This work presents a survey of blue-stain fungi found in Northwestern Ontario, characterization of a homing endonuclease gene within Grosmannia piceiperda and finally an examination of the introns and homing endonuclease genes found in the large ribosomal subunit gene in species of Ceratocystis; using molecular techniques and phylogenetic analysis, we studied the molecular evolution of these mobile genetic elements. The blue-stain fungi of Northwestern Ontario were identified based on phylogenic analysis of rDNA internal transcribed spacer region sequences. This data was supplemented with morphological characteristics of the fungal cultures. The second project was an examination of a LAGLIDADG homing endonuclease and its IC2 group I intron. This intron is uniquely positioned within the group I intron-encoded rps3 gene of the large subunit ribosomal RNA gene. The final chapter is an investigation of the large subunit ribosomal RNA gene in species of Ceratocystis. The 3’ segment of this gene contains several novel introns and homing endonuclease genes. There is also much diversity between strains despite their close relation on the rDNA internal transcribed spacer region phylogenetic tree. Further, our data also suggest that the single motif LAGLIDADG homing endonuclease of the rDNA mL1923 intron is likely to be an ancestor to other homing endonucleases in the area. The results of these studies demonstrate the role that these elements play in the genetic diversity observed in the blue-stain fungi.

xii, 83 p. : ill. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / My dissertation research has centered on understanding how nuclear encoded proteins affect chloroplast gene expression in higher plants. I investigated the functions of three proteins that belong to families whose members function solely or primarily in mitochondrial and chloroplast gene expression; the Whirly family (ZmWHY1) and the pentatricopeptide repeat (PPR) family (ZmPPR5 and ZmPPR10). The Whirly family is a plant specific protein family whose members have been described as nuclear DNA-binding proteins involved in transcription and telomere maintenance. I have shown that ZmWHY1 is localized to the chloroplast where it binds nonspecifically to DNA and also binds specifically to the atpF group II intron RNA. Why1 mutants show reduced atpF intron splicing suggesting that WHY1 is directly involved in atpF RNA maturation. Why1 mutants also have aberrant 23S rRNA metabolism resulting in a lack of plastid ribosomes. The PPR protein family is found in all eukaryotes but is greatly expanded in land plants. Most PPR proteins are predicted to localize to the mitochondria or chloroplasts where they are involved in many RNA-related processes including splicing, cleavage, editing, stabilization and translational control. Our results with PPR5 and PPR10 suggest that most of these activities may result directly from the unusually long RNA binding surface predicted for PPR proteins, which we have shown imparts two biochemical properties: site-specific protection of RNA from other proteins and site-specific RNA unfolding activity. I narrowed down the binding site for PPR5 and PPR10 to ∼45 nt and 19 nt, respectively. I showed that PPR5 contributes to the splicing of its group II intron ligand by restructuring sequences that are important for splicing. I used in vitro assays with purified PPR10 to confirm that PPR10 can block exonucleolytic RNA decay from both the 5' and 3' directions, as predicted by prior in vivo data. I also present evidence that PPR10 promotes translation by restructuring its RNA ligand to allow access to the ribosome. These findings illustrate how the unusually long RNA interaction surface predicted for PPR proteins can have diverse effects on RNA metabolism. This dissertation includes both previously published and unpublished co-authored material. / Committee in charge: Eric Selker, Chairperson, Biology; Alice Barkan, Advisor, Biology; Victoria Herman, Member, Biology; Karen Guillemin, Member, Biology; J. Andrew Berglund, Outside Member, Chemistry

Chemical bath deposition (CBD) is the analog in liquid phase of the well-known chemical vapor deposition technique in the vapor phase. In CBD, deposition of thin films takes place from aqueous solutions at low temperatures by a chemical reaction between dissolved precursors, with the help of a complexing agent. Among all techniques used to grow Group II-VI semiconductors, CBD has the advantage of being a simple, low temperature, and inexpensive large-area deposition technique. So far, its contribution in thin film solar cells industry has been mainly limited to growing n-type CdS and/or ZnS window layers for CdTe-based and CIGS-based solar cells. In this work we first optimize the CBD process of CdS using nitrilotriacetic acid and hydrazine as complexing agents as an alternative to ammonia. We then study the effect of the cadmium precursor on the optical/electrical properties, as well as crystal structure, morphology, and composition of CBD-CdS films. A better understanding of the CBD process of CdS as a whole has been achieved and high quality CBD-CdS films have been obtained. Next, we investigate in-situ doping of CBD-CdS with group III elements, such as B, Al, In, and Ga. The objective is to show that CBD is capable of not only growing CdS but also of doping it to reduce its resistivity and, as a result, facilitate its use in solar cells as well as other optoelectronic device fabrication. A four orders of magnitude drop of film resistivity has been achieved without a significant change in film bandgap, structure, or morphology. Finally, we test the possibility of using CBD to grow transparent conducting oxide (TCO) films, such as Al-doped ZnO films and cadmium stannate films. First, we study CBD of ZnO and later in-situ doping of ZnO using Al. High quality ZnO thin films have been grown using CBD with the help of four different complexing agents. Post heat treatment in argon ambient helped reduce resistivity of CBD-ZnO undoped films to ~ 10-1 Ω-cm. In-situ doping of such films using Al shows promising results. Such films could be an alternative to indium tin oxide (ITO) layers that are commonly used as TCO layers for solar cells. Another approach is to use CBD to grow CdO and SnO2 thin films, with the goal of obtaining Cd2SnO4 by later annealing of these two layers. Cadmium stannate is another TCO candidate that could replace ITO in the near future. We have succeeded in growing CBD-CdO thin films using three different complexing agents. Undoped CBD-CdO films with a resistivity as low as 1.01 x10-2 Ω-cm and a carrier density as high as 2.59 x 1020 cm-3 have been obtained. SnO2 films have been successfully grown using CBD. Fabrication of Cadmium stannate thin films using CBD is investigated. In summary, our objective to expand the use of CBD beyond just growing CdS and ZnS, and to test the possibility of using it for in-situ doping of group II-VI semiconductors as well as TCO layers fabrication proved to be successful. We believe that this may have a significant impact on solar cells as well as other optoelectronic devices fabrication industry, due to the simplicity and the cost-effectiveness of CBD.

The paper describes the comparison and the difference of modern hydraulic fluids compared to conventional hydraulic fluids. A comparison of different base oil groups, solvent neutrals, group I and comparison with hydrotreated/hydroprocessed group II and/or group III base oils is presented. The influence on oxidation stability, elastomer compatibility, carbon distribution and physical properties is outlined.

Les introns de groupe II forment une classe d’ARN connus avant tout pour leur activité ribozymique, qui leur permet de catalyser leur propre réaction d’épissage. Sous certaines conditions, ces introns peuvent s’exciser des ARN précurseurs dont ils font partie et assurer la ligation des exons qui les bordent sans l’aide d’aucune protéine. Les introns de groupe II sont généralement excisés sous forme d’un lariat, semblable à celui formé par les introns des prémessagers nucléaires, dont l’épissage est assurée par le spliceosome. De telles similarités dans le mécanisme d’épissage suggèrent que les introns de groupe II et les introns des prémessagers nucléaires pourraient avoir un ancêtre évolutif commun.Malgré leurs séquences très diverses, les introns de groupe II peuvent être définis par une structure secondaire commune, hautement conservée. Celle-ci est formée de six domaines (domaine I à domaine VI ; D1-D6), émergeant d’une roue centrale. L’épissage des introns de groupe II comprend deux étapes, et autant de réactions de transestérification, qui produisent les exons liés et l’intron excisé sous forme lariat. Il est généralement admis que la structure du ribozyme subit des changements conformationnels entre les deux étapes de l’épissage et que le domaine VI est un acteur clé dans ce phénomène. Cependant, malgré l’identification d’un certain nombre d’interactions tertiaires entre domaines, ni la RMN, ni les études faisant appel à des modifications chimiques ne sont parvenues à déterminer l’environnement immédiat, au niveau du site actif du ribozyme, de l’adénosine qui sert de point de branchement de la structure en lariat, ainsi que des nucléotides qui entourent cette adénosine au sein du domaine VI. A l’aide d’analyses phylogénétiques et d’une modélisation moléculaire tridimensionnelle, nous avons identifié plusieurs sections du ribozyme susceptibles de constituer le site de fixation du domaine VI au cours de l’étape de branchement. Des mutations ont été introduites dans ces sites de fixation potentiels et la cinétique de réaction des ARN mutants résultants a été déterminée. Afin de démontrer formellement l’interaction du domaine VI avec le site récepteur le plus probable, une molécule de ribozyme dont la réaction de branchement est assurée par l’addition d’oligonucléotides ADN ou ARN qui positionnent correctement le domaine VI vis-à-vis de son partenaire a été construite. En combinant l’information apportée par différentes expériences de ce type, nous avons pu générer un modèle à résolution atomique du complexe formé par le domaine VI, son site de branchement et le reste de l’intron au moment où l’épissage est initié. / Group II introns are a class of RNAs best known for their ribozyme-catalyzed, self-splicing reaction. Under certain conditions, the introns can excise themselves from precursor mRNAs and ligate together their flanking exons, without the aid of proteins. Group II introns generally excise from pre-mRNA as a lariat, like the one formed by spliceosomal introns, similarities in the splicing mechanism suggest that group II introns and nuclear spliceosomal introns may share a common evolutionary ancestor.Despite their very diverse primary sequences, group II introns are defined by a highly conserved secondary structure. This generally consists of six domains (Domain I-Domain VI; D1-D6) radiating from a central wheel. Each of the six intronic domains has a specific role in folding, conformational rearrangements or catalysis. The native conformation of a group II intron is sustained by intra- and interdomain long-range tertiary interactions, which are critical either for folding of the intron to the native state or for its catalytic activity. In brief, Domain V interacts with Domain I to form the minimal catalytic core; Domain VI contains a highly conserved bulged adenosine serving as the branch-point nucleotide. DII and Domain III contribute to RNA folding and catalytic efficiency. Domain IV, which encodes the intron ORF, is dispensable for ribozyme activity.Group II intron splicing proceeds through two step transesterification reactions which yield ligated exons and an excised intron lariat. It is initiated by the 2’-hydroxyl group of the bulged adenosine within Domain 6, which serves as a branch point and attacks the phosphate at the 5’-end of the intron, thus releasing the 5’-exon while forming a lariat structure in the first step. The released 5’-exon, which is bound to the intron through base pairing interactions, is then positioned correctly to attack the 3’-splice site with its free 3’-OH in the second step of splicing. It is generally believed that the structure of a group II ribozyme undergoes conformational rearrangements between first step and second step and domain VI must play a central role in the process. However, despite the identification of several interdomain tertiary interactions, neither NMR nor chemical probing studies have been successful in determining the local surroundings of the branch-point adenosine and neighboring domain VI nucleotides in the ribozyme active site. By using phylogenetic analysis and molecular modelling, we have identified several areas of the molecule which have the potential to constitute the docking site of domain VI. Mutations were introduced in putative binding sites and the resulting, mutant RNAs have been kinetically characterized. This has allowed us to identify a site within the ribozyme that appears to be specifically involved in the branching reaction. In order to further investigate the interaction between that site and domain VI, we set up a system in which the docking of domain VI into its presumed binding site is ensured by the addition of DNA/RNA oligos that position the two RNA elements in an appropriate orientation. By combining the information from such experiments, we have built an atomic-resolution model of the complex formed by domain VI, the branch site and the rest of the intron at the time at which splicing is initiated.

Die chloroplastidäre Genexpression ist durch charakteristische posttranskriptionelle Ereignisse, wie RNA-Prozessierung, RNA-Stabilität, RNA-Edierung oder RNA-Spleißen gekennzeichnet. Diese Prozesse werden fast ausnahmslos durch kernkodierte Proteine realisiert. PPR-Proteine (Pentatricopeptid repeat) stellen unter diesen kernkodierten Faktoren die größte Proteinfamilie dar. Das plastidäre Protein P67 gehört zur kleinen Untergruppe der PPR-Proteine mit SMR-Domäne (small MutS-related), deren molekulare Funktion im organellären Nukleinsäuremetabolismus bislang unverstanden ist. P67 zeigt eine nahe Verwandtschaft zu GUN1, einem zentralen Bestandteil retrograder Signalwege. Der hier analysierte P67-Knockout in Mais verursacht hellgrüne Phänotypen, eine drastische Reduktion der plastidären ATPase und Keimlingsletalität, was die essentielle Beteiligung von P67 an den Prozessen der Chloroplastenbiogenese und der Expression der plastidär kodierten ATPase-Untereinheiten vermuten lässt. Mögliche Implikationen eines fehlenden Phänotyps von Mutanten des P67-Orthologs aus Arabidopsis thaliana werden diskutiert. Eine Ausnahmestellung unter den Proteinen des chloroplastidären RNA-Metabolismus nimmt der einzige plastidär kodierte RNA-Reifungsfaktor MatK ein. Die genomische Position des matK-Gens im Intron der trnK-UUU ist in allen grünen Landpflanzen konserviert. MatK ist mit bakteriellen Maturasen verwandt, die spezifisch den Spleißprozess ihres Heimatintrons unterstützen. Dagegen deuten genetische und phylogenetische Studien zusätzliche MatK-Funktionen in trans an. In der vorliegenden Arbeit wird die spezifische Interaktion von MatK mit sieben Gruppe-IIA-Intron enthaltenden Transkripten in vivo gezeigt. Darunter befinden sich vier tRNA-Vorläufer (trnK-UUU mit dem matK-Heimatintron sowie trnV-UAC, trnI-GAU, trnA-UGC) und drei proteinkodierende Vorläufertranskripte (rpl2, rps12, atpF). Die Feinkartierung der MatK-Bindung im trnK-Heimatintron zeigt eine Assoziation mit multiplen Regionen. Organelläre Gruppe-II-Introns gelten als Vorläufer der spleißosomalen Introns. Die Assoziation mit multiplen Gruppe-II-Introns macht MatK somit zu einem interessanten Modell für die Evolution der transaktiven Spleißaktivität im Kern. Analysen der Expression von MatK und seinen Zielen deuten auf ein komplexes Muster möglicher regulativer Interaktionen hin. / Chloroplast gene expression is characterized by posttranscriptional events including RNA cleavage, RNA stability, RNA editing, and RNA splicing. The underlying processing machinery is almost exclusively encoded in the nucleus. PPR proteins (pentatricopeptide repeat) form the biggest protein family among these factors and are major players of the aforementioned posttranscriptional processes. The plastidial protein P67 is a member of a small subgroup of PPR proteins with SMR domain (small MutS-related). Molecular functions of this protein family in organellar nucleic acid metabolism are yet unknown. P67 is a close relative of GUN1, an essential component of the chloroplast to nucleus retrograde signalling pathway. It is shown here that a P67 knockout in maize causes pale green phenotypes, a dramatic reduction in ATPase levels, and seedling lethality. This indicates an essential role of P67 for chloroplast biogenesis and expression of the plastid encoded ATPase. The finding that mutants of the P67-orthologe in Arabidopsis lack a phenotype is discussed against the background of physiological differences between maize and Arabidopsis. A special case among proteins involved in plastid RNA metabolism is MatK - the only plastid encoded RNA maturation factor. The genomic position of the matK gene in the trnK-UUU intron is conserved throughout autotrophic land plants. MatK is related to bacterial maturases - highly specific splice factors supporting splice processes of their respective home introns. There is, however, indirect genetic and phylogenetic evidence that MatK acts also in trans as a common plastidial splice factor serving various group II introns. This study shows that MatK interacts specifically with seven group IIA introns in vivo. Among them are four tRNA precursor transcripts (trnK-UUU including the matK home intron as well as trnV-UAC, trnI-GAU, trnA-UGC) and three protein-coding precursors (rpl2, rps12, atpF). Fine mapping of MatK binding sites within the trnK home intron uncovers protein RNA interactions with diverse intron regions. Organellar introns have been suggested as evolutionary ancestors of nuclear spliceosomal introns. Consequently, association of MatK with multiple group II intron ligands makes the plastidial maturase an attractive model for an early trans-acting nuclear splice activity. Analyses of the expression of MatK and its targets revealed a complex pattern of possible regulatory interactions.

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

The paper describes the comparison and the difference of modern hydraulic fluids compared to conventional hydraulic fluids. A comparison of different base oil groups, solvent neutrals, group I and comparison with hydrotreated/hydroprocessed group II and/or group III base oils is presented. The influence on oxidation stability, elastomer compatibility, carbon distribution and physical properties is outlined.

No description available.

In Chloroplasten durchlaufen primäre Transkripte eine großen Anzahl von bzw. Reifungsprozesse. Diese Ereignisse spielen eine wichtige Rolle bei der Regulation der Genexpression und sind im Wesentlichen durch Proteinfaktoren, insbesondere RNA-Bindeproteine, reguliert. Der plastidäre Spleißfaktor MatK zählt zu den prokaryotischen Gruppe-II-Intron. MatK aus Nicotiana tabacum interagiert mit seinem Heimatintron trnK und sechs weiteren Gruppe IIA Introns. In dieser Untersuchung, MatK-Bindestellen konnten unterschiedlichen Regionen der Gruppe-II-Introns zugewiesen werden mit RIP-seq in Nicotiana tabacum. Die vorliegenden Ergebnisse zeigen, dass MatK im Vergleich zu seinen bakteriellen Vorfahren an Vielseitigkeit in der RNA-Erkennung gewonnen hat. MatK zeigt somit beispielhaft, wie eine Maturase die Fähigkeit erworben haben könnte, in trans auf mehrere Introns zu wirken. Quantitative Untersuchung und mathematische Modellierung der Expression von MatK und dessen Zielen offenbart ein komplexes Muster möglicher regulatorischer Feedback-Mechanismen. In dieser Studie konnte ein möglicher Feedback- Mechanismus durch Analyse von polysomal gebundenen Transkripten ausgeschlossen werden. Stabile Bindung von Proteinen an spezifische RNA-Bindestellen und anschließender Abbau der ungeschützten RNA kann zu Akkumulation von kleinen RNAs (sRNAs) führen. Solche Footprints von RNA-Bindeproteinen wurden durch die Untersuchung von Datensätzen kleiner RNAs in Chlamydomonas reinhardtii identifiziert. Zwei der sRNAs entsprechen den 5'' Enden der reifen psbB und psbH mRNAs. Beide sRNAs sind abhängig von Mbb1, einem TPR (Tetratrico-peptide repeat) Protein. Die beiden sRNAs besitzen eine hohe Ähnlichkeit in ihrer Primärsequenz und fehlen in der mbb1 Mutante. Dies legt nahe, dass auch andere der hier identifizierten sRNAs an 5'' Enden plastidärer mRNAs Protein-Bindestellen repräsentieren, die für die korrekte RNA-Prozessierung und RNA-Stabilisierung in Chlamydomonas Chloroplasten erforderlich sind. / In chloroplasts, primary transcripts are subjected to a number of processing events. These events play important roles in the regulation of gene expression and are extensively controlled by protein factors, especially by RNA-binding proteins. Chloroplast splicing factor MatK is related to prokaryotic group II intron maturases. Nicotiana tabacum MatK interacts with its home intron trnK and six additional group IIA introns. In this study, binding sites of MatK were narrowed down to varying regions of its group II targets by RIP-seq in Nicotiana tabacum. The results obtained demonstrate that MatK has gained versatility in RNA recognition relative to its bacterial ancestors. MatK thus exemplifies how a maturase could have gained the ability to act in trans on multiple introns during the dispersion of the group II introns through the eukaryotic genome early in the eukaryote evolution. Quantitative investigation and mathematical modeling of the expression of MatK and its targets revealed a complex pattern of possible feedback regulatory interactions. In this study, one possible feedback regulation mechanism was ruled out by the analysis of polysome associated transcripts. Stable binding of proteins to specific RNA sites and subsequent degradation of the unprotected RNA regions can result in small RNA, footprint of the RNA binding protein. Such footprints were identified by examining small RNA datasets of Chlamydomonas reinhardtii. Two of the sRNAs correspond to the 5’ ends of mature psbB and psbH mRNAs. Both sRNAs are dependent on Mbb1, a nuclear-encoded TPR (Tetratrico-peptide repeat) protein. The two sRNAs have high similarity in primary sequence, and both are absent in the mbb1 mutant. This suggests that sRNAs at the 5’ ends of chloroplast mRNAs identified here generally represent the binding sites of proteins, which function in RNA processing and RNA stabilization in Chlamydomonas chloroplast.