@Article{IPB-2192, author = {Nishiyama, T. and Sakayama, H. and de Vries, J. and Buschmann, H. and Saint-Marcoux, D. and Ullrich, K. K. and Haas, F. B. and Vanderstraeten, L. and Becker, D. and Lang, D. and Vosolsobě, S. and Rombauts, S. and Wilhelmsson, P. K. I. and Janitza, P. and Kern, R. and Heyl, A. and Rümpler, F and Calderón Villalobos, L. I. A. and Clay, J. M. and Skokan, R. and Toyoda, A. and Suzuki, Y. and Kagoshima, H. and Schijlen, E. and Tajeshwar, N. and Catarino, B. and Hetherington, A. J. and Saltykova, A. and Bonnot, C. and Breuninger, H. and Symeonidi, A. and Radhakrishnan, G. V. and Van Nieuwerburgh, F. and Deforce, D. and Chang, C. and Karol, K. G. and Hedrich, R. and Ulvskov, P. and Glöckner, G. and Delwiche, C. F. and Petrášek, J. and Van de Peer, Y. and Friml, J. and Beilby, M. and Dolan, L. and Kohara, Y. and Sugano, S. and Fujiyama, A. and Delaux, P.-M. and Quint, M. and Theißen, G. and Hagemann, M. and Harholt, J. and Dunand, C. and Zachgo, S. and Langdale, J. and Maumus, F. and Van Der Straeten, D. and Gould, S. B. and Rensing, S. A.}, title = {{The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization}}, year = {2018}, pages = {448-464.e24}, journal = {Cell}, doi = {10.1016/j.cell.2018.06.033}, url = {https://www.sciencedirect.com/science/article/pii/S0092867418308018}, volume = {174}, abstract = {Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.} } @Article{IPB-1536, author = {Wasternack, C. and Hause, B.}, title = {{Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany}}, year = {2013}, pages = {1021-1058}, journal = { Annals of Botany}, doi = {10.1093/aob/mct067}, volume = {111}, abstract = {Background: Jasmonates are important regulators in plant responses to biotic and abiotic stresses as well as indevelopment. Synthesized from lipid-constituents, the initially formed jasmonic acid is converted to differentmetabolites including the conjugate with isoleucine. Important new components of jasmonate signalling includingits receptor were identified, providing deeper insight into the role of jasmonate signalling pathways in stressresponses and development.Scope: The present review is an update of the review on jasmonates published in this journal in 2007. New dataof the last five years are described with emphasis on metabolites of jasmonates, on jasmonate perception andsignalling, on cross-talk to other plant hormones and on jasmonate signalling in response to herbivores and pathogens,in symbiotic interactions, in flower development, in root growth and in light perception.Conclusions: The last few years have seen breakthroughs in the identification of JASMONATE ZIM DOMAIN(JAZ) proteins and their interactors such as transcription factors and co-repressors, and the crystallization of thejasmonate receptor as well as of the enzyme conjugating jasmonate to amino acids. Now, the complex nature ofnetworks of jasmonate signalling in stress responses and development including hormone cross-talk can beaddressed.} } @Article{IPB-1140, author = {Abel, S. and Savchenko, T. and Levy, M.}, title = {{Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa}}, year = {2005}, pages = {72 (1-25)}, journal = {BMC Evolutionary Biology}, url = {http://www.biomedcentral.com/1471-2148/5/72}, volume = {5}, abstract = { We identified and analyzed 33 and 29 IQD1-like genes in Arabidopsis thaliana and Oryza sativa, respectively. The encoded IQD proteins contain a plant-specific domain of 67 conserved amino acid residues, referred to as the IQ67 domain, which is characterized by a unique and repetitive arrangement of three different calmodulin recruitment motifs, known as the IQ, 1-5-10, and 1-8-14 motifs. We demonstrated calmodulin binding for IQD20, the smallest IQD protein in Arabidopsis, which consists of a C-terminal IQ67 domain and a short N-terminal extension. A striking feature of IQD proteins is the high isoelectric point (~10.3) and frequency of serine residues (~11%). We compared the Arabidopsis and rice IQD gene families in terms of gene structure, chromosome location, predicted protein properties and motifs, phylogenetic relationships, and evolutionary history. The existence of an IQD-like gene in bryophytes suggests that IQD proteins are an ancient family of calmodulin-binding proteins and arose during the early evolution of land plants. Comparative phylogenetic analyses indicate that the major IQD gene lineages originated before the monocot-eudicot divergence. The extant IQD loci in Arabidopsis primarily resulted from segmental duplication and reflect preferential retention of paralogous genes, which is characteristic for proteins with regulatory functions. Interaction of IQD1 and IQD20 with calmodulin and the presence of predicted calmodulin binding sites in all IQD family members suggest that IQD proteins are a new class of calmodulin targets. The basic isoelectric point of IQD proteins and their frequently predicted nuclear localization suggest that IQD proteins link calcium signaling pathways to the regulation of gene expression. Our comparative genomics analysis of IQD genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of putative calmodulin targets.} }