mol. Biol., 52, 1135, 10.1023/B:PLAN.0000004309.06973.16 Laxa, 2017, Intron-mediated enhancement: a tool for heterologous gene expression in plants?, Front. Plant Sci., 7, 1977, 10.3389/fpls.2016.01977 Gallegos, 2017, Intron DNA sequences can be more important than the proximal promoter in determining the site of transcript initiation, Plant Cell, 29, 843, 10.1105/tpc.17.00020 Huang, 1997, The Arabidopsis ACT11 actin gene is strongly expressed in tissues of the emerging inflorescence, pollen, and developing ovules, Plant Mol. Biol., 33, 125, 10.1023/A:1005741514764 Rose, 2000, Intron-mediated enhancement of gene expression independent of unique intron sequences and splicing, Plant Physiol., 122, 535, 10.1104/pp.122.2.535 Clancy, 2000, Splicing of the maize Sh1 first intron is essential for enhancement of gene expression, and a T-rich motif increases expression without affecting splicing, Plant Physiol., 130, 918, 10.1104/pp.008235 Mun, 2002, Petunia actin-depolymerizing factor is mainly accumulated in vascular tissue and its gene expression is enhanced by the first intron, Gene, 292, 233, 10.1016/S0378-1119(02)00646-7 Jeong, 2007, An upstream region in the first intron of petunia actin-depolymerizing factor 1 affects tissue-specific expression in transgenic Arabidopsis (Arabidopsis thaliana), Plant J., 50, 230, 10.1111/j.1365-313X.2007.03053.x Parra, 2011, Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants, Nucl. Acids Res., 39, 5328, 10.1093/nar/gkr043 Winter, 2007, An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets, PLoS One, 2, e718, 10.1371/journal.pone.0000718 Liepman, 2003, Alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes of Arabidopsis, Plant Physiol., 131, 215, 10.1104/pp.011460 Kendziorek, 2012, Differential regulation of alanine aminotransferase homologues by abiotic stresses in wheat (Triticum aestivum L.) seedlings, Plant Cell Rep., 31, 1105, 10.1007/s00299-012-1231-2 Taler, 2004, Genes that encode photorespiratory enzymes confer resistance against disease, Plant Cell, 16, 172, 10.1105/tpc.016352 Barak, 2001, Transcriptional and posttranscriptional regulation of the glycolate oxidase gene in tobacco seedlings, Plant Mol. Biol., 45, 399, 10.1023/A:1010688804719 van Oosten, 1994, Regulation of the expression of photosynthetic nuclear genes by CO2 is mimicked by regulation by carbohydrates: a mechanism for the acclimation of photosynthesis to high CO2?, Plant Cell Environ., 17, 913, 10.1111/j.1365-3040.1994.tb00320.x van Oosten, 1992, Long-term effects of a CO2 enriched atmosphere on enzymes of the primary carbon metabolism of spruce trees, Plant Physiol. Biochem., 30, 541