In this research, important stress and redox regulatory genes present in Hydra vulgaris were isolated and characterized to facilitate our understanding of the evolution and mechanisms of stress response. H. vulgaris heat shock protein 70 (HvHSP70), extracellular copper zinc superoxide dismutase (HvECCuZnSOD), manganese superoxide dismutase (HvMnSOD), phospholipid peroxidase glutathione peroxidase (HvPHGPx) and monofunctional catalase (HvCatalase) were cloned and characterized with regard to stress response, phylogeny and molecular structure. The HSP70 gene isolated from H. vulgaris encodes a polypeptide of 650 amino acids (Mw=710,037) and is interrupted by three intron sequences. The 5' non-coding region of the HvHSP70 possessed the canonical heat shock elements. Phylogenetically HvHSP70 formed a distinct lineage. A molecular model generated for the N-terminal fragment of the HvHSP70 displayed the heat shock protein fold and domains of phosphotransferases. The EC-CuZnSOD cDNA isolated from H. vulgaris encodes a protein of 189 amino acids (Mw=20959.73); the first 19 amino acids constitute the presumed signal peptide. Phylogenetically HvEC-CuZnSOD is grouped with ECCuZnSODs from several organisms. A molecular model generated for the HvEC-CuZnSOD displayed the CuZnSOD (beta)-barrel fold. The MnSOD cDNA isolated from H. vulgaris encodes a protein of 219 amino acids (Mw=24348.75); the first 21 amino acids constitute the presumed mitochondria-targeting signal peptide. Phylogenetically HvMnSOD is clustered with mollusk and crustacean MnSODs. A molecular model generated for the HvMnSOD displayed the N-terminal long alpha antiparallel hairpin and the Cterminal mixed alpha/beta fold characteristic of MnSODs. The PHGPx gene isolated from H. vulgaris encodes a polypeptide of 168 amino acids (Mw=18746.51) including a TGA-encoded selenocysteine at residue 44 and lacks any intron. Phylogenetically HvPHGPx is grouped with PHGPxs from several organisms. A molecular model generated for the HvPHGPx displayed the thioredoxin fold. The 3'-end of a cDNA sequence encoding for 168 amino acids of the Cterminal end of a catalase was isolated from H. vulgaris. Phylogenetically HvCatalase is grouped with heme-containing monofunctional catalases. Hydrae exposed to thermal, starvation, oxidative and metal stress responded by regulating respective mRNA transcriptions suggesting that these genes are involved in stress and (anti)oxidative processes and may have potential as molecular biomarkers for assessing aquatic environment quality.

Hox genes are regulatory genes encoding small proteins containing a highly conserved 61-amino acid motif, the homeodomain, that enables Hox proteins to bind to DNA at specifically recognised binding sites and transcriptionally activate their target genes. In mammalian species there are 39 Hox genes and they are structural and functional homologs of the Drosophila homeotic complex (Horn-C). During embryogenesis and early development the Hox genes are expressed in a spatiotemporal fashion, where they operate as master transcriptional regulators. Hox genes are further expressed in fully differentiated adult cells, potentially in a tissue-specific manner involving maintenance of the normal phenotype. In selected oncogenic transformations, dysregulated Hox gene expression has been observed, indicating an involvement of these transcriptional regulators in carcinogenesis and metastasis. Utilising quantitative real-time PCR assays, these studies investigated the expression patterns of 20 Hox genes and two wellcharacterised Hox cofactors (Pbx and Meis) in malignant and non-malignant human breast and skin cancer cells. Dysregulated Hox expression was observed for all malignancies tested, of which some misexpressed Hox genes seemed random, whereas other Hox transcripts showed altered levels potentially corresponding with the invasive capacity of the cells. Also, the Hox cofactors Pbx and Meis showed no marked changes in expression levels from the non-malignant to the malignant phenotypes, indicating that it is dysregulated Hox gene expression rather than dysregulated gene expression of Hox cofactors that potentially commit the cell to redifferentiate and undergo oncogenic transformation. Although the Hox proteins are known to be key transcriptional regulators of development, the mechanisms by which they gain their in vivo functional specificity is still largely unknown. They all show strikingly similar transcriptional specificity in vitro, yet show unique specificity in their in vivo environment. This paradox has been the subject of intense scrutiny, however very few direct Hox target genes have been identified, making it a difficult task to decipher the exact manner in which Hox proteins exert their functional potential. Therefore, the studies presented herein were aimed at identifying further Hox target genes in the human system. Utilising differential display approaches, several potential downstream target genes were isolated. Substantiated with real-time PCR assays, one of these potential targets was selected as a likely direct Hox gene target, and as such subjected to further studies. By the combination of bioinformatic analyses, transfection protocols and luciferase assays, a gene encoding the SR-related protein SRrpl3O was shown to be trans-activated in vitro by HOXD4 via a putative Hox binding element within its promoter region. This is the first reported link between Hox transcription factors and the SR and SR-related family of pre-mRNA splicing proteins, offering a new and exciting insight into the complex nature of Hox functional specificity. Finally, this thesis also puts forward new ideas regarding how the Hox proteins gain their transcriptional and functional specificity. Utilising bioinformatic tools in conjunction with performing an extensive review of the disparate catalogue of Hox-related research reports, work herein offers the first comprehensive analysis of the mammalian Hox gene targets in relation to their promoter structures, as well as with respect to the expanded Hox DNA-binding elements. This work reports that identified Hox targets generally contain TATA-less core promoters, many of which have several GC-box elements. The Hox binding elements show no apparent preference regarding their location relative to the transcription start site (TSS), as they are found both upstream and downstream of the TSS, as well as being located close to proximal core promoter elements for some genes and at more distant positions in other gene promoters. Finally, the core Hox binding element TAAT/ATTA contains only part of the necessary recognition sequence involved in Hox-DNA binding, and the notion that flanking base pairs dictate trans-regulatory potential is further explored with the hypothesis that the immediate 3' base pair dictates an activator/repressor-switch of the Hox trans-regulatory effect.

‘Heterosis’ is a term used in genetics and breeding referring to hybrid vigour or the superiority of hybrids over their parents in terms of traits such as size, growth rate, biomass, fertility, yield, nutrient content, disease resistance or tolerance to abiotic and abiotic stress. Parental plants which are two different inbred (pure) lines that have desired traits are crossed to obtain hybrids. Maximum heterosis is observed in the first generation (F1) of crosses. Heterosis has been utilised in plant and animal breeding programs for at least 90 years: by the end of the 21st century, 65% of worldwide maize production was hybrid-based. Generally, it is believed that an understanding of the molecular basis of heterosis will allow the creation of new superior genotypes which could either be used directly as F1 hybrids or form the basis for the future breeding selection programmes. Two selected accessions of a research model plant Arabidopsis thaliana (thale cress) were crossed to obtain hybrids. These typically exhibited a 60-80% increase of biomass when compared to the average weight of both parents. This PhD project focused on investigating the role of selected regulatory genes given their potentially key involvement in heterosis. In the first part of the project, the most appropriate developmental stage for this heterosis study was determined by metabolite level measurements and growth observations in parents and hybrids. At the selected stage, around 60 candidate regulatory genes (i.e. differentially expressed in hybrids when compared to parents) were identified. Of these, the majority were transcription factors, genes that coordinate the expression of other genes. Subsequent expression analyses of the candidate genes in biomass-heterotic hybrids of other Arabidopsis accessions revealed a differential expression in a gene subset, highlighting their relevance for heterosis. Moreover, a fraction of the candidate regulatory genes were found within DNA regions closely linked to the genes that underlie the biomass or growth heterosis. Additional analyses to validate the role of selected candidate regulatory genes in heterosis appeared insufficient to establish their role in heterosis. This uncovered a need for using novel approaches as discussed in the thesis. Taken together, the work provided an insight into studies on the molecular mechanisms underlying heterosis. Although studies on heterosis date back to more than one hundred years, this project as many others revealed that more investigations will be needed to uncover this phenomenon. / „Heterosis“ ist ein in der Genetik und der Züchtung verwendeter Begriff, der die Hybridwüchsigkeit oder die Überlegenheit der Hybriden über ihre Eltern in Bezug auf Eigenschaften wie Größe, Wachstumsrate, Biomasse, Fruchtbarkeit, Ertrag, Nährstoffgehalt, Widerstand gegen Krankheiten oder Toleranz in Bezug auf biotischen oder abiotischen Stress bezeichnet. Um Hybriden zu erzeugen, werden aus zwei verschiedenen Inzuchtlinien (reine Linien) bestehende Elternpflanzen, welche die gewünschten Eigenschaften besitzen, miteinander gekreuzt. Der stärkste Heterosiseffekt wird in der ersten Kreuzungsgeneration (F1) beobachtet. Heterosis wird in Pflanzen- und Tierzuchtprogrammen schon seit mindestens 90 Jahren genutzt. So beruhte zum Ende des 20. Jahrhunderts 65% der weltweiten Maisproduktion auf Hybridzüchtung. Es wird angenommen, dass ein Verständnis der molekularen Grundlagen der Heterosis die Schaffung neuer, überlegener Genotypen erlaubt, die dann direkt als F1-Hybriden verwendet, oder als Grundlage für zukünftige Zucht- und Selektionsprogramme dienen können. Zwei ausgewählte Akzessionen der Modellpflanze Arabidopsis thaliana (Ackerschmalwand) wurden miteinander gekreuzt, um Hybriden zu erzeugen. Verglichen mit dem durchschnittlichen Gewicht ihren beiden Elternlinien zeigten diese eine 60-80%ige Zunahme an Biomasse. Diese Doktorarbeit befasst sich damit, die Rolle ausgewählter, regulatorischer Gene und ihre mögliche Schlüsselrolle bei der Heterosis zu untersuchen. Im ersten Teil der Arbeit wurde anhand der Gehaltsbestimmung ausgewählter Stoffwechselprodukte und Wachstumsbeobachtungen bei den Eltern und Hybriden das günstigste Entwicklungsstadium für diese Heterosisstudie bestimmt. In diesem Entwicklungsstadium wurden ungefähr 60 regulatorische Gene (d.h. Expressionsunterschiede zwischen Hybriden und Elternlinien) als Kandidaten identifiziert. Ein Großteil dieser Kandidaten waren Transkriptionsfaktoren, also Gene, die die Expression anderer Gene regulieren. Die nachfolgende Expressionsanalyse dieser Kandidatengene in Biomasse-Heterosis Hybriden anderer Arabidopsis Akzessionen zeigte bei einem Teil dieser Gene Expressionsunterschiede, die ihre Bedeutung bei der Heterosis betonen. Darüber hinaus wurde ein Teil dieser regulatorischen Kandidatengene innerhalb von DNS-Regionen gefunden, die eng mit Biomasse- oder Wachstumsheterosis in Verbindung stehen, und somit ihre Wichtigkeit in Bezug auf Heterosis unterstreichen. Weitergehende Analysen um die Rolle dieser ausgewählten regulatorischen Kandidatengene bei der Heterosis aufzuklären, waren nicht aussagekräftig genug, um ihre Rolle bei der Heterosis zu bestätigen. In der Doktorarbeit wird die Notwendigkeit neue Wege zur Aufklärung der Heterosis zu finden, diskutiert. Zusammenfassend gibt diese Doktorarbeit einen Einblick über Studien der molekularen Mechanismen, die der Heterosis zugrunde liegen. Diese Arbeit zeigt, dass obwohl Heterosis bereits seit mehr als hundert Jahren studiert wird, weitere Untersuchungen zur Aufklärung dieses Phänomens notwendig sind.

In this study, regulatory gene effects on recombinant human growth hormone (rhGH) production by Bacillus subtilis were investigated. For this purpose, firstly Bacillus strains, which are deficient in abrB, aprE, degQ, degS, degU, scoC, sinI, sinR, and spo0A genes, were selected according to the regulatory gene network of aprE gene (serine alkaline protease gene of B. subtilis) since due to the degQ promoter and the pre-signal sequence of subC gene cloned in front of the hGH gene, hGH is produced by mimicking the serine alkaline protease synthesis. R-Bacillus strains were constructed by transformation of pMK4::pre(subC)::hGH plasmid to the selected strains. Thereafter, by the laboratory scale experiments, strains having the highest hGH production capacity were determined as scoC, aprE, sinR, and degU knockout strains. Using these strains, fermentation experiments were carried out in pilot-scale bioreactor in defined medium. Effect of pH control was also investigated and the highest cell and hGH concentration was obtained by scoC knockout strain in pH controlled operation as 1.62 kg m-3 and 126 g m-3, respectively. By this strain, the overall product and cell yield on total substrate were found as 16.12 g kg-1 and 0.15 g g-1, respectively. Furthermore, the highest total protease activity was attained by degU knockout strain as 65 U cm-3. On the other hand, maximum total organic acid secretion was determined as 1.31 kg m-3 in aprE knockout strain.

Os genes Hox padronizam o corpo dos vertebrados durante o desenvolvimento embrionário, e a compreensão de sua evolução pode elucidar mecanismos genéticos subjacentes à evolução morfológica. A evolução molecular dos genes Hox imprime assinaturas em regiões regulatórias, as quais potencialmente afetam sua expressão gênica, como os elementos cis-regulatórios (CREs) que ladeiam o cluster D de Hox e seus RNAs não-codificantes (ncRNAs). Essa Tese de Doutorado enfoca a evolução regulatória de genes HoxD envolvidos no estabelecimento dos eixos corpóreos axial ântero-posterior (AP) e apendiculares em linhagens de aminiotas que exibem características morfológicas homoplásticas peculiares: os squamatas serpentiformes (Capítulos I e II) e os marsupiais Diprotodontia (Capítulo III). No Capítulo I investigou-se, em serpentes e anfisbênias, se assinaturas regulatórias envolvidas no estabelecimento das morfologias serpentiformes foram impressas na Sequência Conservada B (Conserved Sequence B, CsB), um CRE centromérico de Hoxd10-13. Usando lagartos e outros tetrápodes como referência para a morfologia serpentiforme, regiões conservadas de CsB foram sequenciadas em 38 espécies de Squamata, cujos TFBS foram preditos e comparados. Ambas linhagens serpentiformes exibem assinaturas regulatórias divergentes e convergentes ausentes em lagartos; a convergência localizou-se em um segmento de CsB que concentra perda nas linhagens serpentiformes de diversos TFBS com funções no desenvolvimento de membros e a aquisição de um sítio de ligação para PBX1. Essa assinatura convergente impressa durante evoluções independentes da morfologia serpentiforme pode estar relacionada à elongação corpórea e à perda dos membros, evidenciando um papel do CsB no desenvolvimento do eixo AP. No Capítulo II, foi investigado se um CRE telomérico (CNS65) e um centromérico (Island I) de Hoxd, os quais regulam respectivamente regiões proximais e distais dos membros tetrápodes em desenvolvimento, retêm suas capacidades regulatórias em Serpentes. Expressões de gene repórter desses CREs de serpentes foram realizadas em camundongo transgênico, revelando deficiência de suas atividades regulatórias nos brotos de membro. A comparação dos TFBS preditos nesses elementos entre serpentes e outros tetrápodes revelou que TFBS relacionados ao desenvolvimento dos membros foram perdidos nas sequências das serpentes. Ainda, essa comparação indicou um elemento em CNS65 potencialmente envolvido especificamente na regulação da formação de estilopódio/zeugopódio, e três elementos na Island I exclusivamente reguladores do desenvolvimento autopodial. A perda de membros em x serpentes aparentemente imprimiu assinaturas nesses CREs de Hoxd que possivelmente contribuíram para sua degeneração funcional, putativamente indicando módulos específicos de regulação nos membros. No Capítulo III, ncRNAs do cluster D de Hox foram estudados no contexto da evolução morfológica do autopódio posterior e heterocronia entre o desenvolvimento de membros anteriores e posteriores em Macropus eugenii. Os ncRNAs mapeados sobre o cluster D de Hox foram selecionados a partir de transcritoma de membros de embriões de M. eugenii nos dias 23 (d23) e 25 (d25) de gravidez, e sua conservação, perfis transcricionais e padrões de expressão foram explorados. A comparação com sequências ortólogas de outros mamíferos revelou cinco ncRNAs conservados em mamíferos, e três aparentemente exclusivos dos marsupiais. Os perfis transcricionais de genes HOXD10-13 e dos ncRNAs do cluster D de Hox foram predominantemente equivalentes. Os padrões de expressão de XLOC46 foi similar aos dos genes HOXD terminais de camundongo e M. eugenii, enquanto que XLOC52 e XLOC53 apresentaram expressão idêntica à desses genes em M. eugenii, exceto pela baixa expressão de XLOC53 no d25. Os ncRNAs intergênicos/intrônicos aos genes HOXD9-12 possivelmente regulam a expressão de genes HOXD terminais em mamíferos, enquanto que XLOC52 e XLOC53 constituem bons candidatos para investigação relacionada à evolução dos membros de marsupiais. Esta Tese demonstra como estudos de assinaturas regulatórias na evolução de genes do desenvolvimento contribuem para o entendimento das histórias evolutivas de divergência entre linhagens e d / Hox genes pattern the vertebrate body during embryonic development, and understanding their evolution may unravel genetic mechanisms subjacent to morphological evolution. Molecular evolution of Hox genes entails signatures in regulatory regions that potentially affect gene expression, such as the cis-regulatory elements (CREs) that surround the HoxD cluster and its noncoding RNAs (ncRNAs). In this PhD Thesis, I have explored regulatory evolution of HoxD genes engaged in the development of appendicular and anterior-posterior body (AP) axes in amniotic lineages that exhibit homoplastic morphological peculiarities: snakelike squamates (Chapters I and II) and diprotodontid marsupials (Chapter III). In Chapter I, I investigated in snakes and amphisbaenians, whether equivalent regulatory signatures were registered in the Conserved Sequence B (CsB), a centromeric Hoxd10-13 CRE, during evolution of snakelike morphologies. Using lizards and other tetrapods to represent the lacertiform morphology, conserved regions within CsB were sequenced from 38 squamate species, and transcription factor binding sites (TFBS) were predicted and compared among groups. Both snakelike lineages carry divergent and convergent regulatory signatures not identified in lizards; the convergence located in one CsB segment comprised loss of limb-related TFBS and gain of a binding site for PBX1. This convergent regulatory signature registered along two independent processes of snakelike evolution may relate to body elongation and limb loss, and evidences a role of CsB for AP axis development. In Chapter II, I investigated whether a telomeric (CNS65) and a centromeric (Island I) Hoxd enhancer that regulate gene expression respectively at proximal and distal regions of developing limbs retain their regulatory capacities in Serpentes. Gene reporter expression of these CREs from snakes were performed in transgenic mice and revealed that their regulatory activities were abrogated in limb buds. Comparison of predicted TFBS in these elements between snakes and limbed tetrapods revealed limb-related TFBS apparently lost in snakes, and pointed to one potential stilopodium/zeugopodium-specific element in CNS65 and three likely autopodium-specific elements in Island I. Limb loss in snakes registered signatures in Hoxd CREs that possibly contributed for their functional impairment, putatively indicating limb-specific modules. Finally, in the chapter III, I studied ncRNAs from HoxD cluster in the context of hindlimb morphological evolution and heterochrony between fore and hindlimb development in the tammar wallaby Macropus eugenii. The ncRNAs mapped to HoxD cluster were selected from transcriptome performed using tammar embryo limbs at days 23 (d23) and 25 (d25) of viii pregnancy, and their conservation, transcriptional profiles and expression patterns were explored. Comparison with orthologous sequences in other mammals revealed five ncRNAs conserved among mammals, and three transcripts apparently exclusive to marsupials. Transcriptional profiles of HOXD10-13 and HoxD ncRNAs were mostly equivalent. XLOC46 expression patterns resembled those of mouse and tammar terminal HOXD genes, whereas XLOC52 and XLOC53 showed identical expression patterns to those genes of tammar, except for XLOC53 low expression at d25. The ncRNAs intergenic/intronic to HOXD9-12 may regulate expression of terminal HOXD genes in mammals, and XLOC52 and XLOC53 are suitable for investigation regarding limb evolution in marsupial. This PhD Thesis demonstrates how studies of evolutionary footprints in regulatory elements of developmental genes contribute for elucidating specific processes during lineages divergence as well as functional aspects of these genes during development.