Die Transkription der Chloroplasten ist erstaunlich komplex. Ihr relativ kleines Genom kodiert für Komponenten der Photosynthese und der eigenen Genexpressionsmaschine. Es wird mindestens durch zwei RNA Polymerasen transkribiert. Neben der plastidär kodierten RNA Polymerase (PEP), existiert mindestens eine weitere kernkodierte RNA Polymerase (NEP). Die PEP spielt eine wichtige Rolle bei der Expression der Photosynthesegene und ist essentiell für die Biogenese der Chloroplasten und schließlich für das Überleben der Pflanzen. In der vorliegenden Arbeit wird erstmals die spezifische Interaktion der PEP mit ihren Transkriptionseinheiten unter verschiedenen Lichtbedingungen in vivo auf plastomweiter Ebene gezeigt. Darunter befinden sich hauptsächlich DNA Fragmente, die Photosynthesegene repräsentieren. Außerdem zeigt die PEP eine eindeutige Präferenz zu den rRNA Genen und einigen tRNA Genen. Eine Reduktion dieser Assoziation der PEP in Dunkelperioden lässt einen lichtabhängigen Prozess bei der PEP-DNA Assoziation vermuten. Außerdem wurde die PEP Aktivität an den bestimmten DNA Regionen in vivo ermittelt durch die Analyse naszierender Transkripte. Ein Großteil der plastidären RNA Spezies kopräzipitiert mit der PEP, aber sie scheint präferentiell mit tRNAs zu interagieren. Die Analyse der Verteilung der PEP bewies erstmals, dass sie hauptsächlich mit den Membranen assoziiert. Dort befindet sich auch das transkriptionsaktive Chromosom (TAC). Im TAC wurden vor kurzem neben der PEP auch Mitglieder von RNA Prozessierungsfaktoren identifiziert, was auf eine mögliche Kopplung von Transkription und posttranskriptionellen Prozessen hindeutet. Für einen Einblick in dieses Interaktionsnetzwerk wurden Transkriptanalysen des TACs ausgeführt. Mit wenigen Ausnahmen assoziieren alle plastidären RNA Spezies mit dem TAC. Einige RNAs liegen bereits prozessiert vor, was eine Verbindung zwischen Transkription und posttranskriptionellen Prozessen noch im TAC vermuten lässt. / Chloroplast transcription is astonishingly complex. The relative small genome of plastids, which codes for components of the photosynthetic machinery as well as for components of their own gene expression machinery, is transcribed by at least two different RNA polymerases. Beside the plastid-encoded plastid RNA polymerase (PEP) a nuclear-encoded plastid RNA polymerase (NEP) exists as well. PEP plays a major role in the expression of photosynthesis genes and is essential for chloroplast biogenesis and thus for plant survival. This work shows the specific in vivo interaction between PEP and its transcription units under different light conditions on a plastome-wide scale. Among them are DNA fragments that represent photosynthetic genes. In addition, PEP shows clear preferences to rRNA and tRNA genes. Furthermore, the association of PEP with photosynthesis-related genes was reduced during the dark period, indicating that PEP-DNA association is a light-dependent process. To survey PEP activity in vivo on plastid DNA regions, the association to nascent transcripts was analyzed. The majority of plastid RNA species could be found in PEP precipitates, but PEP seems to interact more strongly with tRNAs. Analysis of the suborganellar distribution of PEP shows that PEP is preferably associated with chloroplastmembranes. The transcriptionally active chromosome (TAC) was also found to be membrane-attached. Beside PEP different RNA processing factors were identified within the TAC and related purifications, indicating a possible coupling of transcription and posttranscriptional processes. To gain more insights into this interaction network, transcripts of TAC were analyzed. It is shown that nearly all plastid RNA species with only a few exceptions are associated to the TAC and that at least selected transcripts are already processed. This indicates that there is a link between transcription and posttranscriptional processes already within the TAC.

Plastid genomes of flowering plants are largely identical in gene order and content, but a few lineages have been identified with many gene and intron losses, genomic rearrangements, and accelerated rates of nucleotide substitutions. These aberrant lineages present an opportunity to understand the modes of selection acting on these genomes as well as their long-term stability. My research has focused on two areas within plastid genome evolution in Geraniaceae: first, an investigation of the diversity of unusual plastid genomes in a single genus, Erodium (Geraniaceae) for chapters one and three. Chapter two focuses on the evolution of subunits of the plastid-encoded RNA polymerase (PEP). The first chapter described the loss of plastid-encoded NADPH dehydrogenase (ndh) genes from a clade of 13 Erodium species. Divergence time estimates indicate this clade is less than 5 million years old. This recent loss of ndh genes in Erodium presents an opportunity to investigate changes in photosynthetic function through comparative biochemistry between Erodium species with and without plastid-encoded ndh genes. Second, I examined the evolution of the gene encoding the alpha subunit (rpoA) of PEP in three disparate angiosperm lineages—Pelargonium (Geraniaceae), Passiflora (Passifloraceae), and Annonaceae—in which this gene has diverged so greatly that it is barely recognizable. PEP is conserved in the plastid genomes of all photosynthetic angiosperms. I found multiple lines of evidence indicating that the genes remain functional despite retaining only ~30% sequence identity with rpoA genes from outgroups. The genomes containing these divergent rpoA genes have undergone significant rearrangement due to illegitimate recombination and gene conversion, and I hypothesized that these phenomena have also driven the divergence of rpoA. Third, I conducted a survey of plastid genome evolution in Erodium with the completion of 15 additional whole genomes. Except for Erodium and some legumes, all angiosperm plastid genomes share a quadripartite structure with large and small single copy regions (LSC, SSC) and two inverted repeats (IR). I discovered a species of Erodium that has re-formed a large inverted repeat. Demonstrating a precedent for loss and regain of the IR also impacts models of evolution for other highly rearranged plastid genomes. / text