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In order to develop hypotheses presented in the introduction, we have undertaken several experiments, which we describe in the following chapters. The chapters have been published or submitted for publication, however for the purposes of this thesis, some of them have been adapted to make sure the thesis is a coherent stand-alone publication. Some of the chapters have been furthermore updated in order to keep them in accordance with most recent findings in the field. Chapter 2 shows the history of transcriptomics research in thermophiles and hyperthermophiles. We look at a wide range of research questions that transcriptome allows answering and showcase some of the most influential research on thermophile transcriptomics in last decades. Chapter 3 describes the multi-omics toolbox we developed for S. solfataricus research. Standardisation of methodology is a key aspect when it comes to combining experimental work and modelling, we propose a complete collection of methods together with results showing the S. solfataricus Central Carbon Metabolism in shifting temperatures. Chapter 4 focuses on the poorly studied and potentially important membrane proteome of S. solfataricus. We show that better methods allow us elucidating the composition of membrane proteome, and from there, its function. We detect and increased the number of membrane peptides and show a differential protein pattern after cultivation at optimal and at suboptimal temperatures. Chapter 5 addresses the transcription regulation within the S. solfataricus genome. Based on the results from previous chapters we find a putative regulatory sequence responsive to the temperature change and confirm the transcription patterns using RT-qPCR. Chapter 6 looks at experimental evolution as a tool for confirming adaptive traits in S. solfataricus. Looking at sub and super-optimal growth temperatures we try to elucidate whether the selection in fluctuating conditions is selecting for a more generalist growth pattern as opposed to constant selective pressure, which should result in selection for specialists in a given condition. Chapter 7 presents the general conclusions of this thesis focusing on multi approach strategy of looking at biological systems. We try to show how combination of complementary techniques driven by an overreaching hypothesis can aid in finding answers unattainable otherwise. We focus on the links between the previous chapters and propose how findings from one experiment can drive further research.

Zooming in: from multi-omics to single function in hyperthermophilic archaeon Sulfolobus solfataricus