An overview of how rubisco and carbohydrate metabolism may be regulated at elevated atmospheric [CO2] and temperature

Selostus: Hiilihydraatti- ja proteiiniaineenvaihdunnan säätely kohonneen hiilidioksidipitoisuuden ja lämpötilan vallitessa

Functional studies on bacterial nucleotide-regulated inorganic pyrophosphatases

CBS domains are ~60 amino acid tandemly repeated regulatory modules forming a widely distributed domain superfamily. Found in thousands of proteins from all kingdoms of life, CBS domains have adopted a variety of functions during evolution, one of which is regulation of enzyme activity through binding of adenylate-containing compounds in a hydrophobic cavity. Mutations in human CBS domain-containing proteins cause hereditary diseases. Inorganic pyrophosphatases (PPases) are ubiquitous enzymes, which pull pyrophosphate (PPi) producing reactions forward by hydrolyzing PPi into phosphate. Of the two nonhomologous soluble PPases, dimeric family II PPases, belonging to the DHH family of phosphoesterases, require a transition metal and magnesium for maximal activity. A quarter of the almost 500 family II PPases, found in bacteria and archaea, contain a 120-250 amino acid N-terminal insertion, comprised of two CBS domains separated in sequence by a DRTGG domain. These enzymes are thus named CBS-PPases. The function of the DRTGG domain in proteins is unknown. The aim of this PhD thesis was to elucidate the structural and functional differences of CBS-PPases in comparison to family II PPases lacking the regulatory insert. To this end, we expressed, purified and characterized the CBS-PPases from Clostridium perfringens (cpCBS-PPase) and Moorella thermoacetica (mtCBS-PPase), the latter lacking a DRTGG domain. Both enzymes are homodimers in solution and display maximal activity against PPi in the presence of Co2+ and Mg2+. Uniquely, the DRTGG domain was found to enable tripolyphosphate hydrolysis at rates similar to that of PPi. Additionally, we found that AMP and ADP inhibit, while ATP and AP4A activate CBSPPases, thus enabling regulation in response to changes in cellular energy status. We then observed substrate- and nucleotide-induced conformational transitions in mtCBS-PPase and found that the enzyme exists in two differentially active conformations, interconverted through substrate binding and resulting in a 2.5-fold enzyme activation. AMP binding was shown to produce an alternate conformation, which is reached through a different pathway than the substrate-induced conformation. We solved the structure of the regulatory insert from cpCBS-PPase in complex with AMP and AP4A and proposed that conformational changes in the loops connecting the catalytic and regulatory domains enable activity regulation. We examined the effects of mutations in the CBS domains of mtCBS-PPase on catalytic activity, as well as, nucleotide binding and inhibition.

Novel CO2 Regulated Proteins in Synechocystis PCC 6803

The large biodiversity of cyanobacteria together with the increasing genomics and proteomics metadata provide novel information for finding new commercially valuable metabolites. With the advent of global warming, there is growing interest in the processes that results in efficient CO2 capture through the use of photosynthetic microorganisms such as cyanobacteria. This requires a detailed knowledge of how cyanobacteria respond to the ambient CO2. My study was aimed at understanding the changes in the protein profile of the model organism, Synechocystis PCC 6803 towards the varying CO₂ level. In order to achieve this goal I have employed modern proteomics tools such as iTRAQ and DIGE, recombinant DNA techniques to construct different mutants in cyanobacteria and biophysical methods to study the photosynthetic properties. The proteomics study revealed several novel proteins, apart from the well characterized proteins involved in carbon concentrating mechanisms (CCMs), that were upregulated upon shift of the cells from high CO₂ concentration (3%) to that in air level (0.039%). The unknown proteins, Slr0006 and flavodiiron proteins (FDPs) Sll0217-Flv4 and Sll0219-Flv2, were selected for further characterization. Although slr0006 was substantially upregulated under C_i limiting conditions, inactivation of the gene did not result in any visual phenotype under various environmental conditions indicating that this protein is not essential for cell survival. However, quantitative proteomics showed the induction of novel plasmid and chromosome encoded proteins in deltaslr0006 under air level CO₂ conditions. The expression of the slr0006 gene was found to be strictly dependent on active photosynthetic electron transfer. Slr0006 contains conserved dsRNA binding domain that belongs to the Sua5/YrdC/YciO protein family. Structural modelling of Slr0006 showed an alpha/beta twisted open-sheet structure and a positively charged cavity, indicating a possible binding site for RNA. The 3D model and the co-localization of Slr0006 with ribosomal subunits suggest that it might play a role in translation or ribosome biogenesis. On the other hand, deletions in the sll0217-sll218- sll0219 operon resulted in enhanced photodamage of PSII and distorted energy transfer from phycobilisome (PBS) to PSII, suggesting a dynamic photoprotection role of the operon. Constructed homology models also suggest efficient electron transfer in heterodimeric Flv2/Flv4, apparently involved in PSII photoprotection. Both Slr0006 and FDPs exhibited several common features, including negative regulation by NdhR and ambiguous cellular localization when subjected to different concentrations of divalent ions. This strong association with the membranes remained undisturbed even in the presence of detergent or high salt. My finding brings ample information on three novel proteins and their functions towards carbon limitation. Nevertheless, many pathways and related proteins remain unexplored. The comprehensive understanding of the acclimation processes in cyanobacteria towards varying environmental CO₂ levels will help to uncover adaptive mechanisms in other organisms, including higher plants.

A new & accurate map of the North Pole with all the countries hitherto discovered situated near or adjacent to it as well as some others more remote. Drawn from the latest and best authorities and regulated by astronom.l observat.ns by Eman. Bowen.

0-meridiaani: Lontoo. - Koordinaattiasteikko: N90°-55°[50°].

Designing new learning experiences? : exploring corporate E-learners’ self-regulated learning

The context of this study is corporate e-learning, with an explicit focus on how digital learning design can facilitate self-regulated learning (SRL). The field of e-learning is growing rapidly. An increasing number of corporations use digital technology and elearning for training their work force and customers. E-learning may offer economic benefits, as well as opportunities for interaction and communication that traditional teaching cannot provide. However, the evolving variety of digital learning contexts makes new demands on learners, requiring them to develop strategies to adapt and cope with novel learning tools. This study derives from the need to learn more about learning experiences in digital contexts in order to be able to design these properly for learning. The research question targets how the design of an e-learning course influences participants’ self-regulated learning actions and intentions. SRL involves learners’ ability to exercise agency in their learning. Micro-level SRL processes were targeted by exploring behaviour, cognition, and affect/motivation in relation to the design of the digital context. Two iterations of an e-learning course were tested on two groups of participants (N=17). However, the exploration of SRL extends beyond the educational design research perspective of comparing the effects of the changes to the course designs. The study was conducted in a laboratory with each participant individually. Multiple types of data were collected. However, the results presented in this thesis are based on screen observations (including eye tracking) and video-stimulated recall interviews. These data were integrated in order to achieve a broad perspective on SRL. The most essential change evident in the second course iteration was the addition of feedback during practice and the final test. Without feedback on actions there was an observable difference between those who were instruction-directed and those who were self-directed in manipulating the context and, thus, persisted whenever faced with problems. In the second course iteration, including the feedback, this kind of difference was not found. Feedback provided the tipping point for participants to regulate their learning by identifying their knowledge gaps and to explore the learning context in a targeted manner. Furthermore, the course content was consistently seen from a pragmatic perspective, which influenced the participants’ choice of actions, showing that real life relevance is an important need of corporate learners. This also relates to assessment and the consideration of its purpose in relation to participants’ work situation. The rigidity of the multiple choice questions, focusing on the memorisation of details, influenced the participants to adapt to an approach for surface learning. It also caused frustration in cases where the participants’ epistemic beliefs were incompatible with this kind of assessment style. Triggers of positive and negative emotions could be categorized into four levels: personal factors, instructional design of content, interface design of context, and technical solution. In summary, the key design choices for creating a positive learning experience involve feedback, flexibility, functionality, fun, and freedom. The design of the context impacts regulation of behaviour, cognition, as well as affect and motivation. The learners’ awareness of these areas of regulation in relation to learning in a specific context is their ability for design-based epistemic metareflection. I describe this metareflection as knowing how to manipulate the context behaviourally for maximum learning, being metacognitively aware of one’s learning process, and being aware of how emotions can be regulated to maintain volitional control of the learning situation. Attention needs to be paid to how the design of a digital learning context supports learners’ metareflective development as digital learners. Every digital context has its own affordances and constraints, which influence the possibilities for micro-level SRL processes. Empowering learners in developing their ability for design-based epistemic metareflection is, therefore, essential for building their digital literacy in relation to these affordances and constraints. It was evident that the implementation of e-learning in the workplace is not unproblematic and needs new ways of thinking about learning and how we create learning spaces. Digital contexts bring a new culture of learning that demands attitude change in how we value knowledge, measure it, define who owns it, and who creates it. Based on the results, I argue that digital solutions for corporate learning ought to be built as an integrated system that facilitates socio-cultural connectivism within the corporation. The focus needs to shift from designing static e-learning material to managing networks of social meaning negotiation as part of a holistic corporate learning ecology.