Evolutionary study of plastid and mitochondrial DNA insertions into the nucleus of flowering plants
The aim of this study was to characterize the structure of functional and non-functional nuclear inserts of organelle DNA as well the expression of photosynthetic genes which are transferred during endosymbiosis into the nucleus with the final scope to determine the impact of organelle DNA on gene and genome evolution.In Chapter 1 a general description of the chloroplast organelle is given. Its functions emphasizing photosynthesis by which plants, algae, some bacteria, and protists convert the energy of sunlight to chemical energy. An overview on plastid membranes is provided as well. The origin of organelles is described. Mitochondria and chloroplast were once free living bacteria, a-proteobacteria or cyanobacteria, respectively. As a first endosymbiotic event, the mitochondrion was created by the endosymbiosis ofa proteobacteriumwith an ancestor cell containing no mitochondria. Later, a secondendosymbioticevent involving cyanobacteria and the primary ancestor cell, led to the creation of chloroplasts. Also, a description of the import machinery of chloroplasts and mitochondria is provided.In Chapter 2 as a first approach the integration of relative large insertions of organelle DNA into the nucleus was studied using Arabidopsis and rice organelles and genomes. Thirteen integrants were identified in Arabidopsis and rice genomes. Nuclear genomes are exposed to a continuous influx of DNA from mitochondria and plastids. These insertions can occur during the illegitimate repair of double stranded breaks. After integration, nuclear organelle DNA is modified by point mutations and by deletions. Overall, the numbers of insertion and deletion events after integration of the thirteensegmentsof organelle DNA into the nucleus are almost equal. Deletions are associated with the removal of DNA between perfect repeats, indicating that replication slippage has caused them. Two general types of nuclear insertions coexist; one is characterized by long sequence stretches that are colinear with organelle DNA, the other type consists of mosaics of organelle DNA, often derived from both plastids and mitochondria. The levels of sequence divergence of the two types exclude their common descent, implying that at least two independent modes of DNA transfer from organelle to nucleus operate.In addition to the integration of large insertions of organelle DNA into the nucleus of organisms there are small pieces of organelle DNA integrated into functional genes. In Chapter 3 these insertions of organelle DNA into functional genes are described. This analysis was performed in human, yeast, rice and Arabidopsis. In general these insertions were small. In Arabidopsis there was only one insertion event per gene. On the contrary, in all other organisms more than one insertion in the genes, reported having insertions, could be detected. For all proteins, which had an organellar insertion, homologous proteins were analyzed and assigned lacking the organelle insertion, meaning that these organelle insertions might contribute to better functionality of the genes. Many of the genes needed for the proper function of organelles are nuclear encoded. It is believed that they were transferred during endosymbiosis from the organelles to the nucleus where they were exposed to several mutation events in order to adapt to the new environment. These genes acquireatransit peptide in order to be targeted back to the organelle they were coming from.In Chapter 4 the expression of nuclear encoded genes which are of chloroplast origin is studied. The expression of 3292 nuclear Arabidopsis genes, encoding mostly chloroplast proteins, were determined from 101 different environmental and genetic conditions. The 1590 most-regulated genes fell into 23 distinct groups of coregulated genes (regulons). With the exception of regulons 1 and 2, the rest are heterogeneous and consist of genes coding for proteins with different subcellular locations or contributing to several biochemical functions. The co-expression of nuclear genes coding for subunits of the photosystems or encoding proteins involved in the transcription/translation of plastome genes (particularly ribosome polypeptides) (regulons 1 and 2, respectively) implies the existence of a novel mechanism that coordinates plastid and nuclear gene expression and involves nuclear control of plastid ribosome abundance. The co-regulation of genes for photosystem and plastid ribosome proteins escapes a previously described general control of nuclear chloroplast proteins imposed by a transcriptional master switch, highlighting a mode of transcriptional regulation of photosynthesis which is different compared to other chloroplast functions. From an evolutionary standpoint, the results provided indicate that functional integration of the proto-chloroplast into the eukaryotic cell was associated with the establishment of different layers of nuclear transcriptional control.The majority of the light harvesting complex genes are in regulon 1. In Chapter 5 a detailed expression analysis of the genes belonging to Lhc supergene family, which is of chloroplast origin, was performed by using poplar and Arabidopsis. The analysis was done in silico. Four rarely expressed Lhcgenes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3 were studied in details. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS, a subunit of photosystem II and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.Chapter 6represents the general discussion of the thesis emphasizing on the roles that organelle insertions can have in the evolution of genes and genomes. Also open questions still existing on the continuous migration of DNA from the organelles to the nucleus are discussed.In conclusion, DNA transfer from the organelles can have a neutral role by integrating into the nucleus and in areas where no functional elements exist. In addition, it gave rise to the creation of genes which are important for the proper function of the organelles. In this case the transfer of DNA took place in order to have better coordination of the regulation of the chloroplast and mitochondria. In addition there is transfer of small pieces of DNA into the open reading frame of functional genes which might contribute to better functionality of these genes where the insertions are taking place.
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| Format: | Doctoral thesis biblioteca |
| Language: | English |
| Subjects: | dna, flowering plants, genomes, mitochondria, mitochondrial dna, nuclei, plants, plastids, bloeiende planten, celkernen, genomen, mitochondriaal dna, planten, plastiden, |
| Online Access: | https://research.wur.nl/en/publications/evolutionary-study-of-plastid-and-mitochondrial-dna-insertions-in |
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| Summary: | The aim of this study was to characterize the structure of functional and non-functional nuclear inserts of organelle DNA as well the expression of photosynthetic genes which are transferred during endosymbiosis into the nucleus with the final scope to determine the impact of organelle DNA on gene and genome evolution.In Chapter 1 a general description of the chloroplast organelle is given. Its functions emphasizing photosynthesis by which plants, algae, some bacteria, and protists convert the energy of sunlight to chemical energy. An overview on plastid membranes is provided as well. The origin of organelles is described. Mitochondria and chloroplast were once free living bacteria, a-proteobacteria or cyanobacteria, respectively. As a first endosymbiotic event, the mitochondrion was created by the endosymbiosis ofa proteobacteriumwith an ancestor cell containing no mitochondria. Later, a secondendosymbioticevent involving cyanobacteria and the primary ancestor cell, led to the creation of chloroplasts. Also, a description of the import machinery of chloroplasts and mitochondria is provided.In Chapter 2 as a first approach the integration of relative large insertions of organelle DNA into the nucleus was studied using Arabidopsis and rice organelles and genomes. Thirteen integrants were identified in Arabidopsis and rice genomes. Nuclear genomes are exposed to a continuous influx of DNA from mitochondria and plastids. These insertions can occur during the illegitimate repair of double stranded breaks. After integration, nuclear organelle DNA is modified by point mutations and by deletions. Overall, the numbers of insertion and deletion events after integration of the thirteensegmentsof organelle DNA into the nucleus are almost equal. Deletions are associated with the removal of DNA between perfect repeats, indicating that replication slippage has caused them. Two general types of nuclear insertions coexist; one is characterized by long sequence stretches that are colinear with organelle DNA, the other type consists of mosaics of organelle DNA, often derived from both plastids and mitochondria. The levels of sequence divergence of the two types exclude their common descent, implying that at least two independent modes of DNA transfer from organelle to nucleus operate.In addition to the integration of large insertions of organelle DNA into the nucleus of organisms there are small pieces of organelle DNA integrated into functional genes. In Chapter 3 these insertions of organelle DNA into functional genes are described. This analysis was performed in human, yeast, rice and Arabidopsis. In general these insertions were small. In Arabidopsis there was only one insertion event per gene. On the contrary, in all other organisms more than one insertion in the genes, reported having insertions, could be detected. For all proteins, which had an organellar insertion, homologous proteins were analyzed and assigned lacking the organelle insertion, meaning that these organelle insertions might contribute to better functionality of the genes. Many of the genes needed for the proper function of organelles are nuclear encoded. It is believed that they were transferred during endosymbiosis from the organelles to the nucleus where they were exposed to several mutation events in order to adapt to the new environment. These genes acquireatransit peptide in order to be targeted back to the organelle they were coming from.In Chapter 4 the expression of nuclear encoded genes which are of chloroplast origin is studied. The expression of 3292 nuclear Arabidopsis genes, encoding mostly chloroplast proteins, were determined from 101 different environmental and genetic conditions. The 1590 most-regulated genes fell into 23 distinct groups of coregulated genes (regulons). With the exception of regulons 1 and 2, the rest are heterogeneous and consist of genes coding for proteins with different subcellular locations or contributing to several biochemical functions. The co-expression of nuclear genes coding for subunits of the photosystems or encoding proteins involved in the transcription/translation of plastome genes (particularly ribosome polypeptides) (regulons 1 and 2, respectively) implies the existence of a novel mechanism that coordinates plastid and nuclear gene expression and involves nuclear control of plastid ribosome abundance. The co-regulation of genes for photosystem and plastid ribosome proteins escapes a previously described general control of nuclear chloroplast proteins imposed by a transcriptional master switch, highlighting a mode of transcriptional regulation of photosynthesis which is different compared to other chloroplast functions. From an evolutionary standpoint, the results provided indicate that functional integration of the proto-chloroplast into the eukaryotic cell was associated with the establishment of different layers of nuclear transcriptional control.The majority of the light harvesting complex genes are in regulon 1. In Chapter 5 a detailed expression analysis of the genes belonging to Lhc supergene family, which is of chloroplast origin, was performed by using poplar and Arabidopsis. The analysis was done in silico. Four rarely expressed Lhcgenes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3 were studied in details. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS, a subunit of photosystem II and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.Chapter 6represents the general discussion of the thesis emphasizing on the roles that organelle insertions can have in the evolution of genes and genomes. Also open questions still existing on the continuous migration of DNA from the organelles to the nucleus are discussed.In conclusion, DNA transfer from the organelles can have a neutral role by integrating into the nucleus and in areas where no functional elements exist. In addition, it gave rise to the creation of genes which are important for the proper function of the organelles. In this case the transfer of DNA took place in order to have better coordination of the regulation of the chloroplast and mitochondria. In addition there is transfer of small pieces of DNA into the open reading frame of functional genes which might contribute to better functionality of these genes where the insertions are taking place. |
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