Evolutionär konservierte, kleine offene Leserahmen (upstream open reading frames, uORFs) sind translational aktive Kontrollelemente, die bevorzugt in Boten-Ribonukleinsäuren von Schlüsselgenen zur Regulation von Zellwachstum, Proliferation und Differenzierung vorkommen. In dieser Arbeit wurden Mäuse analysiert, die defizient für das uORF Initiationscodon des Transkriptionsfaktors CCAAT/enhancer binding protein beta (C/EBPbeta-Delta-uORF) sind. Proteinanalysen verschiedener Gewebe zeigten, dass C/EBPbeta-Delta-uORF Mäuse im Gegensatz zu Wildtyptieren nicht in der Lage sind, die kurze, auto-antagonistische C/EBPbeta LIP Isoform zu induzieren. Die verminderte LIP Expression verursachte eine gestörte Differenzierung knochenabbauender Osteoklasten und ging mit einer Zunahme von mineralisiertem Knochengewebe in C/EBPbeta-Delta-uORF Mäusen einher. Nach partieller Hepatektomie führte der Verlust der uORF-vermittelten Induktion von LIP in regenerierenden C/EBPbeta-Delta-uORF Lebern zu einer Überaktivierung C/EBPbeta-regulierter Akute Phase Gene. Im Vergleich zum Wildtyp wiesen Hepatozyten von C/EBPbeta-Delta-uORF Tieren einen verzögerten und abgeschwächten Wiedereintritt in die S-Phase des Zellzyklus auf. Genomweite Genexpressionsanalysen zeigten, dass die verminderte S-Phase Aktivität in regenerierenden C/EBPbeta-Delta-uORF Lebern mit einer persistierenden Repression von Zellzyklusgenen korrelierte, wobei insbesondere die verminderte Expression zahlreicher E2F-regulierter Gene auffällig wurde. Chromatinimmunpräzipitations- und Reportergenexperimente führten zur Entwicklung eines mechanistischen Modells, das eine isoformspezifische C/EBPbeta-Koregulation E2F-kontrollierter Zellzyklusgene vorschlägt. Die Analyse der C/EBPbeta-Delta-uORF Mäuse belegt erstmals die Funktionalität der uORF-gesteuerten translationalen Kontrolle im Säugetier und weist auf eine entscheidende Bedeutung dieses Kontrollmechanismus bei zahlreichen physiologischen und pathopysiologischen Prozessen hin. / Evolutionary conserved small upstream open reading frames (uORFs) are translational control elements predominantly prevalent in the 5'' mRNA regions of key regulatory genes of growth, proliferation, and differentiation. This thesis comprises the evaluation of mice deficient for the uORF initiation codon of the transcription factor CCAAT/enhancer binding protein beta (C/EBPbeta-Delta-uORF). Protein analysis of various tissues demonstrated that C/EBPbeta-Delta-uORF mice, in contrast to wildtype control animals (C/EBPbeta-WT), fail to induce translation of the truncated, auto-antagonistic C/EBPbeta LIP isoform. The reduced expression of LIP was associated with impaired differentiation of bone resorbing osteclasts and resulted in an increased bone volume of C/EBPbeta-Delta-uORF mice. After partial hepatectomy the loss of uORF-mediated LIP induction resulted in super activation of acute phase response genes in regenerating livers. Furthermore, C/EBPbeta-Delta-uORF hepatocytes showed a delayed and blunted re-entry into the cell cycle after partial hepatectomy as compared to C/EBPbeta-WT animals. Genome-wide transcript expression analyses revealed that the reduced S-phase activity in regenerating C/EBPbeta-Delta-uORF livers correlated with a persistent repression of cell cycle regulatory genes and showed a remarkable underrepresentation of genes regulated by the E2F family of transcription factors. Chromatinimmunoprecipitations and luciferase reporter gene assays allowed the development of a mechanistic model that suggests C/EBPbeta isoform-specific co-regulation of E2F-controled cell cycle genes. The analysis of C/EBPbeta-Delta-uORF mice validates the functionality of uORF-mediated translational control in vertebrates and suggests a comprehensive role of uORF regulation in physiology and the etiology of disease.

Indiana University-Purdue University Indianapolis (IUPUI) / Gene expression is a highly coordinated process that relies upon appropriate regulation of translation for protein homeostasis. Regulation of protein synthesis largely occurs at the initiation step in which the translational start site is selected by ribosomes and associated initiating factors. In addition to the coding sequences (CDS) for protein products, short upstream open reading frames (uORFs) located in the 5’-leader of mRNAs are selected for translation initiation. While uORFs are largely considered to be inhibitory to translation at the downstream CDS, uORFs can also promote initiation of CDS translation in response to environmental stresses. Multiple transcripts associated with stress adaptation are preferentially translated through uORF-mediated mechanisms during activation of the Integrated Stress Response (ISR). In the ISR, phosphorylation of α subunit of the translation initiation factor eIF2α (eIF2α~P) during environmental stresses results in a global reduction in protein synthesis that functions to conserve energy and nutrient resources and facilitate reprogramming of gene expression. Many key regulators of the ISR network are subject to preferential translation in the response to eIF2α-P. These preferentially translated genes include the pro-apoptotic transcriptional activator Chop that modifies gene expression programs, feedback regulator Gadd34 that targets the catalytic subunit of protein phosphatase 1 to dephosphorylate eIF2α~P, and glutamyl-prolyl tRNA synthetase Eprs that increases the charged tRNA pool and primes the cell for resumption of protein synthesis after stress remediation. Ribosome bypass of at least one inhibitory uORF is a common theme between Chop, Gadd34, and Eprs, which allows for their regulated expression in response to cellular stress. However, different features encoded within the uORFs of the Chop, Gadd34, and Eprs mRNAs provide for regulation of their inhibitory functions, illustrating the complexities of uORF-mediated regulation of gene-specific translation. Importantly, preferentially translated ISR targets can also be transcriptionally regulated in response to cellular stress and misregulation of transcriptional or translational expression of Gadd34 can elicit maladaptive cell responses that contribute to disease. These mechanisms of translation control are conserved throughout species, emphasizing the importance of translation control in appropriate gene expression and the maintenance of protein homeostasis and health in diverse cellular conditions.

Multidrug resistance protein 2 (MRP2) is the second member the C subfamily in the superfamily of adenosine triphosphate (ATP)-binding cassette (ABC) efflux transporters. MRP2 is a critical player for generation of bile acidindependent bile flow and biliary excretion of glutathione, glucuronate and sulfate conjugates of endo- and xenobiotics. Dysfunctional expression of MRP2 is associated with Dubin-Johnson Syndrome. Pathological and physiological states or xenobiotics change the MRP2 expression level. Under some conditions, expression of the human MRP2 and rat Mrp2 proteins are regulated at the translation level. There are several transcription initiation sites in MRP2/Mrp2 gene. The 5’ untranslated regions (5’UTRs) of MRP2/Mrp2 contains multiple translation start codons. The focus of this study, therefore, was investigation of the translational regulatory mechanisms mediated by the upstream open reading frames (uORF) of MRP2/Mrp2. Using in vitro translation assays and transient cotransfection assays in HepG2 cells, we showed that the rat uORF1 starting at position -109 (relative to the ATG of Mrp2) and the human uORF2 starting at position -105 (relative to the ATG of MRP2) are two major cis-acting inhibitors of translation among the rat and human multiple uORFs, respectively. Translational regulation mediated by the uORFs in the rat Mrp2 mRNA is a combined effect of the leaky scanning model and the reinitiation model, and also results from interaction of the multiple uORFs. In addition, by Ribonuclease Protection Assays (RPA), we detected multiple transcription initiation sites of MRP2/Mrp2 gene in tissues. We also found that the relative abundance of the rat Mrp2 mRNA isoforms with different 5’UTRs differed in the rat liver, kidney, jejunum, ileum, placenta, and lung. This is the first study on the translational regulatory mechanisms of the MRP2/Mrp2 gene.

[ES] El correcto desarrollo de tejidos vasculares depende del ajuste preciso entre la proliferación de células vasculares y la diferenciación celular. En Arabidopsis thaliana, la proliferación de células vasculares en el cambium es potenciada por la citoquinina, la síntesi de la cual está promovida por la actividad dependiente de auxina de un heterodímero de factores de transcripción (TF) formado por LONESOME HIGHWAY (LHW) y por TARGET OF MONOPTEROS 5 (TMO5). Como mecanismo de seguridad, las auxinas también activan un módulo inhibidor que implica la inducción precisa de la Termospermina (Tspm) sintasa ACAULIS5 (ACL5) en células vasculares proliferantes por acción conjunta de las auxinas y del TF Class III HD-ZIP (C3HDZ) AtHB8. Entonces, la Tspm permite la traducción de las proteínas SACL de forma celular autónoma, que perjudican la actividad de LHW. Sin embargo, la observación de que estos elementos están presentes en los genomas de todas las plantas terrestres - y no sólo de las plantas vasculares - plantea dos preguntas desde una perspectiva evolutiva: (i) ¿cuál es la función de estos genes en las plantas terrestres no vasculares? y (ii) ¿cuándo se creó el módulo regulador concreto? En esta Tesis, mediante la combinación de análisis filogenéticos, celulares y moleculares con la hepática Marchantia polymorpha, proponemos que la auxina y C3HDZ son reguladores ancestrales de la expresión de ACL5, y que esta conexión se mantiene en las traqueófitas y las briófitas existentes. Por el contrario, la traducción dependiente de Tspm de SACL parece ser específica de las traqueófitas, basado en la aparición de un uORF conservado en la secuencia 5' líder de los tránscritos de SACL y en evidencia experimental basada en ensayos transitorios para la traducción de SACL. De acuerdo con estas observaciones, las funciones de MpACL5 y MpSACL son diferentes en M. polymorpha. MpACL5 se expresa en "notches" apicales y modula la bifurcación de los meristemos. Por otro lado, la expresión de MpSACL está mayoritariamente excluida de los "notches" apicales y su actividad afecta negativamente la producción de gemas y rizoides mediante la interacción con MpRSL1. Finalmente, la hibridación de ARN in situ de ortólogos de C3HDZ, ACL5 y SACL en la gimnosperma Ginkgo biloba, el helecho Ceratopteris richardii y la licófita Selaginella kraussiana indican que la expresión de los tres genes se solapa en los tejidos vasculares. Nuestros resultados sugieren que la función de C3HDZ, ACL5 y SACL ha seguido trayectorias evolutivas divergentes en briófitas y traqueófitas, para controlar, finalmente, diferentes funciones específicas dentro de cada linaje. Sólo en las traqueófitas se formó el módulo regulador y se asoció con la restricción de la proliferación de células vasculares. / [CA] El correcte desenvolupament dels teixits vasculars depèn del precís ajust entre la proliferació de cèl·lules vasculars i la diferenciació cel·lular. En Arabidopsis thaliana, la proliferació de cèl·lules vasculars al càmbium és potenciada per la citoquinina, la síntesi de la qual està promoguda per l'activitat dependent d'auxina d'un heterodímer de factors de transcripció (TF) format per LONESOME HIGHWAY (LHW) i TARGET OF MONOPTEROS 5 (TMO5). Com a mecanisme de seguretat, l'auxina també activa un mòdul inhibidor que implica la inducció precisa de la Termospermina (Tspm) sintasa ACAULIS5 (ACL5) en cèl·lules vasculars proliferants per l'acció conjunta de l'auxina i del TF Class III HD-ZIP (C3HDZ) AtHB8. Llavors, la Tspm permet la traducció de les proteïnes SACL de forma autònoma cel·lular, que perjudiquen l'activitat de LHW. Tanmateix, l'observació de que aquests elements estan presents en els genomes de totes les plantes terrestres - i no només de les plantes vasculars - planteja dues preguntes des d'una perspectiva evolutiva: (i) quina és la funció d'aquests gens en les plantes terrestres no vasculars? i (ii) quan es va crear el mòdul regulador complet? En aquesta Tesi, mitjançant la combinació d'anàlisis filogenètics, cel·lulars i moleculars amb la hepàtica Marchantia polymorpha, proposem que l'auxina i C3HDZ són reguladors ancestrals de l'expressió d'ACL5, i que aquesta connexió es mantén en els traqueòfits i briòfits existents. Per contra, la traducció depenent de Tspm de SACL sembla ser específica dels traqueòfits, basat en l'aparició d'un uORF conservat a la seqüència 5' líder dels trànscrits de SACL i en evidència experimental basada en assajos transitoris per a la traducció de SACL. D'acord amb aquestes observacions, les funcions de MpACL5 i MpSACL són diferents a M. polymorpha. MpACL5 s'expressa en "notch" apicals i modula la bifurcació dels meristems. D'altra banda, l'expressió de MpSACL està majoritàriament exclosa dels "notch" apicals i la seva activitat afecta negativament la producció de gemmes i rizoids mitjançant la interacció amb MpRSL1. Finalment, la hibridació d'ARN in situ d'ortòlegs de C3HDZ, ACL5 i SACL a la gimnosperma Ginkgo biloba, la falguera Ceratopteris richardii i el licòfit Selaginella kraussiana indica que l'expressió dels tres gens es solapa als teixits vasculars. Els nostres resultats suggereixen que la funció de C3HDZ, ACL5 i SACL va seguir trajectòries evolutives divergents en briòfits i traqueòfits, per controlar, finalment, diferents funcions específiques dins de cada llinatge. Només en els traqueòfits es va formar el mòdul regulador i es va associar amb la restricció de la proliferació de cèl·lules vasculars. / [EN] The correct development of vascular tissues depends on the precise adjustment between vascular cell proliferation and cell differentiation. In Arabidopsis thaliana, vascular cell proliferation in the cambium is enhanced by cytokinin, whose synthesis is promoted by the auxin-dependent activity of a transcription factor (TF) heterodimer formed by LONESOME HIGHWAY (LHW) and TARGET OF MONOPTEROS 5 (TMO5). As a safety mechanism, auxin also deploys a negative feedforward regulatory module which involves the precise induction of the Thermospermine (Tspm) synthase ACAULIS5 (ACL5) in proliferating vascular cells by the joint action of auxin and the class-III HD-ZIP (C3HDZ) AtHB8 TF. Tspm then allows the cell-autonomous translation of the SACL proteins, which impair the activity of LHW. However, the observation that these elements are present in the genomes of all land plants -and not only vascular plants- poses two questions from an evolutionary perspective: (i) what is the function of these genes in non-vascular land plants? and (ii) when was the full regulatory module assembled? In this Thesis, through the combination of phylogenetic, cellular, and molecular genetic analyses with the liverwort Marchantia polymorpha, we propose that auxin and C3HDZ are ancestral regulators of ACL5 expression, and that this connection is maintained in extant tracheophytes and bryophytes. On the contrary, thermospermine-dependent translation of SACL seems to be specific of tracheophytes, based on the appearance of a conserved uORF in the 5' leader sequence of SACL transcripts and on experimental evidence using transient assays for SACL translation. In agreement with these observations, the functions of MpACL5 and MpSACL are different in M. polymorpha. MpACL5 is expressed in apical notches and modulates meristem bifurcation. On the other hand, MpSACL expression is mostly excluded from apical notches and its activity negatively affects gemmae and rhizoid production through the interaction with MpRSL1. Finally, in situ RNA hibridization of C3HDZ, ACL5 and SACL orthologs in the gymnosperm Ginkgo biloba, the fern Ceratopteris richardi and the lycophyte Selaginella kraussiana indicates that the expression of the three genes overlaps in vascular tissues. Our results suggest that the function of C3HDZ, ACL5 and SACL followed divergent evolutionary trajectories in bryophytes and tracheophytes, to ultimately control different lineage-specific functions. Only in tracheophytes was the regulatory module assembled and associated with the restriction of vascular cell proliferation. / Solé Gil, A. (2023). Origin & Evolution of the C3HDZ-ACL5-SACL Regulatory Module in Land Plants [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/196681