TY - JOUR A1 - Botero, David A1 - Monk, Jonathan A1 - Rodriguez Cubillos, Maria Juliana A1 - Rodriguez Cubillos, Andres Eduardo A1 - Restrepo, Mariana A1 - Bernal-Galeano, Vivian A1 - Reyes, Alejandro A1 - Gonzalez Barrios, Andres A1 - Palsson, Bernhard O. A1 - Restrepo, Silvia A1 - Bernal, Adriana T1 - Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis BT - an approach to elucidate pathogenicity at the metabolic level JF - Frontiers in genetics N2 - Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)(+) balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species. KW - Xanthomonas KW - Xpm KW - cassava bacterial blight KW - genome-scale metabolic KW - model KW - quorum sensing Y1 - 2020 U6 - https://doi.org/10.3389/fgene.2020.00837 SN - 1664-8021 VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - THES A1 - Rodriguez Cubillos, Andres Eduardo T1 - Understanding the impact of heterozygosity on metabolism, growth and hybrid necrosis within a local Arabidopsis thaliana collection site T1 - Den Einfluss von Heterozygotie auf Stoffwechsel, Wachstum und Hybridnekrose innerhalb einer lokalen Arabidopsis thaliana-Sammelstelle verstehen N2 - Plants are unable to move away from unwanted environments and therefore have to locally adapt to changing conditions. Arabidopsis thaliana (Arabidopsis), a model organism in plant biology, has been able to rapidly colonize a wide spectrum of environments with different biotic and abiotic challenges. In recent years, natural variation in Arabidopsis has shown to be an excellent resource to study genes underlying adaptive traits and hybridization’s impact on natural diversity. Studies on Arabidopsis hybrids have provided information on the genetic basis of hybrid incompatibilities and heterosis, as well as inheritance patterns in hybrids. However, previous studies have focused mainly on global accessions and yet much remains to be known about variation happening within a local growth habitat. In my PhD, I investigated the impact of heterozygosity at a local collection site of Arabidopsis and its role in local adaptation. I focused on two different projects, both including hybrids among Arabidopsis individuals collected around Tübingen in Southern Germany. The first project sought to understand the impact of hybridization on metabolism and growth within a local Arabidopsis collection site. For this, the inheritance patterns in primary and secondary metabolism, together with rosette size of full diallel crosses among seven parents originating from Southern Germany were analyzed. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed pronounced non-additive inheritance patterns. In addition, defense metabolites, mainly glucosinolates, displayed the highest degree of variation from the midparent values and were positively correlated with a proxy for plant size. In the second project, the role of ACCELERATED CELL DEATH 6 (ACD6) in the defense response pathway of Arabidopsis necrotic hybrids was further characterized. Allelic interactions of ACD6 have been previously linked to hybrid necrosis, both among global and local Arabidopsis accessions. Hence, I characterized the early metabolic and ionic changes induced by ACD6, together with marker gene expression assays of physiological responses linked to its activation. An upregulation of simple sugars and metabolites linked to non-enzymatic antioxidants and the TCA cycle were detected, together with putrescine and acids linked to abiotic stress responses. Senescence was found to be induced earlier in necrotic hybrids and cytoplasmic calcium signaling was unaffected in response to temperature. In parallel, GFP-tagged constructs of ACD6 were developed. This work therefore gave novel insights on the role of heterozygosity in natural variation and adaptation and expanded our current knowledge on the physiological and molecular responses associated with ACD6 activation. N2 - Pflanzen sind sessile Organismen, die nicht in der Lage sind sich unerwünschten Lebensräumen zu entziehen, sodass sie sich an verschiedene Umweltbedingungen anpassen müssen. Arabidopsis thaliana (Arabidopsis) als Modellorganismus der Pflanzenbiologie war in der Lage eine Vielzahl von Lebensräumen zu kolonisieren und dabei verschiedenen biotischen und abiotischen Problemen zu trotzen. Natürliche Variation in Arabidopsis hat sich in den letzten Jahren als Mittel bewährt, um Gene zu analysieren, welche für adaptive Eigenschaften und natürliche Vielfalt verantwortlich sind. Studien über Arabidopsis-Hybride haben Erkenntnisse über die genetische Basis von Hybridinkompatibilitäten, Heterosis und Vererbungsmustern von Hybriden geliefert. Jedoch haben diese sich bisher lediglich mit globalen ökotyp befasst, sodass noch viele Informationen über Variation in einem lokalen Wachstumsgebiet fehlen. In meiner Doktorarbeit habe ich den Einfluss von Heterozygotie in einer lokalen Arabidopsis-Population und deren Rolle bei der Adaption untersucht. Dabei habe ich mich auf zwei Themen fokussiert. Beide Themen beinhalteten Arabidopsis-Hybride zwischen Individuen, welche in der Region um Tübingen in Deutschland gesammelt wurden. Das erste Projekt zielte darauf ab, den Einfluss der Hybridisierung auf den Metabolismus und das Wachstum der Pflanzen in einer lokalen Arabidopsis-Population zu verstehen. Dafür wurden das Vererbungsmuster von Primär- und Sekundärmetaboliten, sowie die Rosettengröße von diallelen Kreuzungen zwischen sieben Elternpflanzen analysiert. Im Vergleich zum Primärstoffwechsel variierten Sekundärmetabolite stärker und zeigten nicht-additive Vererbungsmuster. Zusätzlich zeigten Abwehrstoffe – hauptsächlich Glukosinolate – die höchste Abweichung vom Mittelwert beider Eltern und waren in positiver Korrelation mit der Größe der Pflanzen. In dem zweiten Projekt wurde die Rolle von ACCELERATED CELL DEATH 6 (ACD6) im Abwehrsignalweg von nekrotischen Arabidopsis-Hybriden detaillierter charakterisiert. Da die genetische Interaktion zwischen ACD6-Allelen von globalen und lokalen Arabidopsis-ökotypen bereits mit Hybridnekrose verknüpft wurde, habe ich frühe Metaboliten-, Ionen- und Expressionsänderungen von Markergenen charakterisiert, welche durch die Aktivierung von ACD6 induziert wurden. Eine Erhöhung von einfachen Zuckern und Metaboliten nicht-enzymatischer Antioxidantien und dem TCA-Zyklus wurde detektiert, sowie von Putrescin und anderen Säuren abiotischer Stressantworten. Es wurde nachgewiesen, dass Seneszenz früher in nekrotischen Hybriden induziert und zytoplasmatisches Calcium-Signaling nicht durch Temperatur beeinflusst wurde. Zusätzlich wurden GFP-markierte Konstrukte von ACD6 generiert. Zusammenfassend kann gesagt werden, dass diese Arbeit weitere Erkenntnisse über die Rolle von Heterozygotie in natürlicher Variation und Adaptation liefert und sie unser Wissen über die physiologischen und molekularen Veränderungen, verursacht durch die ACD6-Aktivierung, erweitert. KW - arabidopsis KW - diallel KW - nonadditive KW - inheritance KW - metabolism KW - variation KW - ACD6 KW - adaptation KW - defense KW - necrosis KW - Arabidopsis KW - Dialel KW - nicht additiv KW - Erbe KW - Stoffwechsel KW - Variation KW - ACD6 KW - Anpassung KW - Verteidigung KW - Nekrose Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-416758 ER - TY - JOUR A1 - Rodriguez Cubillos, Andres Eduardo A1 - Tong, Hao A1 - Alseekh, Saleh A1 - de Abreu e Lima, Francisco Anastacio A1 - Yu, Jing A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran A1 - Laitinen, Roosa A. E. T1 - Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat JF - Heredity N2 - Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed more pronounced non-additive inheritance patterns which could be attributed to epistasis. In addition, we showed that glucosinolates, among other secondary metabolites, were positively correlated with a proxy for plant size. Therefore, our study demonstrates that heterozygosity in local A. thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism. Y1 - 2018 U6 - https://doi.org/10.1038/s41437-017-0030-5 SN - 0018-067X SN - 1365-2540 VL - 120 IS - 5 SP - 463 EP - 473 PB - Nature Publ. Group CY - London ER -