Gene expression in developing watermelon fruit

<p>Abstract</p> <p>Background</p> <p>Cultivated watermelon form large fruits that are highly variable in size, shape, color, and content, yet have extremely narrow genetic diversity. Whereas a plethora of genes involved in cell wall metabolism, ethylene biosynthesis, fruit softening, and secondary metabolism during fruit development and ripening have been identified in other plant species, little is known of the genes involved in these processes in watermelon. A microarray and quantitative Real-Time PCR-based study was conducted in watermelon [<it>Citrullus lanatus </it>(Thunb.) Matsum. & Nakai var. lanatus] in order to elucidate the flow of events associated with fruit development and ripening in this species. RNA from three different maturation stages of watermelon fruits, as well as leaf, were collected from field grown plants during three consecutive years, and analyzed for gene expression using high-density photolithography microarrays and quantitative PCR.</p> <p>Results</p> <p>High-density photolithography arrays, composed of probes of 832 EST-unigenes from a subtracted, fruit development, cDNA library of watermelon were utilized to examine gene expression at three distinct time-points in watermelon fruit development. Analysis was performed with field-grown fruits over three consecutive growing seasons. Microarray analysis identified three hundred and thirty-five unique ESTs that are differentially regulated by at least two-fold in watermelon fruits during the early, ripening, or mature stage when compared to leaf. Of the 335 ESTs identified, 211 share significant homology with known gene products and 96 had no significant matches with any database accession. Of the modulated watermelon ESTs related to annotated genes, a significant number were found to be associated with or involved in the vascular system, carotenoid biosynthesis, transcriptional regulation, pathogen and stress response, and ethylene biosynthesis. Ethylene bioassays, performed with a closely related watermelon genotype with a similar phenotype, i.e. seeded, bright red flesh, dark green rind, etc., determined that ethylene levels were highest during the green fruit stage followed by a decrease during the white and pink fruit stages. Additionally, quantitative Real-Time PCR was used to validate modulation of 127 ESTs that were differentially expressed in developing and ripening fruits based on array analysis.</p> <p>Conclusion</p> <p>This study identified numerous ESTs with putative involvement in the watermelon fruit developmental and ripening process, in particular the involvement of the vascular system and ethylene. The production of ethylene during fruit development in watermelon gives further support to the role of ethylene in fruit development in non-climacteric fruits.</p

An intermolecular disulfide-based light switch for chloroplast psbD gene expression in Chlamydomonas reinhardtii

Expression of the chloroplast psbD gene encoding the D2 protein of the photosystem II reaction center is regulated by light. In the green alga Chlamydomonas reinhardtii, D2 synthesis requires a high-molecular-weight complex containing the RNA stabilization factor Nac2 and the translational activator RBP40. Based on size exclusion chromatography analyses, we provide evidence that light control of D2 synthesis depends on dynamic formation of the Nac2/RBP40 complex. Furthermore, 2D redox SDS-PAGE assays suggest an intermolecular disulfide bridge between Nac2 and Cys11 of RBP40 as the putative molecular basis for attachment of RBP40 to the complex in light-grown cells. This covalent link is reduced in the dark, most likely via NADPH-dependent thioredoxin reductase C, supporting the idea of a direct relationship between chloroplast gene expression and chloroplast carbon metabolism during dark adaption of algal cells. © 2012 Blackwell Publishing Ltd.España Ministerio de Ciencia e Innovación BIO20010-15430Junta de Andalucía BIO-182 and CVI-591

Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches

[EN] The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis geneCitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotypeMM) into partial andromonoecy (genotypeMm) or andromonoecy (genotypemm). We phenotyped and genotyped, for theM/mlocus, a panel of 207 C. lanatusaccessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite beingMM. A cosegregation analysis between a SNV inCitACS4and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent onCitACS4, but conferred by an unlinked recessive gene which we calledpa. Two different approaches were performed to map thepagene in the genome ofC. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates thatpamaps onto a genomic region expanding across 32.24-36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down thepalocus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.This work has been funded by grant UAL18-BIO-B017-B, awarded by the call "Proyectos UAL-FEDER " within the framework of the 2014-2020 FEDER-Andalusia Operational Program, as well as by the research group BIO293 of the University of Almeria.Aguado, E.; García, A.; Iglesias-Moya, J.; Romero, J.; Wehner, TC.; Gómez-Guillamón, ML.; Picó Sirvent, MB.... (2020). Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches. Frontiers in Plant Science. 11:1-16. https://doi.org/10.3389/fpls.2020.01243S11611Aguado, E., García, A., Manzano, S., Valenzuela, J. L., Cuevas, J., Pinillos, V., & Jamilena, M. (2018). The sex-determining gene CitACS4 is a pleiotropic regulator of flower and fruit development in watermelon (Citrullus lanatus). Plant Reproduction, 31(4), 411-426. doi:10.1007/s00497-018-0346-1Bo, K., Miao, H., Wang, M., Xie, X., Song, Z., Xie, Q., … Gu, X. (2018). Novel loci fsd6.1 and Csgl3 regulate ultra-high fruit spine density in cucumber. Theoretical and Applied Genetics, 132(1), 27-40. doi:10.1007/s00122-018-3191-6Bo, K., Wei, S., Wang, W., Miao, H., Dong, S., Zhang, S., & Gu, X. (2019). QTL mapping and genome-wide association study reveal two novel loci associated with green flesh color in cucumber. BMC Plant Biology, 19(1). doi:10.1186/s12870-019-1835-6Boualem, A., Fergany, M., Fernandez, R., Troadec, C., Martin, A., Morin, H., … Bendahmane, A. (2008). A Conserved Mutation in an Ethylene Biosynthesis Enzyme Leads to Andromonoecy in Melons. Science, 321(5890), 836-838. doi:10.1126/science.1159023Boualem, A., Troadec, C., Kovalski, I., Sari, M.-A., Perl-Treves, R., & Bendahmane, A. (2009). A Conserved Ethylene Biosynthesis Enzyme Leads to Andromonoecy in Two Cucumis Species. PLoS ONE, 4(7), e6144. doi:10.1371/journal.pone.0006144Boualem, A., Troadec, C., Camps, C., Lemhemdi, A., Morin, H., Sari, M.-A., … Bendahmane, A. (2015). A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges. Science, 350(6261), 688-691. doi:10.1126/science.aac8370Boualem, A., Lemhemdi, A., Sari, M.-A., Pignoly, S., Troadec, C., Abou Choucha, F., … Bendahmane, A. (2016). The Andromonoecious Sex Determination Gene Predates the Separation of Cucumis and Citrullus Genera. PLOS ONE, 11(5), e0155444. doi:10.1371/journal.pone.0155444Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., & Buckler, E. S. (2007). TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23(19), 2633-2635. doi:10.1093/bioinformatics/btm308Chae, E., Tan, Q. K.-G., Hill, T. A., & Irish, V. F. (2008). AnArabidopsisF-box protein acts as a transcriptional co-factor to regulate floral development. Development, 135(7), 1235-1245. doi:10.1242/dev.015842Chen, H., Sun, J., Li, S., Cui, Q., Zhang, H., Xin, F., … Huang, S. (2016). An ACC Oxidase Gene Essential for Cucumber Carpel Development. Molecular Plant, 9(9), 1315-1327. doi:10.1016/j.molp.2016.06.018Crow, J. F. (1990). Mapping functions. Genetics, 125(4), 669-671. doi:10.1093/genetics/125.4.669DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., … Daly, M. J. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43(5), 491-498. doi:10.1038/ng.806Díaz, A., Zarouri, B., Fergany, M., Eduardo, I., Álvarez, J. M., Picó, B., & Monforte, A. J. (2014). Mapping and Introgression of QTL Involved in Fruit Shape Transgressive Segregation into ‘Piel de Sapo’ Melon (Cucucumis melo L.). PLoS ONE, 9(8), e104188. doi:10.1371/journal.pone.0104188Dou, J., Lu, X., Ali, A., Zhao, S., Zhang, L., He, N., & Liu, W. (2018). Genetic mapping reveals a marker for yellow skin in watermelon (Citrullus lanatus L.). PLOS ONE, 13(9), e0200617. doi:10.1371/journal.pone.0200617Dou, J., Zhao, S., Lu, X., He, N., Zhang, L., Ali, A., … Liu, W. (2018). Genetic mapping reveals a candidate gene (ClFS1) for fruit shape in watermelon (Citrullus lanatus L.). Theoretical and Applied Genetics, 131(4), 947-958. doi:10.1007/s00122-018-3050-5Duan, Y., Li, S., Chen, Z., Zheng, L., Diao, Z., Zhou, Y., … Wu, W. (2012). Dwarf and deformed flower 1,encoding an F-box protein, is critical for vegetative and floral development in rice (Oryza sativaL.). The Plant Journal, 72(5), 829-842. doi:10.1111/j.1365-313x.2012.05126.xEstornell, L. H., Landberg, K., Cierlik, I., & Sundberg, E. (2018). SHI/STY Genes Affect Pre- and Post-meiotic Anther Processes in Auxin Sensing Domains in Arabidopsis. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.00150Gagne, J. M., Smalle, J., Gingerich, D. J., Walker, J. M., Yoo, S.-D., Yanagisawa, S., & Vierstra, R. D. (2004). Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action and promote growth by directing EIN3 degradation. Proceedings of the National Academy of Sciences, 101(17), 6803-6808. doi:10.1073/pnas.0401698101García, A., Aguado, E., Martínez, C., Loska, D., Beltrán, S., Valenzuela, J. L., … Jamilena, M. (2019). The ethylene receptors CpETR1A and CpETR2B cooperate in the control of sex determination in Cucurbita pepo. Journal of Experimental Botany, 71(1), 154-167. doi:10.1093/jxb/erz417Gebremeskel, H., Dou, J., Li, B., Zhao, S., Muhammad, U., Lu, X., … Liu, W. (2019). Molecular Mapping and Candidate Gene Analysis for GA3 Responsive Short Internode in Watermelon (Citrullus lanatus). International Journal of Molecular Sciences, 21(1), 290. doi:10.3390/ijms21010290Giovannoni, J. J., Wing, R. A., Ganal, M. W., & Tanksley, S. D. (1991). Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Research, 19(23), 6553-6568. doi:10.1093/nar/19.23.6553Grover, A. (2012). Plant Chitinases: Genetic Diversity and Physiological Roles. Critical Reviews in Plant Sciences, 31(1), 57-73. doi:10.1080/07352689.2011.616043Gu, S.-Y., Wang, L.-C., Cheuh, C.-M., & Lo, W.-S. (2019). CHITINASE LIKE1 Regulates Root Development of Dark-Grown Seedlings by Modulating Ethylene Biosynthesis in Arabidopsis thaliana. Frontiers in Plant Science, 10. doi:10.3389/fpls.2019.00600Guo, H., & Ecker, J. R. (2003). Plant Responses to Ethylene Gas Are Mediated by SCFEBF1/EBF2-Dependent Proteolysis of EIN3 Transcription Factor. Cell, 115(6), 667-677. doi:10.1016/s0092-8674(03)00969-3Guo, S., Zhao, S., Sun, H., Wang, X., Wu, S., Lin, T., … Xu, Y. (2019). Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nature Genetics, 51(11), 1616-1623. doi:10.1038/s41588-019-0518-4Gur, A., Tzuri, G., Meir, A., Sa’ar, U., Portnoy, V., Katzir, N., … Tadmor, Y. (2017). Genome-Wide Linkage-Disequilibrium Mapping to the Candidate Gene Level in Melon (Cucumis melo). Scientific Reports, 7(1). doi:10.1038/s41598-017-09987-4Hermans, C., Porco, S., Verbruggen, N., & Bush, D. R. (2009). Chitinase-Like Protein CTL1 Plays a Role in Altering Root System Architecture in Response to Multiple Environmental Conditions      . Plant Physiology, 152(2), 904-917. doi:10.1104/pp.109.149849Hou, J., Zhou, Y.-F., Gao, L.-Y., Wang, Y.-L., Yang, L.-M., Zhu, H.-Y., … Hu, J.-B. (2018). Dissecting the Genetic Architecture of Melon Chilling Tolerance at the Seedling Stage by Association Mapping and Identification of the Elite Alleles. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.01577Hu, B., Li, D., Liu, X., Qi, J., Gao, D., Zhao, S., … Yang, L. (2017). Engineering Non-transgenic Gynoecious Cucumber Using an Improved Transformation Protocol and Optimized CRISPR/Cas9 System. Molecular Plant, 10(12), 1575-1578. doi:10.1016/j.molp.2017.09.005Ji, G., Zhang, J., Gong, G., Shi, J., Zhang, H., Ren, Y., … Xu, Y. (2015). Inheritance of sex forms in watermelon (Citrullus lanatus). Scientia Horticulturae, 193, 367-373. doi:10.1016/j.scienta.2015.07.039Ji, G., Zhang, J., Zhang, H., Sun, H., Gong, G., Shi, J., … Xu, Y. (2016). Mutation in the gene encoding 1-aminocyclopropane-1-carboxylate synthase 4 (CitACS4 ) led to andromonoecy in watermelon. Journal of Integrative Plant Biology, 58(9), 762-765. doi:10.1111/jipb.12466Knopf, R. R., & Trebitsh, T. (2006). The Female-Specific Cs-ACS1G Gene of Cucumber. A Case of Gene Duplication and Recombination between the Non-Sex-Specific 1-Aminocyclopropane-1-Carboxylate Synthase Gene and a Branched-Chain Amino Acid Transaminase Gene. Plant and Cell Physiology, 47(9), 1217-1228. doi:10.1093/pcp/pcj092Kuusk, S., Sohlberg, J. J., Magnus Eklund, D., & Sundberg, E. (2006). Functionally redundantSHIfamily genes regulate Arabidopsis gynoecium development in a dose-dependent manner. The Plant Journal, 47(1), 99-111. doi:10.1111/j.1365-313x.2006.02774.xLevi, A., Jarret, R., Kousik, S., Patrick Wechter, W., Nimmakayala, P., & Reddy, U. K. (2017). Genetic Resources of Watermelon. Plant Genetics and Genomics: Crops and Models, 87-110. doi:10.1007/7397_2016_34Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760. doi:10.1093/bioinformatics/btp324Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352Li, M.-X., Yeung, J. M. Y., Cherny, S. S., & Sham, P. C. (2011). Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Human Genetics, 131(5), 747-756. doi:10.1007/s00439-011-1118-2Lai, Y.-S., Shen, D., Zhang, W., Zhang, X., Qiu, Y., Wang, H., … Li, X. (2018). Temperature and photoperiod changes affect cucumber sex expression by different epigenetic regulations. BMC Plant Biology, 18(1). doi:10.1186/s12870-018-1490-3Li, Z., Han, Y., Niu, H., Wang, Y., Jiang, B., & Weng, Y. (2020). Gynoecy instability in cucumber (Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent Femaleness (F) locus. Horticulture Research, 7(1). doi:10.1038/s41438-020-0251-2Lin, C.-K., Lee, N.-Y., Huang, P.-L., & Do, Y.-Y. (2015). Gene structure and expression characteristics of the auxin receptor TIR1 ortholog in Momordica charantia and developmental analysis of its promoter in transgenic plants. Journal of Plant Biochemistry and Biotechnology, 25(3), 253-262. doi:10.1007/s13562-015-0336-4Lotan, T., Ori, N., & Fluhr, R. (1989). Pathogenesis-related proteins are developmentally regulated in tobacco flowers. The Plant Cell, 1(9), 881-887. doi:10.1105/tpc.1.9.881Mansfeld, B. N., & Grumet, R. (2018). QTLseqr: An R Package for Bulk Segregant Analysis with Next‐Generation Sequencing. The Plant Genome, 11(2), 180006. doi:10.3835/plantgenome2018.01.0006Manzano, S., Martínez, C., García, J. M., Megías, Z., & Jamilena, M. (2014). Involvement of ethylene in sex expression and female flower development in watermelon (Citrullus lanatus). Plant Physiology and Biochemistry, 85, 96-104. doi:10.1016/j.plaphy.2014.11.004Manzano, S., Aguado, E., Martínez, C., Megías, Z., García, A., & Jamilena, M. (2016). The Ethylene Biosynthesis Gene CitACS4 Regulates Monoecy/Andromonoecy in Watermelon (Citrullus lanatus). PLOS ONE, 11(5), e0154362. doi:10.1371/journal.pone.0154362Mara, C. D., & Irish, V. F. (2008). Two GATA Transcription Factors Are Downstream Effectors of Floral Homeotic Gene Action in Arabidopsis    . Plant Physiology, 147(2), 707-718. doi:10.1104/pp.107.115634Martin, A., Troadec, C., Boualem, A., Rajab, M., Fernandez, R., Morin, H., … Bendahmane, A. (2009). A transposon-induced epigenetic change leads to sex determination in melon. Nature, 461(7267), 1135-1138. doi:10.1038/nature08498Martínez, C., Manzano, S., Megías, Z., Barrera, A., Boualem, A., Garrido, D., … Jamilena, M. (2014). Molecular and functional characterization of CpACS27A gene reveals its involvement in monoecy instability and other associated traits in squash (Cucurbita pepo L.). Planta, 239(6), 1201-1215. doi:10.1007/s00425-014-2043-0Matsumoto, N. (2001). A homeobox gene, PRESSED FLOWER, regulates lateral axis-dependent development of Arabidopsis flowers. Genes & Development, 15(24), 3355-3364. doi:10.1101/gad.931001Michelmore, R. W., Paran, I., & Kesseli, R. V. (1991). Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Sciences, 88(21), 9828-9832. doi:10.1073/pnas.88.21.9828Murray, M. G., & Thompson, W. F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8(19), 4321-4326. doi:10.1093/nar/8.19.4321Nimmakayala, P., Tomason, Y. R., Abburi, V. L., Alvarado, A., Saminathan, T., Vajja, V. G., … Reddy, U. K. (2016). Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map. Frontiers in Plant Science, 7. doi:10.3389/fpls.2016.01437Oren, E., Tzuri, G., Vexler, L., Dafna, A., Meir, A., Faigenboim, A., … Gur, A. (2019). The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon. Journal of Experimental Botany, 70(15), 3781-3794. doi:10.1093/jxb/erz182Paris, H. S. (2015). Origin and emergence of the sweet dessert watermelon,Citrullus lanatus. Annals of Botany, 116(2), 133-148. doi:10.1093/aob/mcv077POOLE, C. F., & GRIMBALL, P. C. (1939). INHERITANCE OF NEW SEX FORMS IN CUCUMIS MELO L. Journal of Heredity, 30(1), 21-25. doi:10.1093/oxfordjournals.jhered.a104626Potuschak, T., Lechner, E., Parmentier, Y., Yanagisawa, S., Grava, S., Koncz, C., & Genschik, P. (2003). EIN3-Dependent Regulation of Plant Ethylene Hormone Signaling by Two Arabidopsis F Box Proteins. Cell, 115(6), 679-689. doi:10.1016/s0092-8674(03)00968-1Prothro, J., Abdel-Haleem, H., Bachlava, E., White, V., Knapp, S., & McGregor, C. (2013). Quantitative Trait Loci Associated with Sex Expression in an Inter-subspecific Watermelon Population. Journal of the American Society for Horticultural Science, 138(2), 125-130. doi:10.21273/jashs.138.2.125Pujol, M., Alexiou, K. G., Fontaine, A.-S., Mayor, P., Miras, M., Jahrmann, T., … Aranda, M. A. (2019). Mapping Cucumber Vein Yellowing Virus Resistance in Cucumber (Cucumis sativus L.) by Using BSA-seq Analysis. Frontiers in Plant Science, 10. doi:10.3389/fpls.2019.01583Qiao, H., Chang, K. N., Yazaki, J., & Ecker, J. R. (2009). Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. Genes & Development, 23(4), 512-521. doi:10.1101/gad.1765709Reichheld, J. P., Riondet, C., Delorme, V., Vignols, F., & Meyer, Y. (2010). Thioredoxins and glutaredoxins in development. Plant Science, 178(5), 420-423. doi:10.1016/j.plantsci.2010.03.001Renner, S. S., Chomicki, G., & Greuter, W. (2014). (2313) Proposal to conserve the name Momordica lanata (Citrullus lanatus) (watermelon, Cucurbitaceae), with a conserved type, against Citrullus battich. Taxon, 63(4), 941-942. doi:10.12705/634.29Rosa, J. T. (1928). The inheritance of flower types inCucumisandCitrullus. Hilgardia, 3(9), 233-250. doi:10.3733/hilg.v03n09p233Salman-Minkov, A., Levi, A., Wolf, S., & Trebitsh, T. (2008). ACC Synthase Genes are Polymorphic in Watermelon (Citrullus spp.) and Differentially Expressed in Flowers and in Response to Auxin and Gibberellin. Plant and Cell Physiology, 49(5), 740-750. doi:10.1093/pcp/pcn045Sanders, P. M., Bui, A. Q., Weterings, K., McIntire, K. N., Hsu, Y.-C., Lee, P. Y., … Goldberg, R. B. (1999). Anther developmental defects in Arabidopsis thaliana male-sterile mutants. Sexual Plant Reproduction, 11(6), 297-322. doi:10.1007/s004970050158Singh, S., Yadav, S., Singh, A., Mahima, M., Singh, A., Gautam, V., & Sarkar, A. K. (2019). Auxin signaling modulates LATERAL ROOT PRIMORDIUM 1 ( LRP 1 ) expression during lateral root development in Arabidopsis. The Plant Journal, 101(1), 87-100. doi:10.1111/tpj.14520Takagi, H., Abe, A., Yoshida, K., Kosugi, S., Natsume, S., Mitsuoka, C., … Terauchi, R. (2013). QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. The Plant Journal, 74(1), 174-183. doi:10.1111/tpj.12105Takakura, Y., Ito, T., Saito, H., Inoue, T., Komari, T., & Kuwata, S. (2000). Plant Molecular Biology, 42(6), 883-897. doi:10.1023/a:1006401816145Tan, J., Tao, Q., Niu, H., Zhang, Z., Li, D., Gong, Z., … Li, Z. (2015). A novel allele of monoecious (m) locus is responsible for elongated fruit shape and perfect flowers in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics, 128(12), 2483-2493. doi:10.1007/s00122-015-2603-0Trebitsh, T., Staub, J. E., & O’Neill, S. D. (1997). Identification of a 1-Aminocyclopropane-1-Carboxylic Acid Synthase Gene Linked to the Female (F) Locus That Enhances Female Sex Expression in Cucumber. Plant Physiology, 113(3), 987-995. doi:10.1104/pp.113.3.987Vandenbussche, M., Horstman, A., Zethof, J., Koes, R., Rijpkema, A. S., & Gerats, T. (2009). Differential Recruitment ofWOXTranscription Factors for Lateral Development and Organ Fusion in Petunia andArabidopsis . The Plant Cell, 21(8), 2269-2283. doi:10.1105/tpc.109.065862Wang, X., Bao, K., Reddy, U. K., Bai, Y., Hammar, S. A., Jiao, C., … Fei, Z. (2018). The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development. Horticulture Research, 5(1). doi:10.1038/s41438-018-0080-8Wehner, T. C. (s. f.). Watermelon. Vegetables I, 381-418. doi:10.1007/978-0-387-30443-4_12Wu, S., Wang, X., Reddy, U., Sun, H., Bao, K., Gao, L., … Fei, Z. (2019). Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. Plant Biotechnology Journal, 17(12), 2246-2258. doi:10.1111/pbi.13136Xing, S., & Zachgo, S. (2008). ROXY1 and ROXY2, two Arabidopsis glutaredoxin genes, are required for anther development. The Plant Journal, 53(5), 790-801. doi:10.1111/j.1365-313x.2007.03375.xXing, L., Li, Z., Khalil, R., Ren, Z., & Yang, Y. (2011). Functional identification of a novel F-box/FBA gene in tomato. Physiologia Plantarum, 144(2), 161-168. doi:10.1111/j.1399-3054.2011.01543.xYagcioglu, M., Gulsen, O., Yetisir, H., Solmaz, I., & Sari, N. (2016). Preliminary studies of genom-wide association mapping for some selected morphological characters of watermelons. Scientia Horticulturae, 210, 277-284. doi:10.1016/j.scienta.2016.08.001Yu, L. P., Miller, A. K., & Clark, S. E. (2003). POLTERGEIST Encodes a Protein Phosphatase 2C that Regulates CLAVATA Pathways Controlling Stem Cell Identity at Arabidopsis Shoot and Flower Meristems. Current Biology, 13(3), 179-188. doi:10.1016/s0960-9822(03)00042-3Yu, H., Wu, J., Xu, N., & Peng, M. (2007). Roles of F-box Proteins in Plant Hormone Responses. Acta Biochimica et Biophysica Sinica, 39(12), 915-922. doi:10.1111/j.1745-7270.2007.00358.xZhang, Z., Mao, L., Chen, H., Bu, F., Li, G., Sun, J., … Huang, S. (2015). Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber. The Plant Cell, 27(6), 1595-1604. doi:10.1105/tpc.114.135848ZHANG, J., SHI, J., JI, G., ZHA

Identification of Proteins Targeted by the Thioredoxin Superfamily in Plasmodium falciparum

The malarial parasite Plasmodium falciparum possesses a functional thioredoxin and glutathione system comprising the dithiol-containing redox proteins thioredoxin (Trx) and glutaredoxin (Grx), as well as plasmoredoxin (Plrx), which is exclusively found in Plasmodium species. All three proteins belong to the thioredoxin superfamily and share a conserved Cys-X-X-Cys motif at the active site. Only a few of their target proteins, which are likely to be involved in redox reactions, are currently known. The aim of the present study was to extend our knowledge of the Trx-, Grx-, and Plrx-interactome in Plasmodium. Based on the reaction mechanism, we generated active site mutants of Trx and Grx lacking the resolving cysteine residue. These mutants were bound to affinity columns to trap target proteins from P. falciparum cell extracts after formation of intermolecular disulfide bonds. Covalently linked proteins were eluted with dithiothreitol and analyzed by mass spectrometry. For Trx and Grx, we were able to isolate 17 putatively redox-regulated proteins each. Furthermore, the approach was successfully established for Plrx, leading to the identification of 21 potential target proteins. In addition to confirming known interaction partners, we captured potential target proteins involved in various processes including protein biosynthesis, energy metabolism, and signal transduction. The identification of three enzymes involved in S-adenosylmethionine (SAM) metabolism furthermore suggests that redox control is required to balance the metabolic fluxes of SAM between methyl-group transfer reactions and polyamine synthesis. To substantiate our data, the binding of the redoxins to S-adenosyl-L-homocysteine hydrolase and ornithine aminotransferase (OAT) were verified using BIAcore surface plasmon resonance. In enzymatic assays, Trx was furthermore shown to enhance the activity of OAT. Our approach led to the discovery of several putatively redox-regulated proteins, thereby contributing to our understanding of the redox interactome in malarial parasites

The self-organizing fractal theory as a universal discovery method: the phenomenon of life

A universal discovery method potentially applicable to all disciplines studying organizational phenomena has been developed. This method takes advantage of a new form of global symmetry, namely, scale-invariance of self-organizational dynamics of energy/matter at all levels of organizational hierarchy, from elementary particles through cells and organisms to the Universe as a whole. The method is based on an alternative conceptualization of physical reality postulating that the energy/matter comprising the Universe is far from equilibrium, that it exists as a flow, and that it develops via self-organization in accordance with the empirical laws of nonequilibrium thermodynamics. It is postulated that the energy/matter flowing through and comprising the Universe evolves as a multiscale, self-similar structure-process, i.e., as a self-organizing fractal. This means that certain organizational structures and processes are scale-invariant and are reproduced at all levels of the organizational hierarchy. Being a form of symmetry, scale-invariance naturally lends itself to a new discovery method that allows for the deduction of missing information by comparing scale-invariant organizational patterns across different levels of the organizational hierarchy