Melinka Alonso Butenko

• Lalun, Vilde Olsson & Butenko, Melinka Alonso (2025). Plant Peptide Ligands as Temporal and Spatial Regulators. Annual Review of Plant Biology. ISSN 1543-5008. 76(1), p. 229–253. doi: 10.1146/annurev-arplant-070324-041348. Full text in Research Archive Show summary

  Throughout the life cycle of a plant, numerous responses need to be carefully regulated to ensure proper development and appropriate responses to external stimuli, and plant hormones play a crucial role in this regulation. Since the early 1990s, there has been expansive research elucidating the central role that peptide ligands play as intrinsic short- and long-distance communicators during development and as regulators of phenotypic plasticity. In this review, we focus on recently discovered mechanisms that ensure correct spatial and temporal cellular responses triggered by peptide ligands and provide examples of how peptide processing proteins and apoplastic conditions can regulate peptide activity in a timely manner.

• Trigo, Sergio Galindo; Khandare, Virendrasinh; Roosjen, Mark; Adams, Julian; Wangler, Alexa-Maria & Bayer, Martin [Show all 9 contributors for this article] (2024). A multifaceted kinase axis regulates plant organ abscission through conserved signaling mechanisms. Current Biology. ISSN 0960-9822. 34(13), p. 3020–3030. doi: 10.1016/j.cub.2024.05.057. Full text in Research Archive Show summary

  Plants have evolved mechanisms to abscise organs as they develop or when exposed to unfavorable conditions.1 Uncontrolled abscission of petals, fruits, or leaves can impair agricultural productivity.2,3,4,5 Despite its importance for abscission progression, our understanding of the IDA signaling pathway and its regulation remains incomplete. IDA is secreted to the apoplast, where it is perceived by the receptors HAESA (HAE) and HAESA-LIKE2 (HSL2) and somatic embryogenesis receptor kinase (SERK) co-receptors.6,7,8,9 These plasma membrane receptors activate an intracellular cascade of mitogen-activated protein kinases (MAPKs) by an unknown mechanism.10,11,12 Here, we characterize brassinosteroid signaling kinases (BSKs) as regulators of floral organ abscission in Arabidopsis. BSK1 localizes to the plasma membrane of abscission zone cells, where it interacts with HAESA receptors to regulate abscission. Furthermore, we demonstrate that YODA (YDA) has a leading role among other MAPKKKs in controlling abscission downstream of the HAESA/BSK complex. This kinase axis, comprising a leucine-rich repeat receptor kinase, a BSK, and an MAPKKK, is known to regulate stomatal patterning, early embryo development, and immunity.10,13,14,15,16 How specific cellular responses are obtained despite signaling through common effectors is not well understood. We show that the identified abscission-promoting allele of BSK1 also enhances receptor signaling in other BSK-mediated pathways, suggesting conservation of signaling mechanisms. Furthermore, we provide genetic evidence supporting independence of BSK1 function from its kinase activity in several developmental processes. Together, our findings suggest that BSK1 facilitates signaling between plasma membrane receptor kinases and MAPKKKs via conserved mechanisms across multiple facets of plant development.

• Trigo, Sergio Galindo; Bågman, Anne-Maarit; Ishida, Takashi; Sawa, Shinichiro; Brady, Siobhán M. & Butenko, Melinka Alonso (2024). Dissection of the IDA promoter identifies WRKY transcription factors as abscission regulators in Arabidopsis. Journal of Experimental Botany. ISSN 0022-0957. 75(8), p. 2417–2434. doi: 10.1093/jxb/erae014. Full text in Research Archive Show summary

  Plants shed organs such as leaves, petals, or fruits through the process of abscission. Monitoring cues such as age, resource availability, and biotic and abiotic stresses allow plants to abscise organs in a timely manner. How these signals are integrated into the molecular pathways that drive abscission is largely unknown. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) gene is one of the main drivers of floral organ abscission in Arabidopsis and is known to transcriptionally respond to most abscission-regulating cues. By interrogating the IDA promoter in silico and in vitro, we identified transcription factors that could potentially modulate IDA expression. We probed the importance of ERF- and WRKY-binding sites for IDA expression during floral organ abscission, with WRKYs being of special relevance to mediate IDA up-regulation in response to biotic stress in tissues destined for separation. We further characterized WRKY57 as a positive regulator of IDA and IDA-like gene expression in abscission zones. Our findings highlight the promise of promoter element-targeted approaches to modulate the responsiveness of the IDA signaling pathway to harness controlled abscission timing for improved crop productivity.

• Reinar, William Brynildsen; Krabberød, Anders Kristian; Lalun, Vilde Olsson; Butenko, Melinka Alonso & Jakobsen, Kjetill Sigurd (2024). Short tandem repeats delineate gene bodies across eukaryotes. Nature Communications. 15(1), p. 1–13. doi: 10.1038/s41467-024-55276-w. Full text in Research Archive Show summary

  Short tandem repeats (STRs) have emerged as important and hypermutable sites where genetic variation correlates with gene expression in plant and animal systems. Recently, it has been shown that a broad range of transcription factors (TFs) are affected by STRs near or in the DNA target binding site. Despite this, the distribution of STR motif repetitiveness in eukaryote genomes is still largely unknown. Here, we identify monomer and dimer STR motif repetitiveness in 5.1 billion 10-bp windows upstream of translation starts and downstream of translation stops in 25 million genes spanning 1270 species across the eukaryotic Tree of Life. We report that all surveyed genomes have gene-proximal shifts in motif repetitiveness. Within genomes, variation in gene-proximal repetitiveness landscapes correlated to the function of genes; genes with housekeeping functions were depleted in upstream and downstream repetitiveness. Furthermore, the repetitiveness landscapes correlated with TF binding sites, indicating that gene function has evolved in conjunction with cis-regulatory STRs and TFs that recognize repetitive sites. These results suggest that the hypermutability inherent to STRs is canalized along the genome sequence and contributes to regulatory and eco-evolutionary dynamics in all eukaryotes.

• Lalun, Vilde Olsson; Breiden, Maike; Trigo, Sergio Galindo; Smakowska-Luzan, Elwira; Simon, Rüdiger & Butenko, Melinka Alonso (2023). A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level. eLIFE. 12, p. 1–37. doi: 10.7554/eLife.87912.1. Full text in Research Archive Show summary

  The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-LIKE 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect against pathogen invasion. However, the molecular coordination between abscission and immunity has not been thoroughly explored. Here we show that IDA induces a receptor-dependent release of cytosolic calcium ions (Ca2+) and apoplastic production of reactive oxygen species, which are signatures of early defense responses. In addition, we find that IDA promotes late defense responses by the transcriptional upregulation of genes known to be involved in immunity. When comparing the IDA induced early immune responses to known immune responses, such as those elicited by flagellin22 treatment, we observe both similarities and differences. We propose a molecular mechanism by which IDA promotes signatures of an immune response in cells destined for separation to guard them from pathogen attack.

• Reinar, William Brynildsen; Greulich, Anne; Stø, Ida Myhrer; Knutsen, Jonfinn Mordekai Blix; Reitan, Trond & Tørresen, Ole K. [Show all 9 contributors for this article] (2023). Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis. Science Advances. 9(12), p. 1–10. doi: 10.1126/sciadv.add6960. Full text in Research Archive Show summary

  Intrinsically disordered protein regions are of high importance for biotic and abiotic stress responses in plants. Tracts of identical amino acids accumulate in these regions and can vary in length over generations because of expansions and retractions of short tandem repeats at the genomic level. However, little attention has been paid to what extent length variation is shaped by natural selection. By environmental association analysis on 2514 length variable tracts in 770 whole-genome sequenced Arabidopsis thaliana, we show that length variation in glutamine and asparagine amino acid homopolymers, as well as in interaction hotspots, correlate with local bioclimatic habitat. We determined experimentally that the promoter activity of a light-stress gene depended on polyglutamine length variants in a disordered transcription factor. Our results show that length variations affect protein function and are likely adaptive. Length variants modulating protein function at a global genomic scale has implications for understanding protein evolution and eco-evolutionary biology.

• Breiden, Maike; Olsson, Vilde; Blümke, Patrick; Schlegel, Jenia; Gustavo-Pinto, Karine & Dietrich, Petra [Show all 8 contributors for this article] (2021). The Cell Fate Controlling CLE40 Peptide Requires CNGCs to Trigger Highly Localized Ca2+ Transients in Arabidopsis thaliana Root Meristems. Plant and Cell Physiology. ISSN 0032-0781. 62(8), p. 1290–1301. doi: 10.1093/pcp/pcab079. Full text in Research Archive
• Reinar, William Brynildsen; Olsson, Vilde; Reitan, Trond; Jakobsen, Kjetill Sigurd & Butenko, Melinka Alonso (2021). Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana. The Plant Cell. ISSN 1040-4651. 33(7), p. 2221–2234. doi: 10.1093/plcell/koab107. Full text in Research Archive Show summary

  Abstract The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately influences the phenotype and thus the local adaptation of natural populations. Short tandem repeats (STRs) consisting of repetitive DNA motifs have been shown to regulate gene expression. STRs are variable in length within a population and serve as a heritable, but semi-reversible, reservoir of standing genetic variation. For sessile organisms, such as plants, STRs could be of major importance in fine-tuning gene expression as a response to a shifting local environment. Here, we used a transcriptome dataset from natural accessions of Arabidopsis thaliana to investigate population-wide gene expression patterns in light of genome-wide STR variation. We empirically modeled gene expression as a response to the STR length within and around the gene and demonstrated that an association between gene expression and STR length variation is unequivocally present in the sampled population. To support our model, we explored the promoter activity in a transcriptional regulator involved in root hair formation and provided experimentally determined causality between coding sequence length variation and promoter activity. Our results support a general link between gene expression variation and STR length variation in A. thaliana.

• Hubin, Aliaksandr; Storvik, Geir Olve; Grini, Paul Eivind & Butenko, Melinka Alonso (2020). A Bayesian binomial regression model with latent gaussian processes for modelling DNA methylation. Austrian Journal of Statistics. ISSN 1026-597X. 49(4), p. 46–56. doi: 10.17713/ajs.v49i4.1124. Full text in Research Archive Show summary

  Epigenetic observations are represented by the total number of reads from a given pool of cells and the number of methylated reads, making it reasonable to model this data by a binomial distribution. There are numerous factors that can influence the probability of success in a particular region. Moreover, there is a strong spatial (alongside the genome) dependence of these probabilities. We incorporate dependence on the covariates and the spatial dependence of the methylation probability for observations from a pool of cells by means of a binomial regression model with a latent Gaussian field and a logit link function. We apply a Bayesian approach including prior specifications on model configurations. We run a mode jumping Markov chain Monte Carlo algorithm (MJMCMC) across different choices of covariates in order to obtain the joint posterior distribution of parameters and models. This also allows finding the best set of covariates to model methylation probability within the genomic region of interest and individual marginal inclusion probabilities of the covariates.

• Trigo, Sergio Galindo; Blümke, Patrick; Simon, Rüdiger & Butenko, Melinka Alonso (2020). Emerging mechanisms to fine-tune receptor kinase signaling specificity. Current opinion in plant biology. ISSN 1369-5266. 57, p. 41–51. doi: 10.1016/j.pbi.2020.05.010. Full text in Research Archive Show summary

  Organisms need to constantly inform their cellular machinery about the biochemical and physical status of their surroundings to adapt and thrive. While some external signals are also sensed intracellularly, a considerable share of external information is registered already at the plasma membrane (PM). Receptor kinases (RKs) are crucial for plant cells to integrate such cues from the environment, from microbes, or from other cells to coordinate their physiological response and their development. Early studies on RK signaling depicted the path from external signal to internal response in a linear fashion, but recent findings show that these cellular information highways are highly interconnected and pass signals through molecular intersections. In this review, we first discuss how individual RKs simultaneously contribute to the transduction and deconvolution of a multitude of signals by controlled assembly into diverse RK complexes, exemplified by FERONIA signaling versatility. We then elaborate on how cells can exert highly localized control over the assembly, interaction and composition of such complexes in order to attain essential cellular output specificity.

• Hubin, Aliaksandr; Storvik, Geir Olve; Grini, Paul Eivind & Butenko, Melinka Alonso (2019). Bayesian binomial regression model with a latent Gaussian field for analysis of epigenetic data. In Kharin, Y & Filzmoser, Peter (Ed.), Proceedings of Computer Data Analysis and Modeling: Stochastics and Data Science 2019. Belarusian State University Press. ISSN 9789855668115. p. 167–171. Full text in Research Archive
• Olsson, Vilde; Joos, Lisa; Zhu, Shanshuo; Gevaert, Kris; Butenko, Melinka Alonso & Smet, Ive De (2019). Look closely, the beautiful may be small: Precursor-derived peptides in plants. Annual Review of Plant Biology. ISSN 1543-5008. 70, p. 153–186. doi: 10.1146/annurev-arplant-042817-040413. Full text in Research Archive
• Shi, Chunlin & Butenko, Melinka Alonso (2018). Quantitative Analysis of Floral Organ Abscission in Arabidopsis Via a Petal Breakstrength Assay. In Guo, Yongfeng (Eds.), Plant Senescence: Methods and Protocols (Methods in Molecular Biology). Humana Press. ISSN 9781493976720. p. 81–88. doi: 10.1007/978-1-4939-7672-0_6. Full text in Research Archive
• Shi, Chunlin; Wangenheim, Daniel von; Herrmann, Ullrich; Wildhagen, Mari; Kulik, Ivan & Kopf, Andreas [Show all 16 contributors for this article] (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. ISSN 2055-026X. 4(8), p. 596–604. doi: 10.1038/s41477-018-0212-z. Full text in Research Archive
• Shi, Chunlin & Butenko, Melinka Alonso (2018). Visualizing Morphological Changes of Abscission Zone Cells in Arabidopsis by Scanning Electron Microscope. In Guo, Yongfeng (Eds.), Plant Senescence: Methods and Protocols (Methods in Molecular Biology). Humana Press. ISSN 9781493976720. p. 321–337. doi: 10.1007/978-1-4939-7672-0_26. Full text in Research Archive
• Hohmann, Ulrich; Santiago, Julia; Nicolet, Joel; Olsson, Vilde; Spiga, Fabio M & Hothorn, Ludwig A. [Show all 8 contributors for this article] (2018). Mechanistic basis for the activation of plant membrane receptor kinases by SERK-family coreceptors. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 115(13), p. 3488–3493. doi: 10.1073/pnas.1714972115. Full text in Research Archive
• Mazurek, Sylwester; Garroum, Imène; Daraspe, Jean; Bellis, Damien De; Olsson, Vilde & Mucciolo, Antonio [Show all 9 contributors for this article] (2017). Connecting the molecular structure of cutin to ultrastructure and physical properties of the cuticle in petals of arabidopsis. Plant Physiology. ISSN 0032-0889. 173(2), p. 1146–1163. doi: 10.1104/pp.16.01637. Full text in Research Archive
• Santiago, Julia; Brandt, Benjamin; Wildhagen, Mari; Hohmann, Ulrich; Hothorn, Ludwig A. & Butenko, Melinka Alonso [Show all 7 contributors for this article] (2016). Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission. eLIFE. 5(2016). doi: 10.7554/eLife.15075. Full text in Research Archive
• Butenko, Melinka Alonso & Simon, Rüdiger (2015). Beyond the meristems: Similarities in the CLAVATA3 and INFLORESCENCE DEFICIENT in ABSCISSION peptide mediated signalling pathways. Journal of Experimental Botany. ISSN 0022-0957. 66(17), p. 5195–5203. doi: 10.1093/jxb/erv310. Full text in Research Archive
• Czyzewicz, Nathan; Shi, Chunlin; Vu, Lam Dai; Cotte, Brigitte Van De; Hodgman, Charlie & Butenko, Melinka Alonso [Show all 7 contributors for this article] (2015). Modulation of Arabidopsis and monocot root architecture by CLAVATA3/EMBRYO SURROUNDING REGION 26 peptide. Journal of Experimental Botany. ISSN 0022-0957. 66(17), p. 5229–5243. doi: 10.1093/jxb/erv360. Full text in Research Archive
• Czyzewicz, Nathan; Wildhagen, Mari; Cattaneo, Pietro; Stahl, Yvonne; Pinto, Karine Gustavo & Aalen, Reidunn B. [Show all 10 contributors for this article] (2015). Antagonistic peptide technology for functional dissection of CLE peptides revisited. Journal of Experimental Botany. ISSN 0022-0957. 66(17), p. 5367–5374. doi: 10.1093/jxb/erv284. Full text in Research Archive
• Estornell, Leandro H.; Wildhagen, Mari; Perez-Amador, Miguel A.; Talon, Manuel; Tadeo, Francisco R. & Butenko, Melinka Alonso (2015). The IDA peptide controls abscission in Arabidopsis and citrus. Frontiers in Plant Science. 6(NOVEMBER). doi: 10.3389/fpls.2015.01003. Full text in Research Archive
• Vie, Ane Kjersti; Najafi, Javad; Liu, Bin; Winge, Per; Butenko, Melinka Alonso & Hornslien, Karina Stensland [Show all 10 contributors for this article] (2015). The IDA/IDA-LIKE and PIP/PIP-LIKE gene families in Arabidopsis: Phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide. Journal of Experimental Botany. ISSN 0022-0957. 66(17), p. 5351–5365. doi: 10.1093/jxb/erv285. Full text in Research Archive Show summary

  Peptide ligands play crucial roles in the life cycle of plants by modulating the innate immunity against pathogens and regulating growth and developmental processes. One well-studied example is INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which controls floral organ abscission and lateral root emergence in Arabidopsis thaliana. IDA belongs to a family of five additional IDA-LIKE (IDL) members that have all been suggested to be involved in regulation of Arabidopsis development. Here we present three novel members of the IDL subfamily and show that two of them are strongly and rapidly induced by different biotic and abiotic stresses. Furthermore, we provide data that the recently identified PAMP-INDUCED SECRETED PEPTIDE (PIP) and PIP-LIKE (PIPL) peptides, which show similarity to the IDL and C-TERMINALLY ENCODED PEPTIDE (CEP) peptides, are not only involved in innate immune response in Arabidopsis but are also induced by abiotic stress. Expression patterns of the IDA/IDL and PIP/PIPL genes were analysed using in silico data, qRT-PCR and GUS promoter lines. Transcriptomic responses to PIPL3 peptide treatment suggested a role in regulation of biotic stress responses and cell wall modification.

• Butenko, Melinka Alonso; Wildhagen, Mari; Albert, Markus; Jehle, Anna; Kalbacher, Hubert & Aalen, Reidunn B. [Show all 7 contributors for this article] (2014). Tools and strategies to match peptide-ligand receptor pairs. The Plant Cell. ISSN 1040-4651. 26(5), p. 1838–1847. doi: 10.1105/tpc.113.120071. Full text in Research Archive
• Aalen, Reidunn B.; Wildhagen, Mari; Stø, Ida Myhrer & Butenko, Melinka Alonso (2013). IDA: a peptide ligand regulating cell separation processes in Arabidopsis. Journal of Experimental Botany. ISSN 0022-0957. 64(17), p. 5253–5261. doi: 10.1093/jxb/ert338. Full text in Research Archive
• Liu, Bin; Butenko, Melinka Alonso; Shi, Chunlin; Bolivar, Jenny; Winge, Per & Stenvik, Grethe-Elisabeth [Show all 14 contributors for this article] (2013). NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana. Journal of Experimental Botany. ISSN 0022-0957. 64(17), p. 5345–5357. doi: 10.1093/jxb/ert232. Full text in Research Archive
• Kumpf, Robert; Shi, Chunlin; Larrieu, Antoine; Stø, Ida Myhrer; Butenko, Melinka Alonso & Péret, Benjamin [Show all 9 contributors for this article] (2013). Floral organ abscission peptide IDA and its HAE/HSL2 receptors control cell separation during lateral root emergence. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 110(13), p. 5235–5240. doi: 10.1073/pnas.1210835110. Full text in Research Archive
• Marshall, Alex; Aalen, Reidunn B.; Audenaert, Dominique; Beeckman, Tom; Broadley, Martin R. & Butenko, Melinka Alonso [Show all 27 contributors for this article] (2012). Tackling Drought Stress: RECEPTOR-LIKE KINASES Present New Approaches. The Plant Cell. ISSN 1040-4651. 24(6), p. 2262–2278. doi: 10.1105/tpc.112.096677. Full text in Research Archive
• Shi, Chunlin; Stenvik, Grethe-Elisabeth; Vie, Ane Kjersti; Bones, Atle M.; Pautot, V & Proveniers, M [Show all 8 contributors for this article] (2011). Arabidopsis Class I KNOTTED-Like Homeobox Proteins Act Downstream in the IDA-HAE/HSL2 Floral Abscission Signaling Pathway. The Plant Cell. ISSN 1040-4651. 23(7), p. 2553–2567. doi: 10.1105/tpc.111.084608. Full text in Research Archive
• Tengs, Torstein; Zhang, Haibo; Holst-Jensen, Arne; Bohlin, Jon; Butenko, Melinka Alonso & Kristoffersen, Anja Bråthen [Show all 8 contributors for this article] (2009). Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction. BMC Biotechnology. 9(87). doi: 10.1186/1472-6750-9-87. Full text in Research Archive Show summary

  Background When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown. Results We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya). Conclusion We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.

• Butenko, M; Vie, Ane Kjersti; Brembu, Tore; Aalen, RB & Bones, Atle M. (2009). Plant peptides in signalling: looking for new partners. Trends in Plant Science. ISSN 1360-1385. 14(5), p. 255–263. doi: 10.1016/j.tplants.2009.02.002. Full text in Research Archive
• Stenvik, Grethe-Elisabeth; Tandstad, Nora Martinussen; Guo, Y; Shi, Chunlin; Kristiansen, Wenche & Holmgren, Asbjørn [Show all 9 contributors for this article] (2008). The EPIP peptide of INFLORESCENCE DEFICIENT IN ABSCISSION is sufficient to induce abscission in Arabidopsis through the receptor-like kinases HAESA and HAESA-LIKE2. The Plant Cell. ISSN 1040-4651. 20, p. 1805–1817. doi: 10.1105/tpc.108.059139. Full text in Research Archive
• Mckim, SM; Stenvik, Grethe-Elisabeth; Butenko, Melinka Alonso; Kristiansen, Wenche; Cho, SK & Hepworth, SR [Show all 8 contributors for this article] (2008). The BLADE-ON-PETIOLE genes are essential for abscission zone formation in Arabidopsis. Development. ISSN 0950-1991. 135. doi: 10.1242/dev.012807. Full text in Research Archive
• Stenvik, Grethe-Elisabeth; Butenko, Melinka Alonso & Aalen, Reidunn B. (2008). Identification of a putative receptor-ligand pair controlling cell separation in plants. Article addendum. Plant Signalling & Behavior. ISSN 1559-2316. 3, p. 1109–1110. Full text in Research Archive
• Tengs, Torstein; Kristoffersen, Anja Bråthen; Berdal, Knut G.; Thorstensen, Tage; Butenko, Melinka Alonso & Nesvold, Håvard [Show all 7 contributors for this article] (2007). Microarray-based method for detection of unknown genetic modifications. BMC Biotechnology. 7. doi: 10.1186/1472-6750-7-91. Full text in Research Archive Show summary

  Background Due to the increased use of genetic modifications in crop improvement, there is a need to develop effective methods for the detection of both known and unknown transgene constructs in plants. We have developed a strategy for detection and characterization of unknown genetic modifications and we present a proof of concept for this method using Arabidopsis thaliana and Oryza sativa (rice). The approach relies on direct hybridization of total genomic DNA to high density microarrays designed to have probes tiled throughout a set of reference sequences. Results We show that by using arrays with 25 basepair probes covering both strands of a set of 235 vectors (2 million basepairs) we can detect transgene sequences in transformed lines of A. thaliana and rice without prior knowledge about the transformation vectors or the T-DNA constructs used to generate the studied plants. Conclusion The approach should allow the user to detect the presence of transgene sequences and get sufficient information for further characterization of unknown genetic constructs in plants. The only requirements are access to a small amount of pure transgene plant material, that the genetic construct in question is above a certain size (here ≥ 140 basepairs) and that parts of the construct shows some degree of sequence similarity with published genetic elements.

• Stenvik, Grethe-Elisabeth; Butenko, Melinka Alonso; Urbanowicz, BR; Rose, JKC & Aalen, Reidunn B. (2006). overexpression of inflorescence deficient in abscission activates cell separation in vestigial abscission zones in Arabidopsis. The Plant Cell. ISSN 1040-4651. 18, p. 1467–1476. Full text in Research Archive
• Aalen, Reidunn B.; Butenko, Melinka Alonso; Stenvik, Grethe-Elisabeth; Tandstad, Nora Martinussen & Patterson, Sara E. (2006). Genetic control of floral abscission. In Silva, Jaime A. Teixeira da (Eds.), Floriculture, Ornamental and Plant Biotechnology: Advances and Topical Issues. Global Science Books Ltd.. ISSN 9784903313009. p. 101–108. Full text in Research Archive
• Butenko, Melinka Alonso; Stenvik, Grethe-Elisabeth; Alm, Vibeke; Sæther, Barbro Elisabet; Patterson, Sara E. & Aalen, Reidunn B. (2006). Ethylene dependent and independent pathways controlling floral abscission are revealed to converge using promoter::reporter gene constructs in the ida abscission mutant. Journal of Experimental Botany. ISSN 0022-0957. 57(14), p. 3627–3637. doi: 10.1093/jxb/erl130. Full text in Research Archive Show summary

  The process of floral organ abscission in Arabidopsis thaliana can be modulated by ethylene and involves numerous genes contributing to cell separation. One gene that is absolutely required for abscission is INFLORESCENCE DEFICIENT IN ABSCISSION, IDA, as the ida mutant is completely blocked in abscission. To elucidate the genetic pathways regulating floral abscission, molecular markers expressed in the floral abscission zone have been studied in an ida mutant background. Using plants with promoter–reporter gene constructs including promoters of a novel FLORAL ABSCISSION ASSOCIATED gene (FAA) encoding a putative single-stranded binding protein (BASIL), chitinase (CHIT::GUS) and cellulase (BAC::GUS), it is shown that IDA acts in the last steps of the abscission process. These markers, as well as HAESA, encoding a receptor-like kinase, were unaffected in their temporal expression patterns in ida compared with wild-type plants; thus showing that different regulatory pathways are active in the abscission process. In contrast to BASIL, CHIT::GUS and BAC::GUS showed, however, much weaker induction of expression in an ida background, consistent with a reduction in pathogen-associated responses and a lack of total dissolution of cell walls in the mutant. IDA, encoding a putative secreted peptide ligand, and HAESA appeared to have identical patterns of expression in floral abscission zones. Lastly, to address the role of ethylene, IDA::GUS expression in the wild type and the ethylene-insensitive mutant etr1-1 was compared. Similar temporal patterns, yet restricted spatial expression patterns were observed in etr1-1, suggesting that the pathways regulated by IDA and by ethylene act in parallel, but are, to some degree, interdependent.

• Butenko, Melinka Alonso; Patterson, Sara E.; Grini, Paul Eivind; Stenvik, Grethe-Elisabeth; Amundsen, Svanstrøm Silja & Mandal, Abul [Show all 7 contributors for this article] (2003). INFLORESCENCE DEFICIENT IN ABSCISSION Controls Floral Organ Abscission in Arabidopsis and Identifies a Novel Family of Putative Ligands in Plants. The Plant Cell. ISSN 1040-4651. 15, p. 2296–2307. Full text in Research Archive
• Meza, Trine Johansen; Stangeland, Biljana; Mercy, Inderjit Singh; Skårn, Magne; Nymoen, Dag A. & Berg, Anita [Show all 11 contributors for this article] (2002). Analyses of single-copy Arabidopsis T-DNA transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing. Nucleic Acids Research (NAR). ISSN 0305-1048. 30(20), p. 4556–4566. Full text in Research Archive Show summary

  In genetically transformed plants, transgene silencing has been correlated to multiple and complex insertions of foreign DNA, e.g. T-DNA and vector backbone sequences. Occasionally, single-copy transgenes also suffer transgene silencing. We have compared integration patterns and T-DNA/plant DNA junctions in a collection of 37 single-copy T-DNA transformed Arabidopsis lines, of which 13 displays silencing. Vector sequences were found integrated in five lines, but only one of these displays silencing. Truncated T-DNA copies, positioned in inverse orientation to an intact T-DNA copy, were discovered in three lines. The whole nptII gene with pnos promoter was present in the truncated copy of one such line in which heavy silencing has been observed. In the two other lines no silencing has been observed over five generations. Thus, vector sequences and short additional T-DNA sequences are not sufficient or necessary to induce transgene silencing. DNA methylation of selected restriction endonuclease sites could not be correlated to silencing. Our collection of T-DNA/plants DNA junctions has also been used to evaluate current models of T-DNA integration. Data for some of our lines are compatible with T-DNA integration in double-stranded breaks, while for others initial invasion of plant DNA by the left or by the right T-DNA end seem important.

View all works in NVA

• Reinar, William Brynildsen; Krabberød, Anders Kristian; Lalun, Vilde Olsson; Butenko, Melinka Alonso & Jakobsen, Kjetill Sigurd (2025). Author Correction: Short tandem repeats delineate gene bodies across eukaryotes. Nature Communications. 16(1), p. 1350–1350. doi: 10.1038/s41467-025-56684-2. Full text in Research Archive
• Bjerkan, Katrine; Butenko, Melinka Alonso & Brysting, Anne Krag (2020). The weed that conquered plant scientists: the model organism Arabidopsis thaliana. NBS-nytt. ISSN 0801-3535. 1, p. 8–11. Full text in Research Archive
• Hubin, Aliaksandr; Storvik, Geir Olve; Grini, Paul Eivind & Butenko, Melinka Alonso (2019). Bayesian binomial regression model with a latent Gaussian field for analysis of epigenetic data. Full text in Research Archive
• Thorstensen, Tage; Andersen, Heidi Lie; Hamann, Thorsten & Butenko, Melinka Alonso (2017). Uvitenskapelig motstand mot genredigering av matplanter. Full text in Research Archive
• Herrmann, Ullrich; WILDHAGEN, Mari; Butenko, Melinka Alonso & Aalen, Reidunn B. (2014). Small peptides are involved in cell separation processes in the root. Full text in Research Archive
• Herrmann, Ullrich; WILDHAGEN, Mari; Stø, Ida Myhrer; Butenko, Melinka Alonso & Aalen, Reidunn B. (2014). Secreted IDA-LIKE peptide ligands and their receptors regulate crucial aspects of root development – root cap sloughing, gravitropism and meristem length. Full text in Research Archive
• Vie, Ane Kjersti; Najafi, Javad; Liu, Bin; Winge, Per; Butenko, Melinka Alonso & Hornslien, K [Show all 10 contributors for this article] (2012). Expression of the extended IDA gene family in Arabidopsis thaliana: evidence for post-transcriptional regulation by mRNA decapping. Full text in Research Archive
• Butenko, Melinka Alonso; Shi, Chunlin & Aalen, Reidunn B. (2010). Class I KNOX proteins involved in floral abscission downstream in the IDA-HAE/HSL2 signaling pathway. Full text in Research Archive
• Aalen, Reidunn B.; Stenvik, Grethe-Elisabeth; Shi, Chunlin & Butenko, Melinka Alonso (2009). Identification of putative peptide ligands and receptors involved in control of cell-separation processes in plants. Full text in Research Archive Show summary

  The novel ligand/receptor pair, IDA and the closely related receptor-like kinases (RLKs) HAESA (HAE) and HAESA-LIKE 2 (HSL2), controls floral organ abscission in Arabidopsis. The IDA gene encodes a protein of 77 amino acids (aa), with a N-terminal signal sequence exporting the protein. Genes encoding IDA-LIKE proteins, that share a common C-terminal 12aa motif (PIP), are present both in Arabidopsis and other plant species. The active IDA peptide resided within an extended PIP motif (EPIP). IDA-LIKE (IDL) proteins can in part substitute for IDA function. The IDL expression patterns indicate involvement in regulation of various cell separation events, e.g. root cap sloughing and seed dispersal. Plants constitutively overexpressing IDA exhibit earlier abscission of floral organs and ectopic abscission of flowers, branches and cauline leaves and overexpression of the IDL proteins mimic this phenotype. The over-expression phenotype is dependent on functional HAE and HSL2 RLKs. We suggest that the IDL peptides interact with HEASA-LIKE receptors to control cell-separation processes, and that new peptide-ligand/receptor pairs may be identified by a hypothesis-driven approach with the aid of genetics and new methods to identify active peptides and direct peptide-RLK interactions.

• Aalen, Reidunn B.; Stenvik, Grethe-Elisabeth; Butenko, Melinka Alonso & Shi, Chunlin (2009). Identification of putative peptide ligands and receptors involved in control of cell-separation processes in plants. Full text in Research Archive Show summary

  Recently a novel ligand/receptor pair, IDA and the closely related receptor-like kinases (RLKs) HAESA (HAE) and HAESA-LIKE 2 (HSL2), was revealed to control floral organ abscission in Arabidopsis (Stenvik et al., 2008, Plant Cell, 20: 1805-1817). The IDA gene encodes a protein of only 77 amino acids (aa), with a N-terminal signal sequence that exports the protein out of the cell. There is evidence suggesting that the protein is processed to release a small peptide from the C-terminal end. Genes encoding IDA-LIKE proteins have been identified both in Arabidopsis and other plant species. They are all less than 100 aa, with a N-terminal signal peptide and a common C-terminal motif called PIP (Butenko et al., 2003, Plant Cell, 15: 2296-2307). The active IDA peptide resided within an extended PIP motif (EPIP) of 20 aa (Stenvik et al., 2008). In Arabidopsis IDA-LIKE (IDL) proteins can in part substitute for IDA function. Promoter:GUS expression studies of the IDL genes indicate that these genes may be involved in regulating various cell separation events such as root cap sloughing, stomata development and formation of hydathodes. A 35S:IDA line constitutively overexpressing IDA exhibit earlier abscission of floral organs and ectopic abscission at the bases of the pedicel, branches of the inflorescence, and cauline leaves (Stenvik et al. 2006, Plant Cell 18: 1467-1476) and overexpression of the IDL proteins mimic this phenotype (Stenvik et al., 2008). The over-expression phenotype is dependent on functional HAE and HSL2 RLKs. We suggest that the IDL peptides interact with HEASA-LIKE receptors to control cell-separation processes. Interestingly, The IDA/IDL-HAE/HSL2 signalling system shows similarities to that of CLV3/CLE-CLV1/CLV2 involved in meristem maintenance. We propose that new peptide-ligand/receptor pairs may be identified by a hypothesis-driven approach, and the aid of genetics, as well as new methods to identify active peptides and direct peptide-RLK interactions.

• Aalen, Reidunn B.; Stenvik, Grethe-Elisabeth; Shi, Chunlin & Butenko, Melinka Alonso (2009). Peptide ligands and receptors involved in control of cell-separation processes in Arabidopsis. Full text in Research Archive Show summary

  Cell separation events take place throughout the life cycle of plants, and facilitate organ loss, root cap sloughing, dehiscence, fruit and seed shedding. After pollination has taken place in Arabidopsis, floral organs abscise. INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) that encodes a protein of 77 amino acids (aa) including an N-terminal export signal, is absolutely required for this process. Genetic evidence suggests that IDA is a small peptide ligand interacting with the receptor-like kinases (RLKs) HEASA and HEASA-LIKE2. Thus this is one of the few plant ligand/receptor pairs identified to date [3]. Genes encoding IDA-LIKE proteins, that share a common C-terminal 12aa motif (PIP), are present both in Arabidopsis and other plant species. The active IDA peptide resided within an extended PIP motif (EPIP). IDA-LIKE (IDL) proteins can in part substitute for IDA function, however, the IDL expression patterns indicate involvement in regulation of various other cell separation events, e.g. root cap sloughing and seed dispersal. Plants constitutively overexpressing IDA exhibit earlier abscission of floral organs and ectopic abscission of flowers, branches and cauline leaves and overexpression of the IDL proteins mimic this phenotype. The over-expression phenotype is dependent on functional HAE and HSL2 RLKs. We suggest that the IDL peptides interact with HEASA-LIKE receptors to control cell-separation processes, and that new peptide-ligand/receptor pairs may be identified by a hypothesis-driven approach with the aid of genetics and new methods to identify active peptides and direct peptide-RLK interactions.

• Aalen, Reidunn B.; Stenvik, Grethe-Elisabeth; Shi, Chunlin & Butenko, Melinka Alonso (2009). HAE and HSL receptors in cell separation events. Full text in Research Archive
• Stenvik, Grethe-Elisabeth; Tandstad, Nora Martinussen; Holmgren, Asbjørn; Kristiansen, Wenche; Butenko, Melinka Alonso & Aalen, Reidunn B. (2007). INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) AND IDA-LIKE (IDL) PEPTIDES AND THEIR ROLES IN PLANT DEVELOPMENT. Full text in Research Archive
• Stenvik, Grethe-Elisabeth; Tandstad, Nora Martinussen; Butenko, Melinka Alonso & Aalen, Reidunn B. (2007). INFLORESCENCE DEFICIENT IN ABSCISSION (IDA)AND IDA-LIKE (IDL) PEPTIDES AND THEIR ROLES IN CELL SEPARATION PROCESSES. Full text in Research Archive
• Thorstensen, Tage; Grini, Paul Eivind; Alm, Vibeke; Butenko, Melinka Alonso; Rosenhave, E. Maryann & Aalen, Reidunn (2004). Identification of new gene families and their function using bioinformatics tools and reverse genetics. Full text in Research Archive
• Butenko, Melinka Alonso; Patterson, Sara E.; Stenvik, Grethe-Elisabeth; Grini, Paul Eivind; Thorstensen, Tage & Mandal, Abul [Show all 7 contributors for this article] (2003). The IDA gene, controlling floral organ abscission in Arabidopsis, identifies a novel family of putative ligands in plants. Full text in Research Archive
• Butenko, Melinka Alonso; Patterson, Sara E.; Grini, Paul Eivind; Stenvik, Grethe-Elisabeth; Amundsen, Svanstrøm Silja & Mandal, Abul [Show all 7 contributors for this article] (2003). IDA controls floral organ abscission in Arabidopsis, and identifies a novel family of putative ligands in plants. Full text in Research Archive
• Mercy, Inderjit Singh; Meza, Trine Johansen; Skårn, Magne; Butenko, Melinka Alonso; Håkelien, Anne-Mari & Halsekås, Camilla [Show all 9 contributors for this article] (2001). ). Molecluar studies of single-copy silencing lines. Full text in Research Archive
• Thorstensen, Tage; Butenko, Melinka Alonso; Meza, Trine Johansen; Johnsen, Sylvia; Davies, William & Aalen, Reidunn (2001). Characterization of two SET-domain encoding Arabidopsis genes with similarity to Drosophila SUPPRESSOR OF VARIEGATION (3-9). Full text in Research Archive
• Aalen, Reidunn; Butenko, Melinka Alonso; Stacy, Robin Anne Prentice & Mandal, Abul (2000). Genetic characterization of an Arabidopsis thaliana mutant deficient in floral abscission. Full text in Research Archive Show summary

  We have identified a T-DNA transformed mutant line of Arabidopsis thaliana, named inflorescence deficient in abscission (ida), showing no floral abscission and an occasional reversion of floral meristems to inflorescence meristems. Backcrosses and segregation analysis showed that the mutant phenotype is inherited as a single-locus recessive trait. PCR amplification of the nptII-marker gene in the T-DNA segregants strongly indicates that the mutation is caused by the T-DNA insertion. Similar late abscising phenotypes have previously been described for ethylene insensitive mutants, where flowers are retained longer and tend to become senescent before being shed. However, ida seeds germinated on medium containing ACC, gave rise to seedling featuring the typical triple response of ethylene sensitive plants.

• Butenko, Melinka Alonso; Mandal, Abul & Aalen, Reidunn (2000). Absence of floral abscission and meristem determinacy in the ethylene-sensitive Arabidopsis thaliana mutant inflorescence deficient in abscission (ida). Full text in Research Archive Show summary

  We have identified a T-DNA transformed mutant line of Arabidopsis thaliana, named inflorescence deficient in abscission (ida), showing no floral abscission and an occasional reversion of floral meristems to inflorescence meristems. Backcrosses and segregation analysis showed that the mutant phenotype is inherited as a single-locus recessive trait. Although abscission zone (AZ) cells develop in the ida mutant, vivid, turgid floral organs showing no signs of senescence are found attached to full-grown, green siliques. The petals, sepals and stamens dry out completely and still remain attached to the dry septum after the shedding of mature seeds. ida seedlings feature the typical triple response of ethylene-sensitive plants indicating that the IDA gene is involved in an ethylene-independent developmental pathway controlling floral abscission, and that the ida mutant is different from both etr1 and ein1mutants.

• Butenko, Melinka Alonso; Aalen, Reidunn; Stacy, Robin Anne Prentice & Campillo, Elena del (1999). Differential expression of two distinct classes of Endo-1,4-b-D glucanases (cellulases) genes in Arabidopsis. Full text in Research Archive
• Riiser, Even Sannes; Aalen, Reidunn B. & Butenko, Melinka Alonso (2009). Ligand-receptor matchmaking: The IDA-HAE/HSL2 signaling system and the IDL and HSL relatives. Universitetet i Oslo. Full text in Research Archive Show summary

  Until recently, most intercellular communication in plants has been explained by the signaling and perception of non-peptide plant hormones. It is, however, becoming increasingly clear that plant cell communication also makes use of small peptide signals. One example is the IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) peptide that is believed to signal through the receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2) to induce the cell separation process necessary for floral organ abscission. Several genes closely related to IDA and HAE have been identified, and it is conceivable that the IDL (IDA-LIKE) proteins interact with HSL proteins to control different cell-separation processes. A main aim of this thesis has been to match the expression of IDL and HSL genes as a first approach to identifying putative ligand-receptor pairs. Furthermore, the roles of IDA, HAE and HSL2 in root development have been examined by mutant studies, and finally, the interaction between IDA and HAE, HSL1 and HSL2 has been investigated using yeast direct mating and a genetic approach. Based on overlapping promoter:reporter gene expression patterns, several novel IDL-HSL ligand-receptor pairs have been suggested in this thesis. HSL2 may for instance influence the growth of the main root together with IDL1. Furthermore, IDA has been shown to facilitate the emergence of lateral roots, which also involves a cell-separation process. No direct, biochemical interaction between IDA and HAE, HSL2 or the closely related HSL1 was detected in a yeast direct mating experiment. However, by performing a genetic study it was revealed that IDA has a higher in vivo affinity for HAE than for HSL2. Finally, a genotype lethal during seed development in the presence of ectopic IDA expression was identified that may explain the strongly reduced fertility seen in plants overexpressing IDA.

• Butenko, Melinka Alonso & Aalen, Reidunn B. (2006). A genetic and molecular study of floral organ abscission in Arabidopsis thaliana using the mutant inflorescence deficient in abscission. Universitetet i Oslo. Full text in Research Archive

View all works in NVA