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EF-Tu PROTEIN DOMAINS Functions and Thermostability
Šanderová, Hana ; Jonák, Jiří (advisor) ; Pichová, Iva (referee) ; Mikulík, Karel (referee)
6 % The bacterial elongation factor Tu (EF-Tu) has been extensively studied for decades as it plays a key role in protein biosynthesis. It is a model, multifunctional GTP-protein. This protein is also in the centre of interest as a possible target for new antibiotics. Moreover, the high homology in structure and function makes EF-Tu proteins suitable for the studies of evolutionary relationships between organisms and for elucidation of the structural features of adaptation to various living conditions. Furthermore, since all known EF-Tu proteins are composed of three distinct domains, they can also serve as suitable models for the understanding of domain organization in proteins. One of the main research projects of the Department of Gene Expression at the Institute of Molecular Genetics AS CR, where I did my PhD studies, was the study of the primary structure, transcription regulation and functions of bacterial elongation factors Tu from Gram positive thermophilic bacterium Bacillus stearothermophilus and from Gram negative mesophilic bacterium Escherichia coli. In this work, we focused on the structure-function relationships between EF-Tu proteins and their domains. The domain effect had been before our studies tested mainly by truncated EF-Tu forms lacking one or two domains. In contrast, we decided to...
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Jiří Mucha. Portrait of an Author
Jonák, Jiří
Studie si klade dva hlavní cíle: 1)Zachytit Muchův pohnutý život, který měl pro jeho tvorbu mnohem bezprostřednější význam, než bývá u českých spisovatelů zvykem; život charismatického umělce, dobrodruha, cestovatele, dobrovolného vězně pracovních táborů, život člověka s nekompromisními občanskými postoji, život muže, který se nebál smrti. 2) Vytipovat základní tématické okruhy Muchových děl, zdokumentovat jeho jednotlivé autorské počiny a jejich kritické ohlasy a pokusit se o objektivní zařazení autora do kontextu české poválečné literatury. Powered by TCPDF (www.tcpdf.org)
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Structural studies and tissue distribution of human GCPII and characterization of its rat and porcine orthologs
Rovenská, Miroslava ; Konvalinka, Jan (advisor) ; Jonák, Jiří (referee) ; Martásek, Pavel (referee)
Since GCPII is a potential pharmacological target, it is being extensively snrdied in many labs all around the world and these studies comprise many topics. This is minored also by this PhD thesis. The papers included here concem two major issues: 1. analysis ofGCPII structure and interactions with ligands; 2. study of CCPII distribution in tissues of human and two other species considered as potential animal models and kinetic characterization of the corresponding GCPII orthologs. Structural studies of GCPII active site and substrate binding are driven by the attempt to broaden the information that could help the rational design of novel small GCPII ligands, functioning either as inhibitors in neuronal damage or as imaging agents in cancer diagnosis. Two papers included in this thesis describe ligand binding in the GCPII active site in detail, with particular ernphasis on the Sl'pocket in one case and on the Sl pocket in the other' Based on our findings, we can describe a set of interactions goveming GCPII affinity to a substrate, accommodations that CCPII active site is capable of during ligand binding, the limits imposed on the ligand and tolerance of the enzyme to varying ligand nature. All these pieces of infomation are useful for the design of novel compounds with high affinity to GCPII' sufÍicient...
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Bacillus subtilis ribosomes: regulation of ribosomal RNA biosynthesis and identification of the new ribosomal protein YbxF
Sojka, Luděk ; Jonák, Jiří (advisor) ; Valášek, Leoš (referee) ; Lichá, Irena (referee)
1 Abstract The biology of the bacterial ribosome of gram positive bacterium Bacillus subtilis is the central point of this thesis that includes studies of both ribosomal components - ribosomal RNA (rRNA) and one of ribosomal proteins. The first part of the thesis focuses on the regulation of rRNA synthesis and the second part focuses on the identification and characterization of a new ribosomal protein, YbxF. rRNA synthesis is mostly regulated at the level of transcription initiation. Initiating nucleoside triphosphates (iNTPs) are important molecule effectors that regulate this process. Varying iNTP concentration in the cell directly affects RNA polymerase (RNAP) at rRNA promoters as these promoters are sensitive to [iNTP] in vivo. Most of the knowledge about this regulation is derived from Escherichia coli, where the rRNA promoter sequence is key for this regulation. Nevertheless, sequence characteristics of [iNTP]-regulated rRNA promoters from gram positive bacterium B. subtilis do not emulate the sequence characteristics derived from [iNTP]-regulated rRNA promoters from gram negative bacterium E. coli. Using a combination of in vitro and in vivo approaches, we determined promoter DNA elements that are responsible for [iNTP] sensitivity of ribosomal and non ribosomal promoters in B. subtilis. The second...
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Gene expression in early development of Xenopus laevis
Šindelka, Radek ; Jonák, Jiří (advisor) ; Beneš, Vladimír (referee) ; Svoboda, Petr (referee)
Everyhigherorganismconsistsof severalhundredsof differentcell types.The cell differentiationis a processwhich requireshighlypreciseregulationof mRNA productionand subsequentlyproteinsynthesis.Duringdevelopmentof an organism eachcellgainsa uniquepaletteof mRNAand proteinmolecules,whichreflectsthe cell'sfate.To understandthe basicfunction and regulationof genesthat are importantduringdevelopment,mRNA expressionprofilingis an irreplaceabletool. However, most techniquesto determine the mRNA content, such as Northern blot, microarraysand in situ hybridizationhave some limitationsin their specificity,dynamicrangeand/or sensitivity.Quantitativereal-timePCR analysis(qPCR)for nucleicacids quantificationwas introduced in the last decade and it has overcome the above mentioned drawbacks.qPCR has rapidly becomethe goldenstandardin basicresearchas well as in manyaspectsof appliedresearchsuchas moleculardiagnostic,food pathogendetectionand geneticallymodifiedorganism(GMO)analysis. We decidedto applyqPCRin studieswhere it helpsus to understandbasicbiologicalprocessesthattake placein the developingorganism.One of the focusareasof the Laboratoryof gene expressionat IMG AS CR,where Idid my PhDthesis,was the role of Src tyrosine kinasesin the early developmentof vertebratesstudied on the African clawed frog Xenopus...
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EF-Tu PROTEIN DOMAINS Functions and Thermostability
Šanderová, Hana ; Jonák, Jiří (advisor) ; Pichová, Iva (referee) ; Mikulík, Karel (referee)
6 % The bacterial elongation factor Tu (EF-Tu) has been extensively studied for decades as it plays a key role in protein biosynthesis. It is a model, multifunctional GTP-protein. This protein is also in the centre of interest as a possible target for new antibiotics. Moreover, the high homology in structure and function makes EF-Tu proteins suitable for the studies of evolutionary relationships between organisms and for elucidation of the structural features of adaptation to various living conditions. Furthermore, since all known EF-Tu proteins are composed of three distinct domains, they can also serve as suitable models for the understanding of domain organization in proteins. One of the main research projects of the Department of Gene Expression at the Institute of Molecular Genetics AS CR, where I did my PhD studies, was the study of the primary structure, transcription regulation and functions of bacterial elongation factors Tu from Gram positive thermophilic bacterium Bacillus stearothermophilus and from Gram negative mesophilic bacterium Escherichia coli. In this work, we focused on the structure-function relationships between EF-Tu proteins and their domains. The domain effect had been before our studies tested mainly by truncated EF-Tu forms lacking one or two domains. In contrast, we decided to...
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Jiří Mucha. Portrait of an Author
Jonák, Jiří
Studie si klade dva hlavní cíle: 1)Zachytit Muchův pohnutý život, který měl pro jeho tvorbu mnohem bezprostřednější význam, než bývá u českých spisovatelů zvykem; život charismatického umělce, dobrodruha, cestovatele, dobrovolného vězně pracovních táborů, život člověka s nekompromisními občanskými postoji, život muže, který se nebál smrti. 2) Vytipovat základní tématické okruhy Muchových děl, zdokumentovat jeho jednotlivé autorské počiny a jejich kritické ohlasy a pokusit se o objektivní zařazení autora do kontextu české poválečné literatury. Powered by TCPDF (www.tcpdf.org)
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Microsatellite region in the murine oncogene src - its primary structure and variability during evolution
Fučík, Vladimír ; Šindelka, Radek ; Beran, Jaroslav ; Ferjentsik, Zoltán ; Jonák, Jiří
In the fifth intron of the Mus musculus oncogene src a complex microsatellite was discovered that consists of a CA run and 31 bp apart followed by track of TG dinucleotides interrupted by extra Gs in specific intervals. As the 31 bp interlink can assume a hairpin structure, the whole region can be viewed as an imperfect inverted repeat. The microsatellite was sequenced in imbred lines of M. m. musculus and M. m. domesticus, as well as in mice of both subspecies trapped near the hybrid zone. Differences in the length of repeat regions, insertion/deletions and simple base changes characterize the strains. Hybrids between the two species could be identified by sequencing of cloned PCR products. The structure of the microsatellite in more distant species was found to be conspicuously different. Instead of frequent (CA)18-25, we can see only (CA)8 in M. spretus, CATGCGCCCCCCA in Mus pahari and CACCCCCC in Mus caroli. No similar structure is present in the corresponding human src intron.
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