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Grapevine (Vitis vinifera L.) is one of the most significant crops in the world. Today’s richness in grapevine diversity results from a complex domestication history over multiple historical periods. Here, we employed whole genome resequencing to elucidate different aspects of the recent evolutionary history of this crop. Our results support a model in which a central domestication event in grapevine was followed by post-domestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties, which show large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by geneflow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.
S. Freitas; M.A. Gazda; M. Rebelo; A.J. Muñoz-Pajares; C. Vila-Viçosa; A. Muñoz-Mérida; L.M. Gonçalves; D. Azevedo-Silva; S. Afonso; I. Castro; P.H. Castro; M. Sottomayor; A. Beja-Pereira; J. Tereso; N. Ferrand; E. Gonçalves; A. Martins; M. Carneiro; H. Azevedo. Evidence of post-domestication hybridization and adaptive introgression in Western European grapevine varieties. 2021, 1 .
AMA StyleS. Freitas, M.A. Gazda, M. Rebelo, A.J. Muñoz-Pajares, C. Vila-Viçosa, A. Muñoz-Mérida, L.M. Gonçalves, D. Azevedo-Silva, S. Afonso, I. Castro, P.H. Castro, M. Sottomayor, A. Beja-Pereira, J. Tereso, N. Ferrand, E. Gonçalves, A. Martins, M. Carneiro, H. Azevedo. Evidence of post-domestication hybridization and adaptive introgression in Western European grapevine varieties. . 2021; ():1.
Chicago/Turabian StyleS. Freitas; M.A. Gazda; M. Rebelo; A.J. Muñoz-Pajares; C. Vila-Viçosa; A. Muñoz-Mérida; L.M. Gonçalves; D. Azevedo-Silva; S. Afonso; I. Castro; P.H. Castro; M. Sottomayor; A. Beja-Pereira; J. Tereso; N. Ferrand; E. Gonçalves; A. Martins; M. Carneiro; H. Azevedo. 2021. "Evidence of post-domestication hybridization and adaptive introgression in Western European grapevine varieties." , no. : 1.
Zinc (Zn) is an essential micronutrient for plants and animals owing to its structural and catalytic roles in many proteins1. Zn deficiency affects around 2 billion people, mainly those who live on plant-based diets relying on crops from Zn-deficient soils2,3. Plants maintain adequate Zn levels through tightly regulated Zn homeostasis mechanisms involving Zn uptake, distribution and storage4, but evidence of how they sense Zn status is lacking. Here, we use in vitro and in planta approaches to show that the Arabidopsis thaliana F-group bZIP transcription factors bZIP19 and bZIP23, which are the central regulators of the Zn deficiency response, function as Zn sensors by binding Zn2+ ions to a Zn-sensor motif. Deletions or modifications of this Zn-sensor motif disrupt Zn binding, leading to a constitutive transcriptional Zn deficiency response, which causes a significant increase in plant and seed Zn accumulation. As the Zn-sensor motif is highly conserved in F-group bZIP proteins across land plants, the identification of this plant Zn sensor will promote new strategies to improve the Zn nutritional quality of plant-derived food and feed, and contribute to tackling the global Zn-deficiency health problem. Zinc (Zn) is one of the essential micronutrients for plant growth and development, but the Zn-sensing mechanisms are poorly understood in plants. Two Arabidopsis bZIP transcription factors were previously shown to modulate plant responses to Zn deficiency. In this study, the authors find that they are indeed the sensors of Zn in Arabidopsis.
Grmay H. Lilay; Daniel P. Persson; Pedro Humberto Castro; Feixue Liao; Ross D. Alexander; Mark G. M. Aarts; Ana G. L. Assunção. Arabidopsis bZIP19 and bZIP23 act as zinc sensors to control plant zinc status. Nature Plants 2021, 7, 137 -143.
AMA StyleGrmay H. Lilay, Daniel P. Persson, Pedro Humberto Castro, Feixue Liao, Ross D. Alexander, Mark G. M. Aarts, Ana G. L. Assunção. Arabidopsis bZIP19 and bZIP23 act as zinc sensors to control plant zinc status. Nature Plants. 2021; 7 (2):137-143.
Chicago/Turabian StyleGrmay H. Lilay; Daniel P. Persson; Pedro Humberto Castro; Feixue Liao; Ross D. Alexander; Mark G. M. Aarts; Ana G. L. Assunção. 2021. "Arabidopsis bZIP19 and bZIP23 act as zinc sensors to control plant zinc status." Nature Plants 7, no. 2: 137-143.
Pedro Humberto Castro; Sara Freitas; Herlander Azevedo. Plant hexokinase phylogenetic analysis highlights a possible regulation by the posttranslational modifier SUMO. 2020, 2020, 1 .
AMA StylePedro Humberto Castro, Sara Freitas, Herlander Azevedo. Plant hexokinase phylogenetic analysis highlights a possible regulation by the posttranslational modifier SUMO. . 2020; 2020 ():1.
Chicago/Turabian StylePedro Humberto Castro; Sara Freitas; Herlander Azevedo. 2020. "Plant hexokinase phylogenetic analysis highlights a possible regulation by the posttranslational modifier SUMO." 2020, no. : 1.
Pedro Humberto Castro; Nuno Verde; Herlander Azevedo. Arabidopsis thaliana growth is independently controlled by the SUMO E3 ligase SIZ1 and Hexokinase 1. 2020, 2020, 1 .
AMA StylePedro Humberto Castro, Nuno Verde, Herlander Azevedo. Arabidopsis thaliana growth is independently controlled by the SUMO E3 ligase SIZ1 and Hexokinase 1. . 2020; 2020 ():1.
Chicago/Turabian StylePedro Humberto Castro; Nuno Verde; Herlander Azevedo. 2020. "Arabidopsis thaliana growth is independently controlled by the SUMO E3 ligase SIZ1 and Hexokinase 1." 2020, no. : 1.
Zinc (Zn) is an essential micronutrient for plants and animals because of its structural and catalytic roles in many proteins. Zn deficiency affects ca. two billion people, mainly those living on plant-based diets that rely on crops from Zn deficient soils. Plants maintain adequate Zn levels through tightly regulated Zn homeostasis mechanisms, involving Zn uptake, distribution and storage, but it was not known how they sense Zn status. We use in vitro and in planta approaches to show that the Arabidopsis thaliana F-group bZIP transcription factors bZIP19 and bZIP23, which are the central regulators of the Zn deficiency response, act as Zn sensors by binding Zn2+ ions to a Zn sensor motif (ZSM). Deletions or modifications of this ZSM disrupts Zn binding, leading to a constitutive transcriptional Zn deficiency response, which causes a significant increase in plant and seed Zn accumulation. Since the ZSM is highly conserved in F-bZIPs across land plants, the identification of the first plant Zn-sensor will promote new strategies to improve the Zn nutritional quality of plant-derived food and feed, and contribute to tackle the global Zn deficiency health problem.
Grmay Hailu Lilay; Daniel P. Persson; Pedro Humberto Castro; Feixue Liao; Ross D. Alexander; Mark G.M. Aarts; Ana G.L. Assunção. The Arabidopsis bZIP19 and bZIP23 transcription factors act as zinc-sensors to control plant zinc status. 2020, 1 .
AMA StyleGrmay Hailu Lilay, Daniel P. Persson, Pedro Humberto Castro, Feixue Liao, Ross D. Alexander, Mark G.M. Aarts, Ana G.L. Assunção. The Arabidopsis bZIP19 and bZIP23 transcription factors act as zinc-sensors to control plant zinc status. . 2020; ():1.
Chicago/Turabian StyleGrmay Hailu Lilay; Daniel P. Persson; Pedro Humberto Castro; Feixue Liao; Ross D. Alexander; Mark G.M. Aarts; Ana G.L. Assunção. 2020. "The Arabidopsis bZIP19 and bZIP23 transcription factors act as zinc-sensors to control plant zinc status." , no. : 1.
All living organisms require zinc as an essential micronutrient. Maintaining appropriate intracellular zinc supply, and avoiding deficiency or toxic excess, requires a tight regulation of zinc homeostasis. In Arabidopsis, bZIP19 and bZIP23 (basic-leucine zipper) transcription factors are the central regulators of the zinc deficiency response. Their targets include members of the ZIP (Zrt/Irt-like Protein) transporter family, involved in cellular zinc uptake, which are up-regulated at zinc deficiency. However, the mechanisms by which these transcription factors are regulated by cellular zinc status are not yet known. Here, to further our insight, we took advantage of the zinc deficiency hypersensitive phenotype of the bzip19 bzip23 double mutant, and used it as background to produce complementation lines of each Arabidopsis F-bZIP transcription factor, including bZIP24. On these lines, we performed complementation and localization studies, analyzed the transcript level of a subset of putative target genes, and performed elemental tissue profiling. We find evidence supporting that the zinc-dependent activity of bZIP19 and bZIP23 is modulated by zinc at protein level, in the nucleus, where cellular zinc sufficiency represses their activity and zinc deficiency is required. In addition, we show that these two transcription factors are functionally redundant to a large extent, and that differential tissue-specific expression patterns might, at least partly, explain distinct regulatory activities. Finally, we show that bZIP24 does not play a central role in the Zn deficiency response. Overall, we provide novel information that advances our understanding of the regulatory activity of bZIP19 and bZIP23.
Grmay H. Lilay; Pedro Humberto Castro; Ana Campilho; Ana G. L. Assunção. The Arabidopsis bZIP19 and bZIP23 Activity Requires Zinc Deficiency – Insight on Regulation From Complementation Lines. Frontiers in Plant Science 2019, 9, 1 .
AMA StyleGrmay H. Lilay, Pedro Humberto Castro, Ana Campilho, Ana G. L. Assunção. The Arabidopsis bZIP19 and bZIP23 Activity Requires Zinc Deficiency – Insight on Regulation From Complementation Lines. Frontiers in Plant Science. 2019; 9 ():1.
Chicago/Turabian StyleGrmay H. Lilay; Pedro Humberto Castro; Ana Campilho; Ana G. L. Assunção. 2019. "The Arabidopsis bZIP19 and bZIP23 Activity Requires Zinc Deficiency – Insight on Regulation From Complementation Lines." Frontiers in Plant Science 9, no. : 1.
Functional insight on the post-translational modifier SUMO and its biochemical pathway in plants has steadily increased over the past decade. In contrast to the low number of core components that catalytically control SUMO attachment to targets, the enzymes that control deconjugation and SUMO maturation seem to have diversified in terms of both gene number and biological function. However, studies on these deSUMOylating proteases have been accompanied by diversity in nomenclature and unclear evolutionary categorization. We provide a state-of-the-art assessment of the evolutionary subclades within the ULP gene family of plant deSUMOylating proteases, and propose a nomenclature for this protease subgroup for consistent annotation of ULP-encoding genes in plant genomes.
Pedro Humberto Castro; Andreas Bachmair; Eduardo R Bejarano; George Coupland; L. Maria Lois; Ari Sadanandom; Harrold A Van Den Burg; Richard D Vierstra; Herlander Azevedo. Revised nomenclature and functional overview of the ULP gene family of plant deSUMOylating proteases. Journal of Experimental Botany 2018, 69, 4505 -4509.
AMA StylePedro Humberto Castro, Andreas Bachmair, Eduardo R Bejarano, George Coupland, L. Maria Lois, Ari Sadanandom, Harrold A Van Den Burg, Richard D Vierstra, Herlander Azevedo. Revised nomenclature and functional overview of the ULP gene family of plant deSUMOylating proteases. Journal of Experimental Botany. 2018; 69 (19):4505-4509.
Chicago/Turabian StylePedro Humberto Castro; Andreas Bachmair; Eduardo R Bejarano; George Coupland; L. Maria Lois; Ari Sadanandom; Harrold A Van Den Burg; Richard D Vierstra; Herlander Azevedo. 2018. "Revised nomenclature and functional overview of the ULP gene family of plant deSUMOylating proteases." Journal of Experimental Botany 69, no. 19: 4505-4509.
SPF1 and SPF2 are nuclear-located SUMO proteases that contribute to balancing the levels of SUMO conjugates downstream of SIZ1 and are involved in the regulation of plant development.
Pedro Humberto Castro; Miguel Ângelo Santos; Sara Freitas; Pepe Cana-Quijada; Tiago Lourenço; Mafalda A A Rodrigues; Fátima Fonseca; Javier Ruiz-Albert; Jorge E Azevedo; Rui Manuel Tavares; Araceli G Castillo; Eduardo R Bejarano; Herlander Azevedo. Arabidopsis thaliana SPF1 and SPF2 are nuclear-located ULP2-like SUMO proteases that act downstream of SIZ1 in plant development. Journal of Experimental Botany 2018, 69, 4633 -4649.
AMA StylePedro Humberto Castro, Miguel Ângelo Santos, Sara Freitas, Pepe Cana-Quijada, Tiago Lourenço, Mafalda A A Rodrigues, Fátima Fonseca, Javier Ruiz-Albert, Jorge E Azevedo, Rui Manuel Tavares, Araceli G Castillo, Eduardo R Bejarano, Herlander Azevedo. Arabidopsis thaliana SPF1 and SPF2 are nuclear-located ULP2-like SUMO proteases that act downstream of SIZ1 in plant development. Journal of Experimental Botany. 2018; 69 (19):4633-4649.
Chicago/Turabian StylePedro Humberto Castro; Miguel Ângelo Santos; Sara Freitas; Pepe Cana-Quijada; Tiago Lourenço; Mafalda A A Rodrigues; Fátima Fonseca; Javier Ruiz-Albert; Jorge E Azevedo; Rui Manuel Tavares; Araceli G Castillo; Eduardo R Bejarano; Herlander Azevedo. 2018. "Arabidopsis thaliana SPF1 and SPF2 are nuclear-located ULP2-like SUMO proteases that act downstream of SIZ1 in plant development." Journal of Experimental Botany 69, no. 19: 4633-4649.
SUMO is a modifying peptide that regulates protein activity and is essential to eukaryotes. In plants, SUMO plays an important role in both development and the response to environmental stimuli. The best described sumoylation pathway component is the SUMO E3 ligase SIZ1. Its mutant displays inefficient responses to nutrient imbalance in phosphate, nitrate and copper. Recently, we reported that siz1 also displays altered responses to exogenous sugar supplementation. The siz1 mutant is a salicylic acid (SA) accumulator, and SA may interfere with sugar-dependent responses and signaling events. Here, we extended our previous studies to determine the importance of SA in the SIZ1 response to sugars, by introducing the bacterial salicylate hydroxylase NahG into the siz1 background. Results demonstrate that siz1 phenotypes involving delayed germination are partially dependent of SA levels, whereas the sugar-signaling effect of sugars is independent of SA.
Pedro Humberto Castro; Nuno Verde; Rui Tavares; Eduardo Rodríguez Bejarano; Herlânder Azevedo. Sugar signaling regulation by arabidopsis SIZ1-driven sumoylation is independent of salicylic acid. Plant Signaling & Behavior 2018, 13, e1179417 .
AMA StylePedro Humberto Castro, Nuno Verde, Rui Tavares, Eduardo Rodríguez Bejarano, Herlânder Azevedo. Sugar signaling regulation by arabidopsis SIZ1-driven sumoylation is independent of salicylic acid. Plant Signaling & Behavior. 2018; 13 (4):e1179417.
Chicago/Turabian StylePedro Humberto Castro; Nuno Verde; Rui Tavares; Eduardo Rodríguez Bejarano; Herlânder Azevedo. 2018. "Sugar signaling regulation by arabidopsis SIZ1-driven sumoylation is independent of salicylic acid." Plant Signaling & Behavior 13, no. 4: e1179417.
Silicon (Si) has many beneficial effects in plants, especially for the survival of biotic and abiotic stresses. However, Si may negatively affect the quality of lignocellulosic biomass for bioenergy purposes. Despite many studies, the regulation of Si distribution and deposition in plants remains to be fully understood. Here, we have identified the Brachypodium distachyon mutant low-silicon 1 (Bdlsi1-1), with impaired channelling function of the Si influx transporter BdLSI1, resulting in a substantial reduction of Si in shoots. Bioimaging by Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) showed that the wild-type plants deposit Si mainly in the bracts, awns, and leaf macrohairs. The Bdlsi1-1 mutants showed substantial (>90%) reduction of Si in the mature shoot. The Bdlsi1-1 leaves had fewer, shorter macrohairs, but the overall pattern of Si distribution in bracts and leaf tissues was similar to that in the wild type. The Bdlsi1-1 plants supplied with Si had significantly lower seed weights, compared to the wild type. In low-Si media, the seed weight of wild-type plants was similar to that of Bdlsi1-1 mutants supplied with Si, while the Bdlsi1-1 seed weight decreased further. We conclude that Si deficiency results in widespread alterations in leaf surface morphology and seed formation in Brachypodium, showing the importance of Si for successful development in grasses.
Sylwia Emilia Glazowska; Emiko Murozuka; Daniel Pergament Persson; Pedro Humberto Castro; Jan K. Schjoerring. Silicon affects seed development and leaf macrohair formation inBrachypodium distachyon. Physiologia Plantarum 2018, 163, 231 -246.
AMA StyleSylwia Emilia Glazowska, Emiko Murozuka, Daniel Pergament Persson, Pedro Humberto Castro, Jan K. Schjoerring. Silicon affects seed development and leaf macrohair formation inBrachypodium distachyon. Physiologia Plantarum. 2018; 163 (2):231-246.
Chicago/Turabian StyleSylwia Emilia Glazowska; Emiko Murozuka; Daniel Pergament Persson; Pedro Humberto Castro; Jan K. Schjoerring. 2018. "Silicon affects seed development and leaf macrohair formation inBrachypodium distachyon." Physiologia Plantarum 163, no. 2: 231-246.
Pedro Humberto Castro; Grmay H. Lilay; Ana G.L. Assunção. Regulation of Micronutrient Homeostasis and Deficiency Response in Plants. Plant Micronutrient Use Efficiency 2018, 1 -15.
AMA StylePedro Humberto Castro, Grmay H. Lilay, Ana G.L. Assunção. Regulation of Micronutrient Homeostasis and Deficiency Response in Plants. Plant Micronutrient Use Efficiency. 2018; ():1-15.
Chicago/Turabian StylePedro Humberto Castro; Grmay H. Lilay; Ana G.L. Assunção. 2018. "Regulation of Micronutrient Homeostasis and Deficiency Response in Plants." Plant Micronutrient Use Efficiency , no. : 1-15.
Surekha Agarwal; Chamizo-Ampudia Alejandro; Llamas Angel; Ana G.L. Assunção; Galvan Aurora; Khurram Bashir; Begoña Blasco; Juan J. Camacho-Cristóbal; Pedro Humberto Castro; Theocharis Chatzistathis; Sardar Alam Cheema; André R. Dos Reis; Fernández Emilio; Muhammad Farooq; Agustin Gonzalez-Fontes; Kathleen L. Hefferon; María B. Herrera-Rodríguez; David Hopff; Aysha Kiran; Grmay H. Lilay; Sabine Lüthje; Karolina Malas; Satendra K. Mangrauthia; Tejada-Jimenez Manuel; Juan D. Marques Fong; Tsugiyuki Masunaga; Claudia N. Meisrimler; Paloma K. Menguer; Magdalena Migocka; Larissa A.C. Moraes; Adônis Moreira; Niluka Nakandalage; María T. Navarro-Gochicoa; Eloy Navarro-León; Miroslav Nikolić; Levent Oztürk; Jelena Pavlovic; Hafeez Ur Rehman; Jesus Rexach; Felipe K. Ricachenevsky; Juan M. Ruiz; Neelamraju Sarla; Saman Seneweera; Raul A. Sperotto; Abdul Wakeel. Contributors. Plant Micronutrient Use Efficiency 2018, 1 .
AMA StyleSurekha Agarwal, Chamizo-Ampudia Alejandro, Llamas Angel, Ana G.L. Assunção, Galvan Aurora, Khurram Bashir, Begoña Blasco, Juan J. Camacho-Cristóbal, Pedro Humberto Castro, Theocharis Chatzistathis, Sardar Alam Cheema, André R. Dos Reis, Fernández Emilio, Muhammad Farooq, Agustin Gonzalez-Fontes, Kathleen L. Hefferon, María B. Herrera-Rodríguez, David Hopff, Aysha Kiran, Grmay H. Lilay, Sabine Lüthje, Karolina Malas, Satendra K. Mangrauthia, Tejada-Jimenez Manuel, Juan D. Marques Fong, Tsugiyuki Masunaga, Claudia N. Meisrimler, Paloma K. Menguer, Magdalena Migocka, Larissa A.C. Moraes, Adônis Moreira, Niluka Nakandalage, María T. Navarro-Gochicoa, Eloy Navarro-León, Miroslav Nikolić, Levent Oztürk, Jelena Pavlovic, Hafeez Ur Rehman, Jesus Rexach, Felipe K. Ricachenevsky, Juan M. Ruiz, Neelamraju Sarla, Saman Seneweera, Raul A. Sperotto, Abdul Wakeel. Contributors. Plant Micronutrient Use Efficiency. 2018; ():1.
Chicago/Turabian StyleSurekha Agarwal; Chamizo-Ampudia Alejandro; Llamas Angel; Ana G.L. Assunção; Galvan Aurora; Khurram Bashir; Begoña Blasco; Juan J. Camacho-Cristóbal; Pedro Humberto Castro; Theocharis Chatzistathis; Sardar Alam Cheema; André R. Dos Reis; Fernández Emilio; Muhammad Farooq; Agustin Gonzalez-Fontes; Kathleen L. Hefferon; María B. Herrera-Rodríguez; David Hopff; Aysha Kiran; Grmay H. Lilay; Sabine Lüthje; Karolina Malas; Satendra K. Mangrauthia; Tejada-Jimenez Manuel; Juan D. Marques Fong; Tsugiyuki Masunaga; Claudia N. Meisrimler; Paloma K. Menguer; Magdalena Migocka; Larissa A.C. Moraes; Adônis Moreira; Niluka Nakandalage; María T. Navarro-Gochicoa; Eloy Navarro-León; Miroslav Nikolić; Levent Oztürk; Jelena Pavlovic; Hafeez Ur Rehman; Jesus Rexach; Felipe K. Ricachenevsky; Juan M. Ruiz; Neelamraju Sarla; Saman Seneweera; Raul A. Sperotto; Abdul Wakeel. 2018. "Contributors." Plant Micronutrient Use Efficiency , no. : 1.
Basic leucine zipper (bZIP) transcription factors control important developmental and physiological processes in plants. In Arabidopsis thaliana, the three gene F-bZIP subfamily has been associated with zinc deficiency and salt stress response. Benefiting from the present abundance of plant genomic data, we performed an evolutionary and structural characterization of plant F-bZIPs. We observed divergence during seed plant evolution, into two groups and inferred different selective pressures for each. Group 1 contains AtbZIP19 and AtbZIP23 and appears more conserved, whereas Group 2, containing AtbZIP24, is more prone to gene loss and expansion events. Transcriptomic and experimental data reinforced AtbZIP19/23 as pivotal regulators of the zinc deficiency response, mostly via the activation of genes from the ZIP metal transporter family, and revealed that they are the main regulatory switch of AtZIP4. A survey of AtZIP4 orthologs promoters across different plant taxa revealed an enrichment of the Zinc Deficiency Response Element (ZDRE) to which both AtbZIP19/23 bind. Overall, our results indicate that while the AtbZIP24 function in the regulation of the salt stress response may be the result of neo-functionalization, the AtbZIP19/23 function in the regulation of the zinc deficiency response may be conserved in land plants (Embryophytes).
Pedro Humberto Castro; Grmay Hailu Lilay; Antonio Muñoz-Mérida; Jan K. Schjoerring; Herlander Azevedo; Ana G. L. Assunção. Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants. Scientific Reports 2017, 7, 1 -14.
AMA StylePedro Humberto Castro, Grmay Hailu Lilay, Antonio Muñoz-Mérida, Jan K. Schjoerring, Herlander Azevedo, Ana G. L. Assunção. Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants. Scientific Reports. 2017; 7 (1):1-14.
Chicago/Turabian StylePedro Humberto Castro; Grmay Hailu Lilay; Antonio Muñoz-Mérida; Jan K. Schjoerring; Herlander Azevedo; Ana G. L. Assunção. 2017. "Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants." Scientific Reports 7, no. 1: 1-14.
Plant sumoylation research has seen significant advances in recent years, particularly since high-throughput proteomics strategies have enabled the discovery of hundreds of potential SUMO targets and interactors of SUMO pathway components. In the present chapter, we introduce the SUMO Gene Network (SGN), a curated assembly of Arabidopsis thaliana genes that have been functionally associated with sumoylation, from SUMO pathway components to targets and interactors. The enclosed tutorial helps interpret and manage these datasets, and details bioinformatics tools that can be used for in silico-based hypothesis generation. The latter include tools for sumoylation site prediction, comparative genomics, and gene network analysis.
Pedro Humberto Castro; Miguel Ângelo Santos; Alexandre Papadopoulos Magalhães; Rui Manuel Tavares; Herlânder Azevedo; L. Maria Lois; Rune Matthiesen. Bioinformatics Tools for Exploring the SUMO Gene Network. Advanced Structural Safety Studies 2016, 1450, 285 -301.
AMA StylePedro Humberto Castro, Miguel Ângelo Santos, Alexandre Papadopoulos Magalhães, Rui Manuel Tavares, Herlânder Azevedo, L. Maria Lois, Rune Matthiesen. Bioinformatics Tools for Exploring the SUMO Gene Network. Advanced Structural Safety Studies. 2016; 1450 ():285-301.
Chicago/Turabian StylePedro Humberto Castro; Miguel Ângelo Santos; Alexandre Papadopoulos Magalhães; Rui Manuel Tavares; Herlânder Azevedo; L. Maria Lois; Rune Matthiesen. 2016. "Bioinformatics Tools for Exploring the SUMO Gene Network." Advanced Structural Safety Studies 1450, no. : 285-301.
Sumoylation is an essential post-translational regulator of plant development and the response to environmental stimuli. SUMO conjugation occurs via an E1-E2-E3 cascade, and can be removed by SUMO proteases (ULPs). ULPs are numerous and likely to function as sources of specificity within the pathway, yet most ULPs remain functionally unresolved. In this report we used loss-of-function reverse genetics and transcriptomics to functionally characterize Arabidopsis thaliana ULP1c and ULP1d SUMO proteases. GUS reporter assays implicated ULP1c/d in various developmental stages, and subsequent defects in growth and germination were uncovered using loss-of-function mutants. Microarray analysis evidenced not only a deregulation of genes involved in development, but also in genes controlled by various drought-associated transcriptional regulators. We demonstrated that ulp1c ulp1d displayed diminished in vitro root growth under low water potential and higher stomatal aperture, yet leaf transpirational water loss and whole drought tolerance were not significantly altered. Generation of a triple siz1 ulp1c ulp1d mutant suggests that ULP1c/d and the SUMO E3 ligase SIZ1 may display separate functions in development yet operate epistatically in response to water deficit. We provide experimental evidence that Arabidopsis ULP1c and ULP1d proteases act redundantly as positive regulators of growth, and operate mainly as isopeptidases downstream of SIZ1 in the control of water deficit responses.
Pedro Humberto Castro; Daniel Couto; Sara Freitas; Nuno Verde; Alberto P. Macho; Stéphanie Huguet; Miguel Angel Botella; Javier Ruiz-Albert; Rui Manuel Tavares; Eduardo Rodríguez Bejarano; Herlânder Azevedo. SUMO proteases ULP1c and ULP1d are required for development and osmotic stress responses in Arabidopsis thaliana. Plant Molecular Biology 2016, 92, 143 -159.
AMA StylePedro Humberto Castro, Daniel Couto, Sara Freitas, Nuno Verde, Alberto P. Macho, Stéphanie Huguet, Miguel Angel Botella, Javier Ruiz-Albert, Rui Manuel Tavares, Eduardo Rodríguez Bejarano, Herlânder Azevedo. SUMO proteases ULP1c and ULP1d are required for development and osmotic stress responses in Arabidopsis thaliana. Plant Molecular Biology. 2016; 92 (1):143-159.
Chicago/Turabian StylePedro Humberto Castro; Daniel Couto; Sara Freitas; Nuno Verde; Alberto P. Macho; Stéphanie Huguet; Miguel Angel Botella; Javier Ruiz-Albert; Rui Manuel Tavares; Eduardo Rodríguez Bejarano; Herlânder Azevedo. 2016. "SUMO proteases ULP1c and ULP1d are required for development and osmotic stress responses in Arabidopsis thaliana." Plant Molecular Biology 92, no. 1: 143-159.
Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1]. This information should contribute to the development of plant-based solutions with improved nutrient-use-efficiency traits in crops. Previously, the transcription factors bZIP19 and bZIP23 were identified as essential regulators of the response to zinc deficiency in Arabidopsis thaliana [2]. A microarray experiment comparing gene expression between roots of wild-type and the mutant bzip19 bzip23, exposed to zinc deficiency, led to the identification of differentially expressed genes related with zinc homeostasis, namely its transport and plant internal translocation [2]. Here, we provide the detailed methodology, bioinformatics analysis and quality controls related to the microarray gene expression profiling published by Assunção and co-workers [2]. Most significantly, the present dataset comprises new experimental variables, including analysis of shoot tissue, and zinc sufficiency and excess supply. Thus, it expands from 8 to 42 microarrays hybridizations, which have been deposited at the Gene Expression Omnibus (GEO) under the accession number GSE77286. Overall, it provides a resource for research on the molecular basis and regulatory events of the plant response to zinc supply, emphasizing the importance of Arabidopsis bZIP19 and bZIP23 transcription factors.
Herlânder Azevedo; Sarah Gaspar Azinheiro; Antonio Muñoz-Mérida; Pedro Humberto Castro; Bruno Huettel; Mark G.M. Aarts; Ana G.L. Assunção. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply. Genomics Data 2016, 7, 256 -258.
AMA StyleHerlânder Azevedo, Sarah Gaspar Azinheiro, Antonio Muñoz-Mérida, Pedro Humberto Castro, Bruno Huettel, Mark G.M. Aarts, Ana G.L. Assunção. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply. Genomics Data. 2016; 7 ():256-258.
Chicago/Turabian StyleHerlânder Azevedo; Sarah Gaspar Azinheiro; Antonio Muñoz-Mérida; Pedro Humberto Castro; Bruno Huettel; Mark G.M. Aarts; Ana G.L. Assunção. 2016. "Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply." Genomics Data 7, no. : 256-258.
Quercus suber (cork oak) is a West Mediterranean species of key economic interest, being extensively explored for its ability to generate cork. Like other Mediterranean plants, Q. suber is significantly threatened by climatic changes, imposing the need to quickly understand its physiological and molecular adaptability to drought stress imposition. In the present report, we uncovered the differential transcriptome of Q. suber roots exposed to long-term drought, using an RNA-Seq approach. 454 sequencing reads were used to de novo assemble a reference transcriptome, and mapping of reads allowed the identification of 546 differentially expressed unigenes. These were enriched in both effector genes (e.g. LEA, chaperones, transporters) as well as regulatory genes, including transcription factors (TFs) belonging to various different classes, and genes associated with protein turnover. To further extend functional characterization, we identified the orthologs of differentially expressed unigenes in the model species Arabidopsis thaliana, which then allowed us to perform in silico functional inference, including gene network analysis for protein function, protein subcellular localization and gene co-expression, and in silico enrichment analysis for TFs and cis-elements. Results indicated the existence of extensive transcriptional regulatory events, including activation of ABA-responsive genes and ABF-dependent signaling. We were then able to establish that all components of a core ABA-signaling pathway involving PP2C-SnRK2-ABF components was induced in stressed Q. suber roots, identifying a key mechanism in this species’ response to drought.
Alexandre P. Magalhães; Nuno Verde; Francisca Reis; Inês Martins; Daniela Costa; Teresa Lino-Neto; Pedro Humberto Castro; Rui M. Tavares; Herlânder Azevedo. RNA-Seq and Gene Network Analysis Uncover Activation of an ABA-Dependent Signalosome During the Cork Oak Root Response to Drought. Frontiers in Plant Science 2016, 6, 1195 -1195.
AMA StyleAlexandre P. Magalhães, Nuno Verde, Francisca Reis, Inês Martins, Daniela Costa, Teresa Lino-Neto, Pedro Humberto Castro, Rui M. Tavares, Herlânder Azevedo. RNA-Seq and Gene Network Analysis Uncover Activation of an ABA-Dependent Signalosome During the Cork Oak Root Response to Drought. Frontiers in Plant Science. 2016; 6 ():1195-1195.
Chicago/Turabian StyleAlexandre P. Magalhães; Nuno Verde; Francisca Reis; Inês Martins; Daniela Costa; Teresa Lino-Neto; Pedro Humberto Castro; Rui M. Tavares; Herlânder Azevedo. 2016. "RNA-Seq and Gene Network Analysis Uncover Activation of an ABA-Dependent Signalosome During the Cork Oak Root Response to Drought." Frontiers in Plant Science 6, no. : 1195-1195.
Pedro Humberto Castro; Nuno Verde; Tiago Lourenço; Alexandre Papadopoulos Magalhães; Rui Manuel Tavares; Eduardo Rodríguez Bejarano; Herlânder Azevedo. SIZ1-Dependent Post-Translational Modification by SUMO Modulates Sugar Signaling and Metabolism inArabidopsis thaliana. Plant and Cell Physiology 2015, 56, 2297 -2311.
AMA StylePedro Humberto Castro, Nuno Verde, Tiago Lourenço, Alexandre Papadopoulos Magalhães, Rui Manuel Tavares, Eduardo Rodríguez Bejarano, Herlânder Azevedo. SIZ1-Dependent Post-Translational Modification by SUMO Modulates Sugar Signaling and Metabolism inArabidopsis thaliana. Plant and Cell Physiology. 2015; 56 (12):2297-2311.
Chicago/Turabian StylePedro Humberto Castro; Nuno Verde; Tiago Lourenço; Alexandre Papadopoulos Magalhães; Rui Manuel Tavares; Eduardo Rodríguez Bejarano; Herlânder Azevedo. 2015. "SIZ1-Dependent Post-Translational Modification by SUMO Modulates Sugar Signaling and Metabolism inArabidopsis thaliana." Plant and Cell Physiology 56, no. 12: 2297-2311.
Programmed cell death is a fundamental aspect of plant development and defense. In suspension cultures of maritime pine (Pinus pinaster Ait.), cell death was associated with the simultaneous depletion of sugar and phosphate. This present work suggests that sugar rather than phosphate deprivation induced programmed cell death events, including degradation of nuclear DNA and remobilization of phosphate. However, phosphate starvation may have a synergistic effect on programmed cell death mediated by the lack of carbon source. Sugar and phosphate analogs were used to evaluate the nature of signaling events, and results suggested that programmed cell death induction by sugar starvation occurs downstream of hexokinase-based sugar sensing mechanisms, and that the synergistic effect of lack of phosphate is independent of phosphate sensing.
Herlânder Azevedo; Pedro Humberto Castro; Joana Ferreira Gonçalves; Teresa Lino-Neto; Rui Tavares. Impact of carbon and phosphate starvation on growth and programmed cell death of maritime pine suspension cells. In Vitro Cellular & Developmental Biology - Animal 2014, 50, 478 -486.
AMA StyleHerlânder Azevedo, Pedro Humberto Castro, Joana Ferreira Gonçalves, Teresa Lino-Neto, Rui Tavares. Impact of carbon and phosphate starvation on growth and programmed cell death of maritime pine suspension cells. In Vitro Cellular & Developmental Biology - Animal. 2014; 50 (4):478-486.
Chicago/Turabian StyleHerlânder Azevedo; Pedro Humberto Castro; Joana Ferreira Gonçalves; Teresa Lino-Neto; Rui Tavares. 2014. "Impact of carbon and phosphate starvation on growth and programmed cell death of maritime pine suspension cells." In Vitro Cellular & Developmental Biology - Animal 50, no. 4: 478-486.
Protein post-translational modifications diversify the proteome and install new regulatory levels that are crucial for the maintenance of cellular homeostasis. Over the last decade, the ubiquitin-like modifying peptide small ubiquitin-like modifier (SUMO) has been shown to regulate various nuclear processes, including transcriptional control. In plants, the sumoylation pathway has been significantly implicated in the response to environmental stimuli, including heat, cold, drought, and salt stresses, modulation of abscisic acid and other hormones, and nutrient homeostasis. This review focuses on the emerging importance of SUMO in the abiotic stress response, summarizing the molecular implications of sumoylation and emphasizing how high-throughput approaches aimed at identifying the full set of SUMO targets will greatly enhance our understanding of the SUMO–abiotic stress association.
Pedro Humberto Castro; Rui Tavares; Eduardo Bejarano; Herlânder Azevedo. SUMO, a heavyweight player in plant abiotic stress responses. Cellular and Molecular Life Sciences 2012, 69, 3269 -3283.
AMA StylePedro Humberto Castro, Rui Tavares, Eduardo Bejarano, Herlânder Azevedo. SUMO, a heavyweight player in plant abiotic stress responses. Cellular and Molecular Life Sciences. 2012; 69 (19):3269-3283.
Chicago/Turabian StylePedro Humberto Castro; Rui Tavares; Eduardo Bejarano; Herlânder Azevedo. 2012. "SUMO, a heavyweight player in plant abiotic stress responses." Cellular and Molecular Life Sciences 69, no. 19: 3269-3283.